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MCAT Biochemistry Review

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Amino Acid
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Dipolar compound containing an amino group and a carboxyl group
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Amino Group
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-NH2
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Carboxyl Group
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-COOH
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Alpha Carbon
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Central carbon atom in amino acid Attached to amino & carboxyl groups, H atom, and side chain
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Side Chain
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The variable component of an amino acid that gives the amino acid its identity and chemical properties also called R-group
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Chiral
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A molecule with a nonsuperimposable mirror image All amino acids (except glycine) are chiral
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(S) Absolute Configuration
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All amino acids (except cysteine) have an (S) absolute configuration
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L-amino Acid
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All amino acids found in eukaryotes
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Nonpolar, Nonaromatic Amino Acids
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Glycine, alanine, valine, leucine, isoleucine, methionine, proline
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Glycine
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Single H atom as side chain Achiral Smallest amino acid
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Alanine
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Alkyl side chain (1C)
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Valine
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Alkyl side chain (3C)
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Leucine
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Alkyl side chain (4C)
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Isoleucine
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Alkyl side chain (4C)
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Methionine
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Methyl side chain (-CH3) Contains S atom in side chain
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Proline
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Cyclic amino acid N from amino group becomes part of side chain, forming five-part ring, limiting where is can appear on a protein Rigid/constraints on flexibility
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Aromatic Amino Acids
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Tryptophan, phenylalanine, tyrosine
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Aromaticity
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The ability of a molecule to delocalize pi electrons around a conjucated ring, creating exceptional stability
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Tryptophan
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Double-ring system Contains N atom in one ring Largest of aromatic amino acids
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Phenylalanine
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Benzyl side chain (benzene ring + -CH2 group) Smallest aromatic amino acid Relatively nonpolar
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Tyrosine
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Phenylalanine + -OH group Relatively polar
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Polar Amino Acids
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Serine, threonine, asparagine, glutamine, cysteine
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Polarity
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An uneven sharing of electrons in a molecule, creating a slightly positive side and a slightly negative side
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Serine
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-OH group in side chain Highly polar – participate in H-bonding
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Threonine
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-OH group in side chain Highly polar – participate in H-bonding
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Asparagine
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Amide (-NH2) side chain Amide N do not gain or lose protons with changes in pH – do not become charged
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Glutamine
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Amide (-NH2) side chain Amide N do not gain or lose protons with changes in pH – do not become charged
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Cysteine
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Thiol (-SH) side chain – weaker than OH bond Prone to oxidation
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Negatively-charged (Acidic) Amino Acids
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Aspartic acid (aspartate), glutamic acid (glutamate)
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Aspartic Acid (Aspartate)
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Carboxylate (-COO(-)) group in side chain Deprotonated form of asparagine
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Glutamic Acid (Glutamate)
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Carboxylate (-COO(-)) group in side chain Deprotonated form of glutamine
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Positively-charged (Basic) Amino Acids
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Lysine, arginine, histidine
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Lysine
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Terminal primary amino group
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Arginine
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Has 3 N atoms in side chain Charge delocalized over all three N atoms
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Histidine
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Has aromatic ring with 2 N atoms (ring is called an imidazole) At pH 7.4, one N is protonated and the other isn’t Under acidic conditions, the 2nd N becomes protonated, making it positively charged
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Hydrophobic Amino Acids
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Being repelled by water Alanine, isoleucine, leucine, valine, phenylalanine More likely to be found in center of protein Nonpolar, uncharged compounds Long alkyl chains
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Hydrophilic Amino Acids
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Being attracted to water Histidine, arginine, lysine, glutamate, aspartate, asparagine, glutamine Polar and charged compounds and those that participate in H-bonding
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Neither Really Hydrophobic/-philic
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Cysteine, threonine, serine, tyrosine, tryptophan, proline, methionine, glycine
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Amphoteric
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Ability to act as an acid or a base Can either accept or donate a proton For ionizable groups: tend to be protonated at low pH; deprotonated at high pH
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pKa
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The pH at which half of the species are deprotonated [HA] = [A(-)]
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pKa1
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pKa for carboxyl group Usually around 2
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pKa2
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pKa for amino group Usually between 9 and 10
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pKa3
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For amino acids with ionizable side chains
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Amino Acids in Acidic Conditions
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Amino acid is fully protonated i.e. (-NH3+) and (-COOH)
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Amino Acids in Neutral Conditions
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Form zwitterions pH is near pI of amino acid i.e. (-COO(-)) and (-NH3(+))
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Zwitterion
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A molecule that contains charges, but is neutral overall
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Amino Acids in Basic Conditions
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Amino acid is fully deprotonated i.e. (-COO(-)) and (-NH2)
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Isoelectric Point (pI)
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The pH at which every molecule in solution is electrically neutral Predominantly in zwitterion form
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pI(neutral amino acid) =
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(pKa(NH3+) + pKa(COOH))/2 For amino acids with neutral side chains Have relatively neutral pI values (~6)
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Buffer
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When pH of a solution is approximately = pKa of solute The pH doesn’t change very much, even when acid or base are added to solution
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pI(acidic amino acid) =
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(pKa(R group) + pKa(COOH))/2 For amino acids with negatively charged side chains Have relatively low pI values (~3.2)
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pI(basic amino acid) =
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(pKa(NH3+) + pKa(R group))/2 For amino acids with positively charged side chains Have relatively high pI values (~9.75)
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Titration
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A laboratory technique in which a solution of unknown concentration is mixed with a solution of known concentration to determine the unknown concentration
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Titration Curves for Amino Acids
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Curve is nearly flat at pKa values of amino acids Nearly vertical at pI of amino acid
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Peptides
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A molecule composed of more than one amino acid Can be subdivided into dipeptides, tripeptides, oligopeptides, and polypeptides
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Dipeptide
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Two amino acid residues
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Tripeptide
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Three amino acid residues
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Oligopeptide
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Relatively small peptides (up to ~20 residues) (Single amino acid does not count as oligopeptide)
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Polypeptides
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Long chains of residues (>20 residue)
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Peptide Bonds
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An amide bond between the carboxyl group of one amino acid and the amino group of another amino acid Forms functional group -C(O)NH(-)
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Peptide (Amide) Bond Formation
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Condensation/Dehydration Loss of H2O molecule So strong because of resonance
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N-terminus
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Free amino end of a polypeptide On left side of drawings Read from N-terminus -> C-terminus
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C-terminus
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Free carboxyl end of a polypeptide On right side of drawings Read from N-terminus -> C-terminus
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Cleavage of Peptides
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Hydrolysis – hydrolytic enzymes break the amide bond by adding an H atom to amide nitrogen and adding an OH group to the carbonyl carbon.
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Trypsin
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Hydrolytic enzyme Cleaves carboxyl end of arginine and lysine
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Chymotrypsin
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Hydrolytic enzyme Cleaves carboxyl end of tryptophan, phenylalanine, and tyrosine
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Proteins
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Polypeptides Can be enzymes, hormones, membrane pores and receptors, elements of cell structure
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Primary Protein Structure
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Linear sequence of amino acids in a polypeptide Stabilized by formation of covalent peptide bonds between adjacent amino acids Encodes all info needed for folding at all higher structural levels
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Secondary Protein Structure
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Local structure of neighboring amino acids – most commonly alpha-helices and beta-pleated sheets Primarily result of intramolecular H-bonds between residues Proline can interrupt secondary structure because of rigid structure
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Alpha-Helices
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An element of secondary structure, marked by clockwise coiling of amino acids around a central axis Stabilized by intramolecular H-bonds between carbonyl O and amide H atom 4 residues down the chain Side chains point away from center
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Beta-Pleated Sheets
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An element of secondary structure, marked by peptide chains lying alongside one another, forming rows or strands Held together by intramolecular H-bonds between carbonyl O and amide H in adjacent chain Residues point above and below plane
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Tertiary Structure
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The 3D shape of a polypeptide, stabilized by numerous interactions between R groups Mainly determined by hydrophobic/-philic interactions Can also be determined by H-bonds and acid/base interactions with AA with charged side chains (creating salt bridges)
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Disulfide Bonds
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A covalent interaction between the -SH groups of 2 cysteine residues Form cystine Create loops in protein chains Results in loss of 2 e- and 2H+
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Molten Globule
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Intermediate states in the folding of a protein
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Quarternary Structure
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Interactions between different subunits of a multi-subunit protein Stabilized by R group interactions Can further reduce SA Can reduce amount of DNA needed for coding Can bring catalytic sites closer together Can induce cooperativity (allosteric effects)
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Cooperativity
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The interaction between subunits in a multi-subunit protein in which binding of substrate to one subunit increases the affinity of other subunits for the substrate Unbinding of substrate from one unit decreases the affinity of other subunits for the substrate
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Conjucated Proteins
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A protein that derives part of its function from covalently attached molecules (prosthetic groups)
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Lipoproteins, Glycoproteins, Nucleoproteins
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Proteins with lipid, carbohydrate, and nucleic acid prosthetic groups
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Prosthetic Groups
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A cofactor or coenzyme that is covalently bonded to a protein to permit its function Play major role in determining function of proteins Can be a metal ion, vitamin, lipid, carbohydrate, or nucleic acid
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Denaturation
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The loss of secondary, tertiary, or quarternay structure in a protein, leading to loss of function Often irreversible Cannot catalyze reactions Caused by heat and solutes
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Catalysts
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Speed up reaction process
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Enzyme Features
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A biological molecule with catalytic activity; includes many proteins and RNA molecules Lower activation energy Increase reaction rate Do not alter equilibrium constant Neither changed nor consumed in reaction pH- and temperature-sensitive Specific for particular reaction or class of reactions Do not alter free energy (deltaG) or enthalpy (deltaH)
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Substrates
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Molecules upon which enzymes act
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Oxidoreductases
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Catalyze oxidation-reduction reactions Often have cofactor that acts like an e- carrier (i.e. NAD+ or NADP+) Usually contain dehydrogenase and reductase in name or oxidase in O is final e- acceptor
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Reductant
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Electron donor
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Oxidant
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Electron acceptor
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Transferases
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Catalyzes the transfer of a functional group
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Kinases
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A specific transferase protein that catalyzes the movement of a phosphate group, generally from ATP, to a molecule of interest
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Adenosine triphosphate (ATP)
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The primary energy molecule of the body; it releases energy by breaking the bond with the terminal phosphate to form ADP and inorganic phosphate
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Hydrolases
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Catalyzes cleavage of a molecule with the addition of H2O Include phosphatase, peptidases, nucleases, lipases
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Lyases
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Catalyzes the cleavage or synthesis of a molecule without the addition or loss of H2O Include synthases (catalyze 2 molecules into 1 molecule)
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Isomerases
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Catalyzes the constitutional or stereochemical rearrangement of a molecule
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Ligases
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Catalyzes the synthesis of large polymeric biomolecules, most commonly nucleic acids Often require ATP
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Endergonic Reaction
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Requires energy input (deltaG>0)
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Exergonic Reaction
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Energy is given off (deltaG<0)
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Enzyme-Substrate Complex
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Physical interaction between enzyme and substrate
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Active Site (Enzyme)
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The catalytically active portion of an enzyme Has a defined spatial arrangement
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Lock and Key Theory
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One of two theories of enzyme specificity; states that the enzyme and the substrate have a static by complimentary state
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Induced Fit Model
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States that enzyme and substrate experience a change in conformation during binding to increase complementarity A substrate of the wrong type will not induce the correct conformational change
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Cofactors/Coenzymes
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Nonprotein molecules that participate in catalysis Usually by carrying charge through ionization, protonation, deprotonation Usually kept in small quantities
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Cofactors
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An inorganic molecule or ion that helps an enzyme carry out its function
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Coenzymes
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An organic molecule that helps an enzyme carry out its function Often vitamins or derivatives of vitamins
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Apoenzymes
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Enzymes devoid of the prosthetic group, coenzyme, or cofactor necessary for normal activity
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Holoenzymes
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Enzymes that have already bound a required prosthetic group, coenzyme, or cofactor
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Prosthetic Group
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A cofactor or coenzyme that is covalently bonded to a protein to permit its function
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B1
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Thiamine
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B2
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Riboflavin
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B3
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Niacin
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B5
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Pantothenic Acid
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B6
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Pyridoxal Phosphate
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B7
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Biotin
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B9
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Folic Acid
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B12
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Cyanocobalamin
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Saturation
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The presence or absence of double bonds in a fatty acid; saturated fatty acids only have single bonds, whereas unsaturated fatty acids have at least one double bond
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Saturation Kinetics
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As substrate concentration increases, the reaction rate does as well until a maximum value is reached
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Maximum Velocity
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vmax Only way to increase vmax is to increase enzyme concentration – can be accomplished by inducing expression of the gene encoding the enzyme
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Michaelis-Menten Equation
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Represented as a hyperbola x-axis = [S] y-axis = v E + S ES -> E + P E=enzyme; S=substrate; P=product E+S->ES = k1 ES->E+S = k2 ES->E+P = k3
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Relationship of Velocity to [Substrate]
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v = (vmax[S])/(Km+[S]) At 1/2 vmax, Km = [S]
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Km
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Concentration of substrate at which an enzyme runs at half its maximal velocity Michaelis Constant – measures affinity of an enzyme for its substrate Higher Km has lower affinity; lower has higher affinity (requires higher substrate concentration to be half-saturated) Intrinsic property – cannot be changed by concentration of substrate or enzyme
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Km Affect on Rate
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Concentrations below Km will greatly affect rate Concentrations above Km will affect rate more slowly until it reaches vmax
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Lineweaver-Burk Plots
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Interpret the same data as Michaelis-Menten graphs, but do so in a straight line y-intercept = 1/vmax x-intercept = -1/Km Useful for determining type of inhibition an enzyme is experiencing because vmax and Km can be compared without estimation
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Cooperative Enzymes
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Produce sigmoidal (S-curve) curve because of the change in activity with substrate binding Have a low-affinity tense state (T) and high-affinity relaxed state (R) Often regulatory enzymes in pathways
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Enzyme Activity/Velocity/Rate
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Affected by temperature, pH, and salinity
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Temperature Effects on Enzymes
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Typically double v for every 10 degC until optimal temperature, then drop off significantly – optimal = 37 degC in humans
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pH Effects on Enzymes
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pH affects the ionization of the active sight Optimal = 7.4 in humans
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Salinity Effects on Enzymes
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In vitro; Can disrupt H and ionic bonds, causing partial changes in conformation of enzyme at higher levels
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Feedback Regulation
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Regulation by products further down a metabolic pathway
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Feedback Inhibition
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The inhibition of an enzyme by its product (or a product further down in a metabolic pathway) Used for homeostasis Negative feedback
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Feed-forward Regulation
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The stimulation of an enzyme by an intermediate that precedes the enzyme in a metabolic pathway
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Reversible Inhibition
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Characterized by the ability to replace the inhibitor with a compound of a greater affinity or to remove it using mild lab treatment
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Four Types of Reversible Inhibition
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Competitive*, noncompetitive*, mixed, uncompetitive
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Competitive Inhibition
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Results when inhibitor is similar to the substrate and binds at the active site Can be overcome by adding for substrate vmax and Km increase Substrate can outcompete inhibitor Increases Km ([S] must be higher to reach 1/2 vmax)
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Noncompetitive Inhibitor
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Results when inhibitor binds with equal affinity to the enzyme and E-S complex vmax decreases (less enzyme to react), Km is unchanged (any enzyme left still has some affinity) Bind to allosteric site instead of active site – changes conformation
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Mixed Inhibition
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Results when inhibitor binds with unequal affinity to the enzyme and E-S complex vmax decreases, Km is increased (prefers enzyme) or decreased (prefers E-S complex) Bind allosteric sight
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Uncompetitive Inhibitors
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Bind only to E-S complex – basically lock S in the enzyme, preventing release Must bind allosteric site vmax and Km decrease
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Irreversible Inhibition
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Alters the enzyme in such a way that the active sight is unavailable for a prolonged duration or permanently; new enzyme molecules must be synthesized for the reaction to occur again
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Allosteric Enzymes
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Can be occupied by activators which increase either affinity or enzyme turnover Have multiple binding sites Alternate active and inactive forms Activators make active sight more available for binding, inhibitors make is less available
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Covalently Modified Enzymes
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Often subject to covalent modifications Can be (de)activated by phosphorylation or dephosphorylation
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Phosphorylation
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Addition of phosphates by protein kinases to activate or deactivate proteins
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Glycosylation
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The addition of sugars to a molecule
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Zymogens
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An enzyme that is secreted in an inactive form and must be activated by cleavage (i.e. digestive enzymes) Contain catalytic (active) domain and regulatory domain Regulatory domain must be removed/altered to expose active site Most have suffix -ogen
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Structural Proteins
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Compose the cytoskeleton, anchoring proteins, and much of the extracellular matrix Fibrous in nature
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Collagen (Structural)
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Characteristic trihelical fiber (3 alpha-helices woven to form a secondary helix) Makes up most of extracellular matrix connective tissue Provides strength/flexibility
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Elastin (Structural)
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Important to extracellular matrix of connective tissue Restores original shape of tissue by stretching and recoiling
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Keratins (Structural)
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Intermediate filament proteins found in epithelial cells Mechanical integrity of cell/regulatory proteins Hair and nails
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Actin (Structural)
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Makes up microfilaments and thin filaments in myofibrils Most abundant protein in eukaryotic cells Have + and – sides, allowing unidirectional movement
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Tubulin (Structural)
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Protein that makes up microtubules Polar – negative end usually located adjacent to nucleus, positive usually in periphery of cell
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Motor Proteins
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Have one or more heads capable of force generation through conformational change Have catalytic activity, acting as ATPases to power movement Common functions: muscle contraction, vesicle movement within cells, and cell motility
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Myosin
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Primary motor protein – interacts with actin Can be involved with cellular transport Movement at neck of protein is responsible for power stroke of sarcomere contraction
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Kinesins
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Motor protein associated with microtubules Two heads Aligns chromosomes during metaphase and depolymerizing microtubules during anaphase of mitosis Bring vesicles toward + end
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Dyneins
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Motor protein associated with microtubules Two heads Sliding movement of cilia and flagella Bring tubules toward – end
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Binding Proteins
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Bind a specific substrate, either to sequester it in the body or hold its concentration at a specific concentration Hemoglobin, calcium-binding proteins, DNA-binding proteins Transport/sequester molecules by binding to them
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Cadherins
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Ca-dependent Glycoproteins that hold similar cells together
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Integrins
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Have 2 membrane-spanning chains and permit cells to adhere to proteins in extracellular matrix- alpha+beta Cellular signaling
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Selectins
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Allow cells to bind to carbohydrate molecules on the surface of other cells and are most commonly used in immune system Weakest cell adhesion molecule On white blood cells and endothelial cells that line blood vessels
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Antibodies
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aka Immunoglobulins (Ig) Proteins produced by B-cells Recruit other cells to eliminate threat Has 2 identical heavy chains; 2 identical light chains Disulfide linkages/noncovalent interactions hold heavy and light chains together Contain constant region and variable region (responsible for antigen binding)
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Antigen-binding Region
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On antibodies Tips of the Y Polypeptide sequences that will bind only 1 antigen Variable region
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Possible Outcomes of Antibody
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1) Neutralize antigen 2) Opsonization – marks pathogen for destruction by other white blood cells 3) Agglutination – clumping together antigen and antibody to make protein complexes to be phagocytized and digested by macrophages
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Biosignaling
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Process in which cells receive and act on signals
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Ion Channels
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Proteins that create specific pathways for charged molecules Used for regulating ion flow into or out of cell
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Ungated Channels
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Have no gates and are unregulated Always open Regulate membrane potential
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Voltage-gated Channels
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Gate is regulated by the membrane potential change near channel Open within a range of membrane potentials
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Ligand-gated Channels
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Open in presence of specific binding substance, usually a hormone or neurotransmitter Binding of specific substance or ligand to the channel
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Enzyme-linked Receptors
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Participate in extracellular signaling through extracellular ligand binding and initiation of 2nd messenger cascades
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Three Domains of Enzyme-linked Receptors
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Membrane-spanning domain – anchors receptor to cell membrane Ligand-binding domain – stimulated by appropriate ligand and induces conformational change Catalytic domain
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G-Protein Coupled Receptors (GPCRs)
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Have a membrane bound protein associated with a trimeric G-protein Integral membrane proteins involved in signal transduction 7 membrane-spanning alpha-helices
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Three main types of GPCR
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1) Gs – stimulates adenylate cyclase – increases cAMP in cell 2) Gi – inhibits adenylate cyclase – decreases cAMP in cell 3) Gq – activates phospholipase C (cleaves a phospholipid from PIP2)
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Homogenization
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Crushing, grinding, blending tissue into an evenly distributed mixture
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Electrophoresis
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Uses a gel matrix to observe the migration of proteins in response to an electric field A positive molecule will move toward a negative electrode and vice versa
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Electrophoresis(?) Equation
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v = Ez/f v=migration velocity z=net charge of molecule E=electric field strength f=frictional coefficient (dependent on mass and shape of molecule)
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Native PAGE
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Polyacrylamide Gel Electrophoresis Maintains protein’s shape, but results are difficult are difficult to compare because the mass-to-charge ratio differs for each protein
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SDS-PAGE
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Sodium Dodecyl Sulfate-PAGE Separates proteins on basis of mass alone Denatures the proteins and masks the native charge so that comparison of size of more accurate, but the functional protein cannot be recaptured from the gel
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Isoelectric Focusing
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Type of electrophoresis Proteins can be separated based on their isoelectric point (pI); protein migrates toward an electrode until it reaches a region of the gel where pH=pI of the protein Exploits the acidic and basic properties of amino acids A+: Anode has acidic (H+ rich) gel and a (+) charge
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Chromatography
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Separates protein mixtures on the basis of their affinity for a stationary phase or mobile phase Preferred over electrophoresis when large amounts of protein are being separated
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Column Chromatography
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Uses beads of a polar compound, like silica or alumina (stationary phase) with a nonpolar solvent (mobile phase)
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Ion-exchange Chromatography
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Uses a charged column and a variably saline eluent
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Size-exlusion Chromatography
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Relies on porous beads Larger molecules elute first because they are not trapped in the small pores
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Affinity Chromatography
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Uses a bound receptor or ligand and an eluent with free ligand or a receptor for the protein of interest
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X-ray Crystallography
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A method of determining molecular structure using apparent bond angles and diffraction and refraction of x-rays
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NMR Spectroscopy
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A method of determining molecular structure that uses the relative position of carbons and hydrogens determined by the relative shielding and spins of electrons observed when a molecule is exposed to a magnetic field
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Edman Degredation
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A stepwise process for determining the amino acid sequence in an isolated protein ~50-70 amino acids
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UV Spectroscopy
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A method of determining the concentration of protein in an isolate by comparison against a protein standard; relies on the presence of aromatic amino acids Can also be used with nucleic acids and other compounds
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Bradford Protein Assay
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A colorimetric method od determining the concentration of protein in an isolate against a protein standard Relies on a transition absorption between bound and unbound Coomassie Brilliant Blue dye
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Monosaccharide
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A single sugar monomer Common examples are glucose, galactose, and fructose Every carbon except the carbonyl carbon will carry and hydroxyl (-OH) group Contain alcohols and either aldoses or ketoses
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Glucose
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The primary monosaccharide used for fuel by all cells of the body, with the formula C6H12O6
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Fructose
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A monosaccharide found predominantly in fruit and honey
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Galactose
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A monosaccharide found predominantly in dairy
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Triose
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The simplest monosaccharide that contains 3C
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Tetrose
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A carbohydrate with 4C
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Pentose
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A carbohydrate with 5C
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Hexose
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A carbohydrate with 6C
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Aldose
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A sugar in which the highest-order functional group is an aldehyde; can be categorized by number of carbons Carbohydrates that contain an aldehyde group as their most oxidized functional group Aldehyde carbon is always C-1
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Ketose
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A sugar in which the highest-order functional group is a ketone; can be categorized by number of carbons Carbohydrates with a ketone group as their most oxidized functional group Ketose carbon is usually C-2 (also where glycosidic linkages can happen)
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Glyceraldehyde
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Simplest aldose (an aldotriose)
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Glycosidic Linkage
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The bond between the anomeric (aldehyde) carbon of a sugar and another molecule Called glycosyl residues Dehydration reaction Breaking this bond requires hydrolysis
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Stereoisomer
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Compounds that have the same chemical formula and backbone, differing only in their spatial orientation aka optical isomers
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Enantiomers
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Compounds that are nonsuperimposable mirror images; have the same chemical and physical properties except for rotation of plane-polarized light and interaction with a chiral environment Same sugars, different optical families i.e. D- and L-sugars
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Equation for Stereoisomers
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Number of stereoisomers with common backbone = 2^n n=number of chiral carbons
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Fisher Projection
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A method of drawing organic molecules in which horizontal lines are coming out of the page (wedges) and vertical lines are going into the page (dashes) All D-sugars have the -OH of their highest-numberd chiral center on the right; L-sugars on the left side
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Diastereomers
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Compounds with at least one – but not all – chiral carbons in inverted configurations differ in physical properties Same family (i.e. both kotoses or aldoses) but not mirror images and not identical
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Epimers
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A subtype of diastereomers that differ in absolute configuration at exactly one chiral carbon
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Nucleophile
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A chemical species that donates an electron pair to an electrophile to form a chemical bond in relation to a reaction Hydroxyl group in a monosaccharide
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Electrophile
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A reagent attracted to electrons that participates in a chemical reaction by accepting an electron pair in order to bond a nucleophile Carbonyl group in a monosaccharide
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Carbonyl Group
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C (double bond) O
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Hemiacetals
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A carbon atom bonded to an alkyl group, an -OR group, an -OH group, and a hydrogen From aldoses Formed from intermolecular reactions from electro- and nucleophiles
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Hemiketals
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A carbon atom bonded to two alkyl groups, an -OR group, and an -OH group From ketoses Formed from intermolecular reactions from electro- and nucleophiles
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Pyranose
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A six-membered ring sugar One of two stable cyclic molecules
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Furanose
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A five-membered ring sugar One of two stable cyclic molecules
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Anomeric Carbon
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New chiral center formed in ring closure – the carbon from the carbonyl end of the straight chain
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Anomers
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A subtype of epimers in which the chiral carbon with inverted configuration was the carbonyl carbon (anomeric carbon)
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Alpha-anomer
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Has the -OH group of C-1 trans to the -CH2OH substituent (axial and down)
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Beta-anomer
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Has the -OH group of the C-1 cis to the -CH2OH substituent (equatorial and up)
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Haworth Projection
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A method for depicting cyclic sugars as planar rings with -OH groups sticking up or down from the plane of the sugar
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Mutarotation
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The rapid interconversion between different anomers of a sugar The single bond between C-1 and C-2 can rotate freely, forming either alpha- or beta-anomers Occurs in water Contains both alpha-and beta-anomers in equilibrium concentrations (36% alpha, 64% beta for glucose)
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Aldonic Acids
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Oxidized aldoses Reducing agents
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Reducing Sugar
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Any monosaccharide with a hemiacetal ring
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Lactone
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A cyclic ester with a carbonyl group persisting on the anomeric carbon
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Tollen’s Reagent
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Utilizes Ag(NH3)2+ as an oxidizing agent to find the presence of reducing sugars A positive test shows aldehydes reducing Ag+ to metallic silver
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Benedict’s Reagent
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The aldehyde group of an aldose is readily oxidized, indicated by a red precipitate of Cu2O, to show presence of reducing sugars
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Tautomerization
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The rearrangement of bonds within a compound, usually by moving a hydrogen and forming a double bond
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Enol
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A compound with a double bond and an alcohol group
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Alditol
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A compound where the aldehyde group of an aldose is reduced to an alcohol Reduced aldose
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Deoxy Sugar
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Contains a hydrogen that replaces a hydroxyl group on the sugar
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D-2 Deoxyribose
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The carbohydrate found in DNA
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Esterification
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Sugars that react with carboxylic acids or carboxylic acid derivatives, forming esters
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Acetals/Ketals
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Product of reaction between hemiacetals/hemiketals and alcohols
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Furanosides
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Glycosides derived from furanose rings
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Pyranosides
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Glycosides derived from pyranose rings
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Disaccharide
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Results when glycosidic bonds are formed between hydroxyl groups of two monosaccharides
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Important Disaccharides
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Sucrose (glucose-alpha-1,2-fructose) lactose (galactose-beta-1,4-glucose) maltose (glucose-alpha-1,4-glucose)
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Polysaccharides
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Long chains of monosaccharides linked together by glycosidic bonds
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Homopolysaccharide
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A polysaccharide composed of one type on monosaccharide
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Heterosaccharide
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A polysaccharide made up of more than one type of monosaccharide
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Important Polysaccharides
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Cellulose, starch, glycogen
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Cellulose
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Main structural component of plants Homopolysaccharide Chain of beta-D-glucose molecules linked by beta-1,4 glycosidic bonds, with hydrogen bonds holding the actual polymer chain together for support Main source of fiber in human diet
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Humans cannot digest ____
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beta-linked sugars
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Starches
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Polysaccharides that are more digestible by humans because they are alpha-D-glucose monomers
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Amylose
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A linear glucose polymer linked by alpha-1,4 glycosidic bonds Type of starch – stored by plants Degraded by alpha-amylase and beta-amylase
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Beta-Amylase
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Cleaves amylose at the reducing end of the polymer (end with anomeric carbon) to yield maltose
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Alpha-Amylase
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Cleaves randomly along chain to yield shorter polysaccharide chains, maltose, and glucose
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Amylopectin
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Has alpha-1,4 glycosidic bonds, bur also contains branches via alpha-1,6 glycosidic bonds Debranching enzymes break down amylopectin
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Glycogen (1)
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A carbohydrate storage unit in animals Has more alpha-1,6 glycosidic bonds than starch Highly branches compound, making it more soluble in solution
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Glycogen Phosphorylase (1)
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Functions by cleaving glucose from nonreducing end of a glycogen branch (side with no free anomeric carbon)
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Lipid
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A molecule that is insoluble in water and soluble in nonpolar organic solvents
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Amphipathic
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Having both hydrophobic and hydrophilic regions
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Phospholipid
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A lipid containing a phosphate and alcohol (glycerol or sphingosine) joined to hydrophobic fatty acid tails by phosphodiesterase linkages
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Glycerol
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A three-carbon alcohol Forms phosphoglycerides or glycerophospholipids
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Sphingosine
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Form sphingolipids (though not all sphingolipids are phospholipids)
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Saturated Fatty Acid
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Have only single bond Carbon atom is considered saturated when it is bonded to four other atoms with no pi bonds Greater van der Waals forces More stable overall structure Usually solids at room temp
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Unsaturated Fatty Acid
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Have one or more double bonds Form kinks in chains, making it hard for stacking Usually liquids at room temp
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Glycerophospholipids
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A lipid containing a glycerol backbone with a phosphate group, bound by ester linkages at two fatty acids and a phosphodiester linkage to the head All glycerophospholipids are phospholipids aka phosphoglycerides
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Sphingolipid
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A lipid containing a sphingosine or sphingoid backbone, bound to fatty acid tails Include ceramide, sphingomyelins, glycosphingolipids, and gangliosides
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Glycolipid
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Any lipid linked to a sugar
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Ceramide
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Simplest sphingolipid Has a hydrogen atom as its head group
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Sphingomyelins
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Also phospholipids Have either phosphatidycholine or phosphatidyethanolamine as a head group Bound by phosphodiester bond These head groups have no net charge
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Glycosphingolipids
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Sphingolipids with head groups composed of sugars bound by glycosidic linkages Not phospholipids Found mainly on outer surface of plasma membrane Can be broken down into cerebrosides and globosides
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Cerebrosides
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Have a single sugar Have no net charge
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Globosides
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Have two or more sugars Have no net charge
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Gangliosides
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Most complex sphingolipids Glycolipids that have polar head groups composed of oligosaccharides with one or more N-acetulneuraminic acid (NANA or sialic acid) molecules at the terminus and a negative charge Considered glycolipids Play major role in cell recognition, interaction, and signal transduction
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Wax
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A high-melting point lipid composed of very long chain alcohol and a very long chain fatty acid Form pliable solids at room temp
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Terpene
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A class of lipids built from isoprene (C5H8) moieties; have carbon groups in multiples of five Metabolic precursors to steroids and other signaling molecules Produced mainly by plants and some insects Strongly scented Grouped according to how many isoprene units it has
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Monoterpenes
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C10H16 – two isoprene units
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Sesquiterpenes
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C15H24 – three isoprene units
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Diterpenes
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C20H32 – four isoprene units Vitamin A
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Triterpene
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Six isoprene units Can be converted into cholesterol and various steroids
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Tetraterpenes
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Eight isoprene units Contain carotenoids group (i.e. beta-carotene and lutein)
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Polyterpene
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Many isoprene units i.e. rubber (~1000 – 5000 units)
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Terpenoids
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A terpene derivative that has undergone oxygenation or rearrangement of the carbon skeleton Named similarly to terpenes
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Steroid
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A derivative of cholesterol Metabolic derivatives of terpenes Have four cycloalkane rings fused together – three cyclohexane and one cyclopentane Functionality dependent on oxidation of rings and functional groups attached to them Nonpolar
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Steroid Hormones
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Steroids that act as hormones, meaning they are secreted by endocrine glands into the blood stream and travel on protein carriers to distant sites, where they alter gene expression levels Examples: testosterone, various estrogens, cortisol, aldosterone
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Cholesterol
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A molecule containing four linked aromatic rings; cholesterol provides both fluidity and stability to cell membranes and is the precursor for steroid hormones, bile acids, and vitamin D Amphipathic
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Prostaglandin
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A group of 20-carbon molecules that are unsaturated carboxylic acids derived from arachidonic acid; act as paracrine or autocrine hormones Regulate synthesis of cAMP Have effects on smooth muscle function, sleep-wake cycle, and elevations of bod temp associated with fever and pain
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Vitamin
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An essential organic coenzyme that assists an enzyme in carrying out its action Cannot be adequately synthesized by the body, must be consumed in diet
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Fat-Soluble Vitamins
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A, D, E, and K
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Vitamin A
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Carotene – an unsaturated hydrocarbon important for vision, growth and development, and immune function
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Retinal
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Aldehyde form of vitamin A Component of light-sensing molecular system in human eye
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Retinol
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Storage form of vitamin A Also oxidized to retinoic acid, which regualtes gene expression during epithelial development
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Vitamin D
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Cholecalciferol – can be consumed or formed un a UV-driven reaction on skin Converted to calcitriol (1,25-(OH)2D3) in liver and kidneys – increases calcium and phosphate uptake in intestines, which promotes bone production Lack of vitamin D can cause rickets – an elongation and curvature of the bones and impeded growth
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Vitamin E
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Tocopherols and tocotrienols – characterized by a substituted aromatic ring with a long isoprenoid side chain and are hydrophobic Tocopherols are biological antioxidants – the aromatic ring reacts with free radicals
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Vitamin K
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A group of compounds including phylloquinone (K1) and menaquinone (K2) Important to posttranslational modification for prothrombin, an important clotting factor in blood The aromatic ring undergoes oxidation and reduction during prothrombin formation Also required to introduce calcium-binding sites on Ca-dependent factors
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Triacylglycerols (Triglycerides)
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A glycerol molecule esterified to three fatty acid molecules; the most common form of fat storage in the body Overall nonpolar and hydrophobic Can be seen in oily droplets
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Adipocyte
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A cell specializing in fat storage Found primarily under the skin, around mammary glands, and in the abdominal cavity
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Free Fatty Acids
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Unesterified fatty acids with a free carboxylate group Circulate in the blood bound noncovalently to serum albumin Make up soap
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Saponification
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The reaction between a fatty acid and a strong base, resulting in a negatively charged fatty acid anion bound to a metal ion; creates soap Base is traditionally lye (NaOH or KOH) Can form colloids
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Surfactant
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A compound that lowers the surface tension between two solutions, acting as a detergent or emulsifier
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Micelles
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Tiny aggregates of soap with the hydrophobic tails inward and the hydrophilic heads outward Nonpolar compounds can dissolve in the interior Important for absorption of fat-soluble vitamins and complicated lipids
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Deoxyribonucleic acid (DNA)
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A nucleic acid found exclusively in the nucleus that codes for all of the genes necessary for life; transcribed into mRNA and is read 5′ to 3′ Mostly found in chromosomes, but also in mitochondria and chloroplasts A polydeoxyribonucleotide
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Ribonucleic Acid (RNA)
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A nucleic acid found in both the nucleus and cytoplasm and most closely linked with transcription and translation, as well as some gene regulation
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Nucleosides
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Composed of five-carbon sugar (pentose) bound to a nitrogenous base and formed by covalently linking the base to C-1′ of the sugar Prime denotes carbon atoms on the sugar, not the nitrogenous base
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Nucleotides
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Formed when one or more phosphate groups are attached to C-5′ of a nucleoside The building blocks of DNA
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Why ATP Releases Energy
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Due to all the negative charges in close proximity, removing the terminal phosphate from ATP actually releases energy
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Deoxyribose
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A pentose Ribose with the 2′ -OH replaced with -H
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Backbone of DNA
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Composed of alternating sugar and phosphate groups – determines directionality of DNA Nucleotides are joined by 3′-5′ phosphodiester bonds (a phosphate group links the 3′ carbon of one sugar to the 5′ phosphate group of the next) DNA and RNA strands have an overall negative charge C-5′ will have either an -OH group or phosphate group attached; C-3′ will have a free -OH
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Purines
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Contain two rings in their structure Adenine (A) and guanine (G)
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Pyrimidines
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Contain only one ring in their structure Cytosine (C), thymine (T), Uracil (U) Thymine is found in DNA, uracil in RNA
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Purines and Pyrimidine Characteristics
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Biological aromatic heterocycles
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Aromatic
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Any unusually stable ring system that adheres to four rules: 1) the compound is cyclic; 2) the compound is planar; 3) the compound is conjugated (creates at least one unhybridized p-orbital for each atom in the ring); 4) The compound has 4n+2 pi electrons (HĂŒckel’s rule) (n=any integer) aromatic molecules are fairly unreactive Why nucleic acids are very stable and used for genetic storage
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Double Helix
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Two linear polynucleotide chains of DNA that are wound together in a spiral orientation along a common axis
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Watson-Crick Model Features
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1) Two strands of DNA are antiparallel (oriented in opposite directions) 2) Sugar-phosphate backbone is on the outside of the helix with nitrogenous bases on inside 3) Specific base-pairing rules (A-T vis two H-bonds and C-G via three H-bonds) 4) Chargaff’s Rule – the amount of A always equals that of T and same with C and G; total purines will be equal to total pyrimidines overall
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B-DNA
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Makes a turn once every 3.4nm and contains ~10 bases in each turn Have major and minor grooves that are the sites of protein binding Right-handed helix
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Z-DNA
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Left-handed helix Has a turn every 4.6nm with 12 bases in each turn Unstable
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Denaturing DNA
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Where the double helix “melts” into single strands Caused by heat, alkaline pH, and chemicals (i.e. formaldehyde and urea)
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Reannealing DNA
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Bringing the strands back together Can happen if the denaturing process is slowly removed (i.e. if DNA denatured by heat is slowly cooled, then the strands can reanneal)
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Histone
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A structural protein about which DNA is coiled in eukaryotic cells Five histone proteins in eukaryotic cells
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Nucleosome
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Composed of DNA wrapped around histones A protein complex composed of two copies of each protein (H2A, H2B, H3, and H4) and ~200 DNA base pairs H1 seals of the DNA as it enters and leaves the nucleosome
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Nucleoproteins
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Proteins that associate with DNA
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Heterochromatin
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A small percentage of the chromatin that remains compacted during interphase Appears dark under light microscopy Is transcriptionally silent Often consists of DNA with highly repetitive sequences Dense, dark, and silent
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Euchromatin
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Appears light under light microscopy Contains genetically active DNA Dispersed chromatin Light, uncondensed, expressed
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Telomere
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A simple repeating unit (TTAGGG) at the end of a DNA sequence The high C-G content creates exceptionally strong strand attractions at the end of chromosomes to prevent unraveling
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Centromeres
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Region of DNA found in the center of chromosomes Form noticeable indentations Composed of heterochromatin Contain high C-G content and repeating sequences Sister chromatids can remain connected during anaphase
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Replication Complex (Replisome)
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Set of specialized proteins that assist AND polymerases
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Origins od Replication
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Where DNA unwinds
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Replication Fork
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Where the new double stranded DNA splits into two strands on both sides of the origin Form on both sides of origin, increasing efficiency of replication
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Centromere
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Where sister chromatids remain connected
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Helicase
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Enzyme responsible for unwinding DNA, generating two single-stranded template strands ahead of the polymerase
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Single-Stranded DNA-Binding Proteins
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Bind to the unraveled strand, preventing reassociation of the DNA strands and the degradation of DNA by nucleases (DNA becomes “sticky” when unraveled – the bases look for other molecules to H-bond with)
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Supercoiling
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A wrapping of DNA on itself as its helical structure is pushed over further toward the telomeres during replication
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DNA Gyrase (DNA Topoisomerase II)
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Introduces negative supercoils It works ahead of helicase, nicking both strands, passing the DNA through the nick and releasing both strands
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Semiconservative Replication
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A new double helix is made of one old parent strand and one new daughter strand
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DNA Polymerases
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Responsible for reading the DNA template (parental strand) and synthesizing a new daughter strand Reads 3′-5′ and synthesizes 5′-3′
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Leading Strand
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The strand that is copied in a continuous fashion, in the same direction as the advancing replication fork Read 3′-5′ and its compliment will be synthesized 5′-3′
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Lagging Strand
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Strand that is copied in the opposite direction of the replication fork Parental strand has 5′-3′ polarity Okazaki fragments are porduced
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DNA replication Process
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RNA Primer is laid down Primase synthesizes a short primer (~10 molecules) in 5′-3′ direction to start replication on each strand RNA sequences are constantly added to lagging strand because each new Okazaki fragments must start with a new primer; there are only a few RNA sequences on the leading strand DNA polymerase III (prokaryotes) or DNA polymerase alpha and delta (eukaryotes) begin synthesizing daughter strand in 5′-3′ manner Incoming nucleotides are 5′ deoxyribonucleotide triphosphates (dATP, dCTP, dGTP, and dTTP) A free pyrophosphate (PP1) is released as new phosphodiester bond is made
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RNase H
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removes RNA for sanctity of genome DNA polymerase I in prokaryotes
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DNA Polymerase Delta
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Adds DNA nucleotides where the RNA primer was DNA polymerase I in prokaryotes
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DNA Ligase
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Seals ends of DNA molecules together, creating a continuous strand of DNA
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DNA Polymerases Alpha and Delta
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Work together to synthesize leading and lagging strands Delta also fills in gaps left behind when RNA primer is removed
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DNA Polymerase Gamma
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Replicates mitochondrial DNA
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DNA Polymerases Beta and Epsilon
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Mostly participate in DNA repair
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DNA Polymerases Delta and Epsilon
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Assisted by PNCA protein, which assembles into a trimer to form the sliding clamp (helps to strengthen interaction between DNA polymerases and template strand)
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Cancer
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Cells that proliferate excessively because they are able to divide without stimulation from other cells and are no longer subject to the normal controls on cell proliferation
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Metastasis
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A migration to distant tissues by the bloodstream or lymphatic system
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Oncogenes
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Mutated genes that cause cancer
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Antioncogenes
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Tumor supressor genes p53 or Rb (retinoblastoma) Normally function to stop tumor progression
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Proofreading
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If an incorrect DNA base is paired, the H-bonds are unstable, so the incorrect base is expelled and the correct one replaces it Looks for methylation to determine if it is the parent or daughter strand
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Mismatch Pair
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Machinery in G2 phase of cell cycle These genes encoded by MSH2 and MLH1, which detect and remove errors that were missed in the S phase (MutS and MutL in prokaryotes)
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Nucleotide Excision Repair (NER)
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Eliminate thymine dimers Proteins scan and detect and bulge in the DNA strand; an excision endonuclease makes nicks in the phosphodiester bond of the damaged strand and removes the oligonucleotide DNA polymerase then fills in the gap; the nick in the strand is fixed by DNA ligase
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Base Excision Repair
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The affected base is detected and removed by a glycosylase enzyme, leaving behind an apurinic/apyramidinic (AP) site (abasic site); AP site is recognized by AP endonuclease and removed the damaged sequence DNA polymerase and DNA ligase fill in the gap and seal it
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Recombinant DNA
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DNA composed of nucleotides from two different sources
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DNA Cloning
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Allows for production of recombinant proteins, or identification and characterization of DNA by increasing its volume and purity Can produce large amounts of a desired sequence
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Vectors for Cloning
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Usually bacterial or viral plasmids that can be transferred to a host bacterium after insertion of the DNA of interest Require an origin of replication and at least one gene for antibiotic resistance
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Restriction Enzymes (Restriction Endonucleases)
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Enzymes that recognize specific double-stranded DNA sequences (palindromic sequences – the 5′-3′ of one strand matches the 5′-3′ strand of another in antiparallel fashion)
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DNA Libraries
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Large collections of known DNA sequences
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Genomic Libraries
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Contain large fragments of DNA and include both coding (exon) and noncoding (intron) regions of the genome Requires restriction endonuclease and DNA ligase
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cDNA (Complimentary DNA) Libraries
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Constructed by reverse-transcribing processed mRNA Lacks noncoding regions (i.e. introns) Only includes the genes that are expressed in tissue from which the mRNA was isolated Sometimes called expression libraries Only library reliable enough to sequence genes, identify disease-causing mutations, produce recombinant proteins, or produce transgenic animals Requires reverse transcriptase and DNA ligase
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Hybridization
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The joining of complimentary base pair sequences Can be DNA-DNA or DNA-RNA recognition
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Polymerase Chain Reaction (PCR)
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An automated process that can produce millions of copies of a DNA sequence without amplifying the DNA in bacteria Requires primers (complimentary to the DNA that flanks the region of interest, nucleotides, and DNA polymerase) Heat is needed to denature DNA, but DNA polymerase cannot work in this heat, so the DNA polymerase from Thermus aquaticus (a bacteria found in Yellowstone) is used instead
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Gel Electrophoresis
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A technique used to separate macromolecules by size and charge All DNA strand will migrate toward the anode of an electrochemical cell Preferred gel is agarose gel The longer the DNA strand, the slower its migration
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Southern Blot
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Used to detect the presence and quantity of various strands of DNA in a sample DNA is cut by restriction enzymes then separated by gel electrophoresis The DNA fragments are then transferred to a membrane A probe is sent in and will bind with its complimentary strand Probes are labeled with radioisotopes or indicator proteins
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DNA Sequencing
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Requires template DNA, primers, DNA polymerase, all deoxyribonucleotide triphosphates, and a modified base in small quantities call dideoxyribonucleotide (contains an H at C-3′ instead of an -OH) – the polymerase can no longer be added to the chain The sequence will be broken into fragments and separated using gel electrophoresis
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Gene Therapy
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Offers potential cures for individuals with inherited diseases
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Transgenic Mice
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Mice whose germ line has been altered by introducing a cloned gene into fertilized ova or into embryonic stem cells
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Transgene
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The gene introduced into transgenic mice
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Knockout Mice
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A gene has been intentionally removed from a sequence
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Central Dogma of Molecular Biology
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The major steps in the transfer of genetic information, from transcription of DNA to RNA to translation of that RNA to protein
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Gene
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A unit of DNA that encodes a specific protein or RNA molecule, and through transcription and translation, that gene can be expressed
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Flow of Genetic Info from DNA to Protein
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mRNA is synthesized 5′-3′ and is complimentary and antiparallel to the DNA template strand Ribosome translates mRNA 5′-3′ as it synthesizes the protein N-terminus to C-terminus
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Messenger RNA (mRNA)
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Carries the information specifying the amino acid sequence of the protein to the ribosome Transcribed by RNA polymerase Read in codons Is monocistronic in eukaryotes (each mRNA molecule translates into only one protein product); polycistronic in prokaryotes Most abundant type of RNA
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Transfer RNA (tRNA)
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Responsible for converting the language of nucleic acids to the language of amino acids and peptides Each molecule contains a 3-nucleotide anticodon – pairs with the appropriate codon on an mRNA molecule while in the ribosome Amino acids are connected to a specific tRNA (these are charged or activated) Second most abundant type of RNA
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Aminoacyl-tRNA Synthase
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Activates the amino acids that attach to tRNA Each amino acid is attached with a different synthase Requires two ATP bonds (energy-rich) Transfers amino acid to 3′ end of tRNA Each tRNA molecule has a CCA nucleotide sequence where the amino acid binds The aminonacyl-tRNA bond will be used to supply energy needed to create a peptide bond in translation
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Ribosomal RNA (rRNA)
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Synthesized in nucleolus and functions as an integral part of the ribosomal machinery used during protein assembly in the cytoplasm Many function as ribozymes (enzymes made of RNA molecules instead of peptides) Helps catalyze formation of peptide bonds Important in splicing out its own introns Least abundant type of RNA
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Codon
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A three-nucleotide sequence in an mRNA molecule that pairs with an appropriate tRNA anticodon during translation
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Start Codon
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Every preprocessed eukaryotic protein starts with methionine (AUG)
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Stop Codons
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UGA, UAA, UAG There are no charged tRNA molecules that recognize these sequences, so the protein releases from the ribosome
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Degeneracy
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A characteristic of the genetic code, in which more than one codon can specify a single amino acid A mutation within an intron will not change protein sequence
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Wobble
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The third nucleotide of a codon that often plays no role in specifying an amino acid; an evolutionary development designed to protect against mutations
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Point Mutation
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The substitution of one nucleotide for another in DNA Expressed mutations (two types: missense and nonsense)
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Missense Mutation
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A mutation in which one amino acid is substituted for by a different amino acid
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Nonsense Mutation
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A mutation in which a coding codon is changed to a stop codon; also called a truncation mutation
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Reading Frame
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The three nucleotides of a codon
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Frameshift Mutation
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A change in DNA in which the reading frame of the codons in mRNA is shifted due to the insertion or deletion of nucleotides (other than multiples of three)
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Transcription
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The production of an mRNA molecule from a strand of DNA
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Template Strand (Antisense Strand)
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One of the two nucleotide strands of DNA that synthesizes mRNA using transcription
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RNA Polymerase
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Synthesizes RNA Locates genes by searching for specialized DNA regions called promoters Travels along the 3′-5′ route, and synthesizes 5′-3′ Does not proofread, so the transcript isn’t edited
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Promoter Region
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The portion of DNA upstream from a gene; contains the TATA box, which is the site where RNA polymerase II (eukaryotes) binds to start transcription
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TATA Box
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The site of binding for RNA polymerase II during transcription; named for its high concentration of thymine and adenine bases Usually falls around base number -25
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Transcription Factors
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Proteins that help RNA polymerase II locate and bind to the promoter region of DNA RNA polymerase does not require an RNA primer to start transcription
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RNA Polymerase I
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Synthesizes rRNA Located in nucleolus
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RNA Polymerase II
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Synthesizes hnRNA (pre-processed mRNA) and some small nuclear RNA (snRNA) Located in nucleus
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RNA Polymerase III
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Synthesizes tRNA and some rRNA Located in nucleus
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Coding Strand (Sense Strand)
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Not used during transcription because it is also complimentary to the template strand, making it exactly the same as the mRNA strand
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Base Numbering for Transcription
answer

The first base transcribed from DNA to RNA is defined as +1; bases to the left of this position (toward the 5′ end) are given negative numbers (-1, -2, -3…); numbers to the right of this position are given positive numbers (+2, +3, +4…) No base is position 0
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Heterogenous Nuclear RNA (hnRNA)
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Primary transcript formed Precursor to mRNA – produces mRNA via posttranscriptional modifications
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Splicing: Introns and Exons
answer

Posttranscriptional processing Introns = noncoding regions Exons = ligate coding sequences Accomplished by spliceosome – snRNA couples with small nuclear ribonucleoproteins (snRNPs); snRNP/snRNA complex recognizes the 5′ and 3′ ends of the intron, then excised in the form of a lariat and degraded
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Lariat
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The lasso-shaped structure formed during the removal of introns in mRNA processing
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5′ Cap
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Posttranscriptional processing a 7-methylguanylate triphosphate cap is added to the 5′ end of the hnRNA molecule – recognized by ribosome as binding sight and protects mRNA from degradation in cytoplasm
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3′ Poly-A Tail
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Posttranscriptional processing Polyadenosyl (poly-A) tail is added to the 3′ end of the mRNA transcript and protects message from rapid degradation Assists with export of mature mRNA from nucleus
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Alternative Splicing
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The production of multiple different but related mRNA molecules from a single primary transcript of hnRNA
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Nuclear Pore
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A hole in the nuclear envelope that permits the entrance and exit of substrates
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Translation
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The production of a protein from an mRNA molecule Requires mRNA, tRNA, ribosomes, amino acids, and energy in the form of GTP Occurs in cytoplasm of cell
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Ribosome
answer

Composed of proteins and rRNA Made of small and large subunits that bind together during protein synthesis Has three binding site for tRNA: A site (aminoacyl), P site (peptidyl), and E site (exit) Contain 4 strands of rRNA (28S, 18S, 5.8S, and 5S) Genes used to construct the 28S, 18S, 5.8S, and 5S are found in nucleolus and transcribed by RNA polymerase I as a single unit, which results in a 45S precursor RNA RNA polymerase III transcribes the 5S rRNA, and happens outside the nucleolus 18S is found in small subunit; others in large subunit
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Steps of Translation
answer

Initiation, Elongation, Termination
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Initiation
answer

The start of translation, in which the small subunit of the ribosome binds to the mRNA molecule, and the first tRNA (methionine or N-formylmethionine) is bound to the start codon (AUG) Small ribosomal subunit binds 5′ cap on the mRNA (eukaryotes); binds Shine-Dalgarno sequence in the 5′ UTR of the mRNA (prokaryotes) Base pairing occurs in A site in ribosome Initiation factors help bind the large and small ribosomal subunits
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Elongation
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The three-step cycle that is repeated for each amino acid being added to a protein during translation Synthesized N- to C-terminus Elongation factors locate and recruit aminoacyl-tRNA and GTP, and removes GDP after use
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A Site
answer

Holds incoming aminoacyl-tRNA complex This is the amino acid being added next
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P Site
answer

Holds the tRNA that carries the growing polypeptide chain Where methionine binds A peptide bond is formed – requires peptidyl transferase (part of large subunit) – GTP is used as energy for bond formation
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E Site
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Where not inactivated tRNA pauses before exiting the ribosome Quickly unbinds mRNA and is ready to be recharged
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Termination
answer

A stop codon enter the A site and release factors bind the stop codon, causing an H2O molecule to be added to the chain, which allows peptidyl transferase to hydrolyze the chain Protein will be released, and the ribosome sununits dissociate
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Chaperones
answer

Proteins that assist in protein folding during posttranslational processing
question

Carboxylation
answer

Addition of carboxylic acid groups, usually to serve as calcium-binding sites
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Glycosylation (Translation)
answer

Addition of oligosaccharides as proteins pass through the ER and Golgi apparatus to determine cellular destination
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Prenylation
answer

Addition of lipid groups to certain membrane-bound enzymes
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Major Postranslational Modifications
answer

Proper protein folding by chaperones Formation of quarternary structure, Cleavage of protein/signal sequence Addition of other biomolecules (phosphorylation, carboxylation, glycosylation, prenylation)
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Operon
answer

In prokaryotes, a cluster of genes transcribed as a single mRNA that can be regulated by repressors or inducers, depending on the system
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Jacob-Monod Model
answer

The description of the structure and the function of operons in prokaryotes, in which operons have structural genes, and operator site, a promoter site, and a regulator gene
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Structural Gene
answer

Codes for the protein of interest
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Operator Site
answer

A nontranscribable region of DNA that is capable of binding a repressor protein
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Promoter Site
answer

Provides a place for RNA polymerase to bind
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Regulator Gene
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Codes for repressor protein
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Inducible Systems
answer

An operon that requires an inducer to remove a repressor protein from the operator site to begin transcription of the relevant gene The repressor otherwise binds the operator and doesn’t allow RNA polymerase to move down the gene Positive control mechanisms
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Repressible Systems
answer

A operon that requires a repressor to bind to a corepressor before binding to the operator site to stop transcription of the relevant gene Negative control system
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DNA-Binding Domain
answer

Part of transcription factors Binds to a specific nucleotide sequence in the promoter region or to a DNA response element to help recruit transcriptional machinery
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Response Element
answer

A sequence of DNA that binds only to specific transcription factors
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Activation Domain
answer

Allows for binding of several transcription factors and other important regulatory proteins
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Enhancers
answer

A collection of several response elements that allow for the control of one gene’s expression by multiple signals
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Gene Duplication
answer

Cells can increase expression of a gene product by duplicating a relevant gene Can be duplicated in series on the same chromosome, making many copies of the same genetic info in a row Can also be duplicated in parallel – opening up the gene and allowing DNA replication
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Histone Acetylation
answer

A coactivator – involved in chromatin remodeling They acetylate lysine residues found in the amino terminal tail regions of histone proteins
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Acetylation of Histone Proteins
answer

Decreases charge of lysine residues and weakens the interaction of histone with DNA, which opens up chromatin conformation and allows for easier access of transcriptional machinery to DNA
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Histone Deacetylases
answer

Proteins that function to remove acetyl groups from histones, which closes chromatin conformation and decreases gene expression
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DNA Methylation
answer

Involved in chromatin remodeling and regulation of gene expression DNA methylases add methyl groups to cytosine and adenine nucleotides Often associated with silencing gene expression Heterochromatin regions are more heavily methylated
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Cell (Plasma) Membrane
answer

Semipermeable phospholipid bilayer Can select which materials come in and out of the cell – permits fat-soluble compounds easy access; large and water-soluble compounds are harder to cross
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Fluid Mosaic Model
answer

The representation of the plasma membrane as a dynamic phospholipid bilayer with interactions of cholesterol, proteins, and carbohydrates
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Lipid Rafts
answer

Collections of similar lipids with or without associated proteins that serve as attachment points for other biomolecules
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Flippases
answer

Assist phospholipids in their move from between layers of the cell membrane
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Fatty Acids
answer

Carboxylic acids that contain a hydrocarbon chain and terminal carboxyl group
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Cholesterol in Cell Membranes
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Cholesterol stabilizes adjacent phospholipids and occupies the space between them, which prevents the formation of crystals and keeps the membrane fluid Composes ~20% of the membrane by mass and ~50% by mole fraction
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Transmembrane Proteins
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Pass completely through the lipid bilayer Transporters, channels, receptors
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Embedded Proteins
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Associated with the interior (cytoplasmic) or exterior (extracellular) surface of the cell membrane
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Integral Proteins
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Transmembrane and embedded proteins, because of their association with the inside of the plasma membrane
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Membrane-Associated (Peripheral) Proteins
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May be bound through electrostatic interactions with the lipid bilayer, especially at lipid rafts or to other transmembrane/embedded proteins, like G proteins
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Carbohydrates on Cell Membrane
answer

Generally attached to proteins on extracellular surface Can act as signaling and recognition molecules
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Membrane Receptors
answer

Transmembrane protein molecules that act enzymatically or as ion channels to participate in signal transduction
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Cell Adhesion Molecules (CAM)
answer

Specialized structural proteins that are involved in cell-cell junctions as transient cellular interactions; common cell adhesion molecules are cadherins, integrins, and selectins Allow cells to recognize each other and contribute to proper cell differentiation and development
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Gap Junction
answer

Allow for direct cell-cell communication; often found in small bunches Gap junctions = connexons; comprised of six molecules called connexins Permit movement of H2O and some solutes
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Tight Junctions
answer

Cell-cell junctions that prevent the paracellular transport of materials; tight junctions form a collar around cells and link cells within a single layer Prevent solutes from leaking into cell Found in epithelial cells
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Desmosomes
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Bind adjacent cells by anchoring their cytoskeletons Formed by interactions between transmembrane proteins associated with intermediate filaments inside adjacent cells
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Passive Transport
answer

Does not require energy; spontaneous -deltaG Uses concentration gradient
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Active Transport
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Requires energy; nonspontaneous +deltaG
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Simple Diffusion
answer

Substrates move down their concentration gradient directly across the membrane
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Osmosis
answer

The simple diffusion of water Water moves from an area with lower solute (more water) concentration to one with a higher solute concentration (less water)
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Hypotonic
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Concentration of solutes in cell is much higher than outside the cell Will cause a cell to swell as water rushes in (sometimes to the point of bursting)
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Hypertonic
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Concentration of solutes in cell is much lower than outside cell Water will move out of the cell (shrivel)
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Isotonic
answer

When the cell and solution have the same concentration of solute Prevents *net* movement of particles
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Osmotic Pressure
answer

Driving force behind osmosis Colligative property (dependent only on concentrations, not types of solute) II = iMRT (M=molarity of soln; R=ideal gas constant; T=absolute temp (K); i=van ‘t Hoff factor=number of particles obtained from the molecule when in soln) Maintained against cell membrane, not the force of gravity
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Facilitated Diffusion
answer

Type of passive transport – diffusion of molecules down a concentration gradient through a channel in the membrane Used for large, polar, or charged particles
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Carrier Protein
answer

Facilitated diffusion Only open on one side of the cell membrane at any given point – think revolving door Binding of a substrate creates an occluded state (carrier is not open to either side of the bilayer)
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Channels
answer

Facilitated diffusion Have an open or closed conformation When open, they are exposed to both sides of the membrane (like a tunnel)
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Primary Active Transport
answer

Uses ATP or another energy molecule to directly transport molecules across the membrane Generally involves help of a transmembrane ATPase
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Secondary Active Transport
answer

aka coupled transport No direct coupling to ATP hydrolysis Takes energy from one particle going down its electrochemical gradient to drive a different particle up its gradient
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Symport
answer

When both particles from secondary active transport flow in the same direction
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Antiport
answer

When the particles from secondary active transport flow in opposite directions
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Endocytosis
answer

The transport of molecules into a cell through invagination of cell membrane and the formation of a vesicle; phagocytosis is the endocytosis of solid, pinocytosis is the endocytosis of a liquid Substrate binding to specific receptors will activate endocytosis
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Exocytosis
answer

The transport of molecules out of a cell by release from a transport vesicle; the vesicle fuses to the cell membrane during secretion
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Sarcolemma
answer

Must maintain a membrane potential for muscle contraction to occur
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Membrane Potential
answer

The difference in electrical potential across cell membranes (Vm) ~-40 to -80mV Maintaining Vm requires energy
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Nernst Equation
answer

E=RT/zF(ln[ion(outside)/ion(inside)]) = 61.5/z(log[ion(outside)/ion(inside)]) F=96,485 C/mol(e-)
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Goldman-Hodkin-Katz Voltage Equation
answer

*Refer to photo*
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Sodium-Potassium (Na+/K+) Pump
answer

Pumps three Na ions out of a cell and two K ions in Regulates a high concentration of K ions inside Maintains the negative charge of the membrane Cell membranes are more permeable to K+ because there are more K+ leak channels than Na+ channels
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Outer Mitochondrial Membrane
answer

Highly permeable due to many large pores that allow for passage of ions and small proteins Envelops the inner mitochondrial membrane with a small intermembrane space
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Inner Mitochondrial Membrane
answer

More restricted permeability Have cristae, that increase SA to which proteins bind Also encloses the mitochondrial matrix, where the citric acid cycle occurs Contains a high amount of cardiolipin, and does not contain cholesterol
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Glucose Transport
answer

Driven by concentration, independent of Na Normal glucose concentration is 5.6mM (range: 4-6 mM); 4 glucose transporters: GLUT 1 – GLUT 4 GLUT 2 and GLUT 4 are most significant
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GLUT 2
answer

Low-affinity transporter in hepatocytes and pancreatic cells Captures excess glucose from hepatic portal vein, primarily for storage When glucose levels drop below Km for GLUT 2 (~15mM), the liver will pick up glucose in relation to its concentration in the blood (1st order kinetics) – the liver picks up glucose only after a meal when blood glucose levels are high Serves as a sensor for insulin, along with glucokinase
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GLUT 4
answer

In adipose tissue and muscle and responds to glucose concentration in peripheral blood Rate of transport between these tissues increases with insulin Km ~5mM (close to normal blood concentrations) – the transporter is saturated (0-order kinetics) at only a little above this level Decreased insulin = less GLUT 4 transporters on surface of cells; increased insulin = more GLUT 4 transporters on surface of cells Muscle stores excess glucose as glycogen Adipose tissue need glucose to for dihydroxyacetone phosphate (DHAP), which makes glycerol phosphate to store fatty acids as triacylglycerols
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Glycolysis
answer

The breakdown on glucose into two molecules of pyruvate, with the formation of energy carriers (NADH); occurs under both aerobic and anaerobic conditions In the liver, it converts excess glucose to fatty acids for storage
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Hexokinase
answer

Converts glucose to glucose 6-phosphate in peripheral tissues
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Glucokinase
answer

Converts glucose to glucose 6-phosphate; is present in beta-islet cells in the pancreas as part of glucose sensor and is responsive to glucose in the liver
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Glucose Entrance into Cells
answer

Enters by facilitated diffusion or active transport Kinases convert glucose to glucose 6-phosphate GLUT is specific for glucose (not the phosphorylated form) so it gets trapped inside the cell
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Phosphofructokinase-1 (PFK-1)
answer

Rate-limiting enzyme and main control point in glycolysis Fructose-6 phosphate is phosphorylated to fructose 1,6-bisphosphate using ATP Inhibited by ATP and citrate, and activated by AMP Stimulated by insulin; inhibited by glucagon in hepatocytes
question

Phosphofructokinase-2 (PFK-2)
answer

Activated by insulin, which converts fructose 6-phosphate to fructose 2,6-bisphosphate (F2,6-BP) F2,6-BP activates PFK-1 Glucagon inhibits PFK-2, lowering F2,6-BP and inhibiting PFK-1 Found mostly in liver
question

Glyceraldehyde-3-phosphate Dehydrogenase
answer

Catalyzes an oxidation and addition of inorganic phosphate to its substrate, glyceraldehyde 3-phosphate, which results in the intermediate 1,3-bisphosphoglycerate and reduction on NAD+ to NADH NADH can be oxidized if in aerobic glycolysis by electron transport chain, providing ATP synthesis
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3-Phosphoglycerate Kinase
answer

Transfers the high-energy phosphate from 1,3-bisphosphoglycerate to ADP, forming ATP and 3-phosphoglycerate
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Substrate-Level Phosphorylation
answer

The transfer of a phosphate group from a high-energy compound to ATP or another compound; occurs in glycolysis Only means of phosphorylation in anaerobic conditions, because O2 isn’t needed
question

Pyruvate Kinase
answer

Catalyzes a substrate-level phosphorylation of ADP to ATP using phosphoenolpyruvate (PEP) Activated by fructose 1,6-bisphosphate from PFK-1 reaction (feed-forward activation)
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Fermentation
answer

The conversion of pyruvate to either ethanol and carbon dioxide (yeast) or lactic acid (animal cells); does not require O2 Lactase dehydrogenase = main enzyme in mammalian cells – oxidizes NADH to NAD+, replenishing the oxidized coenzyme for glyceraldehyde-3-phoshphate dehydrogenase No net loss of carbon (pyruvate and lactate are 3-C molecules)
question

Dihydroxyacetone phosphate (DHAP)
answer

Used in hepatic and adipose tissue for triacylglycerol synthesis Formed from fructose 2,6-bisphosphate Can be isomerized to glycerol 3-phosphate, which can be converted to glycerol (the backbone of triacylglycerols)
question

1,3-Bisphosphoglycerate (1,3-BPG) and PEP
answer

High-energy intermediates used to generate ATP by substrate-level phosphorylation Only ATP gained in anaerobic respiration
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Irreversible Enzymes of Glycolysis
answer

Glucokinase or hexokinase, PFK-1, pyruvate kinase Catalyze reactions that are irreversible
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Glycolysis in Erythrocytes
answer

Erythrocytes = red blood cells Anaerobic glycolysis, which yields 2 ATP per glucose molecule Have bisphosphoglycerate mutase, which produces 2,3-BPG from 1,3-BPG in glycolysis 2,3-BPG binds allosterically to the beta-chain of hemoglobin A (HbA) and decreases its affinity for oxygen (Things that promote a right shift in the Hb affinity curve: high 2,3-BPG, low pH, high [H+], high pCO2)
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Mutase
answer

Enzymes that move a functional group from one place in a molecule to another
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Galactose Metabolism
answer

A good source of galactose is lactose (disaccharide) Lactose is hydrolyzed into glucose and galactose, then galactose reached the liver through the hepatic portal vein Galactose -phosphorylated by galactokinase-> galactose 1-phosphate -galactose-1-phosphate uridyltransferase-> glucose 1-phosphate
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Epimerases
answer

Enzymes that catalyze the conversion of one sugar epimer to another
question

Fructose Metabolism
answer

Derived from sucrose (table sugar) Sucrose -sucrase-> glucose + fructose are absorbed by the hepatic portal vein fructose -phosphorylated by fructokinase-> fructose 1-phosphate -cleaved by aldolase B-> glyceraldehyde and DHAP
question

Pyruvate Dehydrogenase
answer

A complex of enzymes carrying out multiple reactions in succession Pyruvate is converted to acetyl-CoA, which is then converted into fatty acids for storage or sent into the citric acid cycle Pyruvate Dehydrogenase Complex (PDH) Requires thiamine pyrophosphate, lipoic acid, CoA, FAD, NAD+ Inhibited by acetyl-CoA
question

Glycogen (2)
answer

A branched polymer of glucose that represents a storage form of glucose Synthesis and degradation occur primarily in liver and skeletal muscle Stored in cytoplasm as granules – each granule has a central protein core and polyglucose strands coming out Those composed entirely of long chains have highest density in the core; those that have branched chains have highest density in periphery
question

Glycogenesis
answer

The synthesis of glycogen granules Begins with a core protein called glycogenin and glucose 1-phosphate, which is activated by coupling uridine diphosphate (UDP), which permits integration by glycogen synthase Glucose 1-phosphate + uridine triphosphate -> UDP-glucose + pyrophosphate
question

Glycogen Synthase
answer

Rate-limiting enzyme of glycogen synthesis, forms alpha-1,4 glycosidic bond in linear glucose chains Stimulated by glucose 6-phosphate and insulin Inhibited by epinephrine and glucagon
question

Branching Enzyme
answer

Glycosyl alpha-1,4:alpha-1,6 transferase Responsible for introducing alpha-1,6-linked branches into the granule as it grows Hydrolyzes one of the alpha-1,4 bonds to release a block of oligoglucose, which is moved and added in a slightly different place Forms an alpha-1,6 bond to form a branch
question

Glycogenolysis
answer

The breakdown of glycogen granules
question

Glycogen Phosphorylase (2)
answer

Breaks alpha-1,4 glycosidic bonds by introducing an inorganic phosphate, releasing glucose 1-phosphate from periphery Cannot break alpha-1,6 bonds Activated by glucagon in the liver, and by AMP and epinephrine in skeletal muscle Inhibited by ATP
question

Debranching Enzyme
answer

Glucosyl alpha-1,4:alpha 1,6 transferase and alpha-1,6 glucosidase (both are needed as a complex) Breaks an alpha-1,4 bond adjacent to the branch and moves small polyglucose chain that is released to the exposed end of the other chain Forms new alpha-1,4 bond Hydrolyzes the alpha-1,6 bond, releasing single residue at the branch point (only free glucose produced)
question

Gluconeogenesis
answer

The production of glucose from other biomolecules; carried out by the liver and kidney Promoted by glucagon and epinephrine Inhibited by insulin
question

Important Substrates of Gluconeogenesis
answer

Glycerol 3-phosphate (from stored fats, or triacylglycerols, in adipose tissue) Lactate (from anaerobic glycolysis) Glucogenic amino acids (from muscle proteins)
question

Glucogenic Amino Acids
answer

Can be converted into intermediates that feed into gluconeogenesis (all except leucine and lysine)
question

Ketogenic Amino Acids
answer

Can be converted into ketone bodies, which can be used as an alternative fuel, especially during starvation Leucine, lysine, isoleucine*, phenylalanine*, threonine*, tryptophan*, and tyrosine* *=also glucogenic
question

Important Intermediates of Gluconeogenesis
answer

Lactate, alanine, glycerol 3-phosphate Lactate -lactase dehydrogenase-> pyruvate Alanine -alanine amino transferase-> pyruvate Glycerol 3-phoshphate -glycerol 3-phoshphate dehydrogenase-> DHAP
question

Pyruvate Carboxylase
answer

Mitochondrial enzyme that is activated by acetyl-CoA (from beta-oxidation) -> oxaloacetate (OAA) -reduced-> malate -> leaves cytoplasm via malate-aspartate shuttle -oxidized-> OAA
question

Phosphoenolpyruvate carboxykinase (PEPCK)
answer

Induced by glucagon and cortisol, which raise blood sugar levels Converts OAA -GTP-> PEP -> fructose 1,6-bisphosphate
question

Fructose 1,6-bisphosphate
answer

A key control point of gluconeogenesis; rate-limiting step Reverses action of phosphofructokinse-1 (rate-limiting step of glycolysis) Produces fructose 6-phosphate Activated by ATP and inhibited by AMP and fructose 2,6-bisphosphate – glucagon lowers F2,6-BP (stimulating gluconeogensis); insulin increases F2,6-BP (inhibiting gluconeogenesis)
question

Glucose-6-phosphate
answer

Found only in lumen of the ER in liver cells Used to circumvent glucokinase and hexokinase Absence in skeletal muscle means glycogen cannot serve as a source of blood glucose, it can only be used in muscle
question

Pentose Phosphate Pathway (PPP)
answer

aka hexose monophosphate (HMP) shunt Produces NADPH and serves as a source of ribose 5-phosphate for nucleotide synthesis Involves glucose-6-phosphate dehydrogenase (G6PD) (induced by insulin) Inhibited by NADPH and activated by NADP+ Pentoses can be made from glycolytic intermediates without going through G6PD reaction – accomplished by transketolase and transaldolase
question

NADPH
answer

Acts as an electron donor in many biochemical reactions; potent reducing agent Needed for: biosynthesis (fatty acids and cholesterol); assisting in cellular bleach production in certain white blood cells; Maintenance of a reduced supply of glutathione to protect against oxidative species; protects cells from free radical oxidative damage caused by peroxides
question

Glutathione
answer

A reducing agent that can help reverse radical formation before damage is done to the cell
question

Citric Acid Cycle
answer

A metabolic pathway that produces GTP, carries energy, and carbon dioxide as it burns acetyl-CoA; also called the Krebs Cycle or tricarboxylic acid (TCA) cycle; can share intermediates with many other metabolic processes including fatty acid and cholesterol synthesis, gluconeogenesis, amino acid metabolism, and others Forms FADH2 and NADH Main function is oxidation of acetyl-CoA to CO2 and H2O
question

Pyruvate Dehydrogenase Complex
answer

Made up of five enzymes: 1) pyruvate dehydrogenase (PDH), 2) dihydropropyl transacetylase, 3) dihydrolipoyl dehydrogenase, 4) pyruvate dehydrogenase kinase, and 5) pyruvate drhydrogenase phosphotase (1), (2), and (3) convert pyruvate to acetyl-CoA; (4) and (5) regulate actions of PDH Overall pyruvate -> acetyl-CoA reaction is exergonic (-33.4 kJ/mol) Inhibited by an accumulation of acetyl-CoA and NADH
question

CoA
answer

A thiol (has an -SH group) CoA forms through a covalent attraction between the acetyl group and -SH group, forming a thioester (-SR, instead of -OR) Enzymes needed for catalysis of acetyl-CoA: PDH, dihydropropyl transacetylase, and dihyrolipoyl dehydrogenase
question

PDH in Acetyl-CoA Formation
answer

Pyruvate is oxidized -> CO2 Remaining 2C molecule binds covalently to thiamine pyrophosphate (vitamin B1, TPP – coenzyme held by noncovalent interactions to PDH) Mg2+ is also required
question

Dihydropropyl Transacetylase in Acetyl-CoA Formation
answer

2C molecule bonded to TPP is oxidized and transferred to lipoic acid (a coenzyme covalently bonded to the enzyme) Lipoic acid’s disulfide group acts as an oxidizing agent, creating the acetyl group Acetyl group bonds to lipoic acid via thioester bond DT catalyzes CoA-SH interaction, causing transfer of acetyl to form acetyl-CoA Lipoic acid is left in reduced form
question

Dihydrolipoyl Dehydrogenase in Acetyl-CoA Formation
answer

Flavin adenine dinucleotide (FAD) is used as a coenzyme to reoxidize lipoic acid, allowing lipoic acid to facilitate acetyl-CoA in further reactions FAD is reduced to FADH2, then in further reactions is reoxidized to FAD, and NAD+ is reduced to NADH
question

Fatty Acid Oxidation (Beta-oxidation)
answer

The catabolism of fatty acids to acetyl-CoA A thioester bond forms between carboxyl groups of fatty acids and CoA -> fatty acyl-CoA is transported to intermembrane space -> transferred to carnitine via transesterification reaction -> acyl-carnitine crosses inner membrane -> transfers acyl to CoA-SH via another transesterification reaction Carnitine transfers fatty acyl from cytosolic CoA to mitochondrial CoA Once acyl-CoA is formed in the matrix, beta-oxidation can begin (removes 2 C from the carboxyl end)
question

Activation
answer

The conversion of a biomolecule to its active or usable form, such as activation of tRNA with an amino acid or activation of a fatty acid with CoA to form fatty acyl-CoA
question

Amino Acid Catabolism
answer

Amino acids must lose their amino group via transamination to form acetyl-CoA (the carbon skeletons can form ketone bodies) Termed ketogenic
question

Ketones
answer

Ketone bodies can be used to synthesize acetyl-CoA under certain conditions Used as brain’s major source of energy during starvation
question

Alcohol
answer

Alcohol dehydrogenase and acetaldehyde dehydrogenase convert alcohol to acetyl-CoA Accompanied by NADH buildup, inhibiting the Krebs cycle Used primarily to synthesize fatty acids
question

Step 1 of Citric Acid Cycle
answer

Citrate formation: acetyl-CoA joins with oxaloacetate from a condensation reaction to form citryl-CoA (an intermediate) Hydrolysis of citryl-CoA -> citrate + CoA-SH Catalyzed by citrate synthase
question

Step 2 of Citric Acid Cycle
answer

Citrate isomerized to isocitrate: achrial citrate is isomerized to one of four isomers of isocitrate Citrate binds at 3 points to aconitase, then H2O is lost -> cis-aconitate -> water is added back to form isocitrate Enzyme (aconitase) is a metalloprotein requiring Fe2+ Necessary to facilitate subsequent oxidative decarboxylation
question

Step 3 of Citric Acid Cycle
answer

Alpha-ketoglutarate and CO2 formation: Isocitrate -oxidized by isocitrate dehydrogenase-> oxalosuccinate -decarboxylated-> alpha-ketoglutarate and CO2 Isocitrate dehydrogenase is the rate-limiting enzyme for the citric acid cycle First C from acetyl-CoA is lost here; first NADH is produced from acetyl-CoA
question

Step 4 of Citric Acid Cycle
answer

Succinyl-CoA and CO2 formation: Carried out by alpha-ketoglutarate dehydrogenase complex, similar in mechanism, cofactors and coenzymes to PDH complex Alpha-ketoglutarate and CoA come together to form a molecule of CO2 (second and last C lost from acetyl-CoA) Another NADH is produced by reducing NAD+
question

Dehydrogenase
answer

Subset of oxidoreductases Transfer a hydride ion (H-) to an electron acceptor, usually NADH or FADH2 (high-energy carrier formation)
question

Step 5 of Citric Acid Cycle
answer

Succinate formation: Succinyl-CoA -hydrolysis of thioester bond-> succinate and CoA-SH Coupled to phosphorylation of GDP to GTP (driven by energy released from thioester hydrolysis) Catalyzed by succinyl-CoA synthetase After GTP is formed, nucleosidediphosphate kinase catalyzes phosphate transfer from GTP to ADP, producing ATP (Only time ATP is produced directly in citric acid cycle)
question

Synthetase
answer

Create new covalent bonds with energy input
question

Step 6 of Citric Acid Cycle
answer

Fumarate formation: Occurs on outer membrane (instead of in mitochondrial matrix) Succinate -oxidation-> fumarate Catalyzed by succinate dehydrogenase (a flavoprotein because it is covalently bonded to FAD) FAD -reduced-> FADH2 -transfers electrons to ETC-> 1.5ATP
question

Step 7 of Citric Acid Cycle
answer

Malate formation: Fumarase catalyzes hydrolysis of alkene bond in fumarate, producing malate (only L-malate forms)
question

Step 8 of Citric Acid Cycle
answer

Oxaloacetate formed again: malate -malate dehydrogenase-> oxaloacetate (oxidation) 3rd NAD+ reduced to NADH
question

Net Results of PDH Complex and Citric Acid Cycle
answer

Steps 3, 4, 8: 1 NADH Step 5: 1 GTP (can be converted to ATP) Step 6: 1 FADH2 2 carbons leave as CO2 Each NADH = 2.5 ATP; wach FADH2 = 1.5 ATP, so 4NADH(2.5) + 1FADH2(1.5) + 1GTP(1) = 12.5 ATP per pyruvate; 25 ATP per glucose Glycolysis yields 2 ATP and one NADH, making 7 more ATP, so net ATP yield from glycolysis through oxidative phosphorylation is 30-32 ATP
question

Pyruvate Dehydrogenase Complex Regulation
answer

Phosphorylation of PDH, facilitated by enzyme pyruvate dehydrogenase kinase When ATP levels rise, phosphorylating PDH inhibits acetyl-CoA production PDH complex is reactivated by pyruvate dehydrogenase phosphotase in response to high ADP levels (abel to reactivate acetyl-CoA production)
question

Citrate Synthase
answer

ATP and NADH function as allosteric inhibitors of citrate synthase Citrate and succinyl-CoA inhibit citrate synthase directly
question

Isocitrate Dehydrogenase
answer

Likely to be inhibited by ATP and NADH ADP and NAD+ function as allosteric activators and enhance its affinity for sustrates
question

Alpha-ketoglutarate dehydrogenase complex
answer

Succinyl-CoA and NADH are inhibitors, as well as ATP Stimulated by ADP and Ca ions
question

Complex I of ETC
answer

NADH-CoQ Oxidoreductase: the transfer of electrons from NADH to CoQ Has ~20 subunits. Two important ones: one that has an iron-sulur cluster and one has a flavoprotein that oxidizes NADH; the flavoprotein has FMN (a cofactor – flavin mononucleotide) attached – a lot like FAD NADH -transfers electrons-> FMN -> NAD+ + FMNH2 -> flavoprotein is oxidized; iron-sulfur cluster is reduced -> Fe-S donates e- it got from FMNH2 to CoQ -> CoQH2 Net effect: passing high-energy e- from NADH to CoQ to form CoQH2 (NADH + H+ + CoQ -> NAD+ + CoQH2
question

Complex II of ETC
answer

Succinate-CoQ oxidoreductase: Transfers e- to CoQ from succinate FAD is covalently bonded to complex II; after succinate is oxidized, it’s converted to FADH2 -reoxidation-> FAD + reduced Fe-S -reoxidation of Fe-S-> reduced CoQ No hydrogen pumping for proton gradient is done here Succinate dehydrogenase (oxidizes succinate) is part of this complex also Net effect: passing high-energy e- from succinate to CoQ to form CoQH2 (succinate + CoQ + 2H+ -> fumarate + CoQH2
question

Complex III of ETC
answer

CoQH2-cytochrome c oxidoreductase (aka cytochrome reductase): facilitates transfer of e- from CoQ to cytochrome c 2 cytochrome c molecules are needed because CoQ can transfer 2 e- Main contribution: Q cycle CoQH2 -2 electrons -> CoQ 2 electrons on heme moieties -> reduce cytochrome c – carrier with Fe and S help carry out this reaction 4 electrons get displaced, so it helps to increase the gradient of proton-motive force across inner mitochondrial membrane
question

Cytochromes
answer

Proteins with heme groups in which iron is reduced to Fe2+ and reoxidized to Fe3+
question

Q Cycle
answer

The shuttling of electrons between ubiquinol (CoQH2) and ubiquinone (CoQ) in the inner mitochondrial membrane as a part of Complex III’s function
question

Complex IV of ETC
answer

Cytochrome c oxidase: transfers e- from cytochrome c to oxygen (final e- acceptor) Culminating step Includes subunits of cytochrome a, cytochrome a3, and Cu2+ ions – cytochromes a and a3 make up cytochrome oxidase Final proton pumping 2cytochrome c [with Fe2+] + 2H+ + 1/2O2 -> 2cytochrome c [with Fe3+] + H2O
question

Electrochemical Gradient
answer

An uneven separation of ions across a biological membrane, resulting in potential energy
question

Proton-motive Force
answer

The proton concentration gradient across the inner mitochondrial membrane that is created in the electron transport chain and used in oxidative phosphorylation pH drops; voltage difference between intermembrane space and matrix increases due to proton pumping
question

Shuttle Mechanism
answer

A method of functionally transferring a compound across a membrane without the actual molecule crossing; common examples are the glycerol 2-phosphate shuttle and the malate-aspartate shuttle
question

Glycerol 3-phosphate Shuttle
answer

One isoform of glycerol 3-phosphate dehydrogenase that reduces FAD to FADH2 FADH2 transfers e- to ETC via complex II, generating 1.5ATP for every molecule of cytosolic NADH in this pathway
question

Malate-Aspartate Shuttle
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Cytosolic oxaloacetate is reduced to malate (which can pass through the inner mitochondrial membrane) – accomplished by malate dehydrogenase NADH -reduction-> NAD+ Once malate crosses the membrane, malate dehydrogenase reverses the reaction and forms mitochondrial NADH, which passes its e- to complex I of ETC and generates 2.5ATP per molecule of NADH
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Chemiosmotic Coupling
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The utilization of the proton-motive force generated by the electron transport chain to drive ATP synthesis in oxidative phosphorylation F0 = the portion of the membrane where the proton-motive force interacts with ATP synthase; acts as an ion channel F1 portion = site where energy is released from the electrochemical gradient to phosphorylate ADP to ATP Exergonic (deltaG’ = -220kJ/mol)
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Conformational Coupling
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A less-accepted mechanism of ATP synthase activity in which the protons cause a conformational change that releases ATP from ATP synthase
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Regulation of Oxidative Phosphorylation
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The rates of the citric acid cycle and oxidative phosphorylation are very close, because the products of the citric acid cycle feed into the ETC, and therefore oxidative phosphorylation
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Respiratory Control
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The coordinated regulation of the different aerobic metabolic processes
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Emulsification
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The mixing of two normally immiscible liquids Occurs in duodenum of small intestine Aided by bile Increases SA of lipids
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Bile
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A mixture of salts,pigments, and cholesterol that acts to emulsify lipids in the small intestine Secreted by liver and stored in the gallbladder
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Pancreas Contribution to Digestion
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Secretes pancreatic lipase, colipase, and cholesterol esterase – these enzymes hydrolyze lipids to 2-monoacylglycerol, free fatty acid, and cholesterol
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Micelle Formation
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Free fatty acids, cholesterol, 2-monoacylglycerol, and bile salts contribute to formation of micelles (soluble in aqueous environment of the intestinal lumen) Vital to digestion, transport, absorption of lipid-soluble substances (beginning with duodenum and ending with ileum)
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Absorption by Micelles
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Diffuse to brush border of intestinal mucosal cells and then absorbed -> digested lipids pass through brush border -> absorbed into mucosa -> re-esterified to form triacylglycerols and cholesteryl esters -> packaged with apoproteins, fat-soluble vitamins, and other lipids into chylomicrons -> leave intestine via lacteals (vessels of the lymphatic system) -> re-enter bloodstream via thoracic duct (long lymphatic vessel that empties into left subclavian vein) Shorter, water-soluble fatty acids can be absorbed directly into the bloodstream
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Lipid Mobilization
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A fall in insulin activates hormone-sensitive lipase (HSL), which hydrolyzes triacylglycerols -> fatty acids and glycerol; HSL can be activated by epinephrine and cortisol; HSL is effective in adipose tissue; released glycerol from fat may be transported to the liver for glycolysis or gluconeogenesis Lipoprotein lipase (LPL) is necessry for metabolism of chylomicrons and very-low-density lipoproteins (VLDL); LPL can release free fatty acids from triacylglycerols in these lipoproteins
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Lipoprotein
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The transport mechanism for lipids within the circulatory and lymphatic systems; includes chylomicrons (least dense; highest fat-to-protein ratio) and VLDL (very low density), which transport triacylglycerols; and HDL (high density), IDL (intermediate density), and LDL (low density), which transport cholesterol and cholesteryl esters
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Apolipoprotein
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Protein molecules responsible for the interaction of lipoproteins with cells and the transfer of lipid molecules between lipoproteins; also called apoproteins
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Chylomicrons
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Highly soluble in lymphatic fluid and blood Transport triacylglycerols, cholesterol, and cholesteryl esters Assembly occurs in intestinal lining
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VLDL
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Produced and assembled in liver cells Metabolism is similar to chylomicrons Transports triacylglycerols to other tissues Contain fatty acids synthesized from excess glucose or retrieved from chylomicron remnants
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IDL
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The particle remaining after triacylglycerol is removed from VLDL Either reabsorbed by the liver by apolipoproteins and some is further processed by the bloodstream Intermediate between triacylglycerol and cholesterol transport
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LDL
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Most cholesterol measured in blood is associated with LDL Delivers cholesterol for biosynthesis Bile salts and acids are made from cholesterol in the liver
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HDL
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Synthesizes in liver and intestines; released as dense, protein-rich particles into the bloodstream HDL contains apolipoproteins used for cleaning up excess cholesterol in the bloodstream Delivers some cholesterol to steroidogenic tissues and transfers apolipoproteins to other lipoproteins
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apoA-I
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activates LCAT, an enzyme that catalyzes cholesterol esterification
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apoB-48
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Mediates chylomicron secretion
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apoB-100
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permits uptake of LDL by liver
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apoC-II
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Activates lipoprotein lipase
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apoE
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permits uptake of chylomicron remnants and VLDL by the liver
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Sources of Cholesterol
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Most derive cholesterol from LDL or HDL, but some is synthesized de novo (occurs in liver and is driven by acetyl-CoA and ATP) Citrate shuttle carries mitochondrial acetyl-CoA to cytoplasm -> NADPH supplies reducing equivalents -> synthesis of mevalonic acid (rate-limiting step) in SER -> catalyzed by 3-hydroxy-3-methylglutaryl (HMG) CoA reductase Control mechanisms: increased levels of cholesterol provide negative feedback; insulin promotes cholesterol synthesis, de novo cholesterol depend on HMG-CoA reductase
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Lecithin-Cholesterol Acetyltransferase
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LCAT – an enzyme found in the bloodstream Activated by HDL apoproteins Adds a fatty acid to cholesterol, which produces soluble cholesteryl esters
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Cholesteryl Ester Transfer Protein
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CETP – facilitates transfer of cholesteryl esters onto apoproteins – HDL to IDL to form LDL
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Nomenclature of Fatty Acids
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Total number of carbons is given, along with double bonds, written as carbons:double bonds
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Alpha-linolenic Acid and Linolenic ACid
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Poly-unsaturated fatty acids Important in maintaining cell membrane fluidity
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Omega Numbering System
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Used for unsaturated fatty acids The omega distinction describes the position of the last double bond relative to the end of the chain and identifies the major precursor fatty acid Double bonds in natural fatty acids are generally in the cis configuration
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Nontemplate Synthesis
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Synthesis of lipids and carbohydrates Called so because they do not need a DNA template for synthesis, unlike nucleic acid and protein synthesis
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Fatty acid Biosynthesis
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Occurs in liver and the products are transported to adipose tissue for storage Major enzymes: acetyl-CoA carboxylase and fatty acid synthase (stimulated by insulin) Primary end product: palmitic acid (palmitate)
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Acetyl-CoA Shuttling
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Citrate diffuses across the mitochondrial membrane, where citrate lyase splits citrate into acetyl-CoA and oxaloacetate in the cytosol and oxaloacetate returns to the mitochodrion to continue moving acetyl-CoA
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Acetyl-CoA Carboxylase
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The rate-limiting step of fatty-acid synthesis Requires both biotin and ATP to function, and adds CO2 to acetyl-CoA to form malonyl-CoA Activated by insulin and citrate Incorporates acetyl-CoA into fatty acids
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Fatty Acid Synthase
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aka palmitate synthase (because palmitate is the only fatty acid humans synthesize de novo) Large multi-enzme complex found in cytosol; rapidly induced in liver after a meal Contains an acyl carrier protein (ACP) that requires vitamin B5 (pantothenic acid) NADPH is also required to reduce acetyl groups added to the fatty acid Eight acetyl-CoA groups are required to form palmitate Steps include: ACP attachment, bonding between activated malonyl-CoA (malonyl-ACP) and growing chain, reduction of a carboxyl group, dehydration, reduction of a double bond (many of these are reversed in beta-oxidation)
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Triacylglycerol (Triglyceride) Synthesis
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Formed by attaching three fatty acids to glycerol Occurs primarily in liver and a little in adipose tissue In the liver, triglycerides are packed and sent to adipose tissue as VLDL, leaving only a small amount of stored triacylglyceriols
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Oxidation of Fatty Acids
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Most fatty acid catabolism occurs via beta-oxidation (reverse of fatty acid synthesis); peroxisomal beta-oxidation also occurs Insulin indirectly inhibits beta-oxidation; glucagon stimulates it
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Activation of Beta-Oxidation
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Become activated first by attachment to CoA -catalyzed-> fatty-acyl-CoA synthase -> products referred to as fatty acyl-CoA or acyl-CoA
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Fatty Acid Entry into Mitochondria
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short- (2-4C) and medium-chain (6-12C) diffuse freely into mitochondria, where they are oxidized Long-chain (14-20C) are oxidized in mitochondria, but are transported in via carnitine shuttle Carnitine acyltransferase I is rate-limiting enzyme of fatty acid oxidation Very long-chain (>20C) are oxidized elsewhere in the cell
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Beta-oxidation in Mitochondria
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Beta-oxidation oxidizes and releases (rather than reducing and linking, as in fatty acid synthesis) acetyl-CoA Repeating 4 steps: 1) oxidation of fatty acid to form double bond; 2) hydration of double bond to form a hydroxyl group; 3) oxidation of hydroxyl group to form a carbonyl (beta-ketoacid); 4) splitting of beta-ketoacid into a shorter acyl-CoA and acetyl-CoA (each cycle reduces one NAD+ and one FAD) NAD+ and FAD -oxidized-> ETC Even-numbered fatty acids produce two acetyl-CoA as its final product; odd-numberd fatty-acids produce one acetyl-CoA and one propionyl-CoA -propionyl-CoA carboxylase (needs vitamin B7)-> methylmalonyl-CoA -methylmalonyl-CoA mutase (needs vitamin B12)-> succinyl-CoA (which goes to the citric acid cycle or gluconeogenesis)
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Enoyl-CoA Isomerase
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Rearranges cis double bonds at the 3,4 position to trans double bonds at the 2,3 position once enough acetyl-CoA has been liberated to isolate the double bond within the first three carbons (permits beta-oxidation to proceed in monounsaturated fats)
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2,4-dienoyl-CoA Reductase
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Converts 2 conjugated double bonds to just one double bond at the 3,4 position, where it will undergo the same rearrangement as monounsaturated fatty acids
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Ketone Bodies
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Excess acetyl-CoA from beta-oxidation gets turned into the ketone bodies “acetoacetate” and “3-hydroxybutyrate (beta-hydrozybutyrate)” During fasting, muscle will metabolize ketones as rapidly as the liver releases them, preventing buildup in the bloodstream
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Ketogenesis
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Occurs in mitochondria of liver cells when excess acetyl-CoA accumulates in fasting state HMG-CoA synthase forms HMG-CoA; HMG-CoA lyase breaks down HMG-CoA into acetoacetate -reduced-> 3-hydroxybutyrate
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Ketolysis
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Acetoacetate is activated in mitochondria by succinyl-CoA acetoacetyl-CoA transferase (thiophorase) – present only in tissues outside the liver 3-hydroxybutyrate is reduced to acetoacetate
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Ketolysis in the Brain
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After ~a week of fasting, the brain uses ketone bodies When ketone bodies are broken down to acetyl-CoA, pyruvate dehydrogenase is inhibited -> glycolysis and glucose uptake in the brain decreases (preserves essential proteins that would otherwise be used up to make glucose)
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Protein Catabolism
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Protein digestion in stomach starts with pepsin -pancreatic proteases-> trypsin, chymotrypsin, carboxypeptidases A and B (all secreted as zymogens) Completes by small intestine brush-border enzymes dipeptidase and aminopeptidase Main products are amino acids, dipeptides, and tripeptides -> absorption is done by secondary active transport linked to Na Catabolized mainly in muscle and liver Released amino acids usually lose their amino groups
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Open Systems
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A system capable of exchanging both matter and energy with the environment
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Closed Systems
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A system capable of exchanging energy, but not matter, with the environment
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Internal Energy (U)
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The sum of all of the different interactions between and within atoms in a system; vibration, rotation, linear motion, and stored chemical energies all contribute deltaU = q – w
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Free Energy
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deltaG – provides info about chemical reactions and can predict whether a chemical reaction is favorable and will occur
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Enthalpy
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deltaH – The overall change in heat of a system during a reaction At constant pressure, deltaH and q are equal
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Entropy
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deltaS – The disorder of a system; systems in which entropy is energetically favored is increased and are generally favored (units = 1/K)
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Gibb’s Free Energy Equation
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deltaG = deltaH – T(deltaS) Predicts whether a reaction will occur spontaneously
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Standard Free energy
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deltaG° – occurs as standard 1M, 1atm, and 25degC deltaG = deltaG° + RT(lnQ) Q=reaction quotient
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Modified Standard State
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[H+] = 10^-7M and pH = 7 Under these conditions, deltaG° becomes deltaG°’ meaning it is standardized to the neutral buffers used in biochemistry
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ATP
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Negative charges on the phosphate groups experience repulsive forces with one another and the ADP and Pi molecules that form after hydrolysis are stabilized by resonance deltaG° = -55kJ/mol (under standard conditions); at pH 7 + excess Mg, deltaG° = -30.5kJ/mol ADP has similar deltaG° values, but AMP has lower values at around -10kJ/mol Donates a Pi to other molecules to (in)activate them
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High-Energy Electron Carriers
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NADH, NADPH, FADH2, ubiquinone, cytochromes, glutathione
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Flavoproteins
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A protein bonded to FAD Contain vitamin B2 (riboflavin) Most notable for their presence in mitochondria and chloroplasts as electron carriers Act as cofactors/coenzymes in oxidation of fatty acids, decrboxylation of pyruvate, and reduction of glutathione
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Homeostasis
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The stable internal state of an organism; homeostasis is not synonymous with equilibrium
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Postprandial State
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aka absorptive or well-fed state Occurs shortly after eating; generally lasts 3-5 hrs Nutrients move from the gut to hepatic portal vein to the liver, where they are stored or distributed to other tissues Increases insulin levels (nervous tissue and red blood cells are insensitive to insulin)
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Anabolism
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Synthesis of biomolecules Greater in postprandial state
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Catabolism
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Breakdown of biomolecules for energy
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Postabsorptive State
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aka fasting state Release counterregulatory hormones (glucagon, cortisol, epinephrine, norepinephrine, and growth hormone)
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Prolonged Fasting State
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aka starvation Gluconeogenesis starts after about 12 hours of fasting, and after about 24 hours of fasting, gluconeogensis is the primary source of glucose Muscle tissue will use fatty acids and the brain will use ketone bodies After several weeks of fasting, the brain gets ~2/3 of its energy from ketones, and 1/3 from glucose Calls that have few (or no) mitochondria continue to be dependent on glucose
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Peptide Hormones
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Able to rapidly adjust the metabolic processes of cells via second messenger cascades Water-soluble example: insulin
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Amino Acid-derivative Hormones
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Enact longer-range effects by exerting regulatory actions at the transcriptional level Fat-soluble example: thyroid hormones
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Insulin
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Peptide hormone secreted by beta-cells of the pancreatic islets of Langerhans Adipose tissue and resting skeletal muscle require insulin for effective glucose uptake Tissues that do not require insulin: nervous tissue, kidney tubules, intestinal mucosa, red blood cells (erythrocytes), beta-cells of the pancreas Increases glycogen synthesis; it also increases: glucose and triglyceride uptake by fat cells, lipoprotein lipase activity (clears VLDL and chylomicrons from the blood), triacylglycerol synthesis (lipogenesis) in adipose tissue and the liver from acetyl-CoA Insulin decreases: triacylglycerol breakdown (lipolysis) in adipose tissue, formation of ketone bodies by the liver Plasma glucose = most important insulin controller
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Glucagon
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Peptide hormone secreted by alpha-cells of the pancreatic islets of Langerhans 1) increases liver glycogenolysis (activates glycogen phosphorylase; inactivates glycogen synthase) 2) increases liver gluconeogenesis (promotes PEP -pyruvate carboxylase-> PEPCK; increases F1,6-BP -fructose 1,6-bisphosphotase-> fructose 6-phsophate 3) increases liver ketogenesis; decreases lipogenesis 4) increases lipolysis in liver (activates HSL; glucagon is not a major fat-mobilizing hormone) Low plasma glucose (hypoglycemia) = most important promoter of glucagon; elevated plasma glucose (hyperglycemia) = most important inhibitor Secreted in response to protein-rich meals
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Glucocorticoids
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Responsible for part of the stress response; from adrenal cortex Example: cortisol Cortisol inhibits glucose uptake in most tissues (muscle, lymphoid, fat); increases hepatic output of glucose via gluconeogenesis
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Catecholamines
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Secreted by adrenal medulla and include epinephrine, norepinephrine (aka adrenaline and noradrenaline, respectively) Increase liver activity and muscle glycogen phosphorylase (promoting glycogenolysis) Increase lipolysis in adipose tissue by activating HSL
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Thyroid Hormones
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Levels are kept more or less consistent, rather than changing with metabolic state Increase basal metabolic rate thyroxine 4 (T4) increases metabolic rate (may last for several hours or days) trĂŒodothyronine (T3) increases metabolic rate for short periods of time -subscripts indicate # of iodine atoms attached -T4 is precursor to T3 (iodine removed by deiodonases) Accelerate cholesterol clearance from plasma and increase rate of glucose absorption from small intestine
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Liver Metabolism
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Two major functions: keep glucose levels relatively constant, synthesize ketones when excess fatty acids are being oxidized Increased insulin -> glycogen and fatty acid synthesis -> triacylglycerols -> released as VLDL During the well-fed state, liver derives its energy from excess amino acid oxidation
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Adipose Tissue Metabolism
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Elevated insulin increases glucose uptake in adipose tissue, also increases lipoprotein lipase Fatty acids taken up by adipose tissue are re-esterified to triacylglycerols for storage During fasting, decreased insuline/increased epinephrine activate HSL
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Resting Muscle Metabolism
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Glucose and fatty acids = main energy sources After a meal, glucose uptake is used for protein synthesis During fasting, uses fatty acids derived from free fatty acids flowing in the bloodstream (ketone bodies may also be used)
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Active Muscle Metabolism
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Short bursts (2-7sec) use creatine phosphate (transfers a phosphate group from ADP to ATP); also supported by anaerobic glycolysis Has stores of glycogen and triacylglycerols High-intensity exercise glucose and fatty acids are oxidized After 1-3 hours of intense exercise, glucose levels become depleted, and declines to a rate that can be supported by oxidation of fatty acids
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Cardiac Muscle Metabolism
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Prefer fatty acids as their major energy source, even in well-fed state Ketones can also be used during fasting In a failing heart, glucose oxidation increases; beta-oxidation decreases
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Brain Metabolism
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Glucose is primary fuel In hypoglycemic conditions (<70mg/dL) hypothalamic centers trigger release of glucagon and epinephrine Fatty-acids can't cross blood-brain barrier, so they are not used at all Only during prolonged starvation can ketone bodies be used by the brain
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Respirometry
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A method of measuring metabolism through the consumption of oxygen
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Respiratory Quotient
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RQ = (CO2 produced)/(O2 consumed) For carbs ~1.0 Lipids ~0.7 Resting individuals ~0.8
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Calorimeter
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A device for measuring the heat change during the course of a reaction
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Basal Metabolic Rate
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The amount of energy consumed in a given period of time by a resting organism
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Hormones that Control Hunger
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Ghrelin, orexin, leptin
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Ghrelin
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Secreted by the stomach in response to signals of an impending meal i.e. sight, sound, taste, and especially smell Increases appetite and stimulates release of orexin
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Orexin
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Increases appetite Also involved in alertness and the sleep-wake cycle Hypoglycemia activates orexin
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Leptin
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Decreases appetite by suppressing orexin production