Biochemistry WGU

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RNA polymerase
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Enzyme that facilitates transcription
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Transcription
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synthesis of an RNA molecule from a DNA template
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Ribosome
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Large macromolecular complex where proteins are synthesized
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tRNA (transfer RNA)
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Form of RNA that is complementary to mRNA. Has a neucleotide anticodon on one end and an amino acid in the other.
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Translation
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decoding of a mRNA message into a polypeptide chain
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Coding strand (DNA)
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The original strand off which the new nucleotide sequence is based. Almost the same as mRNA
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template strand (DNA)
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The strand mRNA uses to make a copy. Complementary to mRNA
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missense mutation
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base substitution results in change in an amino acid
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nonsense mutation
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changes a normal codon into a stop codon
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silent mutation
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change in DNA that codes for the same amino acid
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Replication
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process of copying DNA prior to cell division
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DNA polymerase III
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synthesizes new DNA only in the 5′ to 3′ direction Needs a primer to start
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polymerase chain reaction (PCR)
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Copying DNA in lab. Used to study/diagnose
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PCR needs
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Target DNA dNTPs (deoxyneucleotides) DNA primers Taq polymerase (stable at high temps)
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Helicase
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An enzyme that untwists the double helix of DNA at the replication forks.
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Ligase
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An enzyme that connects two fragments of DNA to make a single fragment
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Repair for damage to bases from harmful molecules (like chemicals)
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Base excision (removes damaged base and replaces it)
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Mismatch repair
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Repair for base mismatches due to errors in replication
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Repair for double stranded breaks in DNA (Radiation/x-rays)
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Homologous recombination (using sister chromosome as model) Non homologous end joining (no model available)
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Nucleotide excision
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Repair for damage from UV which causes adjacent nucleotides to fuse together (thiamine dimers)
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Amino acid sequence wraps around proteins called
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Histones
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Histones organize to form
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Nucleosomes
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Nucleosomes organize to form
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Chromatin
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Chromatin organizes to form
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A chromosome
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Complete dominance
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When the phenotypes of the heterozygote and dominant homozygote are indistinguishable.
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Codominance
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A condition in which neither of two alleles of a gene is dominant or recessive. Both phenotypes are expressed.
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Incomplete dominance
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when the phenotypes of the two alleles blend
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Point mutations
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chemical changes in just one base pair of a gene
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frameshift mutations
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Insertions and deletions
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4 parts of an amino acid
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Carboxyl group Alpha carbon Amino group R side chain
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COO- I H – C – R I NH3+
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Abbreviated structure (amino acid)
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3 types of amino acids
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Hydrophobic Polar Charged
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Bonds in hydrophobic amino acids
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C-C, C-H
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Bonds in polar amino acids
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O-H N-H S-H
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Primary protein structure
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Sequence of amino acids form peptide bonds
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Secondary protein structure
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Hydrogen bonding of the peptide backbone causes amino acids to fold into a repeating pattern
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tertiary protein structure
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3-D folding pattern of a protein due to side chain interactions
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Quaternary protein structure
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Protein consisting of more than one amino acid chain
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hydrophobic interactions
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Weak interactions between amino acids in a protein that come together to avoid water and can be disrupted by heat
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2 types of bonds in polar interactions
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Hydrogen bonds Disulfide bonds
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Hydrogen bond
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Weak bond where hydrogen from a polar amino acid attracts an electronegative atom like O & N. Can be disrupted by heat and change in pH.
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Disulfide bond
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Very strong covalent bond between two sulfur atoms. Can only be broken by chemical agents.
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Ionic bonds
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Bonds in charged interactions between +R group and -R group. Moderately strong, can be broken by change in pH or by salts.
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Dehydration reaction
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Creates a peptide bond by removing water.
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Hydrolysis
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Breaking peptide bonds by adding water.
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protein phosphorylation
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The attachment of a phosphate group of a polar amino acid group.
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Protein dephosphorylation
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Removal of a phosphate group of a polar amino acid.
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competitive inhibitor
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A molecule similar to a substrate that can bind to the enzymes active site. Reversible Increased substrate=increase in reaction
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Non competitive inhibitors (allosteric)
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A molecule that binds to a place on the enzyme other than the active site that changes the shape of the enzyme which interferes with the binding of the substrate. Some reversible, some permanent. Increased substrate does not = increased reaction
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Feedback inhibition
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When end product is no longer being consumed and starts accumulating, the end product binds with the initial enzyme, stopping it from bonding with the substrate. Reversible
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Ways to target enzymes in disease
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Modify diet (like HFI-removing fructose from diet) Enzyme therapy (like CF to increase digestive enzymes) Drugs that increase substrate of an enzyme(like Parkinson’s with LDopa) Drugs that inhibit enzyme activity (like viagra)
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Myoglobin affinity and location
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High O2 affinity, stores O2 in muscles
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Hemoglobin affinity and location
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Lower O2 affinity, picks up O2 in lungs and delivers to body
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Myoglobin structure
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1 protein subunit (1 heme group and 1 iron)
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Hemoglobin structure
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4 protein subunits
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Cooperativity
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In Hgb, if 1 heme gets filled the other 3 want to get filled. If 1 O2 leaves, the others tend to leave.
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Hemoglobin in the lung -5 qualities
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Higher O2 affinity Relaxed state Higher pH Low CO2 Low H+
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Hemoglobin in muscle-5 qualities
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Lower O2 affinity Tense state Lower pH High CO2 Lots of H+
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The Bohr effect
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The difference of O2 affinity at different pH Shift to left= in higher pH- higher affinity Shift to right= in lower pH- lower affinity
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sickle cell anemia cause
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A mutation in the beta subunit of hemoglobin which leads to insertion of valine into the hydrophobic patches on deoxygenated Hgb.
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ATP
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Molecule that fuels our body’s activity
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3 major steps in aerobic metabolism
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Glycolysis Citric acid cycle (CAC) or Kreb’s cycle Electron transport chain (ETC)
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Inputs of cellular respiration
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O2 and sugar
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Outputs of cellular respiration
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CO2, H2O, ATP
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Cellular respiration
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The process our bodies use to convert food to energy.
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Mitochondria
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Organelle of a cell where much of cellular respiration occurs.
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Glycolysis location
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Cytoplasm
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Glycolysis inputs
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Glucose 2 ATP 4 ADP 2 NAD+
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Glycolysis outputs
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2 pyruvate 2 NADH 4 ATP 2 ADP
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Pyruvate moves into the ________ and is converted to ________.
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Matrix, Acetyl CoA
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Citric acid/ Krebs cycle location
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Matrix
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Citric acid/ Krebs cycle inputs
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Acetyl CoA NAD+ GDP FAD
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Citric acid/ Krebs cycle outputs
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CO2 NADH GTP FADH2
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Electron transport chain location
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Inner membrane
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Electron transport chain inputs
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NADH FADH2 O2 ADP + P
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Electron transport chain outputs
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NAD+ FAD H2O ATP
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At the end of the ETC, ATP is formed when
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Protons (H+) in the intermembrane rush through ATP synthase in the inner membrane and into the matrix.
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What occurs when no O2 is present?
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ETC cannot occur. Instead fermentation happens.
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Fermentation converts _________ into __________.
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NADH, NAD+ and 2 lactates
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What happens in the Cori cycle?
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Fermentation To liver where 2 lactates are converted to glucose using 6 ATP Glucose goes back into blood stream and to cells.
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Cori cycle has a net loss of _________.
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4 ATP
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Glut 4
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Cell doorways for glucose.
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Insulin _________ the Glut4 doors.
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Opens
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Glucagon __________ the Glut4 doors.
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Closes
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Glycogenesis
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Glucose forms a chain called glycogen. Happens in the liver when it detects insulin.
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Glycogenolysis
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Break down of glycogen to glucose to be released into blood stream. Happens in liver when it detects glucagon.
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In diabetes, glucose and protein do what?
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Bond to form a glycated protein. Glycated proteins aggregate to form Advanced Glycation End Products (AGEs)

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