Biochemistry: Amino Acids, Peptides, Proteins

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alpha amino acid
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when the amino and carboxyl group are on the same carbon
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Glycine
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only amino acid that is not chiral
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L-amino acids
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all chiral amino acids in eukaryotes, amino group on left side of the fisher projection, S configuration
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Cysteine Configuration
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L- amino acid, R configuration
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Nonpolar nonaromatic amino acids
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Glycine, Alanine, Valine, Leucine, Isoleucine, Methionine, Proline
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Methionine
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1 of 2 with sulfur atom on side chain, nonpolar/nonaromatic
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Proline
Proline
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forms a cyclic amino acid, contrains on flexibility, non polar
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Amino acids with alkyl side chains
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alanine, valine, leucine, isoleucine, phenylalanine, proline
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Aromatic Amino Acids
Aromatic Amino Acids
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Tryptophan, Phenylalanine, Tyrosine
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Tryptophan
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largest aromatic amino acid side chain
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Phenylalanine
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smallest aromatic amino acid side chain, non polar
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Tyrosine
Tyrosine
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relatively polar, aromatic amino acid
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Polar amino acids
Polar amino acids
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Serine, threonine, Asparagine, Glutamine, Cysteine
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Serine and Threonine
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OH makes them highly polar and able to participate in H-bonding
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Asparagine and Glutamine
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amide N’s do NOT gain or lose protons with change in pH
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Cysteine
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thiol group, S is larger than O making the S-H bond weaker than OH Thiol group more prone to oxidation
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Positively Charged Amino Acids
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basic, arginine, lysine, histidine
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Arginine
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positive charge delocalized over 3 nitrogens
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Histidine
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imidazole, at pH 1 atom is protenated at highly acidic pH, 2nd N becomes protenated–>R positive charge
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Hydrophobic Amino Acids
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amino acids with long alkyl chains -alanine, valine, leucine, isoleucine, phenylalanine -found at interior of protein
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Hydrophilic Amino Acids
Hydrophilic Amino Acids
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glutamate, aspartate, histidine, lysine, arginine, glutamine, asparagine
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Negatively Charged Amino Acids
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Aspartic Acid-aspartate, Glutamic Acid-Glutamate
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At a low pH, ionizable groups of aa tend to be _____
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Protenated
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At a high pH, ionizable groups of aa tend to be _____
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deprotenated
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pH<pKa
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majority of species is protenated
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pH>pKa
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majority of species is deprotenated
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pKa
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the pH at which, on average, half of the molecules of a species are deprotenated
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pKa 1 of an amino acid
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Carboxyl group (~2)
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pKa 2 of glycine
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Amino group (~9-10)
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Glycine at pH 1
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-many protons – pH<pKa2=amino group is protenated (+1) -pH<pKa1=carboxy group is protenated (0) -aa is positively charged
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Glycine at Intermediate pH
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zwitterion -pH>pKa1= carboxy group deprotenated (-1) -pH<pKa2=amino group protenated (+1) -neutral molecule
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Glycine under Basic Conditions
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-pH>pKa1= carboxy group deprotenated (-1) -pH>pKa2= amino group deprotenated (0) – -1 charge
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When does the solution during a titration act as a buffer?
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When pH of solution is almost equal to pKa of solute
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Isoelectric Point
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Isoelectric Point
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when the molecule is neutral, very sensitive to pH change
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Equation of isoelectric Point
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pKa2+pKa1/2
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The pI for acidic amino acids is
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lower than neutral amino acids -pKa of R group substitutes amino pKa
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The pI for basic amino acids is
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higher than neutral amino acids -pKa of R group substitutes carboxy pKa
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peptide bond
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COO- — NH3+
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Peptide Bond Formation
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condensation/dehydration removes H20 acyl substitution
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hydrolytic enzymes
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chymotrypsin, trypsin specific and cleave at specific points on peptide chain
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Peptide destruction
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Hydrolysis add H to amide N and OH group to carbonyl C
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Primary structure of Protein
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linear arrangement of amino acids encodes all info needed for folding determined by sequencing
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Secondary Structure of Protein
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local structure of neighboring amino acids result of H-bonding (alpha helices, Beta Pleated Sheets)
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alpha helices
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rod like structure -side chains of aa point away from helix core
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Beta-pleated sheets
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parallel or anti-parallel peptide chains forming rows -rippled and pleated -aa point above or below sheet
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Secondary Structure and Proline
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rigid structure -kink in a-helix -turns between chains of B sheets
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Fibrous Proteins
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structures that resemble long strands and sheets collagen
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Globular Proteins
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spherical globin
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Tertiary Structure
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3D shape determine by hydrophilic and hydrophobic interactions between R groups of amino acids -determined by H bonding -determined by acid base interactions between aa with charged R groups
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Salt Bridges in amino acids
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when R groups of different aa interact with one another
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Disulfide Bond
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2 cysteine molecules oxidized–>cystine
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denaturation
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protein loses tertiary structure
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Entropy in Tertiary Structures of Proteins
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causes hydrophobic regions to move inward, philic to move outward
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Hydrophobic R groups Dissolve Process
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H20 cannot bind to R so it must rearrange to maximize H bonding – -S (entropy) -less disorder -non spontaneous
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Hydrophilic R groups in Dissolve Process
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H20 binds to R–>increase entropy–>increase disorder -spontaneous
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Quarternary Structure
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only exist for proteins with 1+ polypeptide chains -functional form of the protein
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Roles of Quarternary Structure
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1. increase stability, decrease surface area 2. lower amount of DNA needed to encode protein complex 3. bring catalytic sites together 4. induce cooperativity and allosteric effects
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Conjugated Proteins
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derive part of their function from covalently attached molecules called prosthetic groups

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