Biochemistry | Chapter 1 | Amino Acids, Peptides, and Proteins

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Non polar, Nonaromatic Side Chains
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-Glycine -Alanine -Valine -Leucine -Isoleucine -Methionine -Proline
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Glycine
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3 Letter Abbreviation: Gly 1 Letter Abbreviation: G -Single H atom as side chain -Achiral
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Alanine
Alanine
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3 Letter Abbreviation: Ala 1 Letter Abbreviation: A
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Valine
Valine
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3 Letter Abbreviation: V 1 Letter Abbreviation: Val
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Leucine
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3 Letter Abbreviation: Leu 1 Letter Abbreviation: L
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Isoleucine
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3 Letter Abbreviation:Ile 1 Letter Abbreviation: I
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Methionine
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3 Letter Abbreviation: Met 1 Letter Abbreviation: M – One of only 2 amino acids that has a Sulfur atom in its side chain
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Proline
Proline
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3 Letter Abbreviation: Pro 1 Letter Abbreviation: P – Unique, forms a cyclic amino acids – The ring –> LESS flexibility –> Strains its role in secondary structure
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All chiral amino acids used in Eukaryotes are __-amino acids
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L. NOT D.
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Aromatic Side Chains
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-Tryptophan -Phenylalanine -Tyrosine
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Tryptophan
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3 Letter Abbreviation: Trp 1 Letter Abbreviation: W – Largest aromatic A.A.
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Phenylalanine
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3 Letter Abbreviation: Phe 1 Letter Abbreviation: F – Nonpolar
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Tyrosine
Tyrosine
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3 Letter Abbreviation: Tyr 1 Letter Abbreviation: Y – Polar
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Polar, Non-aromatic Side Chains
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-Serine -Threonine -Asparagine -Glutamine -Cysteine
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Serine
Serine
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3 Letter Abbreviation: S 1 Letter Abbreviation: Ser -Highly Polar & Able to participate in H bonding
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Threonine –
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3 Letter Abbreviation: Thr 1 Letter Abbreviation: T -Highly Polar & Able to participate in H bonding
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Asparagine
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3 Letter Abbreviation: Asn 1 Letter Abbreviation: N – Amide side chain
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Glutamine
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3 Letter Abbreviation: Gln 1 Letter Abbreviation: Q -Amide side chain
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Cysteine –
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3 Letter Abbreviation: Cys 1 Letter Abbreviation: C -Thiol side chain – THE ONLY AMINO ACID THAT IS NOT “S”
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Negatively Charged (Acidic) Side Chains
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-Aspartic Acid -Glutamic Acid
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Aspartic Acid (Aspartate = Deprotonated form)
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3 Letter Abbreviation: Asp 1 Letter Abbreviation: D
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Glutamic Acid (Glutamate = Deprotonated form)
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3 Letter Abbreviation: Glu 1 Letter Abbreviation: E
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Positively Charged (Basic) Side Chains
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-Lysine -Arginine -Histidine
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Lysine
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3 Letter Abbreviation: Lys 1 Letter Abbreviation: K
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Arginine
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3 Letter Abbreviation: Arg 1 Letter Abbreviation: R
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Histidine
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3 Letter Abbreviation: His 1 Letter Abbreviation: H
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Hydrophobic Amino Acids
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Long alkyl side chains -Alanine -Valine -Leucine -Isoleucine -Methionine -Tryptophan -Tyrosine -Phenylalanine
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Hydrophilic Amino Acids
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Charged Side chains (+) -Histidine -Arginine -Lysine (-) -Glutamate -Aspartic acid Amides -Asparagine -Glutamine
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Amphoteric Species
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Can either accept or donate a proton
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pH and pKa relationship
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pKa = The pH at which half of the molecules in that substance are protonated Soooooooooo…… [HA] = [A-] [Pronated form] = [Deprotonated form]
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If the ph is smaller than the pka
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A higher percentage of the species will be pronated
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If the pH is larger than the pKa
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A lower percentage of the species will be pronated
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pKa’s of amino acid componenets
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The carboxyl group = ~pKa = 2 The amino group = ~pka = 9-10
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Amino Acids @ low pH’s (pH = 1) (<– Stomach acid)
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So the pH is lower than pKas–> protonated (+) Charged!
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Zwitterions @ Normal pH (~pH=7.4) (<– Blood)
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The carboxyl = Is NOT protonated The amino = IS protonated
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Amino Acids @ high pH’s (pH = 10.5) (<–milk of magnesia)
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So the pH is higher than pKas—> un-protonated (-) Charged!
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Isoelectric point formula
Isoelectric point formula
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pKi = pKa of NH3 pKj = pKa of COOH If acidic, replace NH3 with R group If basic, replace COOH with R group
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Amino acid side chains and PI values relationship
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Acidic Sides chains = pI values below 6 Basic side chains = pI values above 6
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Peptides are composed of amino acids subunits called ______
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Residues
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The residues are joined together through ________ ________
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Peptide bonds
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Peptide bonds
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-Covalent -Water is a byproduct
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Peptide Bond Resonance
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1° Structure
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-Linear arrangement of amino acids -N-terminus –> C-terminus -Encodes all the information for folding at the higher levels of structure -1° Structure can be determined by a technique called sequencing
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2° Structure
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-Result of H-bonding – 2 most common structures – Alpha helix – Beta pleaded sheet AA with proline -RARE in alpha helix -ALTHOUGH, could be the starting residue -RARE in the middle of B sheet also – Found in the turns between he chains
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Alpha Helix
Alpha Helix
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– Stabilized: Intramolecular hydrogen bonds between carbonyl’s O and and the amide’s H four residues down the chain – Side chains point AWAY from the cord – IMPORTANT comp. of keratin
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Beta pleaded sheet
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– can be PARALLEL or ANTIparallel – To accommodate the most hydrogen bonds, this is PLEADED – R groups –> Point ABOVE & BELOW the plane IMPORTANT comp. of Fibroin
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3° Structure
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– The 3D shape Determined by : –Hydrophilic and hydrophobic interactions between the R groups (Phobic = Inside the protein) –H bonds –Disulfide bonds
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Disulfide Bonds
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-When two CYSTEINE molecules are oxidized, they from CYSTINE – These disulfide bonds that are formed from this process create loops in the protein shape
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Molten Globules
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Intermediate stage between secondary and tertiary
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Solvation layer
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A protein is most stable when the hydroPHILIC side chains are on the outside of the protein. This increases entropy, and as a result deems this as spontaneous, and more STABLE
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4° Structure
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-Not all proteins have this -Exists for proteins with more than 1 polypeptide chain -Combination of subunits, and the FUNCTIONAL form of a protein
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Advanteges to having a 4° Structure
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-Stable, because reduces surface area -Reduce the amount of DNA needed to encode the complex -Bring catalytic sites together, allow intermediates from one reaction to be directly shuttled to a second reaction -COOPERTIVITY, or ALLOSTERIC effects
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Conjugated Proteins
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-Function stems from prosthetic groups -Proteins with lipid, carb, or nucleic acid prosthetic groups are lipoproteins, glycoproteins, nucleoproteins
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Prosthetic groups
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-Vitamins -Metals, such as Iron -Heme
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Heme
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Iron group at core Binds to oxygen
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Denaturation & Heat
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Temp increases kinetic energy. BUT, when temp gets TOO high, the hydrophobic compounds in the middle of the compounds, unfold
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Denaturation & Solutes
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Solutes can disrupt the disulfide bonds in cystine, resulting in two cysteine residues, and NO quat/tert structure

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