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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

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3 Letter Abbreviation: Ala 1 Letter Abbreviation: A

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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

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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

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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

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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

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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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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

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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

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

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