Amino Acids and Proteins

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1 Amino Acids and Proteins

2 Proteins are composed of amino acids. There are 20 amino acids commonly found in proteins. All have: N2 C α R COO

3 Amino acids at neutral p are dipolar ions (zwitterions) because their α-carboxyl and α-amino groups are ionized. + N3 C R COO

4 Titration curve for Glycine: pk2 p pk1 COO= COO- N3+= N [NaO]

5 Structure of glycine at differing p values: + N3 C COO + N3 C COO p=1 p=7 N2 C COO p=11

6 pk2 8 N3+ p pk1 COO Isoelectric point (no net charge) 0. 5 [NaO]

7 Aliphatic Non-Polar Amino Acids 2+ N C C 2 3+ N- C - 3+ N- C - C 2 C C 2 proline 3+ C 2 C C 3 C 3 leucine C 3 alanine 3+ C 3 - C - C 3 C 2 isoleucine C 3 C 3 valine 3+ C 2 C 2 S C 3 methionine

8 Aromatic Non-Polar Amino Acids C 2 phenylalanine C 2 C C N tryptophan

9 Polar Uncharged Amino Acids 3+ glycine C 2 O serine pka=13 3+ CO C 3 threonine pka=13 C 2 3+ O tyrosine pka=10.1 C 2 S cysteine pka=8.3

10 Serine and Threonine can be POSPORYLATED: ATP ADP, Pi N - C - C 2 O 2- C 2 OPO 3 serine serine ATP ADP, Pi N - C - CO 2- COPO 3 C 3 threonine C 3 threonine

11 3+ C 2 S S C 2 3+ N- C - Disulfide Bond:Two cysteine residues condense. Disulfide bonds may occur between cyteine residues within the same protein (intrachain) or between two cystein residues occuring in different proteins (interchain). Disulfide formation is a major factor in the determination of protein structure. Permanent waving is the result of the reduction of disulfides in the α-keratin protein (that hair is made of) and spontaneous re-oxidation of those disulfide bonds in air.

12 Polar Uncharged Amino Acids 3+ C 2 C O N 2 asparagine 3+ C 2 C 2 C O N 2 glutamine

13 Acidic Amino Acids O C 2 C O - aspartate pka=3.9 O C 2 C 2 C O - glutamate pka=4.3

14 Basic Amino Acids C 2 C 2 C 2 C 2 N 3 + Lysine pka=10.5 C 2 C 2 C 2 N C 2+ N N 2 arginine pka=12.5 C 2 C= C N N C histidine pka=6.0

15 Chirality in Amino Acids CO O - C - C 2 O L-Glyceraldehyde CO - C - O C 2 O D-Glyceraldehyde COO 3+ C 3 L-Alanine COO + - C - N 3 C 3 D-Alanine L amino acids occur in proteins!

16 The Peptide Bond Bond occurs between the α-amino group of one amino acid and the α-carboxyl group of another amino acid A condensation reaction where the elements of 2 0 are removed

17 O C - O 2 COO

18 O C 2 - O - COO

19 O C 2 - O - COO

20 O C 2 The Peptide Bond!! COO O C 2 COO

21 Functions of Proteins: Enzymes Regulatory Proteins Structural Transport Storage Contractile Three Classes Based on Shape and solubility: Fibrous (collagen) Globular (enzymes) Membrane (CP 43)

22 Conjugated Proteins: Prosthetic groups: non-amino acid components Coenzyme: organic molecules (vitamins) involved in catalysis Metalloproteins Phosphoproteins Glycoproteins Lipoproteins Nucleoproteins

23 Protein chains have a direction. By convention the N-terminus is taken to be the beginning of a polypeptide chain. O O N 2 - C - C - C - COO C 3 Glycine-Glycine-Alanine

24 Protein Architecture Conformation: The spatial arrangement of atoms in a protein. There are 4 levels of organization: 1) Primary Structure: linear sequence of amino acids in a polypeptide. 2) Secondary Structure: local conformation of the peptide backbone.

25 The Peptide Bond is a Resonance Structure: O C 2 COO O - N + C 2 N + - C - COO

26 Peptide bonds are resonance structures and cannot freely rotate Rotation occurs only about the N-C a (phi; φ ) and C-C a (psi; ψ) bonds

27 Each carboxyl oxygen is hydrogen bonded to the amino group of the amino acid four residues above Single turn = 0.56 nm = 3.6 amino acids Stretches of + and - charged amino acids destabilize; proline destabilizes; amino acids with bulky R groups destabilize; polyleucine and polyalanine are good helix formers. α-elix

28 C C N N N C Parallel; 5 sheets or more β-pleated sheet Anti-Parallel: 2 or more sheets; silk is an example C N Glycine and Alanine often found in β-sheets

29 Composed of 4 amino acids; the first is hydrogen bonded to the fourth β-bend Glycine (small and flexible) and proline (kinks) occur in β-bends

30 Secondary structures are arranged into domains or modules. 3) Tertiary Structure: the way in which the secondary structural elements are folded; the spatial distribution of side chains. ydrophobic effect is a major factor in determining the folding pattern Secondary structural elements fold first to maximize -bonds; then interactions between these elements occur

31 4) Quaternary Structure: subunit organization; kinds of subunits, number of subunits and the ways in which they interact with one another. Multisubunit proteins are also referred to as oligomers. Proteins composed of a single type of monomer are homomultimeric; those composed of two or more different subunits are heteromultimeric. emoglobin has two each of two different subunits; it s structure is designated α 2 β 2.

32 Forces Driving Quaternary Association: ydrogen Bonding Electrostatic Interactions Van Der Waals Interactions ydrophobic Interactions

33 Structure determines function: one way to study this relationship is to alter the structure and determine its effect on function. Protein Denaturation: Loss of tertiary and quaternary structure (sometimes 2 o structure). β-mercaptoethanol: disulfide reducing agent SDS: detergent; disrupts hydrophobic core urea: disrupts hydrogen bonds water: disrupts electrostatic interactions organic solvents: disrupts interactions of hydrophobic residues temperature: complete denaturation

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