Amino Acids, Peptides, Proteins - Chemistry

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Amino Acids, Peptides, Proteins. Functions of proteins: Enzymes. Transport and Storage. Motion, muscle contraction. Hormones. Mechanical support. Immune ...
Amino Acids, Peptides, Proteins Functions of proteins: Enzymes Transport and Storage Motion, muscle contraction Hormones Mechanical support Immune protection (Antibodies) Generate and transmit nerve impulses Control growth and differentiation Lens protein in eye Feathers Spider webs Horns Milk proteins Antibiotics Mushroom poison …..

Luciferin, luciferase

Hemoglobin

Amino Acids General structure α carbon, side chain (R group)

Amino Acids

Amino Acids

Amino Acids

Amino Acids

Amino Acids

Amino Acids Amino Acid

Abbreviations

Nonpolar, aliphatic R group Glycine Alanine Proline Valine Leucine Isoleucine Methionine

Gly Ala Pro Val Leu Ile Met

G A P V L I M

Aromatic R groups Phenylalanine Tyrosine Tryptophan

Phe Tyr Trp

F Y W

Polar, uncharged R groups Serine Threonine Cysteine Asparagine Glutamine

Ser Thr Cys Asn Gln

S T C N Q

Positively charge R groups Lysine Histidine Arginine

Lys His Arg

K H R

Negatively charged R groups Aspartate Glutamate

Asp Glu

D E

Amino Acids

Amino Acids Additional properties of Amino Acids Numbering of R group carbons ε 6

CH2

δ 5

CH2

γ 4

CH2

β 3

CH2

+NH 3

α 2

CH

1

COO-

+NH 3

Aromatic side chains absorb UV light

Trp 280 nm Tyr 280 nm Phe 260 nm Peptide bond 210-214 nm

Disulfide bond formation with cysteine

oxidation

reduction

Amino Acids Nonpolar, aliphatic R group Gly, Ala, Pro, Val, Leu, Ile, Met Gly - no steric hindrance Pro - hinders backbone flexibility hydrophobic core of soluble proteins found in transbilayer part of membrane proteins

Aromatic R groups Phe, Tyr, Trp hydrophobic, Stacking Tyr/Trp - H-bonding Tyr - site of phosphorylation

Polar, uncharged R groups Ser, Thr, Cys, Asn, Gln Ser/Thr - H-bonding; phosphorylated, glycosylated; enzyme active sites Cys - disulfide bonds; enzyme active sites; metal ion binding Asn/Gln - very polar, H-bonding

Positively charge R groups Lys, His, Arg His - pKa close to neutrality (catalysis); ligand for metal ions (Zn2+, Fe2+)

Negatively charged R groups Asp, Glu General acids/bases in catalysis (lysozyme) Chelate divalent metal ions (Mg, Ca, Mn, Zn)

Uncommon Amino Acids prothrombin collagen

elastin myosin

Amino Acids Optical Activity of Amino Acids For all AA except glycine the α carbon is bonded to 4 different groups: Carboxyl, amino, hydrogen, and R group (in Gly, R group is hydrogen) Chiral center = ___________________

All AA except Gly

Gly

Amino Acids Optical Activity of Amino Acids 1 Chiral center = ___ stereoisomers

Stereoisomer found in proteins =

Amino acids act as acids and bases “zwitterion” amphoteric

Base = proton acceptor, electron pair donor Acid = proton donor, electron pair acceptor

Amino acid titration Curve

2 buffer regions

pK1 = a carboxyl group pK2 = a amino group isoelectric point (pI)- pH where there is an equal amount of (+) and (-) charges (overall charge of zero) isoelectric point (pI) for glycine is at pH = 5.97 pI = (pK1 + pK2)/2

Chemical environment influences pKa

Titration Curve of Histidine

Histidine R group has pKa = 6.0 No other AA side chain has a pKa near neutral pH So Histidine is really the only AA that can be: an effective buffer at physiological pH (7.0)

Peptides and Proteins Peptide - two amino acids joined covalently by a peptide bond Polypeptide - many AA joined together by peptide bond (M.W.