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

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

Aromatic R groups Phenylalanine Tyrosine Tryptophan

Polar, uncharged R groups Serine Threonine Cysteine Asparagine Glutamine

Positively charge R groups Lysine Histidine Arginine

Negatively charged R groups Aspartate Glutamate

Amino Acid Abbreviations

Gly G Ala A Pro P Val V Leu L Ile I Met M

Phe F Tyr Y Trp W

Ser S Thr T Cys C Asn N Gln Q

Lys K His H Arg R

Asp D Glu E

Amino Acids

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

CH2

+NH3

CH COO- CH2 CH2 CH2

+NH3

α 2

β 3

γ 4

δ 5

ε 6 1

Aromatic side chains absorb UV light

Disulfide bond formation with cysteine

oxidation

reduction

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

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

collagen

myosin

prothrombin

elastin

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 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 = α carbon

All AA except Gly

Gly

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

Stereoisomer found in proteins =

Amino Acids Optical Activity of Amino Acids 1 Chiral center = 2 stereoisomers

Stereoisomer found in proteins = L-amino acids

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

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

2 buffer regions

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.<10,000) Protein - macromolecule with one or more polypeptide chains

condensation

Peptides Ionization

Biologically active Peptides & Polypeptides

Dipeptide (Nutrasweet)

Other small peptides Oxytocin (9 aa) - stimulates uterine contractions Bradykinin (9 aa) - inhibits tissue inflammation Amanitin - mushroom poison

Polypeptides Insulin - pancreatic hormone, needed for sugar metabolism, 2 polypeptide chains (30 aa and 21 aa) Glucagon - pancreatic hormone, opposes action of insulin (29 aa) Corticotropin - anterior pituitary gland hormone, stimulates adrenal cortex (39 aa)

Proteins contain other prosthetic groups

Protein Structure