Amino Acids, Peptides, Proteins

Amino Acids, Peptides, ProteinsFunctions of proteins:

EnzymesTransport and StorageMotion, muscle contractionHormonesMechanical supportImmune protection (Antibodies)Generate and transmit nerve impulsesControl growth and differentiationLens protein in eyeFeathersSpider websHornsMilk proteinsAntibioticsMushroom poison …..

Luciferin, luciferase Hemoglobin

Amino AcidsGeneral structure

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 AcidsAdditional properties of Amino AcidsNumbering of R group carbons

CH2

+NH3

CH COO-CH2 CH2 CH2

+NH3

Aromatic side chains absorb UV light

Disulfide bond formation with cysteine

oxidation

reduction

Trp 280 nmTyr 280 nmPhe 260 nmPeptide bond 210-214 nm

Amino AcidsNonpolar, aliphatic R group

Gly, Ala, Pro, Val, Leu, Ile, Met

Gly - no steric hindrance Pro - hinders backbone flexibility

hydrophobic core of soluble proteinsfound in transbilayer part of membrane proteins

Aromatic R groupsPhe, Tyr, Trp

hydrophobic, StackingTyr/Trp - H-bonding

Tyr - site of phosphorylation

Polar, uncharged R groupsSer, 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 groupsLys, His, Arg

His - pKa close to neutrality (catalysis); ligand for metal ions (Zn2+, Fe2+)

Negatively charged R groupsAsp, Glu

General acids/bases in catalysis (lysozyme)Chelate divalent metal ions (Mg, Ca, Mn, Zn)

Uncommon Amino Acids

collagen

myosin

prothrombin

elastin

Amino AcidsOptical Activity of Amino AcidsFor all AA except glycine the 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 AcidsOptical Activity of Amino AcidsFor all AA except glycine the carbon is bonded to 4 different groups:Carboxyl, amino, hydrogen, and R group (in Gly, R group is hydrogen)

Chiral center = carbon

All AA except Gly

Gly

Amino AcidsOptical Activity of Amino Acids1 Chiral center = ___ stereoisomers

Stereoisomer found in proteins =

Amino AcidsOptical Activity of Amino Acids1 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 donorAcid = proton donor, electron pair acceptor

Amino acid titration Curve

pK1 = a carboxyl grouppK2 = a amino groupisoelectric 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 = 6.0No 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 bondPolypeptide - many AA joined together by peptide bond (M.W.<10,000)Protein - macromolecule with one or more polypeptide chains

condensation

PeptidesIonization

Biologically active Peptides & Polypeptides

Dipeptide (Nutrasweet)

Other small peptidesOxytocin (9 aa) - stimulates uterine contractions Bradykinin (9 aa) - inhibits tissue inflammationAmanitin - mushroom poison PolypeptidesInsulin - 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