Biochem I Exam 1

Ch. 2, 4, 5, 6, 7, 10

zwitterion

neutral molecule with one positive and one negative charge; happens when amino acids are at pH 7

amino acid structure

tetrahedral; alpha carbon always chiral

aliphatic & aromatic

non-polar amino acids

Proline

cyclic, least hydrophobic aliphatic amino acid

Proline codes

Pro, P

Glycine

the only non-chiral amino acid

Glycine codes

Gly, G

Alanine

side chain is a methyl group

Alanine codes

Ala, A

Valine

side chain is an isopropyl group

Valine codes

Val, V

Leucine

side chain is an isobutyl group

Leucine codes

Leu, L

Isoleucine

contains 2 chiral carbons, most hydrophobic of the aliphatic amino acids

Isoleucine codes

Ile, I

aromatic amino acids

VERY hydrophobic, absorb UV at 280 nm

Phenylalanine

Phenylalanine codes

Phe, F

Tyrosine

OH group has a pKa of 10.5

Tyrosine codes

Tyr, Y

Tryptophan

bi-cyclic indole ring, NH group has a pKa of 16-17

Tryptophan codes

Trp, W

Cysteine

important in disulfide linkages, weak acid (R group pKa = 8.3)

Cysteine codes

Cys, C

Methionine

“start” amino acid in majority of proteins, VERY hydrophobic, sulfur present in thioester linkage

Methionine codes

Met, M

acidic amino acids

contain carboxyl group, negatively charged at physiological pH, present as conj. bases

Aspartate

R group pKa = 3.9

Aspartate codes

Asp, D

Glutamate

R group pKa = 4.3

Glutamate codes

Glu, E

basic amino acids

hydrophilic nitrogenous bases, positively charged at physiological pH

Lysine

di-amino acid, protonated at pH 7 (R group pKa = 10.5)

Lysine codes

Lys, K

Arginine

most basic amino acid (R group pKa = 12.5)

Arginine codes

Arg, R

Histidine

the only amino acid that functions as a buffer in physiological range (R group pKa = 6.0)

Histidine codes

His, H

polar uncharged amino acids

polar side groups, hydrophilic

Serine

looks like Alanine with hydroxyl group, protonated at pH 7 (R group pKa = 13)

Serine codes

Ser, S

Threonine

2 chiral carbons, protonated at pH 7, (R group pKa = 13)

Threonine codes

Thr, T

Asparagine

amide of aspartic acid

Asparagine codes

Asn, N

Glutamine

amide of glutamic acid

Glutamine codes

Gln, Q

Selenocysteine

natural amino acid, selenol group (SeH), pKa = 5.2

Selenocysteine codes

Sec, U

Pyrrolysine

found in some methanogenic archaea & bacteria, but not humans, pyrroline side chain, pKa unknown

Pyrrolysine codes

Pyl, O

weak polyprotic

type of acid that amino acids are

alpha-carboxyl group

pKa = 2

alpha-amino group

pKa = 9

asymmetric because the alpha carbon of the amino acid is a chiral center

is the polypeptide chain symmetric or asymmetric?

trans to each other

carbonyl oxygen & amide hydrogen relationship in peptide backbone

peptides

short polymers of amino acids

residue

unit of amino acid

dipeptide

2 residues

tripeptide

3 residues

oligopeptide

12-20 residues

polypeptide

20+ residues

monomeric protein

one polypeptide chain

multimeric protein

more than one polypeptide chain

homomultimer

one kind of polypeptide chain

heteromultimer

2 or more different polypeptide chains

fibrous proteins

relatively simple, regular, linear proteins

globular proteins

proteins that are roughly spherical in shape

primary protein structure

amino acid sequence numbered from N-terminus to C-terminus

secondary protein structure

local structures stabilized by H-bonds, represent 3-dimensional arrangement of polypeptide

alpha helix & beta strand

the 2 major secondary structures of proteins

tertiary protein structure

overall 3-dimensional shape of a protein

quaternary protein structure

subunit organization of protein

prosthetic group

the non-amino acid part of the structure of a protein, tightly linked to apo-protein

primary structure

determined by covalently linked amino acid residues in polypeptide backbone

secondary and higher structures

determined by noncovalent & weak forces

H bonds

peptide backbone forms these bonds, side chain can form these bonds on the surface of a protein with water molecules

hydrophobic interactions

nonpolar side chains of amino acids cluster in nonpolar environments; forming of these bonds minimizes interactions of nonpolar residues with water and is highly favorable

ionic interactions

arise as electrostatic attractions between opposite charges or repulsions between like charges; side chains can carry positive charges or negative charges

on the protein surface because they can interact optimally with the water solvent

where are ionically charged residues usually located? why?

van der waals interactions

includes both attractive & repulsive forces; individual interactions are weak, but many occur in a protein

dipole-induced dipole interactions that arise from fluctuations in the electron charge distributions of adjacent nonbonded atoms

what causes attractive forces in van der waals interactions?

• bond linking the alpha carbon & the carbon of the peptide bond (psi)

• bond linking the nitrogen of the peptide bond & the adjacent alpha carbon (phi)

rotations allowed in secondary structure of protein

alpha helix of secondary structure

forms b/c of each carbonyl forming a H bond w/ the amino group of the 4th residue ahead in the sequence; 3.6 amino acid residues per turn; amphiphilic (hydrophilic + hydrophobic sides)

1.5 A

rise per residue in alpha helix

5.4 A (3.6 residues per turn x 1.5 rise per residue)

rise per turn (pitch) in alpha helix

backbone loop

closed by any H bond in alpha helix

beta sheet of secondary structure

sheet of polypeptides; parallel & antiparallel stable arrangements

parallel beta sheet

adjacent strands run in same direction

antiparallel beta sheet

adjacent strands run in opposite direction

fibrous protein

mechanically strong, insoluble, play structural role

fibroin & beta-keratin

form extensive beta sheets

collagen

triple helix structure, principal component of connective tissue

tropocollagen

basic unit of collagen, 3 intertwined polypeptide chains, composed of hydroxylysine & hydroxyproline

globular proteins

more abundant than fibrous proteins, large functional diversity, composed of domains

globular proteins

broad section of antiparallel beta-sheets, a few beta-turns, several peptide sections without defined secondary structure (random coil)

ribonuclease

globular protein w/ hydrophobic core & hydrophilic surface

globular protein structure

surface structure includes water molecules, alpha-helices on a surface are usually amphiphilic

protein domains

compact, folded protein structures that are usually stable by themselves in aqueous solution

multi-domain proteins

possess the sum of functional properties & behaviors of their constituent domains, 90% are duplicated in other proteins, many proteins contain multiple copies of the same