Biochem chs 3 and 4

protein functions

catalysis, transport, structure, motion

properties of amino acids

capacity to polymerize, useful acid-base properties, varied physical properties, varied chemical functionality

amino acid structure at neutral pH

zwitterion; net charge of 0

alipathic

no benzene ring

amino acid structure at low pH

both groups are pronated

amino acid structure at high pH

both groups are deprotonated

where nonpolar AAs are usually found

hydrophobic core of soluble proteins or in membranes

precursors to epinephrine

Tyr and Phe

how to convert His to histamine

remove acid group

pK1

carboxyl group (COOH)

pK2

amino group (NH2)

isoelectric point (pI)

pH where there is an equal amount of positive and negative charges

peptide

2-15 joined AA

polypeptide

15-50 joined AA

protein

more than 50 AA

molecule made when a peptide bond is formed

water

direction amino acids are numbered

N terminus to C terminus

sequence logos

show AA concentration

examples of peptides with biological activity

oxytocin, bradykinin

examples of polypeptides with biological activity

insulin, glucagon

native fold

specific shape/fold a protein makes to function

what stabilizes protein shape (native fold)

disulfide bonds, noncovalent interactions, hydrophobic effect

primary structure

amino acids sequence held together by polypeptide bonds

secondary structure

formed with hydrogen bonds and disulfate bonds

paralogs

proteins from the same species

orthologs

proteins from different species

random coil

irregular arrangement of polypeptide chain (connector/linker region)

phi

rotation around C-N bond

psi

rotation around C-C bond

reason why psi and phi can’t rotate freely

steric hinderance

only place and AA can change direction

phi and psi bonds

Ramachandran plot

shows the best areas to rotate to avoid steric hinderance

bonds that hold helical backbone together

hydrogen bonds

what n binds to in a helix

n+4 (binds to AA four ahead)

bond that connects n to n+4

hydrogen bonds

direction of H bonds in helix

vertical

direction of H bonds in sheets

horizontal

strong helix formers

small hydrophobic AAs (Ala and Leu

helix breakers

Pro and Gly

why Pro is a helix breaker

rotation around N-C bond is impossible

why Gly is a helix breaker

small R group supports other conformations

helix capping

stabilizing the end of a helix

coiled-coil dimers

formed by amphipathic areas of helixes (hydrophobic areas of two coils wrap around each other)

AAs found in B sheets

large, aromatic (tyr, phe, trp); branched (leu, val, ile)

inner diameter of helix

backbone only

outer diameter of helix

side chains that fit into major groove of DNA

rigid bond

peptide bond

secondary structure

repeating patterns from backbone to hydrogen bonding

tertiary structue

3D shape of polypeptide chain

coil-coil dimers

two coils wrap together, hydrophobic AAs interact

bonds that hold beta sheet together

hydrogen bonds

AA typically in beta sheets

large, aromatic (Tyr, Phe, Trp); branched (Leu, Val, Ile)

AA not typically found in beta sheets

Gly, Pro

why backbone zigzags in beta sheets

peptide bond’s planarity and tetrahedral geometry

side chain arrangement in a beta sheet

alternate up and down

beta turn

180 direction change from 4 AA

stabilizer for beta sheet

H bond spanning AA1-4

globular proteins

enzymes, transport proteins, antibodies, motor proteins, etc

purpose of fibrous proteins

mechanical, structural jobs; typically nonpolar (insoluble)

purpose of globular proteins

dynamic (catalysis, transport, signaling)

collagen

fibrous protein made of three polypeptides (a-chain) supercoiled like a rope (left handed helix)

hemoglobin

globular protein with two copies of two kinds of polypeptides

individual chains

fold into a normal right-handed a-helix

a-Keratin bonds

individual chains into right handed a-helix; two helices are amphipathic; disulfide bonds

perm processes

break disulfide bonds and loosen structure (flexible hair reshapes); oxidizing re-forms new disulfide bonds (resetting crosslinks)

purpose of collagen

give tissue tensile strength

PDI (protein disulfide isomerase)

enzyme that fixes disulfide bonds that form between the wrong amino acids

PPI (peptide prolyl cis-trans isomerase)

enzyme that converts between cis and trans conformation of proline

Hsp 60

chaperonins; provides isolated environment for proteins to fold properly (cap and barrel)

Hsp 70

chaperone protein that “clamps” onto exposed hydrophobic areas of a protein, so the rest of the protein folds around it

purpose of intrinsically disordered proteins

act as scaffolds or diffusion barriers

common amino acids in disordered proteins

Lys, Arg, Glu, and Pro