Bioc 307 - Exam 1

four types of noncovalent interactions

ionic interactions

hydrogen bonds

van der Waals forces

hydrophobic interactions

ionic interaction (charge-charge interaction)

(aka salt bridges) electrostatic attraction/repulsion between charged groups

effect of distance between two charged groups on energy of their interaction

energy most optimal when two atoms approach one another within 4-5 A

relative dielectric constants for nonpolar vs polar solvents

nonpolar = 1-2

polar = 50+

effect of solvent polarity on ionic interactions

more polar → greater interference/dielectric constant → weakens ionic interaction

what type of solvent is water?

super polar

solvent that makes ionic interaction stronger

lower dielectric constant - vacuum, hexanes

H bond donor vs acceptor

H bond donor = the molecule that supplies H

H bond acceptor = the electronegative atom with a lone pair that attracts H

groups that serve as H bond donors

H bonded to an EN atom

groups that serve as H bond acceptors

EN atom w/ lone pair - O, N, F

importance of van der Waals interactions in biochem

weak + nonspecific individually but sum of many can be strong + important for shape

hydrophobic effect

association of nonpolar groups w/ each other in aqueous systems - want to minimize their interaction w/ water

amphipathic

compound w/ both nonpolar and polar aspects - ex: phospholipids

properties of water

polar, bent structure, can H-bond with tetrahedral network

polarity determined by….

1. difference in EN > 0.4 between two atoms sharing covalent bond

2. asymmetric dipole arrangement

coulomb’s law

E = k * [ (Q1 * Q2) / Dr)

clathrate structures

water caged around nonpolar solute - low entropy → unfavorable

water when surrounding nonpolar solutes

highly ordered and low entropy → nonpolar solutes form cluster to increase entropy

basic α-amino acid structure

central C bonded to carboxyl, amino, H, and R group - L-isomer

α-COOH group ionization

weak acid (pKa 2) → donates proton

α-amino group ionization

weak base (pKa 9) → accepts proton

pH

acidity of a sol’n - lower pH → incr [H]

pKa

how tightly molecule holds onto proton - lower pKa → gives up H+

when pH = pKa…

half of the molecules are protonated and half deprotonated

pH < pKa

sol’n has higher [H+] → molecule keeps proton

pH > pKa

sol’n has lower [H+] → molecule kicks out proton

zwitterion

neutral molecule where the charges cancel out to zero

isoelectric point (pI)

pH where zwitterionic form is most likely to be found

pI equation

(pKa 1 + pKa 2) / 2

nonpolar amino acids

ala, val, leu, ile, met, pro, phe, trp

polar, uncharged amino acids

ser, thr, asn, gln, tyr, cys

positively charged amino acids

lys, arg, his

negatively charged amino acids

asp, glu

glycine (g)

achiral, small, flexible, nonpolar, alpha C

alanine (ala)

small and boring, R group = methyl, nonpolar

valine (v)

bulky, hydrophobic, nonpolar

leucine (l)

more bulky/hydrophobic, isobutyl

isoleucine (i)

bulky, hydrophobic, side chain = chiral

methionine (m)

nonpolar, start codon, contains S

proline (p)

nonpolar, connects back to amino group → rigid

phenylalanine (f)

nonpolar, aromatic, hydrophobic - phenyl ring connected to B C

tryptophan (w)

nonpolar, indole group that H bonds

serine (s)

OH group - polar, can H bond and be phosphorylated

threonine (t)

polar w/ secondary alcohol

asparagine (n)

polar w/ amide group - not titratable

glutamine (q)

polar w/ amide group - not titratable

tyrosine (y)

polar phenol group - can H bond, titratable when basic (pKa = 10)

cysteine (c)

thiol group - can’t H bond but titratable to S- (pKa = 8)

lysine (k)

polar, contains amino group (pKa = 11)

arginine (r)

contains guanidino group (pKa = 12) - always polar + positive

histidine (h)

contains polar imidazole group (pKq = 6) - proton pulled off if pH > 7 → neutral

aspartic acid (d)

beta carboxylate group (pKa = 4) - always polar, negatively charged

glutamic acid (e)

gamma carboxylate group (pKa = 4) - always polar, negatively charged

hydropathy of amino acids

if it moves to bilayer → hydrophobic + favorable (-ΔG) - determines protein folding

kinase

enzymes that add a phosphate - specific ones for Ser/Thr and Tyr

phosphatase

enzymes that remove a phosphate

effect of kinases

adds big negative charge → amino acid becomes polar → changes shape + function

disulfide bonds

strong covalent bonds between two cysteines - can only occur in oxidizing environments

if pH = 7 & pI < 7

protein has more acidic residues → overall negative charge

examples of protein secondary structure

alpha-helices and beta-sheets

α-helix structure

secondary structure stabilized by H-bonds in backbone four residues apart

H bond donor/acceptor in α-helix

backbone carbonyl = acceptor

amide’s hydrogen = donor

chirality of α-helix

typically right-handed - (-60, -50)

α-helix # of residues per turn

3.6 residues/turn

orientation of R groups relative to axis of α-helix

R groups facing outside - determines protein’s properties

packing density of atoms in α-helix

distance for 1 full turn pitch = 5.4 A/turn

distance per residue rise = 1.5 A/residue

β-conformation structure

pleated zig-zag shape

H bond donors/acceptors in β-sheets

orientation of R groups in β-pleated sheet

alternatively above and below plane of strand

parallel β conformation

sheets have same directionality - weaker b/c H bond geometry less than ideal

antiparallel β conformation

sheets run in opposite directions - more stable/linear structure + more common

non-covalent interaction stabilizing a-helix and β conformations

hydrogen bonds

tertiary protein structure

overall 3-d conformation of whole polypeptide chain in its folded state

structural domain of protein

structurally independently folded region of a protein - have different functions

6-atom planar peptide group

resonance structure of peptide bond restricts rotation of atoms around omega bond

phi vs psi angles

phi: counter-clockwise between N and α-C

psi: clockwise between α-C and carboxyl-C

Ramachandran plots

shows possible phi and psi values for protein conformations

location of phi angles in Ramachandran plot

fourth quadrant: (-120, +120)

location of psi angles in Ramachandran plot

3rd quadrant (-100, -60) for right handed α-helix and 1st quadrant (60, 60) for left-handed α-helix

conformation

spatial arrangement of atoms/groups that can change by bond rotation with no covalent bond breaking

configuration

spatial arrangement of atoms/groups that cannot change without breaking covalent bonds

peptide bond

amide bond - condensation of acid and amine (catalyzed by ribosome + not spontaneous)

amino acids not found in α-helices

glycine: more energetically stable to be flexible than in ordered conformation

proline: rigid ring + has no proton on N to be H bond acceptor

protein motif

(aka super-secondary structures) smaller, recurring patterns of secondary structures - cannot usually fold on their own, building blocks of protein folding

amino acids most likely buried inside proteins

cysteine, isoleucine, tryptophan, phenylalanine

amino acids most likely facing outside of protein

aspartic acid, glutamic acid, lysine, glycine

protein folding

spontaneously arriving at the correct combo of phi and psi angles for every residue in the polypeptide sequence - becomes functional protein

quaternary structure

multiple independent polypeptide chains coming together to form a functional complex

free energy equation

ΔG = ΔH - TΔS

direction + source of enthalpy change (ΔH) for protein folding

negative b/c of internal interactions

• breaking bonds with water to form stronger bonds

• protein core has lower dielectric constant than water

sources of entropy change (ΔS) for protein folding

positive: conformational constraints - limiting phi and psi angles

negative: hydrophobic effect - collapse of hydrophobic core → liberation of water

under native conditions, how is free energy state of folded vs unfolded form of protein?

overall (-) ΔG so protein folding is spontaneous

free energy funnel

depicts thermodynamics of protein folding - highest energy states has most possibilities but heads towards energy minimum of native structure

significance of lymphotactin

exists as two conformations in equilibrium with two different functions - exception to the one protein = one function rule

other factors beside hydrophobic collapse in protein folding

salt bridge = internal electrostatic interactions that brig opposite charges together inside protein

zinc finger = non-protein cofactor that holds structure together

effects of urea on proteins structure

breaks noncovalent interactions + changes solvent properties of water - more important b/c prevents collapse of hydrophobic core (breaks 2’ and 3’ structures)

effects of B-mercaptoethanol on protein structure

reduces covalent interactions (disulfide bonds) - breaks 3’ and 4’ structures

Anfinsen’s experimental setup

denature native ribonuclease A in a reversible way using urea + B-mercaptoethanol

Anfinsen’s experimental conclusions

reversibly denatured protein was able to spontaneously refold and regain activity → evidence that primary sequence has all the info needed to find it’s tertiary native structure

globular proteins

compact, roughly spherical proteins

water-soluble - often help w/ transport