biochem midterm 1

what amino acid makes disulfide bonds

cysteine

explain ph and pka in relation to eachother

ph>pka deprotonates (basic)(environment is empty. surroundings steal proton) ph<pka protonates (acidic) (environment is full. surroundings gives proton)

whats special about histidine

-the histidine side chain undergoes protonation/deprotonation near physiological pH.

-histidine is near physiological ph(7.4)ph=6

-tiny shifts can make it neutral or positive

asp/glu

pka=4 negatively charged

lys

pka=10 +charged

arg

pka=12 +charged

his

pka=6 + charged at ph=7

tyr

pka=10 (neutral)

cys

pka=8.5 (partial negative at ph=7)

what are amino acids joined by

peptide bonds

peptide bonds are …

-planar

-partial double bond character (resonance form)

-cant rotate

-Trans>Cis

-dehydration synthesis (loss of h2o)

alpha carbon of the amino acid bond rotation

phi and psi (left and right)

-in theory should have -180 to +180 but don’t due to steric hindrance.

-steric hindrance: some angles cannot happen due to R groups or oxygen bumping into each other (ramachandran plot)

secondary structure types

alpha helix (tight coil) and beta sheets (extended)

alpha helix

-side chains point out

-RIGHT HANDED (point right thumb up. follows curve of fingers)

-stabilized by hydrogen bonds between the backbone atoms (the side chains arent involved in forming the helix (they point out)

the rule for hydrogen bonding pattern

the hydrogen bond forms between the carbonyl oxygen of residue i and the amide hydrogen (N-H) of reside i+4

-the 4 residue jump creates a perfect, repeating coil (draw this)

-3 amino acids in the middle (between them)

one full turn of the helix is…

3.6 amino acid residues

the backbone of a beta strand is not a straight line. its a …

zig zag (planar)

for beta sheets, where are the R groups

alternating up and down (sterics-prevents the R chains from bumping into each other by being too close)

where do the hydrogen bonds occur in beta sheets

between the different chains

hydrogen bonding for alpha helix, for beta sheet

a) within the same coil (i+4) b) between different strands

T/F beta sheets are flat

FALSE

parallel vs antiparallel b-sheets

antiparallel: c=o and n-h line up perfectly, so the hydrogen bonds are stronger/shorter

parallel: c=o and n-h groups are slightly staggered, so the hydrogen bonds are more angled, so they’re slightly weaker

turn (reverse turn)

alpha helix or beta strand, U-turns that connect segments so the protein can fold onto itself

the folded structure of most proteins is stabilized chiefly by the …

hydrophobic effect (clumped together rather than being extended)

membrane proteins with hydrophobic effect

water is on the inside, so it doesn’t follow the rules of hydrophobic insides (flips it)

denaturing (anfinsens experiment)

-add urea and BME

-unfolding and folding of ribonuclease

-urea alters the solution so that the hydrophobic effect is weakened

-BME reduces (breaks) the disulfide bonds

-once you remove urea and most of the BME it refolds

proteins folding and refolding is a “cooperative” process

all or nothing. its like a row of dominoes falling or a '“click to fit” mechanism. once it starts, the whole thing snaps into place instantly

if the backbone of each rwsiude can assume any of three different conformations, then the total number N of possible conformations for a proteins of residues would be

3^n

proteins have a ton of conformations. how can folding occur?

the search is restricted by the relative stability of certain states along the way

proteins dont search for the right shape, they use energy landscaping

“folding funnel”

-top (high entropy): protein is loose. thousands of possible wrong shapes

-the descent: protein starts to fold, entropy decreases. forms small, stable structures which narrows down the possibilities

-bottom (native structure): the correct protein fold: lowest gibbs free energy

explain entropy for the folding funnel

the entropy of the protein goes down (folded) but the system reaches the lowest gibbs free energy (entropy increases)

explain form follows function

function (chemical reactivity, catabolic abillty) results from and is best explained by structure

macromolecules vs metabolites

dna, protein // glucose, alanine

draw the dna backbone

-5’ to 3’

-sugar phosphate nitrogenous base

-adenine, thymine, guanine, cytosine (a+t) (2 H-bonds)( c+g) (3 h-bonds)

a , g

purines

c, g

pyrimidines

how many different kinds of nucleotides are there

4 (4 different bases, 4 different nucleotides) 1 nucleotide=sugar,base,phosphate

noncovalent forces in DNA

-ionic: destabilizing. every phosphate carries a negative charge. if two are close they can repel each other. sometimes its stabilizing when positively charged ions (k+, mg2+) hang around dna to shield or neutralize the phosphates negative charges which allows the dna strands to stay close

-london dispersion forces: between atoms of bases stacked together. vertical stability

-hydrophobic effect: hydrophobic bases on interior. shielded from h2o

details about the hydrophobic effect

-water is polar

-water can form h-bonds and can engage in other electrostatic interactions. it has a high affinity for other water molecules, and for polar solutes.

-liquid water has fewer h-bonds than ice (less ordered) you know this

-oil and water don’t mix

-nonpolar solutes do not interact with water but do affect waters organization

-release of water molecules due to the hydrophobic effect is thermodynamically favored (think of the whole system. water is free. entropy (disorder) goes up)

enthalpy (first law of thermodynamics)

deltaH= U+PV

—H releases heat (we like)

-+H absorbed heat

-energy is conserved

entropy (second law of thermodynamics)

-delta S surroundings =delta H system/T

-delta S total = (delta S system - delta H system)/T

-positive process

gibbs free energy

delta G = delta H system- T delta S system

-negative for spontaneous processes

conformation entropy

“freedom of choice” a molecule has regarding its shape

more choices=higher entropy

amino acids by themselves are

zwitterionic (carboxyl gives away proton and amino group has a base that accepts proton)

-explains how proteins can fold and stick together

whatre the steps to deriving the ph equation from ka=H+A-/HA

1. multiply by HA

2. divide by A-

3. take -log

4. ph=-log(H+) and pka=-log(ka)

when rearranging to get the positive log, u have to switch HA and A- so A- is on the top and HA is on the bottom.

A- is…

the version without the proton (nh2, coo-) (Abandoned the proton)

HA is…

the version with the proton (nh3+, cooh) (Has A proton)

protein structures are often diversified further by

posttranslational modification: upgrades (adding the paint, GPS, leather seats)

-by modifying the protein a little bit, the cell can change its activity, location, longevity

ex) green fluorescent protein: PTM produces a fluorophore (glows)

what are the three cases of binding

tight, weak, intermediate

tight binding

shapes are perfectly complimentary and noncovalent forces are maximized

-ligand concentration [L] here is equal to the receptor concentration

weak binding

molecules interact briefly and then bounce away. forces are strong enough to interact and recognize the partner but not enough to stay stuck

-even at high concentration of ligand, very little of the receptor is occupied

intermediate binding

goldilocks zone. strong enough to be specific but reversible enough that the body can regulate it.

-ligand [L] concentration here is sufficient enough to occupy half the receptor (L1/2)

-as the concentration of ligand increases, the slope decreases

example of binding (estrogen receptor and steroid/estradiol ligand)

both of the ligands can bind to the receptor but estradiol binds more strongly.

-the estrogen receptor has a pocket thats complimentary to the estradiol ligand (size of the pocket fits well) +h-bond acceptor

-the pocket is too tight for testosterone

binding is dynamic. what does this mean

dissaociation and association is continuosly occurring. a ligand is NOT stuck together. the molecules are constantly falling off and being replaces with the same or different molecules.

binding of oxygen to myoglobin

-binding curve is hyperbolic

-P50=2 (high affinity) (TIGHTTT binding)

structure of myoglobin

helices wrapped around the heme. myoglobin cannot bind oxygen with amino acids alone. needs help. this is where the heme comes into play.

-heme has a porphyrin ring that holds an iron atom at the center

-this ring has 6 parking spots. 4 by ring. 1 is the distal histidine. the 6th is for oxygen!!!

deoxymyoglobin vs oxymyoglobin

without oxygen . with oxygen

distal histidine

-oxygen isnt the only thing that wants to bind to the heme. carbon monoxide does (toxic. bad [binds 20,000 times stronger than co2])

-myoglobin solves this issue by utilizing the distal histidine

-doesnt touch iron but hangs over o2 binding site

-it forces the o2 to bind at an angle and uses a h-bond to stabilize it

-this makes it physically awkward for CO to bind. dropping affinity

hemoglobin

a cooperative oxygen carrier (it has 4 subunits that talk to each other so they CAN have cooperativity)

-subunits can communicate through shape changes

hemoglobin curve

sigmoidal. when o2 levels are low, its hard for the first o2 to bind. but once that first o2 breaks the ice and binds, it tugs on the rest of the protein making the 3rd 4th and 5th molecules to snap into place

-this binding curve ensures delivery of oxygen to tissues that need it most

-p50=26 (lower affinity for o2 than myoglobin)

T state vs R state

deoxyhemoglobin: the off state. the subunits are held tightly by ionic bonds (salt bridges). affinity for o2 is low. prefers this state in the tissues.

oxyhemoglobin: on state. when o2 binds, it pull the iron atom into the plane of the heem, which pulls and breaks salt bridges. the whole protein relaxes and the affinity for o2 SHOOTS UPPP. prefers this state in the lungs

why is environment important for hemoglobin

if u take it out of the red blood cell it behaves like a hoarder. similar to myoglobin. HIGHHH affinity. binds to o2 more strongly.

-this is due to 2,3BPG : inside a red blood cell, this exists and is an allosteric effector

2,3 BPG is a _____ for hemoglobin

allosteric effector: it binds to a very specific spot on the hemoglobin molecule but only when its on the T state. which makes it harder for oxygen to bind

-hemoglobin’s natural instinct is to stay in the R state. to make it work right, it has to bully the T state using a specific molecule (2,3 BPG- packed with tons of negative charges and creates salt bridges that lock the subunits into the T state)

-basically. 2,3 BPG makes the T state more stable which makes it harder for oxygen to bind

more allosteric effectors

protons: oxygen binds less tightly at lower Ph

(bohr effect)

-his gets protonated (gets positive charge) can form salt bridge now with nearby negative residues. extra bridges act like zip ties that lock the protein into the T state

co2: o2 binds less tightly when co2 is present

1. most co2 is converted by enzymes into bicarbonate and protons which fuel the bohr effect

2. co2 can physically attach itself to hemoglobin binding to the N terminus to form carbamate

• releases even more protons

• negative charge of the carbamate forms additional salt bridges that further stabilize the T state

bohr effect??

co2 and protons decrease hemoglobins affinity for oxygen

aggregation

happens when proteins misbehave and start clumping together. form large, insoluble tangles

what is Kd

the disassociation constant kd=[R][L]/[RL]=keq

disassociation constant

the ligand concentration that gives half occupancy of the receptor

-the concentration of ligand needed to saturate 50% of the protein

do we want a low or high kd for binding?

low! we can use them to quantify the specificity of binding too

at equilibrium.. the rate of dissociation ___ rate of binding

equals

receptors all empty. rate of binding ___ rate of dissociation

> . dissociation = 0 there are no complexes formed yet so nothing can fall apart

receptors all occupied rate of dissociation ___ rate of binding

>. dissociation = a lot. so many complexes, the likelihood of one falling apart is high.