Exam #1

Question 1

Isoelectric Point Calculation

Answer 1

Average the pKas= pKa1+pKa2/2

Question 2

Spontaneous

Answer 2

Delta G < 0, reaction will move to the right

Question 3

Enthalpy

Answer 3

Delta H, Delta H < 0= exothermic and favorable
heat released - Delta H when chemical bonds form
heat absorbed + Delta H when chemical bonds break

Question 3

Non-Spontaneous

Answer 3

Delta G > 0, reaction will move to the left

Question 4

Entropy

Answer 4

Delta S, Disorder of System,
Delta S > 0= favorable

Question 5

Thermodynamics

Answer 5

study of energy, transformation of energy from one form to another

Question 6

Covalent Bonds

Answer 6

atoms share at least 2 electrons

Question 7

Ionic Bonds

Answer 7

no sharing, steals electrons, attractive force from opposite charges

Question 8

Dipole-Dipole Interactions

Answer 8

same as ionic, with something with no definitive charge

Question 9

Hydrogen Bonds

Answer 9

special, don’t bond to H, bond 2 electronegative atoms (O or N) with it and one has a lone pair

Question 10

Van der Waals

Answer 10

low energy, not significant, radius distance between center of atom and end, they come close but don’t invade personal space, when they get too close they repel

Question 11

Hydrophilic

Answer 11

water likes to interact with hydrogen bonds

Question 12

Hydrophobic

Answer 12

doesn’t like interacting with water, does Van der Waals

Question 13

Amphipathic

Answer 13

hates to interact with both

Question 14

Amphiphilic

Answer 14

likes to interact with both

Question 15

Hydrophobic effect

Answer 15

water pushes hydrophobic molecules together

Question 16

Acids

Answer 16

donates proton to water
HA (acid) + H2O (backward and forward arrows) A (CB) + H3O+

Question 17

Base

Answer 17

accepts proton usually from a water
B + H2O (backward and forward arrow which establishes equilibria) BH (CA) + OH-

Question 18

Equilibrium

Answer 18

-logKa= pKa (measure of how much a group wants a proton)

Question 19

pH

Answer 19

measure of how many Hs are in the solution

Question 20

Henderson-Hasselbach Equation

Answer 20

pH= pKa + log [base]/[acid]

Question 21

KEY INFO ABOUT pH esp when COMBINING AMINO ACIDS

Answer 21

when pH is BELOW the pKa, the group is protonated

Question 22

Proteins

Answer 22

bind things

Question 23

Binding Pocket

Answer 23

area on proteins with binding properties
protein will have surface designed to interact with particular ligand

Question 24

Ligand

Answer 24

what it binds to, molecule which protein specifically interacts with

Question 25

Binding a ligand

Answer 25

conformational change of protein catalyze a chemical reaction inhibit or alter normal function of protein do none of the above

Question 26

Types of Interactions

Answer 26

Hydrogen Bonds, electrostatic, van der Waals ALL NON-COVALENT

Question 27

"specific" may not be that specific

Answer 27

protein may have different ligands and ligand may interact with different proteins

Question 28

Affinity

Answer 28

preference of a protein for a ligand is its AFFINITY for that ligand

Question 29

High affinity

Answer 29

binds tightly lots of interactions small Kd

Question 30

Low affinity

Answer 30

binds loosely less interactions large Kd

Question 31

Transiently

Answer 31

proteins w/ ligands transiently--> protein: ligand interaction from equilibria

Question 32

Fraction Disassociation Equation

Answer 32

Theta= [L]/Kd+[L]

Question 33

Two-Log Rule of Affinity

Answer 33

protein-ligand binding is linearly related to [ligand] over a span of two logs relative to the Kd below 0.1XKd there is minimal protein occupancy (drug will have no real effect b/c it won't find its target) above 10XKd saturation approaches (interactions w/ other proteins can lead to side-effects)

Question 34

Myoglobin

Answer 34

oxygen-storer single polypeptide chain made up of 8 alpha helices NO BETA SHEETS Heme prosthetic group--> co-factor, critical (covalently bonded to protein) Binds O2 by means of Fe2+ contained in heme prosthetic group

Question 35

Heme

Answer 35

Nitrogens are holding on to iron equally (heme is conjugated), Fe is what interacts w/ O2, and heme binding to O2 is facilitated by 2 different histidines proximal and distal

Question 36

Distal Histidine

Answer 36

very strong H-bond with molecular oxygen, heme bonds w/ CO much better than O2 x20,000 stronger for free heme alpha CO

Question 37

Myoglobin Binds O2

Answer 37

[L]--> pO2 Kd--> P50 Theta= pO2/P50+pO2 P50 of myoglobin for O2 is 0.26 kPa Myoglobin saturated at most biological pO2s pO2 lungs: 13.3 kPa pO2 tissue: 4 kPa

Question 38

Hemoglobin

Answer 38

transporting O2 throughout body higher P50 than myoglobin tetramer (quaternary structure): 2 pairs of hemoglobins alpha beta, each monomer similar in structure to myoglobin 2 alpha and beta subunits, dimers

Question 39

T State

Answer 39

"tense" LOW AFFINITY FOR O2

Question 40

R State

Answer 40

"relaxed" HIGH AFFINITY FOR O2

Question 41

T--R

Answer 41

O2 binding induces a conformational change O2 coordinating w/ heme causes a conformationmotifs from T to R R state has higher affinity for O2 Shift propagated throughout protein so each monomer enters R state even if it hasn't bound O2 yet

Question 42

Cooperativity

Answer 42

ligand binding at one site affects ligand binding at another site

Question 43

Positive cooperativity

Answer 43

initial binding increases affinity for other ligand nH>1

Question 44

Non-competitive cooperativity

Answer 44

ligand binding is independent for all sites nH=1

Question 45

Negative cooperativity

Answer 45

initial binding decreases affinity for other ligand nH<1

Question 46

Allostery

Answer 46

when protein conformational changes affect protein function

Question 47

Why Hemoglobin is an ideal O2 transporter

Answer 47

cooperativity of hemoglobin makes it effective at both binding and increasing O2, dependent on O2 myoglobin only releases O2, when pO2 is very low other factors enhance O2, release by stabilizing hemoglobin's T state (BPG and pH/CO2 Bohr Effect)

Question 48

Concerted (MWC) Model

Answer 48

only conformational change alters affinity for ligand if one subunit changes state, they ALL change state

Question 49

Sequential (KNF) Model

Answer 49

ligand binding alters affinity of own subunit and adjacent subunits

Question 50

nH

Answer 50

found by looking at the slope where it varies from 1

Question 51

BPG

Answer 51

binds in central cavity of T-state hemoglobin, stabilizing it interacts with three positively charged amino acids (two His and one Lys) on each beta subunit fetal hemoglobin features y subunits instead of beta subunits. Lower affinity for BPG Stabilizing T state reduces affinity for O2 when then leads to release when/where it is needed

Question 52

Bohr Effect

Answer 52

hemoglobin's binding affinity for O2 inversely related to [H+] and pCO2 low pH--> protonation--> forms salt bridges in T-state and can stabilize T-state--> reduce affinity for O2 --> leads to release when/where it is needed CO2 combines w/ H2O to make H2CO3 reducing pH CO2 reacts with N-terminal amine group to form a carbamate, forms salt bridge that stabilizes T-state