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BCHM461 > Exam #1 > Flashcards

Exam #1 Flashcards

1
Q

Isoelectric Point Calculation

A

Average the pKas= pKa1+pKa2/2

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2
Q

Spontaneous

A

Delta G < 0, reaction will move to the right

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3
Q

Enthalpy

A

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

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3
Q

Non-Spontaneous

A

Delta G > 0, reaction will move to the left

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4
Q

Entropy

A

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

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5
Q

Thermodynamics

A

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

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6
Q

Covalent Bonds

A

atoms share at least 2 electrons

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7
Q

Ionic Bonds

A

no sharing, steals electrons, attractive force from opposite charges

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8
Q

Dipole-Dipole Interactions

A

same as ionic, with something with no definitive charge

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9
Q

Hydrogen Bonds

A

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

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10
Q

Van der Waals

A

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

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11
Q

Hydrophilic

A

water likes to interact with hydrogen bonds

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12
Q

Hydrophobic

A

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

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13
Q

Amphipathic

A

hates to interact with both

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14
Q

Amphiphilic

A

likes to interact with both

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15
Q

Hydrophobic effect

A

water pushes hydrophobic molecules together

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16
Q

Acids

A

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

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17
Q

Base

A

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

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18
Q

Equilibrium

A

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

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19
Q

pH

A

measure of how many Hs are in the solution

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20
Q

Henderson-Hasselbach Equation

A

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

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21
Q

KEY INFO ABOUT pH esp when COMBINING AMINO ACIDS

A

when pH is BELOW the pKa, the group is protonated

22
Q

Proteins

A

bind things

23
Q

Binding Pocket

A

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

24
Q

Ligand

A

what it binds to, molecule which protein specifically interacts with

25
Q

Binding a ligand

A

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

26
Q

Types of Interactions

A

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

27
Q

“specific” may not be that specific

A

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

28
Q

Affinity

A

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

29
Q

High affinity

A

binds tightly
lots of interactions
small Kd

30
Q

Low affinity

A

binds loosely
less interactions
large Kd

31
Q

Transiently

A

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

32
Q

Fraction Disassociation Equation

A

Theta= [L]/Kd+[L]

33
Q

Two-Log Rule of Affinity

A

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)

34
Q

Myoglobin

A

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

35
Q

Heme

A

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

36
Q

Distal Histidine

A

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

37
Q

Myoglobin Binds O2

A

[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

38
Q

Hemoglobin

A

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

39
Q

T State

A

“tense” LOW AFFINITY FOR O2

40
Q

R State

A

“relaxed” HIGH AFFINITY FOR O2

41
Q

T–R

A

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

42
Q

Cooperativity

A

ligand binding at one site affects ligand binding at another site

43
Q

Positive cooperativity

A

initial binding increases affinity for other ligand nH>1

44
Q

Non-competitive cooperativity

A

ligand binding is independent for all sites nH=1

45
Q

Negative cooperativity

A

initial binding decreases affinity for other ligand nH<1

46
Q

Allostery

A

when protein conformational changes affect protein function

47
Q

Why Hemoglobin is an ideal O2 transporter

A

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)

48
Q

Concerted (MWC) Model

A

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

49
Q

Sequential (KNF) Model

A

ligand binding alters affinity of own subunit and adjacent subunits

50
Q

nH

A

found by looking at the slope where it varies from 1

51
Q

BPG

A

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

52
Q

Bohr Effect

A

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

BCHM461 (7 decks)

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