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bisc 330 > PINAUD EXAM 2 > Flashcards

PINAUD EXAM 2 Flashcards

1
Q

basic characteristics of enzymes

A

increase rate by lowering AE
do not alter equilibrium constant
often require co-factors
usually proteins, sometimes RNA
highly specific to substrate and reaction

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2
Q

protease

A

catalyzes the hydrolysis of protein peptide bonds

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3
Q

thrombin

A

proteolytic enzyme in blood clotting
Cuts between Arg and Gly

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4
Q

trypsin

A

enzyme in the digestive system
cuts after Arg or Lys

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5
Q

holoenzyme

A

apoenzyme (inactive) + cofactor (coenzyme or metal)

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6
Q

∆G equation

A

∆G = ∆G° + RT ln [products]/[reactants]

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7
Q

Keq equation

A

kf/kr

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8
Q

3 ways to increase the rxn rate (k)

A

increase substrate conc.
increase T
decrease activation energy

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9
Q

ES complex characteristics

A

shape of active catalytic pocket is 3D (via steric hindrances of AA residues) and flexible, often nonpolar
induced fit: change conformation after binding
multiple weak interactions between E and S (H bonding, electrostatic, hydrophobic, VDWs)

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10
Q

transition state

A

short lived chemical state
highest peak of ∆G diagram
strong binding and flexibility of ES complex promotes formation of transition state

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11
Q

kinetic evidence for ES complex

A

rxn rate increases with increases substrate conc until a plateau (enzyme conc)

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12
Q

physical evidence for ES complex

A

x-ray crystallography

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13
Q

binding energy

A

some free energy released upon binding ES, helps form active site and lowers ∆G of transition state

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14
Q

enzymes speed up biochemical rxns by…

A

specific substrate recognition
multiple reactive steps at catalytic site
strong binding to transition state
efficient release of product

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15
Q

first order rxn

A

V = k[S], units s-1

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16
Q

second order rxn

A

V = k[S][B], units M-1 s-1

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17
Q

at low [S]…

A

Vo proportional to [S]

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18
Q

at high [S]…

A

Vo independent of [S]

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19
Q

Km

A

substrate concentration at 1/2(Vmax)

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20
Q

kcat

A

turnover rate (molecules/s), only works when Vmax has been reached

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21
Q

Michaelis-Menten equation

A

Vo = Vmax ([S]/[S] + Km)

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22
Q

what does Km say about the strength of ES complex?

A

low Km = stronger binding
high Km = weaker binding

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23
Q

enzyme efficiency measurement

A

kcat/Km
10^8 to 10^9 is catalytically perfect

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23
Q

lineweaver burke plot

A

reciprocal of Michaelis-Menten curve, linear
1/Vo = (Km/Vmax)(1/[S]) + 1/Vmax

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24
Q

types of reversible enzymatic inhibition

A

competitive, uncompetitive, noncompetitive

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25
Q

irreversible enzymatic inhibition

A

tight binding to enzyme

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26
Q

competitive inhibition

A

enzyme binds to S OR I
enzyme freed from I by increasing [S]
increases Km, Vmax unchanged

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27
Q

DHFR (dihydrofolate reductase)

A

needed for cell division
methotrexate (similar structure) = competitive inhibitor to DHFR, 1000x tighter binding, cancer drug

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28
Q

methotrexate

A

competitive inhibitor to DHFR (structurally similar)
1000x tighter binding than DHFR
cancer drug used to kill rapidly dividing cells

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29
Q

uncompetitive inhibition

A

I binds after S
ESI complex cannot make P
Vmax decreases and cannot be attained
Km decreases
High [S] does not overcome inhibition

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30
Q

noncompetitive inhibition

A

I and S bind at the same time
ESI cannot make P
Vmax decreases
high [S] does not overcome inhibition

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31
Q

4 types of irreversible inhibition

A

group specific modifying agent, affinity labels, suicide inhibitors, transition state analogs

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32
Q

group specific modifying agent

A

react with specific group at modifying site

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33
Q

affinity labels

A

inactivate enzyme by covalent modification

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34
Q

suicide inhibitors

A

chemical mechanism makes enzyme react covalently with inhibitor

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35
Q

transition state analog

A

similar to transition state structure, binds more strongly to E than S

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36
Q

proline racemase

A

enzyme that catalyzes isomerization of proline
pyrrole 2-carboxylic acid acts as transition state analog to planar proline ion (transition state)

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37
Q

penicillin

A

transition state analog and suicide inhibitor
inhibits glycopeptide transpeptidase (forms bacterial cell walls through peptide cross-linking)

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38
Q

statins

A

competitive inhibitors of HMG-CoA reductase (cholesterol synthesis)
similar structure to substrate inhibits cholesterol synthesis

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39
Q

reactive cleft

A

environment favoring S + E interaction
close proximity of substrate to active reading groups
optimized orientation of substrate for rxn
rxn protected from water / hydrolysis

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40
Q

aspirin

A

irreversible covalent inhibitor of prostaglandin H2 synthase (prostaglandin synthesis –> transmission of pain info, inflammation)
acetylation of serine residue in channel to reach active site - anti-inflammatory

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41
Q

induced fit

A

stabilizes various conformations for both E and S
optimized orientation of catalytic groups in enzyme
allows very tight binding to transition state (gives free energy to accelerate catalysis)

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42
Q

covalent catalysis

A

reactive groups of enzyme become covalently attached to substrate
covalent E-S bond highly reactive for next step
usually involves strong Nu-

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43
Q

acid-base catalysis

A

reactive groups of enzymes donate or accept a proton
involves acidic and basic AA residues

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44
Q

metal ion catalysis

A

loosely (Ca2+) or tightly (Zn2+) bound to enzyme
ionic interactions with substrate or enzyme groups
shield neg charges or stabilize charges

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45
Q

serine protease

A

uses Ser 195 as a highly reactive group for catalysis
transient covalent interaction
acetylation & deacetylation

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46
Q

oxyanion hole

A

area of active catalytic site that tightly binds tetrahedral transition intermediate, stabilizes O- charge

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46
Q

catalytic triad

A

making Ser 195 a Nu-
H-bound network between Asp 102, His 57, Ser 195
mutations within triad lead to dramatic decrease in catalytic efficiency

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47
Q

chymotrypsin

A

cuts after bulky hydrophobic AAs, Trp, Phe, Met
pocket is deep and hydrophobic

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48
Q

trypsin

A

cuts after long positive AAs Lys and Arg
Asp (-) at the bottom of pocket

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49
Q

elastase

A

cuts after AAs with small side chains, Ala and Ser
narrow pocket

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50
Q

cysteine protease

A

catalytic mech resembles Ser triad

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51
Q

Aspartyl protease

A

use Asp carboxylate group to activate H2O and attack peptide bonds

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52
Q

Metalloproteases

A

use metal ion to activate H2O
ex. carbonic anhydrase

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53
Q

proton shuttle

A

His 64 removes proton in carbonic anhydrase catalysis to achieve fast catalytic rates

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54
Q

“committed step”

A

first step that makes reaction irreversible, feedback regulation will target the product of the first committed step

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55
Q

homotropic effects

A

caused by substrate itself at catalytic sites
increase catalytic rates

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56
Q

heterotropic effects

A

caused by binding of non-substrate ligands
decrease catalytic rates

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57
Q

R + T states

A

relaxed and tense states of an enzyme, rapid switching

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58
Q

cooperative binding

A

binding of 1 substrate causes increased binding affinity for another

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59
Q

ATCase

A

allosteric enzyme involved in synthesis of pyrimidine nucleotides

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60
Q

end product for ATCase?

A

CTP, which causes negative feedback on ATCase

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61
Q

structure of ATCase

A

12 subunits: 6 catalytic and 6 regulatory

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62
Q

PALA

A

substrate analog, binding to ATCase causes large conformational changes
equilibrium toward R state
(basically a model to understand substrate binding and how it affects catalytic activity)

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63
Q

CTP

A

allosteric inhibitor of ATCase
binds to regulatory subunits in T state, stabilizes low catalytic efficiency, equilibrium toward T, decrease ATCase affinity for substrates

64
Q

ATP (in ATCase)

A

allosteric effector of ATCase
competes with CTP on regulatory subunits
favors R state and pyrimidine synthesis

65
Q

isozyme

A

multiple forms of an enzyme catalyzing the same reaction in different ways or in different tissues
long-term regulation (M and H isozymes of LDH based on aerobic conditions throughout lifespan in rats)

66
Q

kinase and phosphatase

A

kinase > phosphorylates (transfers phosphate group from ATP to AA residue), signal amplification
phosphatase > dephosphorylates (hydrolysis of phosphate ester)
cascade amplification effects!

67
Q

Protein Kinase A (PKA)

A

phosphorylates many proteins!
2 C 2 R subunits
activated by cAMP

68
Q

PKA consensus sequence

A

Arg - Arg - small AA - Ser/Thr - large AA

69
Q

PKA substrates

A

1) consensus seq / pseudosubstrate (inactive)
2) ATP (phosphorylation cascade)

70
Q

PKA shabangle

A

cAMP binding > conf change > frees C subunits (pseudosubstrate) > activates PKA > binds ATP > phosphorylation cascade

71
Q

amplification example

A

1 cAMP causes a lot of phosphorylation
adrenaline causes a lot of G-protein to bind

72
Q

zymogens

A

proenzymes/inactive forms of enzymes
activated by proteolytic cleavage
ex. proteolysis of trypsin activates chymotrypsin

73
Q

reduction in sugars

A

hemiacetal - open - OH - reducing
acetal - locked - OC - nonreducing

74
Q

non-reducing sugar

A

sucrose

75
Q

reducing sugars

A

lactose and maltose

76
Q

lactose

A

galactose + glucose

77
Q

maltose

A

glucose + glucose

78
Q

glycogen

A

glucose polymer
a-1,4 linkages (favor packaging), some a-1,6 for branching
reduce osmotic pressure
maintain glucose inside cell

79
Q

cellulose

A

glucose polymer
B-1,4 linkages (fiber like structure for strength)
humans can’t digest these linkages
no branching

80
Q

glycoproteins

A

protein modified by carbohydrate at specific AA residues via glycosyltransferase
ER and golgi

81
Q

glycoprotein linkages

A

N-glycosidic linkage with Asn in Asn-X-Ser/Thr with X=any but proline

O-glycosidic linkage with Ser or Thr

82
Q

erythropoietin (EPO)

A

blood glycoprotein involved in stimulating RBC production (higher number RBC, limit degradation)

83
Q

recombinant EPO

A

helpful in treating anemia but also in blood doping
can be detected in blood due to different glycosylation pattern

83
Q

blood types

A

based on glycosylation patterns
glycosyltransferase enzymes expressed by body define type

84
Q

mucins

A

highly glycosylated proteins, act as lubricants in secretions (saliva, mucus)
Ser and Thr o-linked glycosylations
localized in VNTR domain

85
Q

O-antigens

A

common oligosaccharide foundation

86
Q

A-type glycosyltransferase

A

adds N-acetylgalactosamine

87
Q

B-type glycosyltransferase

A

adds galactose

88
Q

fatty acids

A

14-24 hydrocarbon chain w carboxyl

89
Q

saturation of fatty acids

A

saturated = higher MP, less fluid
unsaturated = lower MP, more fluid

90
Q

classes of membrane lipids

A

phospholipids (glycerophospholipids, sphingolipids)
glycolipids (sphingolipids)
cholesterol

91
Q

glycerophospholipid

A

glycerol connected to 2 FA chains and PO4 - alcohol

92
Q

phosphosphingolipid

A

sphingosine connected to 1 FA and PO4-choline

93
Q

glycosphingolipid

A

sphingosine connected to 1 FA and mono/oligosaccharide

94
Q

cholesterol structure

A

4 rings, 1 hydroxyl, 1 alkyl chain
parallel to other lipids with OH interacting with heads

95
Q

arrangement of fatty acid chains

A

micelle: single fatty acid chain
liposome: closed lipid bilayer (circle)
formation driven by hydrophobic int, close packing by VDWs

96
Q

liposomes

A

can be used as nanocontainers and reactors
thermodox: targets cancer tissue, heat releases toxins

97
Q

permeability of lipid bilayers

A

low permeability to ions and polar molecules (except water)
highly selectively permeability barriers to ions using protein pumps/channels, maintains ion conc gradient

98
Q

membrane protein functions

A

transport across membranes
signaling/transfer info
maintain electric potential

99
Q

lipid : protein ratio in membranes

A

varies from 1:4 to 4:1

100
Q

3 major types of membrane anchoring

A

transmembrane (very strong association)
electrostatic interaction (weak)
lipid anchoring (strong)

101
Q

alpha helices

A

7-span proteins
20 AA/helix
extensive H-bonding
formed of hydrophobic AA residues

102
Q

bacteriorhodopsin

A

light driven proton pump used by halobacteria, alpha helix

103
Q

hydropathic index

A

uses ∆G when transferred from hydrophobic to aqueous environment
each point measures the AA window average ∆G (slides 1)
∆G > 0 hydrophobic
∆G < 0 hydrophilic
only detects alpha helices not B sheets!
alpha helix criterion level of +84

104
Q

beta sheets

A

common for pore forming proteins
channel protein
extensive H-bonding, barrel structure
alternates between hydrophobic and philic AA
external: hydrophobic, internal: hydrophilic

105
Q

prostaglandin H2 synthase

A

peripheral protein that converts arachidonic acid into prostaglandin in ER membrane
a-helix hydrophilic backbone for partial attachment, hydrophobic channel for arachidonic acid to get to active site

106
Q

FRAP (fluorescence recovery after photobleaching)

A

shows that membrane is dynamic
after bleach, rapid lateral diffusion in the plane of the membrane for both lipids and proteins
recovery time as a measurement of membrane fluidity

107
Q

what affects the overall melting temp of membranes?

A

length of fatty acids and degree of unsaturation
saturation takes priority over length

108
Q

Tm

A

melting T of membrane (solid to fluid)

109
Q

how does cholesterol influence membrane fluidity?

A

increases fluidity in low temperatures by disrupting tight packing
decreases fluidity in high temperatures by interfering with kinetic fatty acids

109
Q

asymmetry in membranes

A

outer and inner membranes differ in lipid composition and associated proteins
maintained because flip-flopping is rare and requires flippase
orientation of transmembrane proteins do not change over time
outer membrane rich in glycosylated proteins and lipids

110
Q

uncharged membrane permeable molecules

A

chemical concentration gradient determines spontaneous movement across membrane

110
Q

charged membrane permeable molecules

A

chemical concentration gradient AND electrical potential term determines movement across molecule

111
Q

∆G trans

A

determines if the transport across a membrane is passive or active

112
Q

membrane pumps

A

primary active transport
drive thermodynamic uphill reactions with ATP
ATP causes conformational changes for open and close

113
Q

membrane carriers

A

secondary active transport
drive thermodynamic uphill reactions using chemical gradient of one molecule to drive transport of a second molecule against own gradient
no ATP

114
Q

membrane channels

A

passive transport
selective pore
can be sensitive to membrane polarization

115
Q

What is SERCA ATPase: Ca2+ pumps

A

rapidly removes excess Ca2+ after Ca2+ triggered muscle contraction
needs ATP
P-type ATPase
10 transmembrane a-helices and 2 domains (A, P, N)

116
Q

SERCA pumps mechanism

A

2 Ca2+ / ATP

1) 2 Ca2+ bind transmembrane domain from cytoplasm
2) ATP binds N domain
3) P domain phosphorylated on Asp residue
4) CC by A domain –> Ca2+ release into SER lumen
5) phosphoaspartate residue hydrolyzed (dephosphorylation)
6) transmembrane domain conformation reset

117
Q

ABC (ATP binding cassette) transporter pumps

A

membrane pumps: 1 transmembrane domain and 2 ABC domains
Exist in equilibrium between open and closed conformations
Substrate binding stabilizes weak closed state, enhances affinity for ATP binding
ATP binding induces strong interaction between ABC domains > CC > substrate release
Reset of ATP pump by hydrolysis

118
Q

types of cotransport

A

antiporter: 2 solutes in opposite directions
symporter: 2 solutes in same direction
no ATP

119
Q

lactose permease symport

A

lactose permease in E. Coli uses H+ gradient to drive entry of lactose against

H+ binding favors lactose binding > CC > lactose release > proton release in cell

120
Q

fastest transporters

A

1000 folds faster than pumps or carriers, close to diffusion rates of ions

121
Q

action potential

A

generated in neurons by membrane depolarization involving Na+ and K+ ion channels

122
Q

patch clamping

A

study ion channels by isolating single channel with a pipette, record changes in current upon opening and closing

123
Q

ion specificity in K channel

A

1) sequence specific peptidic backbone TVGYG provides polar interactions with K+ as replacement for H2O, TVGYG optimal for K+ only and tight binding

2) electrostatic repulsions between K+ ion in channel allows for rapid flow

123
Q

structure of K channel

A

tetramer forming pore through lipid membranes
larger solvated entry into channel, then narrow channel constriction forces passing K+ ion to desolvate (loos H2O) (funnel-like)

124
Q

voltage gating

A

channel will open given a specific change in membrane potential

125
Q

ligand gating

A

channel will open upon binding of specific ligand

126
Q

voltage gating in K+ channels

A

S4++ domain at the bottom of the channel is positively charged
close channel: S4++ domain in the down position
open channel: membrane depolarization causes S4++ to go upward due to electrostatic repulsion, channel opens

127
Q

ball and chain model

A

small peptide fragment is attached by a flexible domain, in open state it occludes the pore and inactivates transport
very quick, time depends on chain length

127
Q

acetylcholine receptors

A

responsible for electrochemical signal transduction at synapses
binding of acetylcholine triggers opening of non-selective channel, Na+ and K+ travel freely, membrane depolarization (-60 to -20)

128
Q

gap junctions

A

large channels
cell to cell communication
long opening times
controlled by membrane potential and phosphorylation

129
Q

action potential mechanism

A

1) neuron firing > acetylcholine release in synaptic cleft
2) acetylcholine binding to receptors open ligand-gated channels
3) entry of Na+ and exit of K+ ions
4) at -40 mV, Na+ channels (voltage gated) open, more Na+ enters, further depolarization
5) Na+ channels inactivate, K+ channels open
6) K+ efflux repolarizes membrane, K+ channels inactivate
7) Na/K pumps use ATP to return to resting potential

130
Q

aquaporins

A

rapid H2O transport
6 a-helices form hydrophilic channel

131
Q

B-Adrenergic Receptor (B-AR) signal transduction

A

1) Adrenaline binds β-AR, activating receptor
2. Heterotrimeric G-protein (G⍺sβƔ) binds receptor and exchanges GDP for GTP
3. G-protein (β + Ɣ) subunits disassociate and G⍺s subunit binds downstream
effector adenylyl cyclase (AMP 1: 1 B-AR to many G⍺s)
4. Adenylyl cyclase converts ATP to cAMP (AMP 2)
5. cAMP activates PKA triggering a phosphorylation cascade and activation of other effectors (AMP 3)

132
Q

Reset of G protein

A

hydrolysis of GTP to GDP
reassociation of G-protein units

132
Q

reset of B-AR receptor

A

dissociation of ligand (adrenaline), phosphorylation of C-terminal tail allows binding of B-arrestin, desensitizes the receptor

132
Q

angiotensin II receptor signal transduction

A

1) G⍺q-GTP binds, activates PLC
2) PLC binds PIP2, cleaves into IP3 and DAG
3) IP3 releases Ca2+ from ER, DAG activates PKC after it receives Ca2+

132
Q

insulin receptor signal transduction

A

1) insulin binding > cross-phosphorylation by tyrosine binding on an activation loop
2) IRS bind receptor, bind PIP2 lipids with a pleckstrin domain, IRS phosphorylated
3) PIP3 Kinase recruited, makes PIP2 > PIP3
4) PIP3 activates PDK1
5) PDK1 phosphorylates Akt > cascade
6) storage of glucose via glycogen synthesis

133
Q

calmodulin

A

Ca2+ binding domains called EF hands, large CC after Ca2+ binding

133
Q

EGF receptor signal transduction

A

EGF stimulates cell growth

1) EGF binding > dimerization of receptor > CC
2) tyrosine kinase activity for cross-phosphorylation
3) recruitment of Grb-2, then SOS
4) Ras activated by GTP binding
Ras binds and activates kinases for P cascade

133
Q

Ca2+ as an intracellular messenger

A

stored in ER, low cytoplasmic Ca2+, binding of Ca2+ to calmodulin = CC and signal transduction

133
Q

adapter proteins

A

specialized domains (SH2, pleckstrin domain, SH3), needed for precise localization of signal transduction

134
Q

kinase examples

A

PKA, PKC, PIP3K, PKB
receptors themselves can have kinase activity: insulin and EGF

134
Q

second messengers

A

provide delocalization of signals in cell, fast amplification effects
Ca2+, cAMP, IP3

134
Q

negative feedback mechanisms in signal transduction pathways

A

clocked deactivation (GTPase activity in G-protein, Ras)
general deactivation by phosphatase
ligand release of receptor internalization

135
Q

Cancer and signal transdutions

A

gene encoding important proteins for signal transduction mutated
Ras gene often mutated, trapped in active form with lost ability to hydrolyze GTP > uncontrolled cell growth

136
Q

cholera

A

toxin alters G-protein activity
Gas constantly active, continuous PKA activation
opening of Cl- channels
excessive loss of H2O and Na+, diarrhea/dehydration/death

137
Q

myosin structure

A

two heads (motors), one long shaft
P-loop ATPase cores, 2 light chains

138
Q

myosin substrate

A

ATP-Mg2+

139
Q

myosin V ATPase activity

A

ATP hydrolysis by nucleophilic attack of H2O (takes off 1 phosphate)
vanadium replaces phosphoryl group
dephosphorylated = swinging lever-arm motion, power stroke state

140
Q

actin binding of myosin, L T Head specific!

A

S1 heads (L and T) bind actin filaments
CC change favors release of Pi

1) T empty (strong actin binding) while L binds ADP + Pi (weak)
2) T binds ATP (detached)
3) ATP does to L head as ADP + Pi

ATP attachment and detachment only from T head

141
Q

two models for myosin V movement

A

hand over hand: like a little human
inchworm: scoochies

142
Q

structure breakdown of muscle fiber

A

thin actin filaments and thick myosin > sarcomeres > myofibrils > muscle fiber
each myosin filament binds 2 actin filaments on either end so able to contract

143
Q

muscle contraction mechanism

A

1) ATP binds to myosin head, myosin releases actin
2) ATP > ADP + Pi, myosin head cocks to high energy conformation
3) Pi released from myosin, CC > myosin power stroke
4) ADP released

144
Q

regulation of actin binding

A

1) action potential causes Ca2+ release
2) Ca2+ binds to troponin on actin, displacing tropomyosin
3) myosin heads can latch to actin

145
Q
A

bisc 330 (3 decks)

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