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Biochemistry > BB450 exam 2 > Flashcards

BB450 exam 2 Flashcards

1
Q

proteases

A

enzymes that cleave peptide bonds

catalyze addition of water

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2
Q

chymotrypsin is a ___ protease

A

serine

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3
Q

catalytic triad

A

serine H - histidine - aspartic acid

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4
Q

catalysis of serine proteases

A
  1. binding of substrate
  2. conformational change –> alkoxide ion
  3. attack of alkoxide ion on carbonyl carbon of peptide bond –> unstable intermediate
  4. stabilization of intermediate –> breaking peptide bond (one side attached to serine, other side released)
  5. water enters active site
  6. activation of water by removal of proton from histidine
  7. attach of hydroxyl on carbonyl carbon attached to serine
  8. release of second peptide and regeneration of original active site
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5
Q

alkoxide ion formation

A

binding of substrate brings histidine closer to hydroxyl group of serine and extracting protein

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6
Q

oxyanion hole

A

stabilizes tetrahedreal intermediate that arises twice during catalysis, keeps intermediate from reacting with enzymes (adjacent to active site/catalytic triad)

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7
Q

S1 pocket

A

where substrate binds and catalysis occurs (adjacent to active site/catalytic triad)
determines serine protease’s specificity

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8
Q

S1 pocket of chymotrypsin

A

hydrophobic and relatively large (to bind to phenylalanine)

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9
Q

S1 pocket of trypsin

A

negatively charged to bind to lysine or arginine

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10
Q

chymotrypsin cuts at

A

adjacent to phenylalanine (and other hydrophobic aa)

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11
Q

aspartyl proteases

A

use 2 aspartic acid side chains to hold water in place; use ion to act as nucleophile to attach peptide bond

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12
Q

metalloproteases

A

use metal ion to hold water in place so can be ionized to act as nucleophile to attach peptide bond

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13
Q

Carbonic Anhydrase

A

enzyme that catalyzes joining of CO2 and water to form carbonic anhydrase

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14
Q

carbonic anhydrase process

A

zinc ion held by 3 histidines in active site bind water molecule
loss of proton my water –> catalysis

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15
Q

carbonic anhydrase max effective at

A

high pH - protons easily removed

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16
Q

limiting step in carbonic anhydrase

A

abstraction of proton from water

buffers and/or bases help facilitate this

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17
Q

restriction enzymes/endonucleases

A

bacterial enzymes that can cleave DNA by breaking phosphodiester bond between adjacent nucleotides

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18
Q

restriction enzymes are defense against ___

A

viruses

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19
Q

___ prevents restriction enzyme from cutting DNA

A 
methyl group (mathylase puts methyl group on nucleotide) 
cellular, methylated DNA remains uncut, invading viral DNA (not methylated) gets cut and destroyed
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20
Q

Myosins

A

translate ATP energy into movement

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21
Q

ATCase catalyzes

A

1st reaction in CTP synthesis (pyrimidine synthesis)

*does not synthesize CTP

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22
Q

substrate of ATCase

A

aspartate - substrate at active site
indicates cell’s readiness to divide
hold in R state (active)

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23
Q

CTP inhibits

A

ATCase - feedback inhibition (mediated allosterically)

CTP locks it in T state (can’t flip to R anymore)

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24
Q

____ activates ATCase

A

ATP and aspartate

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25
Q

ATP and ATCase

A

activates
ATP is a purine, indicates high energy of cell–> cell is ready to divide
hold is R state (active)

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26
Q

structure of ATCase

A

12 subunits: 6 catalytic, 6 regulatory
ATP and CTP bound at regulatory subunit
aspartate bound at catalytic substrate at active site

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27
Q

PALA

A

binds to active site of ATCase covalently
suicide inhibitor
locks enzyme in R state, blocks access to active site
acts like aspartate (proves aspartate is causing to be in R state)

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28
Q

concerted model

A

ATCase can flip between R and T state all by itself, allosteric effects lock it in state
no cause/effect sequential model like hemoglobin

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29
Q

Protein Kinase A

A

attaches phosphates to serine or threonine
controlled by allosteric means
2 regulatory, 2 catalytic subunits: R2C2
control whether enzymes are active or inactive

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30
Q

when catalytic subunits bind to regulatory subunits of Protein Kinase A

A

cannot catalyze reactions

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31
Q

when cAMP binds to regulatory subunits of Protein Kinase A

A

catalytic subunits released and active

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32
Q

phosphatases

A

remove phosphates

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33
Q

cAMP

A

signaling molecule, activated Protein Kinase A

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34
Q

Protein Kinase A activates enzymes involved in…

A

breakdown of glycogen and synthesis of glucose
in liver
epinephrine–>cAMP–>protein kinase A–>phosphorylates enzymes–>activates production of glucose

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35
Q

phosphodiesterase

A

breaks down cAMP

stopping breakdown of glycogen and reducing blood glucose to normal

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36
Q

caffeine…

A

inhibitor of phosphodiesterase, favors high blood glucose levels

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37
Q

zymogens

A

enzymes that are synthesized in an inactive form

activation requires covalent modification, usually proteolytic cleavage

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38
Q

digestive enzymes

A

trypsin, chymotrypsin, elastase, carboxypeptidase

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39
Q

proteolytic enzymes

A

break down proteins, needed for digestion

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40
Q

take ___ to activate a protease

A

another protease

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41
Q

pancreatitis

A

proteolytic enzymes attack pancreas (where they’re made) overly active, get activated closer to pancreas

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42
Q

___ is primary activator or proteolytic enzymes

A

trypsin

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43
Q

chymotrypsinogen –> chymotrypsin

A

requires trypsin
makes initial cleave between aa 15 and 16 (disulfide bonds keep them from coming completely apart)
becomes pi-chymotrypsin, cleaves itself to remove 2 dipeptides–> full chymotrypsin activity (3 polypeptide pieces held together by disulfide bonds)

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44
Q

pi-chymotrypsin

A

intermediately active form

after trypsin makes initial cleave between aa 15 and 16

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45
Q

alpha one antitrypsin

A

protease inhibitor that stops elastase in lungs from getting too active
(plugs up active site of trypsin, works better on elastase but already got name)

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46
Q

elastase

A

breaks down proteins we breath in

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47
Q

is elastase is too active –>

A

emphysema

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48
Q

smokers and alpha one antitrypsin

A

oxidize methionine in alpha one antitrypsin
prevents it from binding to elastase
elastase too active –> emphysema

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49
Q

blood clotting general

A

2 pathways possible

blood clot is self assembly of fibrin

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50
Q

blood clotting pathway

A

prothrombin bind to calcium and held at wound site
prothrombin –> thrombin
thrombin converts fibrinogen –> fibrin
fibrin polymer hardens by glutaminase

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51
Q

fibrinogen

A

alpha, beta, and gamma chains
dimer
alpha has A on end, beta has B on end

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52
Q

fibrinogen –> fibrin

A

thrombin clips A and B portions of alpha and beta of fibrinogen, polymerization
alpha left over fits into gamma
beta left over fits into hole on beta structure

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53
Q

transglutaminase (glutaminase)

A

hardens fibrin polymer
combines side chains of glutamine and lysine with covalent bond
covalent bond gives strength to clot

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54
Q

binding of prothrombin to calcium…

A

anchors prothrombrin in phospholipid membranes derived from blood platelets after injury
prothrombin converted to thrombin at this site

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55
Q

enable prothrombin to bind calcium…

A

glutamate resides must be carboxylated

this reaction catalyzed by enzyme that uses vitamin K as cofactor

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56
Q

block action of vitamin K…

A

anticlotter
how blood thinners works (Coumadin, warfarin)
competitive inhibitor: compete with vit. K for active site

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57
Q

plasmin

A

removal of blood clots

synthesized by plasminogen

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58
Q

t-PA

A

tissue type plasminogen activator
plasminogen –> plasmin
effective in inhibiting cascade to dissolve unwanted clot from stroke or heart attack
serine protease

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59
Q

glucose is an ___

A

aldohexose

most abundant sugar

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60
Q

glyceraldehyde

A

aldo-triose

simplest saccharide we call carb

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61
Q

dihydroxyacetone

A

keto-triose

simplest saccharide we call carb

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62
Q

D

A

2nd to last hydroxyl on right

most biological sugars

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63
Q

L

A

second to last hydroxyl on left

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64
Q

enantiomers

A

non superimposable mirror images

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65
Q

diasteriomers

A

differ in sterioisomeric configuration, not mirror images

epimers and anomers

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66
Q

epimer

A

differ in configuration of 1 carbon

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67
Q

anomer

A

differ in configuration of anomeric carbon

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68
Q

isomer

A

same formula, different structure

enantiomers and diasteriomers (epimers and anomers)

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69
Q

furanoses

A

5 carbon rings

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70
Q

pyranoses

A

6 carbon rings

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71
Q

ring structure arise from…

A

formation of hemiacetals or hemiketals

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72
Q

cyclization creates__

A

a new asymmetric carbon = anomeric carbon

carbon that was aldehyde or ketone

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73
Q

anomeric carbon can be ___

A

alpha (down) or beta (up) configuration

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74
Q

if hydroxyl group on anomeric carbon is unaltered

A

ring and linear forms can reversibly form

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75
Q

if hydroxyl group of anomeric carbon is altered (my methylation)

A

linear structure cannot form and flipping cannot occur

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76
Q

glycoside

A

altering hydroxyl group on anomeric carbon
commonly created during formation of disaccharides and longer carbs
form glycosidic bonds

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77
Q

aldehydes

A

very reactive, readily oxidized

78
Q

ketones not…

A

not readily oxidized

79
Q

chair and boat

A

different conformations

chair favored because less steric hindrance

80
Q

sucrose

A

glucose in alpha + fructose in beta
non reducing
table sugar

81
Q

lactose

A

glucose + galactose
B- 1,4 linkage
reducing sugar

82
Q

maltose

A

glucose + glucose
alpha- 1,4 linkage
reducing sugar

83
Q

reducing sugar

A

has free anomeric hydroxyl
lactose and glucose
in presence of copper 2+, copper will be reduced –> color change

84
Q

oxidize aldehyde –>

A

acid

85
Q

ribose linear structure

A

right, right, right,

86
Q

deoxyribose linear structure

A

right, right, H

87
Q

glucose linear structure

A

right, right, left, right

88
Q

mannose linear structure

A

right, right, left, left

89
Q

galactose linear structure

A

right, left, left, right

90
Q

fructose linear structure

A

right, right, left, ketone

91
Q

right is…

A

down in ring

92
Q

left is…

A

up in ring

93
Q

glycogen

A

energy stores for animals
polymer of glucose (a-1,4) with branches (a-1,6) ~every 10 residues
branches have branches
most in liver and muscles

94
Q

cellulose

A

structural support in plants
only glucose
animals don’t make
b-1,4 linkages

95
Q

starch

A

energy stores in plant, mixture of polysaccharides (amylose and amylopectin)

96
Q

chitin

A

exoskeleton of insects

97
Q

amylose

A

a-1,4 linkages of glucose, plants

one component of starch

98
Q

homopolymers

A

contain only 1 sugar residue

glycogen, cellulose, amylose, amylopectin, chitin

99
Q

amylopectin

A

a-1,4 links with a-1,6 branches ~every 30-50 residues

one component of starch

100
Q

amylopectin/starch not as branched as glycogen…

A

less ends –> slower breakdown into glucose than glycogen because plants need less energy

101
Q

cellulase

A

enzyme that breaks down b-1,4 linkages of cellulose
most animals don’t have it/cant digest cellulose
ruminants (cow, sheep) and ungulates have bacterium that make enzyme is specialized stomach

102
Q

glycosaminoglycans

A

polysaccharides that contain amine group…

polyanionic –> chemical properties

103
Q

proteoglycans

A

complexes or proteins and glycosaminoglycans that form feathery structures (repel each other bc negative charges)
slippery ex: snot and synovial fluid

104
Q

glycoproteins

A

protein linked to oligosaccharide

105
Q

N linkages

A

through N of asparagine
have common core of 5
made in Golgi or ER

106
Q

O linkages

A

across serine or threonine oxygen

made only in Golgi

107
Q

proteins from ER–> Golgi

A

additional modifications

targeting to cell membrane, release from cell, lysosome depending on patter on oligosaccharide surface

108
Q

dolichol phosphate

A

embedded in ER membrane

N glycoprotein core attaches here

109
Q

oligosaccharides to be linked with proteins

A

built on dolichol phosphate on outer portion of ER

then flip inside for attachment

110
Q

hemagluttanin

A

protein on surface of flu viruses

bind specific carb. residues of surface of glycoproteins of blood cells

111
Q

to exit cell, virus…

A

must cleave the sialic acid off w/ neuraminidase enzyme on virus surface

112
Q

anti flu drugs

A

inhibit action on neuraminidase
cant exit cell after it divides
ex: Tamiflu

113
Q

Haworth structure

A

ring form

114
Q

Fischer projection

A

straight chain form

115
Q

first messengers

A

epinephrine/adrenaline
insulin
epidermal growth factor (EGF)

116
Q

second messengers

A 
cAMP
cGMP
Calcium (3rd) 
DAG
PIP3
117
Q

response of signal include

A

enzyme activity, gene expression, cell division

118
Q

7TM Receptors

A

cross cell membrane 7 times
N terminus sticks out, C terminus in cytosol
ex: beta-adrenergic receptor, rhodopsin

119
Q

G protein

A

protein partner of 7TM receptor
on inside of cell that helps transmit signal
3 subunits: alpha, beta, gamma

120
Q

G proteins can bind…

A

guanine nucleotides: GTP or GDP

121
Q

beta-adrenergic receptor

A
  1. epinephrine binds to receptor
  2. G protein interacts with carboxyl tail of receptor and senses change
  3. alpha subunits binds GTP, releases GDP
  4. alpha subunit separate from b and gamma
  5. a subunit moves to adenylate cyclase
  6. conversion of ATP to cAMP
  7. cAMP interacts with protein kinase A–>phosphorylation–>produce glucose
122
Q

alpha subunit of G protein bound to ___ when no signal present

A

GDP

123
Q

when signal is present G protein ..

A

bind GTP and alpha subunits separates from beta and gamma

124
Q

alpha subunits moves to..

A

adenylate cyclase

125
Q

adenylate cyclase

A

membrane bound enzyme

catalyzes conversion of ATP to cAMP

126
Q

turn off beta-adrenergic system..

A

GTP converted back to GDP
dissociation of epinephrine from receptor
receptor kinase to phosphorylate the carboxyl tail
breakdown of cAMP by phosphodiesterase

127
Q

receptor kinase…

A

phosphorylates carboxyl tail of beta-adrenergic receptor –> target for beta arrestin (stops signaling )

128
Q

beta arresting

A

stops signaling

129
Q

Angiotensin receptor system

A
  1. binds to 7TM receptor
  2. activates G protein
  3. activates phospholipase C
  4. breaks down PIP2–> DAG and IP3
  5. DAG stimulates protein kinase A (w/ Calcium)
  6. IP3 stimulates release of calcium from ER–>calcium controls vessel contraction
  7. Calcium bind calmodulin
  8. CaM Kinases phosphorylate proteins.. .
130
Q

Angiotensin

A

regulates blood pressure

131
Q

PIP2

A

component of membrane

broken into DAG and IP3 by phospholipase C

132
Q

DAG

A

2nd messenger
remains in or near lipid bilayer (nonpolar tails)
stimulates protein kinase A

133
Q

protein kinase A stimulated by…

A

calcium and DHE together

located at cell membrane so can interact with DHE

134
Q

IP3

A

2nd messenger
soluble in cytoplasm
binds to receptor in ER
opens channel and Ca from ER come out

135
Q

Calcium…

A

“3rd messenger”
normally kept low to prevent it from binding proteins and precipitating DNA
essential for muscle contraction

136
Q

EF Hands

A

structure in Calcium binding proteins

137
Q

Calmodulin

A

calcium binding protein
keeps concentration low
able to bind other proteins –> CaM Kinases stimulated to phosphorylate proteins

138
Q

Peptide Hormone

A

protein that acts as a hormone

ex: angiotensin, insulin, EGF

139
Q

Insulin released in response to

A

increased glucose in blood, cells take it up

140
Q

insulin receptor

A

not a 7TM, no G protein
in membrane of target cell
dimeric form
2 extracellular alpha subunits, 2 intracellular beta subunits

141
Q

beta subunits of insulin receptor

A

have active site, tyrosine kinase

142
Q

no insulin binding…

A

subunits are non-phosphorylated, kinase is inactive

143
Q

binding of insulin…

A

moves units of dimer closer together –> phosphorylate tyrosine resides on each other –> activation

144
Q

phosphorylated tyrosines on insulin receptor

A

bind IRS-1 via SH2 domain

tyrosines on IRS-1 phosphorylated as well

145
Q

SH2 domain..

A

recognizes and binds phosphorylated tyrosines

146
Q

phosphorylated tyrosines on IRS-1 bind

A

BOB

147
Q

BOB…

A

PIP2–>PIP3 in membrane

148
Q

PIP3 is binding target for

A

PDK1

149
Q

PDK1

A

phosphorylates Akt

150
Q

Akt

A

activates pathway –>GLUT4 to cell surface –>glucose into cell

151
Q

EGF

A

stimulates cells to grow and divide

152
Q

EGF receptor

A

monomer in cell membrane w/out EGF

153
Q

binding of EGF to receptor…

A 
receptor dimerize (interact with another receptor bound to EGF) 
phosphorylate each other at tyrosine
154
Q

phosphorylated tyrosines of EGF receptor bind

A

Grb-2

155
Q

Grb-2b binds

A

SOS

156
Q

SOS…

A

interacts with Ras –> cell division stimulated

157
Q

Ras and G proteins…

A

bad enzymes, hold onto GDP for few minutes before hydrolyze to GTP
on long enough to pass signal

158
Q

oncogene

A

gene in which mutations can happen that lead to uncontrollable growth

159
Q

proto-oncogene

A

normal, unmutated form of protein

important role in controlling cells

160
Q

Ras

A

proto-oncogene
mutations interfere with ability to cleave GTP to GDP–> uncontrolled cell growth
Ras becomes as oncogene

161
Q

src

A

proto-oncogene that participates in controlling cell’s decision to divide
first oncogene discovered: chicken with virus had cancer

162
Q

when src tail are phosphorylated on tyrosine…

A

does not divide

163
Q

when src tail are not phosphorylated on tyrosine…

A

stimulates cell division

164
Q

viral form of src..

A

mutated such that does not have carboxyl tail…favors cancer bc cant be turned off (no tail to phosphorylate)

165
Q

ABL

A

tyrosine kinase that plays role in controlling when cells divide

166
Q

BCR-ABL

A

fusion made in greater quantities than ABL alone –>cells divide uncontrollably

167
Q

BCR-ABL tumors treated with

A

Gleevec tyrosine kinase inhibitor

168
Q

Her

A

related to EGF receptor
proto-oncogene
normally present in low amounts
bind to EGF receptor–>process

169
Q

mutation in Her ..

A

favors Ras and cell division

170
Q

Her and breast cancer

A

block with antibody –> stop process

Herceptin

171
Q

negative delta G

A

goes forward

172
Q

positive delta G

A

reverse favored

173
Q

delta G = zero

A

in equilibrium

174
Q

delta G zero

A

delta G measured under standard conditions, all products and reactants at 1M

175
Q

delta G zero prime

A

prime to encompass aq. solutions at pH 7 for biological systems

176
Q

as reactants increase…

A

products/reactants decreases
ln is negative
delta G is more negative

177
Q

as products increase..

A

products/reactants increase
ln is positive
delta G is more positive

178
Q

products/ reactants >1

A

ln is positive

179
Q

products/reactants <1

A

ln is negative

180
Q

electron carriers

A

NAD+/NADH
FAD/FADH2
NADP+/NADPH

181
Q

6 classes of reactions catalyzed by enzymes

A 
redox 
ligation 
isomerization
group transfer
hydrolytic 
lyases
182
Q

primary way cells get energy

A

oxidation

183
Q

glycolysis step 1

A

hexokinase
glucose + ATP –> G6P
negative delta G zero prime

184
Q

glycolysis step 2

A

phoshpoglucoisomerase

G6P –> F6P

185
Q

glycolysis step 3

A

PFK
F6P –> F-1,6 BP
negative delta G zero prime
most important step for regulation

186
Q

glycolysis step 4

A

aldolase
F-1,6 BP –> DHAP and G3P
positive delta G zero prime, energetically unfavorable
1 6C molecules –> 2 3C molecules

187
Q

glycolysis step 5

A

TPI (perfect enzyme)

DHAP –> G3P

188
Q

at end of energy investment phase…

A

used 2 ATPs (steps 1 and 3)

make 2 G3Ps (steps 4 and 5)

189
Q

glycolysis step 6

A 
G3PDH
G3P --> 1,3-BPG
NAD+ --> NADH 
only redox reaction
energy from oxidation of aldehyde --> acid
190
Q

glycolysis step 7

A 
phosphoglycerate kinase 
1,3-BPG --> 3-phosphoglycerate (3PG)
ADP --> ATP
phosphate from 1,3-BPG to ADP to make ATP
substrate level phosphorylation

Biochemistry (11 decks)

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