BB450 exam 2 Flashcards
1
Q
proteases
A
enzymes that cleave peptide bonds
catalyze addition of water
2
Q
chymotrypsin is a ___ protease
A
serine
3
Q
catalytic triad
A
serine H - histidine - aspartic acid
4
Q
catalysis of serine proteases
A
- binding of substrate
- conformational change –> alkoxide ion
- attack of alkoxide ion on carbonyl carbon of peptide bond –> unstable intermediate
- stabilization of intermediate –> breaking peptide bond (one side attached to serine, other side released)
- water enters active site
- activation of water by removal of proton from histidine
- attach of hydroxyl on carbonyl carbon attached to serine
- release of second peptide and regeneration of original active site
5
Q
alkoxide ion formation
A
binding of substrate brings histidine closer to hydroxyl group of serine and extracting protein
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)
7
Q
S1 pocket
A
where substrate binds and catalysis occurs (adjacent to active site/catalytic triad)
determines serine protease’s specificity
8
Q
S1 pocket of chymotrypsin
A
hydrophobic and relatively large (to bind to phenylalanine)
9
Q
S1 pocket of trypsin
A
negatively charged to bind to lysine or arginine
10
Q
chymotrypsin cuts at
A
adjacent to phenylalanine (and other hydrophobic aa)
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
12
Q
metalloproteases
A
use metal ion to hold water in place so can be ionized to act as nucleophile to attach peptide bond
13
Q
Carbonic Anhydrase
A
enzyme that catalyzes joining of CO2 and water to form carbonic anhydrase
14
Q
carbonic anhydrase process
A
zinc ion held by 3 histidines in active site bind water molecule
loss of proton my water –> catalysis
15
Q
carbonic anhydrase max effective at
A
high pH - protons easily removed
16
Q
limiting step in carbonic anhydrase
A
abstraction of proton from water
buffers and/or bases help facilitate this
17
Q
restriction enzymes/endonucleases
A
bacterial enzymes that can cleave DNA by breaking phosphodiester bond between adjacent nucleotides
18
Q
restriction enzymes are defense against ___
A
viruses
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
20
Q
Myosins
A
translate ATP energy into movement
21
Q
ATCase catalyzes
A
1st reaction in CTP synthesis (pyrimidine synthesis)
*does not synthesize CTP
22
Q
substrate of ATCase
A
aspartate - substrate at active site
indicates cell’s readiness to divide
hold in R state (active)
23
Q
CTP inhibits
A
ATCase - feedback inhibition (mediated allosterically)
CTP locks it in T state (can’t flip to R anymore)
24
Q
____ activates ATCase
A
ATP and aspartate
25
ATP and ATCase
activates
ATP is a purine, indicates high energy of cell--> cell is ready to divide
hold is R state (active)
26
structure of ATCase
12 subunits: 6 catalytic, 6 regulatory
ATP and CTP bound at regulatory subunit
aspartate bound at catalytic substrate at active site
27
PALA
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)
28
concerted model
ATCase can flip between R and T state all by itself, allosteric effects lock it in state
no cause/effect sequential model like hemoglobin
29
Protein Kinase A
attaches phosphates to serine or threonine
controlled by allosteric means
2 regulatory, 2 catalytic subunits: R2C2
control whether enzymes are active or inactive
30
when catalytic subunits bind to regulatory subunits of Protein Kinase A
cannot catalyze reactions
31
when cAMP binds to regulatory subunits of Protein Kinase A
catalytic subunits released and active
32
phosphatases
remove phosphates
33
cAMP
signaling molecule, activated Protein Kinase A
34
Protein Kinase A activates enzymes involved in...
breakdown of glycogen and synthesis of glucose
in liver
epinephrine-->cAMP-->protein kinase A-->phosphorylates enzymes-->activates production of glucose
35
phosphodiesterase
breaks down cAMP
| stopping breakdown of glycogen and reducing blood glucose to normal
36
caffeine...
inhibitor of phosphodiesterase, favors high blood glucose levels
37
zymogens
enzymes that are synthesized in an inactive form
| activation requires covalent modification, usually proteolytic cleavage
38
digestive enzymes
trypsin, chymotrypsin, elastase, carboxypeptidase
39
proteolytic enzymes
break down proteins, needed for digestion
40
take ___ to activate a protease
another protease
41
pancreatitis
proteolytic enzymes attack pancreas (where they're made) overly active, get activated closer to pancreas
42
___ is primary activator or proteolytic enzymes
trypsin
43
chymotrypsinogen --> chymotrypsin
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)
44
pi-chymotrypsin
intermediately active form
| after trypsin makes initial cleave between aa 15 and 16
45
alpha one antitrypsin
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)
46
elastase
breaks down proteins we breath in
47
is elastase is too active -->
emphysema
48
smokers and alpha one antitrypsin
oxidize methionine in alpha one antitrypsin
prevents it from binding to elastase
elastase too active --> emphysema
49
blood clotting general
2 pathways possible
| blood clot is self assembly of fibrin
50
blood clotting pathway
prothrombin bind to calcium and held at wound site
prothrombin --> thrombin
thrombin converts fibrinogen --> fibrin
fibrin polymer hardens by glutaminase
51
fibrinogen
alpha, beta, and gamma chains
dimer
alpha has A on end, beta has B on end
52
fibrinogen --> fibrin
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
53
transglutaminase (glutaminase)
hardens fibrin polymer
combines side chains of glutamine and lysine with covalent bond
covalent bond gives strength to clot
54
binding of prothrombin to calcium...
anchors prothrombrin in phospholipid membranes derived from blood platelets after injury
prothrombin converted to thrombin at this site
55
enable prothrombin to bind calcium...
glutamate resides must be carboxylated
| this reaction catalyzed by enzyme that uses vitamin K as cofactor
56
block action of vitamin K...
anticlotter
how blood thinners works (Coumadin, warfarin)
competitive inhibitor: compete with vit. K for active site
57
plasmin
removal of blood clots
| synthesized by plasminogen
58
t-PA
tissue type plasminogen activator
plasminogen --> plasmin
effective in inhibiting cascade to dissolve unwanted clot from stroke or heart attack
serine protease
59
glucose is an ___
aldohexose
| most abundant sugar
60
glyceraldehyde
aldo-triose
| simplest saccharide we call carb
61
dihydroxyacetone
keto-triose
| simplest saccharide we call carb
62
D
2nd to last hydroxyl on right
| most biological sugars
63
L
second to last hydroxyl on left
64
enantiomers
non superimposable mirror images
65
diasteriomers
differ in sterioisomeric configuration, not mirror images
| epimers and anomers
66
epimer
differ in configuration of 1 carbon
67
anomer
differ in configuration of anomeric carbon
68
isomer
same formula, different structure
| enantiomers and diasteriomers (epimers and anomers)
69
furanoses
5 carbon rings
70
pyranoses
6 carbon rings
71
ring structure arise from...
formation of hemiacetals or hemiketals
72
cyclization creates__
a new asymmetric carbon = anomeric carbon
| carbon that was aldehyde or ketone
73
anomeric carbon can be ___
alpha (down) or beta (up) configuration
74
if hydroxyl group on anomeric carbon is unaltered
ring and linear forms can reversibly form
75
if hydroxyl group of anomeric carbon is altered (my methylation)
linear structure cannot form and flipping cannot occur
76
glycoside
altering hydroxyl group on anomeric carbon
commonly created during formation of disaccharides and longer carbs
form glycosidic bonds
77
aldehydes
very reactive, readily oxidized
78
ketones not...
not readily oxidized
79
chair and boat
different conformations
| chair favored because less steric hindrance
80
sucrose
glucose in alpha + fructose in beta
non reducing
table sugar
81
lactose
glucose + galactose
B- 1,4 linkage
reducing sugar
82
maltose
glucose + glucose
alpha- 1,4 linkage
reducing sugar
83
reducing sugar
has free anomeric hydroxyl
lactose and glucose
in presence of copper 2+, copper will be reduced --> color change
84
oxidize aldehyde -->
acid
85
ribose linear structure
right, right, right,
86
deoxyribose linear structure
right, right, H
87
glucose linear structure
right, right, left, right
88
mannose linear structure
right, right, left, left
89
galactose linear structure
right, left, left, right
90
fructose linear structure
right, right, left, ketone
91
right is...
down in ring
92
left is...
up in ring
93
glycogen
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
cellulose
structural support in plants
only glucose
animals don't make
b-1,4 linkages
95
starch
energy stores in plant, mixture of polysaccharides (amylose and amylopectin)
96
chitin
exoskeleton of insects
97
amylose
a-1,4 linkages of glucose, plants
| one component of starch
98
homopolymers
contain only 1 sugar residue
| glycogen, cellulose, amylose, amylopectin, chitin
99
amylopectin
a-1,4 links with a-1,6 branches ~every 30-50 residues
| one component of starch
100
amylopectin/starch not as branched as glycogen...
less ends --> slower breakdown into glucose than glycogen because plants need less energy
101
cellulase
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
glycosaminoglycans
polysaccharides that contain amine group...
| polyanionic --> chemical properties
103
proteoglycans
complexes or proteins and glycosaminoglycans that form feathery structures (repel each other bc negative charges)
slippery ex: snot and synovial fluid
104
glycoproteins
protein linked to oligosaccharide
105
N linkages
through N of asparagine
have common core of 5
made in Golgi or ER
106
O linkages
across serine or threonine oxygen
| made only in Golgi
107
proteins from ER--> Golgi
additional modifications
| targeting to cell membrane, release from cell, lysosome depending on patter on oligosaccharide surface
108
dolichol phosphate
embedded in ER membrane
| N glycoprotein core attaches here
109
oligosaccharides to be linked with proteins
built on dolichol phosphate on outer portion of ER
| then flip inside for attachment
110
hemagluttanin
protein on surface of flu viruses
| bind specific carb. residues of surface of glycoproteins of blood cells
111
to exit cell, virus...
must cleave the sialic acid off w/ neuraminidase enzyme on virus surface
112
anti flu drugs
inhibit action on neuraminidase
cant exit cell after it divides
ex: Tamiflu
113
Haworth structure
ring form
114
Fischer projection
straight chain form
115
first messengers
epinephrine/adrenaline
insulin
epidermal growth factor (EGF)
116
second messengers
```
cAMP
cGMP
Calcium (3rd)
DAG
PIP3
```
117
response of signal include
enzyme activity, gene expression, cell division
118
7TM Receptors
cross cell membrane 7 times
N terminus sticks out, C terminus in cytosol
ex: beta-adrenergic receptor, rhodopsin
119
G protein
protein partner of 7TM receptor
on inside of cell that helps transmit signal
3 subunits: alpha, beta, gamma
120
G proteins can bind...
guanine nucleotides: GTP or GDP
121
beta-adrenergic receptor
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
alpha subunit of G protein bound to ___ when no signal present
GDP
123
when signal is present G protein ..
bind GTP and alpha subunits separates from beta and gamma
124
alpha subunits moves to..
adenylate cyclase
125
adenylate cyclase
membrane bound enzyme
| catalyzes conversion of ATP to cAMP
126
turn off beta-adrenergic system..
GTP converted back to GDP
dissociation of epinephrine from receptor
receptor kinase to phosphorylate the carboxyl tail
breakdown of cAMP by phosphodiesterase
127
receptor kinase...
phosphorylates carboxyl tail of beta-adrenergic receptor --> target for beta arrestin (stops signaling )
128
beta arresting
stops signaling
129
Angiotensin receptor system
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
Angiotensin
regulates blood pressure
131
PIP2
component of membrane
| broken into DAG and IP3 by phospholipase C
132
DAG
2nd messenger
remains in or near lipid bilayer (nonpolar tails)
stimulates protein kinase A
133
protein kinase A stimulated by...
calcium and DHE together
| located at cell membrane so can interact with DHE
134
IP3
2nd messenger
soluble in cytoplasm
binds to receptor in ER
opens channel and Ca from ER come out
135
Calcium...
"3rd messenger"
normally kept low to prevent it from binding proteins and precipitating DNA
essential for muscle contraction
136
EF Hands
structure in Calcium binding proteins
137
Calmodulin
calcium binding protein
keeps concentration low
able to bind other proteins --> CaM Kinases stimulated to phosphorylate proteins
138
Peptide Hormone
protein that acts as a hormone
| ex: angiotensin, insulin, EGF
139
Insulin released in response to
increased glucose in blood, cells take it up
140
insulin receptor
not a 7TM, no G protein
in membrane of target cell
dimeric form
2 extracellular alpha subunits, 2 intracellular beta subunits
141
beta subunits of insulin receptor
have active site, tyrosine kinase
142
no insulin binding...
subunits are non-phosphorylated, kinase is inactive
143
binding of insulin...
moves units of dimer closer together --> phosphorylate tyrosine resides on each other --> activation
144
phosphorylated tyrosines on insulin receptor
bind IRS-1 via SH2 domain
| tyrosines on IRS-1 phosphorylated as well
145
SH2 domain..
recognizes and binds phosphorylated tyrosines
146
phosphorylated tyrosines on IRS-1 bind
BOB
147
BOB...
PIP2-->PIP3 in membrane
148
PIP3 is binding target for
PDK1
149
PDK1
phosphorylates Akt
150
Akt
activates pathway -->GLUT4 to cell surface -->glucose into cell
151
EGF
stimulates cells to grow and divide
152
EGF receptor
monomer in cell membrane w/out EGF
153
binding of EGF to receptor...
```
receptor dimerize (interact with another receptor bound to EGF)
phosphorylate each other at tyrosine
```
154
phosphorylated tyrosines of EGF receptor bind
Grb-2
155
Grb-2b binds
SOS
156
SOS...
interacts with Ras --> cell division stimulated
157
Ras and G proteins...
bad enzymes, hold onto GDP for few minutes before hydrolyze to GTP
on long enough to pass signal
158
oncogene
gene in which mutations can happen that lead to uncontrollable growth
159
proto-oncogene
normal, unmutated form of protein
| important role in controlling cells
160
Ras
proto-oncogene
mutations interfere with ability to cleave GTP to GDP--> uncontrolled cell growth
Ras becomes as oncogene
161
src
proto-oncogene that participates in controlling cell's decision to divide
first oncogene discovered: chicken with virus had cancer
162
when src tail are phosphorylated on tyrosine...
does not divide
163
when src tail are not phosphorylated on tyrosine...
stimulates cell division
164
viral form of src..
mutated such that does not have carboxyl tail...favors cancer bc cant be turned off (no tail to phosphorylate)
165
ABL
tyrosine kinase that plays role in controlling when cells divide
166
BCR-ABL
fusion made in greater quantities than ABL alone -->cells divide uncontrollably
167
BCR-ABL tumors treated with
Gleevec tyrosine kinase inhibitor
168
Her
related to EGF receptor
proto-oncogene
normally present in low amounts
bind to EGF receptor-->process
169
mutation in Her ..
favors Ras and cell division
170
Her and breast cancer
block with antibody --> stop process
| Herceptin
171
negative delta G
goes forward
172
positive delta G
reverse favored
173
delta G = zero
in equilibrium
174
delta G zero
delta G measured under standard conditions, all products and reactants at 1M
175
delta G zero prime
prime to encompass aq. solutions at pH 7 for biological systems
176
as reactants increase...
products/reactants decreases
ln is negative
delta G is more negative
177
as products increase..
products/reactants increase
ln is positive
delta G is more positive
178
products/ reactants >1
ln is positive
179
products/reactants <1
ln is negative
180
electron carriers
NAD+/NADH
FAD/FADH2
NADP+/NADPH
181
6 classes of reactions catalyzed by enzymes
```
redox
ligation
isomerization
group transfer
hydrolytic
lyases
```
182
primary way cells get energy
oxidation
183
glycolysis step 1
hexokinase
glucose + ATP --> G6P
negative delta G zero prime
184
glycolysis step 2
phoshpoglucoisomerase
| G6P --> F6P
185
glycolysis step 3
PFK
F6P --> F-1,6 BP
negative delta G zero prime
most important step for regulation
186
glycolysis step 4
aldolase
F-1,6 BP --> DHAP and G3P
positive delta G zero prime, energetically unfavorable
1 6C molecules --> 2 3C molecules
187
glycolysis step 5
TPI (perfect enzyme)
| DHAP --> G3P
188
at end of energy investment phase...
used 2 ATPs (steps 1 and 3)
| make 2 G3Ps (steps 4 and 5)
189
glycolysis step 6
```
G3PDH
G3P --> 1,3-BPG
NAD+ --> NADH
only redox reaction
energy from oxidation of aldehyde --> acid
```
190
glycolysis step 7
```
phosphoglycerate kinase
1,3-BPG --> 3-phosphoglycerate (3PG)
ADP --> ATP
phosphate from 1,3-BPG to ADP to make ATP
substrate level phosphorylation
```
