bch210 exam Flashcards
(163 cards)
1
Q
enzymes…
A
lower Ea, inc rate of rxn
2
Q
how are enzymes activated
A
proteolytic cleavage of zymogens
3
Q
how to monitor enzymes
A
chromogenic substances + 405nm absorption
4
Q
how are enzymes regulated
A
gene expression, structural changes, proteasome/lysosome/endocytosis
5
Q
types of enzyme inhibition and their respective vmax, km effect
A
competitive, inc km
uncompetitive, dec km, dec vmax
noncompetitive (allosteric esque), dec vmax
allosteric, sigmoidal kinetics
6
Q
what’s special about allosteric regulators
A
quaternary struc, T/R form, cooperativity
7
Q
x intercept on LB plot
A
1/Km
8
Q
y intercept on LB plot
A
1/vmax
9
Q
x and y axis on LB plot
A
1/[S] and 1/[vo] respectively
10
Q
Keq’<1 =>
A
delta G nought prime < 0
11
Q
delta G < 0 =>
A
exergonic
12
Q
delta G eqn
A
delta G = delta G nought ‘ + RTln([P]/[S])
13
Q
delta G = 0 =>
A
rxn may be reversible, directionality depends on conc.
14
Q
nucleoside diphosphokinase
A
enzyme that can swap P b/w GTP and ADP
15
Q
ATP struc
A
n.t. = adenine + ribose + 3P
16
Q
how do you get delta G nought prime
A
take delta G eqn but set delta G = 0 and use standard conditions (1M, 8.314 = R, 298K, pH 7)
17
Q
vo eqn
A
vo = d[P]/dt
18
Q
MM eqn
A
vo = vmax*[S]/([S]+Km)
19
Q
kcat eqn
A
vmax/[E total]
20
Q
what does km indicate
A
how tight the binding is
21
Q
what does kcat indicate
A
turnover number, describes enzyme efficiency
22
Q
what happens in the muscles to make atp
A
creatine kinase couples phosphocreatine -> creatine rxn w ATP synthesis (at rest we want phosphocreatine)
23
Q
oxioreductase
A
redox rxn, involves nadh fadh2
24
Q
transferase
A
group transfer b/w molecs
25
hydrolase
hydrolysis rxn, func group transferred to water
26
lyase
cleavage rxn, usu DB/cyclization
27
isomerase
group transfer w/i molecules
28
ligase
join 2 molecs, involves ATP/GTP/UTP/CTP
29
translocase
mvmt of ions/molecs *across a membrane*
30
chromogenic substance for chymotrypsin
N-acetyl-L-Phe-P-nitrophenylester (chymotrypsin cuts Phe)
31
catabolism features (3)
breakdown, exergonic, oxidative
32
glucokinase
transfers P onto glc (this does not work for galactose bc km glc < km galac)
33
what type of enzyme is phosphoglucomutase
isomerase
34
what type of enzyme are kinases
transferase
35
L means
OH on the LEFT
36
D means
OH on the RIGHT
37
monosaccharide formula
(CH2O)n
38
furanose
FIVE membered ring
39
pyranose
SIX membered ring
40
alpha
\o/
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beta
/o\
42
glycoprotein O linked will be what AA/molec
ser, thr, sugars
43
glycoprotein N linked will be what AA
asn
44
maltase cleaves
1 4 alpha glyc
45
lactase cleaves
1 4 beta glyc
46
heteropolymer
diff monosach.s
47
detect starch??
starch coil around iodine
48
amylopectin
branched, alpha 1-4 normal, alpha 1-6 branched every 30 units
49
alpha amylase
breaks down starch
50
cellulose struc
beta 1-4, unbranched
51
glycogen struc
alpha 1-6 branch every 8-12 units, regular alpha 1-4
glycogenin dimer at origin w cov linkage to reducing end
52
how do enzymes add/remove glc from glycogen
remove units from non-reducing ends
53
amylose struc
unbranched, alpha 1-4
54
how to detect L/D chirality
mutarotation - a change in optical rotation of polarized light due to alpha and beta anomer interconversion
55
test for reducing sugar
Cu2+ -----> cu2o
56
oligosacch length
3-20 monosacchs
57
what does 1-4 bond mean
anomeric C at carbon 1, attacking oh at carbon 4
58
constitutional isomer
diff order of functional grp
59
stereoisomer
diff bond rotato9in
60
enentiomer
non superimposable mirror img
61
diasterreiomseiorn
non superimposable non mirror img
62
epimer
differ at 1 asymmetric carbon
63
anomer
differ at anomeric carbon
64
SGLT
sodium gluc co-transporters, 2ndary active transport
65
types of GLUT and type of transport
GLUT4: glc
GLUT5: fruc
facilitated diffusion
66
glycolysis general pathway
glc -> pyruvate, 2ATP generated, exergonic
67
glycolysis stage 1 net eqn
2ATP + 1 glc -> 2 GAP
68
glycolysis step 1
hexokinase phosphrylates glc to G6P, uses ATP
69
how are hexokinases activated for glycolysis
Mg2+ and ATP bind -> C6 hydroxyl atks phosphate on ATP
70
how is hexokinase regulated
buildup of G6P inhibits
71
glycolysis step 3
phosphofructosekinase-1 (PFK1) phosphorylates F6P to F1,6BP, uses ATP
72
how is PFK1 inhibited/activated
allosterically inhibited by ATP/citrate (signs of high enrg), activated by AMP, ADP, F2,6BP
73
what does PFK2 do
phosphorylates F6P to F2.6BP
74
how are PFK2 and PFK1 linked
PFK1 activates PFK2 (feed forward regulation)
75
how (chemically) is PFK1 inhibited/activated
has 1 active binding site and 1 allosteric binding site - ATP, AMP, ADP bind to the allosteric site to inhibit/activate it
76
glycolysis stage 2 net eqn
2 GAP -> 4 ATP + 2 NADH + 2 pyruvate
77
glycolysis step 10
pyruvate kinase dephosphorylates PEP to pyruvate, creating ATP
78
how is pyruvate kinase inhibited
inhibited by phosphorylation when blood glc low, inhibited by allosteric regulators: acetyl CoA and alanine (both can be used to generate enrg)
79
how is pyruvate kinase actiated/stimulated
F1.6BP, AMP, high blood glc/insulin
80
how glycogen synthesis
step 1 of glycolysis
phosphoglucomutase isomerizes g6p to g1p
UDP phosphorylase uses UTP to convert g1p to udp-glc
glycogen synthase attaches udp-glc to non reducing ends of glycogen (udp removed after)
81
phosphoglucomutase
isomerizes g6p to g1p during glycogen synthesis
82
how glycogen breakdown/glycogenolysis
glycogen phosphorylase uses P to release G1P from glycogen non reducing end
83
what triggers glycogen breakdown
epi and glucagon signalling => phosphorylation/activation of glycogen phosphorylase and dephosphorylation/inactivation of glycogen synthase
84
how is glycogenolysis regulated
inhibited by high enrg (ATP, G6P) allosterically
stimulated by AMP
85
what happens to the g1p after after glycogn breakdown
phosphoglucomutase converts g1p to g6p to be used in glycolysis
86
what does gluconeogenesis do
supply blood glc (make glc)
87
how does gng
uses 4 enzymes, high enrg intermediates, ATP, GTP, NADH, lactate/glycerol/AA to make glc
88
what does fructose 2, 6 bisphosphate do
activates pfk1 for glycolysis, inhibits fructose 1,6 bisphosphatase for GNG
89
what is the tandem enzyme
pfk2/fbpase2
90
what does tandem enzyme do
makes f2,6bp -> f6p when phosphorylated (fbpase2 active, low glc), and opp when dephosphorylated (pfk2 active, high glc)
91
how is the tandem enzyme regulated
phosphorylation, it's phosphorylated by pka when blood glc is low and dephosphorylated via phosphatase when blood glc is high
92
what is in the outer mitochondrial membrane
porins, beta barrels
93
where does pyruvate production occur
cytoplasm
94
succinate dehydrogenase (SDH) does what
links CAC and oxidative phosphorylation in the mx, turns succinate into fumarate and makes a FADH2
95
PDC struc
multipel copies of 3 subunits: E1, E2, E3 + 5 cofactors
96
PDC cofactors
prosthetic groups: thiamine pyrophosphate (TPP), lipamide, FAD
cosubstrates: coA, NAD+
97
PDC solubility
soluble
98
where does PDC live
mx
99
what does PDC do
turn pyruvate into acetyl coA, makes CO2 and NADH as a result and H+
100
why is PDC rxn favourable
release of CO2 is spontaneous and pyruvate is unstable/charged
101
what does PDC inhibition do
inc in pyruvate => glycolysis inhibited if high enrg, lactate used in gng if low enrg
102
how is PDC regulated allosterically
inc acetyl coa inhibits E2 and stimulates pd kinase
inc nadh inhibited e3 and stimulates pd kinase
dec pyruvate, adp, calcium stimulates pdc by inhibiting pd kinase (except for ca which activates pd phosphatase)
103
what does pd kinase do
phosphorylates pdc to inhibit e1, uses atp
104
what does pd phosphatase do
dephosphorylates pdc to activate e1
105
how is pdc regulated via covalent modification
pd kinase and pd phosphatase
106
what happens when oxygen level drops
etc shuts down, anaerobic metabolism starts, pdc and cac slow. glycolysis is only able to generate the 2 atp
107
how does anaerobic metabolism work
lactate dehydrogenase uses nadh (from glycolysis) to replenish nad+ to continue glycolysis
lactate used in liver in gng
108
cori cycle
low o2 => lactate up
lactate -> pyruvate (via ldh) -> oxaloacetate -> glc (VIA CAC)
in the liver and kidney
109
1 acetyl coa produces what when put into cac
oxaloacetate, coa, 3nadh, fadh2, gtp, 3H+, 3CO2
110
where do co2 carbons originate from in cac cycle
round 1: oxaloacetate
round 2: 50% certainty of acetyl coa
111
parts of cac that can be made from aa
alpha ketoglutarate from glutamate
oxaloacetate from aspartate
112
how can acetyl coa be made
glc, fatty acids, AA
113
stage 2 cac
regenerate oxaloacetate
1 fadh2, 1 nadh, 1 gtp produced
step 8 is relevant to inhibition b/c MDH rxn standard free enrg > 0
114
stage 1 cac general
2 oxidative decarboxylation rxns
co2, 2nadh released
acetyl groups join w oxaloacetate
amphibolic pathway
115
how is cac regulated
at steps 1, 3, 4, 8
low enrg, ca, upstream substrates stimulate cac
high enrg, lack of coenzymes, low product inhibit cac
116
how can oxaloacetate run out
beta oxi using a lot of acetyl coa, glc or glucogenic aa depleted
117
how can oxaloacetate be made
AA, pyruvate
118
pyruvate carboxylase...
turn pyruvate into oxaloacetate (first step of gng)
119
electron transfer/redox potential
a molecule's tendency to be oxidized or reduced
120
redox potential < 0 =>
prefer to lsoe e-, good reducing agents
121
redox potential > 0 =>
prefer to gain e-, good oxidizing agents
122
redox potential formula
standard free enrg = -n*F*redox potential
F = 96485J/mol
123
redox potential formula when given rxn
E = E acceptor - E donor
(donor is on the right side of the rxn)
124
look at the mitochondrial experiment graphs a bit
also!! what do the experiments test
mitchell chemiosmotic hypothesis
125
regulation of oxidative phosphorylation
rotenone and amytal inhibit e- flow from I to Q
antimycin A blocks III
cyanide, azide, CO inhibit IV
oligomycin inhibits V
uncouplers disrupt the H+ gradient
126
types of uncouplers
DNP, salicylate, FCCP
127
what do uncouplers do
disrupt H+ gradient by moving H+ from high to low conc. they can cross the membrane w h.phobic properties and bind H+ with acidic groups
128
where is cac
mx
129
complex I
NADH Q oxidoreductase, pumps 4 protons
130
complex 2
succinate Q reductase
131
complex 3
q cytochrome c oxidoreductase, pumps 4 protons
132
complex 4
cytochrome c oxidase, pumps 2 protons
133
complex 5
atp synthase
134
atp synthase structure
f1 peripheral unit (alpha, beta gamma subunits + strator)
f0 integral unit/rotor
135
purpose of f0 (atp synthase)
anchor enzyme to IMM
136
how does f1 work
gamma rotates when h+ binds to gamma => conformational changes in beta subunits => ATP synthesis
137
how do atp synthase beta subunits work
O state: atp leave
L state: ADP and P bind
T state: ATP bound
138
nadh in etc = ...
10 protons pumped = 2.5 ATP = 3.5 water
139
fadh2 in etc = ...
6 protons pumped = 1.5 atp = 2.5 water
140
p/o ratio
atp:oxygen ratio
141
what connects complex 3 and 4 in etc
cytochrome c
142
what happens when atp synthase functions in reverse
beta subunits rotate in opp direction to move p+ in opp direction after atp hydrolysis
143
acyl coa structure
coa-s-CO-(CH3)n
144
what happens when glc level increases
glycogen synthesis
inc in atp and nadh
=> cac slows => fat synthesis
145
how os cholesterol synthesized
w acetyl coa in cytoplasm. req nadph, atp
146
how is cholesterol synthesis regulated
hmg coa -> mevalonate is a precursor to cholesterol, catalyzed by hmg coa reductase. inhibiting hmg coa reductase will inhibit cholesterol synthesis
147
what is hmg coa reductase and how is it inhibited
catalyzes hmg coa -> mevalonate which is a precursor to cholesterol. inhibited by phosphorylation or statins
148
how are acyl chains activated for pre-carnitine shuttle. what is the caveat
acyl coa synthetase attaches HS-coa, uses ATP. ppi hydrolysis helps make this rxn favourable (ATP -> AMP + ppi)
uses 2 ATP and 1 h2o in total bc 1 atp is used to recover adp from amp
149
pyrophosphate is
ppi
150
what does coa addition do to FA
causes it to be trapped in the cell
151
how does acyl coa get transported across the immune system
carnitine shuttle
152
how carnitine shuttl;e
carnitine acyltransferase I catalyzes carnitine to acyl carnitine (acyl coa -> coa) which goes in. then cat II does the opposite. carnitine can now be transported back across via a TRANSLOCASE!!!!
153
what do lipoproteins do
transport h.phobic fats
154
where are lipoproteins produced
liver/intestine
155
hdl lipoprotein relation
hdl is the lipoprotein that picks up cholesterol for the liver to process
156
what are lipoproteins made of
monolayer of phospholipids and cholesterol
apoproteins on the surface are involved in cell-cell comm.s
157
how does beta oxidation???
acyl coa + h2o + coa -> acetyl coa + nadh + fadh2 + acyl coa with 2 less carbons
a k:0 chain will go through k/2-1 cycles
158
REVIEW ATP CALCULATIONS RN!!
DONE
159
how does citrate shuttle????
acetyl coa -> citrate in cac via citrate synthase
citrate exported to cytoplasm, coa is added to it to turn into acetyl coa + pyruvateand pyruvate can return inside mitochndria
160
FA synthesis?
acetyl in the cytoplasm is carboxylated to malonyl coa via acetyl coa carboxylase (ACC)
fatty acid synthase forms 16:0 FA chains
further modification mayhappen
161
how does ACC work
uses ATP lol nothing else to say
162
how is ACC regulated
inhibited by palmitoyl coa and stimulated by citrate (allosterically for both)
inhibited by phosphorylation(glucagon/epi/amp trigger this)
stimulated by insulin and protein phosphatase
163
