Ford Review Flashcards
1
Q
What are the four types of noncovalent interactions?
A
charge-charge
dipole interactions
van der waals
hydrogen
2
Q
Example of charge-charge interaction
A
salt bridges
3
Q
Example of dipole interaction
A
selectivity filter of K+ channgel
4
Q
Example of van Der Waals interactions
A
nucleotide stacking
5
Q
Example of hydrogen interactions
A
nuclei acid and base pairing/protein secondary structure
6
Q
If pH< pKa what does that mean?
A
protonated
7
Q
If pH> pKa what does that mean
A
deprotonated
8
Q
If pH=pKa what does that mean?
A
just as likely to be protonated as deprotonated
9
Q
what is the equation for pKa?
A
pKa= -logKa = [H+] [A-] / [HA]
10
Q
What does Ka mean?
A
dissociation constant, predicts how likely an acid will donate a proton
11
Q
What is the Henderson-Hasselbalch equation?
A
pH= pKa + log [A-] / [HA]
12
Q
What happens when something is reduced?
A
gains electrons (H)
13
Q
What happens when something is oxidized?
A
loses electrons
14
Q
What amino acid preforms redox?
A
cystein (disulfide linkages are reductions)
15
Q
What are the 3 important electron carriers in cellular metabolism and their reduced and oxidized forms?
A
NAD+/NADH
FAD/FADH2
FMN/FMNH2
16
Q
What is equilibrium?
A
forward rate = reverse rate, no net formation or destruction
17
Q
How does Le Chatlier fit into cellular metabolism?
A
it’s how to drive an unfavorable reaction forward
- make pathway/use up products
- couple it to a favorable reaction like ATP hydrolysis
18
Q
What is the gibs free energy equation?
A
deltaG= deltaH- TdeltaS
19
Q
how does thermodynamics relate to protein folding?
A
change of entropy–protein folds, loses entropy
aqueous environment has more disorder
20
Q
negative delta H
A
energy released
21
Q
postive delta H
A
energy added
22
Q
zero delta H
A
closed system
23
Q
negative delta S
A
decrease disorder
24
Q
positive delta S
A
increase disorder
25
zero delta S
no net change in disorder
26
negative delta G
free energy released
exergonic, favorable
spontaneous reaction
27
positive delta G
free energy required
endergonic, unfavorable
driven reaction
28
zero delta G
equilibrium
29
Give example of cooperative binding
hemoglobin binds oxygen cooperatively
30
Positive cooperativity definition
binding site affinity for ligand increases with every subsequent binding
31
negative cooperativity definition
binding site affinity for ligand decreases with every subsequent binding
32
no cooperativity definition
binding sites are independent, situation can be Michaelis menten enzyme
33
Km definition
Michaelis constat, [S] where reaction rate is half maximal OR half of the active sites are full
Km= [E] [S] / [ES]
34
Vmax definiton
maximum rate possible for a give concentration of enzyme
Vmax= Kcat [E]T
35
Kcat definition
number of substrate molecules concerted per active site per time (first order rate constant)
kcat= K2
36
Kcat/Km definition
measure of enzyme performance by predicting the fate of E*S, how good an enzyme is
Kcat/Km= Kcat/ k-1 +Kcat
37
VIEW DIFFERENT TYPES OF INHIBITORS
pictures on slides
38
similarities between substate level control and feedback control
alters ability of reaction to proceed
39
differences between substate level control and feedback control
substrate: acts on single reaction
feedback: acts on different reaction pathway
40
example of substrate level control
G6P and hexokinase
| Acetyl-CoA inhibits PDH
41
example of feedback control
nucleotide de novo synthesis
| aa biosynthesis
42
similarities between activation and inhibition
alters ability of reaction to proceed, can be substrate or feedback
43
differences between activation and inhibition
activation: adds new or increases existing function
inhibition: decreases or stops existing function
44
example of activation
dephosphorylation of pyruvate kinase
45
example of inhibition
phosphorylation of pyruvate kinase
46
description of reversible covalent modification
+/- small molecule
47
description of irreversible covalent modification
proteolytic activation
48
similarities between reversible covalent modification and irreversible covalent modification
reversible: may be activating
irreversible: activating mechanism only
49
differences between reversible covalent modification and irreversible covalent modification
reversible: may be inhibiting, reversible
irreversible: never inhibiting, irreversible
50
examples of reversible covalent modification
histone modification
adenylation/uridylation
and glutamine synthetase
phosphorylation
51
examples of irreversible covalent modification
protease cascade/digestive enzyme
blood clotting factors
insulin
52
allosteric effector description
binds at unique locations and alters the proteins functionality
53
competitive effector description
competes with intended substate to bind the active site
54
allosteric effector and competitive effector similarities
allosteric: may inhibit function
competitive: always inhibits function
55
allosteric effector and competitive effector differences
allosteric: does not bind active site, may be activating
competitive: binds at active site, can never be activating
56
allosteric effector examples
ATCase
ribonucleotide reductase
phosphofructokinase
57
competitive effector examples
methotrexate vs dihydrofolate for dihydrofolate reductase
58
What does covalent catalysis do?
share electrons
59
What does acid base catalysis do?
share protons
60
What does approximation do in catalysis?
orientation and proximity
61
What does electrostatic catalysis do?
non covalent interactions
62
oxidoreductases description and example
description: redox, move elections
example: dehydrogenase (oxidizers)
reductases (reducers)
63
transferases description and example
move a functional group
kinases add phosphate
phosphotases remove phosphate
64
hydrolases description and example
break a bond by adding water
citrate synthase, lactose
65
lyases description and example
break a bond without water
aldolase in glycolysis
66
isomerases description and example
rearrange order of atoms
TPI
67
ligases description and example
make a covalent bond
aldolase in gluconeogenesis
68
Describe active transport
requires energy
| moves something against/creates a concentration gradient
69
Describe the P-type ATPase
phosphorylates itself
transports ions
4 domains: transmembrane, actuator, nucleotide, binding, phosphorylation
example: Na/K pump
70
Describe the ABC transporter
no phosphorylation of self
transport small molecules
dimeric, contains 2 copies of transmembrane domain and aTP binding cassette (ABC)
example: multidrug resistance protein
71
describe the secondary transport
uses gradient established by primary active transport
moves ion or molecule against its gradient without using energy
example: Na-glucose cotransport
72
describe passive transport
no energy needed
73
describe the ion channel
selectivity filter
| gate: voltage gated, ligand gated
74
describe the aquaporin
selectivity filter
| no gate
75
describe the gap junction
no selectivity filter
| no gate
76
review glycolysis, TCA and ox-phos
look at notes
77
location of glycolysis
cytoplasm
78
rate limiting enzyme of glycolysis
phosphofructokinase
79
how does hexokinase regulate in glycolysis
G6P inhibits
80
how is phosphofructokinase regulated in glycolysis
citrate inhibits
| low ATP is activating
81
how is pyruvate kinase regulated in glycolysis
high ATP is inhibitory
| F16BP activates
82
location of TCA cycle
mitochondrial matrix
83
rate limiting enzyme of TCA cycle
isocitrate dehydrogenase
84
how is the pyruvate dehydrogenase complex regulated in the TCA cycle
ATP, acetyl CoA, NADH are inhibitory (kinase/+PO4)
ADP and pyruvate are activating (phosphatase/-PO4)
85
how is isocitrate dehydrogenase regulated in the TCA cycle
ATP and NADH inhibit
| ADP activates
86
how is alpha-ketoglutarate dehydrogenase complex regulated in TCA cycle
ATP, succinyl CoA and NADH inhibit
87
location of ox phos
mitochondrial inner membrane and inter membrane space
88
glycogenolysis location
cytoplasm
89
glycogenolysis rate limiting enzyme
glycogen phosphorylase
90
glycogenolysis regulated enzyme
glyogen phosphorylase
- dephosphorylation inhibits
- phosphorylation activates
91
amino acid catabolism location
cytoplasm and mitochondrial matrix
| urea cycle only in liver
92
beta oxidation location
```
cytoplasm (activation)
mitochondrial matrix (beta oxidation)
```
93
rate limiting enzyme of beta oxidation
perilipins
94
how is perilipins regulated in beta oxidation
phosphorylation promotes TAG release by inhibiting perilipin
95
location of ketone bodies
only produced in liver, but broken down in non liver cells though
96
location of gluconeogenesis
cytoplasm (ER in liver and kidney only)
97
rate limiting enzyme of gluconeogenesis
fructose- 1,6- bisphophate
98
How is pyruvate carboxylase regulated in gluconeogenesis
ADP inhibits
| acetyl CoA is activating
99
how is PEP carboxykinase regulated in gluconeogenesis
ADP inhibits
100
how is fructose 1,6 bisphoate regulated in gluconeogenesis
low ATP is inhibitory
| citrate activates
101
location of PPP
cytoplasm
102
rate limiting enzyme of PPP
glucose 6 phosphate dehydrogenase
103
how is G6P dehydrogenase regulated in the PPP
monomers inactive, dimers activate
dephosphorylated inactive, phosphorylation activates
insulin activates
104
location of nucleotide de novo synthesis
cytoplasm (except dihydroorotate dehydrogenase in mitochondria)
105
what are the regulated in enzymes in nucleotide de novo synthesis
general theme: feedback regulation
| ribonucleotide reductase: activity site and specificity site
106
amino acid biosynthesis location
cytoplasm and mitochondrial matrix
107
amino acid biosynthesis regulated enzymes
general theme: feedback regulation
glutamine synthetase:
- adenylylation inhibits/deadenylylation actives
- PII is inactivating/ PII-UMP is activating
- feed back inhibition is glutamine
- feed forward activation is alpha ketoglutarate, ATP
108
fatty acid synthesis location
cytoplasm and mitochondrial matrix
109
rate limiting enzyme of fatty acid synthesis
acetyl coA carboxylase
110
how is ATP citrate lyase regulated in fatty acid synthesis
activated by phosphorylation and glucose/insulin
| inhibited by PUFAs and leptin
111
how is acetyl coA carboxylase regulated in fatty acid synthesis
active by citrate, -PO4/ insulin, high carb diet
inhibited by palmitate, +PO4/epinephrine/glucagon/AMP
112
how is fatty acid synthase regulated in fatty acid synthesis
activated by sugar-PO4, insulin, high carb diet
| inhibited by high fat diet, starvation and PUFAs
113
glycogenesis location
cytoplasm
114
glycogenesis rate limiting enzyme
glycogen synthase
115
how is glycogen synthase regulated in glycogenesis
phosphorylation inhibits
| dephosphorylation activates
116
where does TAG synthesis occur
hepatocytes and adipocytes
