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Biochemistry > Test #2 > Flashcards

Test #2 Flashcards

1
Q

serine protease

A

enzymes that catalyze peptide bond hydrolysis

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2
Q

chymotrypsin binding pocket

A

bulky hydrophobic residues

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3
Q

trypsin binding pocket

A

positively charged residues

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4
Q

elastase binding pocket

A

binds small residues like gly, ala, val

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5
Q

catalytic triad

A

serine, histidine and aspartate make up the catalytic machinery

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6
Q

The ______ formed in the transition state is stabilized by the enzyme

A

oxyanion

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7
Q

Delta G0

A

standard conditions of delta G

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8
Q

What point of curve used to measure enzyme

A

> > Km - saturating amounts of substrate

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9
Q

What point of curve used to measure substrate

A

low substrate levels (lower or at Km)

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10
Q

Kcat

A

Vmax/enzyme concentration - or how many substrate molecules that can be used per second

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11
Q

alanine transaminase (ALT)

A

balances amino acid levels, indicative of cell damage

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12
Q

alpha-1 antitrypsin

A

indicator of liver damage when low, secreted by liver and taken up by lung

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13
Q

zymogen

A

enzyme precursor

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14
Q

order of blood clotting cascade

A

damage leads to activated enzyme, cleaves prothrombin to thrombin which cleaves fibrinogen to fibrin which spontaneously forms a cross-linked fibrin clot

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15
Q

prothrombin

A

needs to be cut in two places to become activated thrombin

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16
Q

what needs to be in the right position to make active thrombin

A

Ile16 needs to move closer to the serine

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17
Q

purpose of calcium in clotting cascade

A

gamme-carboxy-glutamate binds metal ions like calcium which promotes binding of prothrombin which can be cleaved when clotting is needed

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18
Q

purpose of vitamin K in clotting cascade

A

needed for the carboxylation of glutamate to bind to calcium to bind to membrane surface

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19
Q

dicournarol and warfarin

A

blocks the carboxylation of glutamate in prothrombin, preventing binding to the membrane

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20
Q

heparin

A

protein inhibitor of clotting, promotes antithrombin-thrombin complex formation, irreversible short acting inhibition

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21
Q

elastase and alpha1-antitrypsin

A

elastase is used by neutrophils to neutralize foreign particles. It is inhibited in tissues by alpha1-antitrypsin. This can be defective in smokers which leads to destroyed elastin

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22
Q

Ki??

A

inversely related to the affinity constant of the inhibitor for the enzymes, the lower the Ki, the tighter it binds

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23
Q

DIPF

A

inhibits serine proteases, an irreversible inhibitor, lowers Vmax

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24
Q

allosteric enzymes

A

multiple subunits, binding sites for affector molecules, regulate a pathway, do not follow michaelis menten

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25
Q

example of allosteric enzyme

A

PFK1, inhibited by high levels of ATP

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26
Q

E2F

A

required to bind to DNA to initiate transcription of genes, when bound to RB, it remains inactive

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27
Q

mechanism of RB

A

in the unphosphorylated activte state, RB is bound to E2F. In the presence of cyclin dependent kinases, Rb is phosphorylated, causing dissociated from E2F, allowing for transcription. Thereby Rb acts as a master brake in preventing transcription.

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28
Q

mechanism of p53

A

in the presence of DNA damage, p53 is able to induce the expression of p21 which binds to the cyclin/Cdk complexes and stops cell cycle, p21 also binds to PCNA

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29
Q

p53 plays a key role in….

A

apoptosis

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30
Q

Rb

A

retinoblastoma

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31
Q

p53

A

sarcomas, carcinomas

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32
Q

NF1

A

neuroblastoma, contains GAP domain, leads to cafe-au-lait spots, defective signal transduction through RAS

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33
Q

APC

A

colon, stomach

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34
Q

example of altered growth factors

A

simian sarcoma oncogene, encodes part of PDGF molecule to induce signal transduction

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35
Q

example of altered growth factor receptors

A

epidermal growth factor receptor in the absence of EGF can stimulate growth (includes ErbB/HER2)

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36
Q

mechanism of Ras

A

active when bound to GTP, inactive when bound to GDP. stuck in active form leads to growth and cancer

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37
Q

Fos and Jun

A

continuous expression of these transcription factors activates AP1 sites and leads to increased growth

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38
Q

Myc

A

regulates 15% of all gene, binds to enhancer sequences and recruits histone acetyltransferases, can have translocation in Burkitt’s lymphoma

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39
Q

Burkitt’s lymphoma

A

caused by translocation, Myc is constitutively expressed

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40
Q

transformation by DNA tumor virus

A

SV40 T-antigen sequesters Rb and p53, leading to uncontrolled proliferation

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41
Q

HPV E6 and E7

A

E6 binds to p53, E7 binds to RB

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42
Q

O blood type leads to increase in….

A

duodenal ulcers

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43
Q

alpha vs beta sugars

A

alpha = anomeric carbon is down, beta is up

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44
Q

maltose

A

2 glucose in alpha 1,4

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45
Q

lactose

A

galactose and glucose in beta 1,4

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46
Q

sucrose

A

glucose and fructose in alpha 1,2

47
Q

amylose

A

unbranched glucose polysaccharide in alpha 1,4 (only in plants)

48
Q

hyaluronic acid

A

repeating residues or glucuronic acid and n-acetylglucosamine

49
Q

examples of GAGs

A

hyaluronic acid, herapin, chondroatin sulfate, heparan sulfate

50
Q

example of glycation

A

hemoglobin A1C, measure of history of blood glucose

51
Q

gangliosides

A

sugars conjugated to lipids

52
Q

except for ______, enzymatic glycosylation is for ______

A

GlcNac, secreted proteins or extracellular facing proteins

53
Q

process of O-linked sugars

A

linked to serine or threonine, added one sugar at a time in the Golgi

54
Q

process of N-linked sugars

A

linked to asparagine, assembled on dolicohol phosphate lipid carrier on the ER membrane, eventually released in the ER lumen

55
Q

tunicamycin

A

inhibits the first step in N-linked protein glycosylation

56
Q

aggrecan

A

proteoglycan that acts as a shock absorber in the knee

57
Q

where do polyaccharides get disested

A

mouth, intestine, colon (not the stomach)

58
Q

digestion in the mouth

A

alpha-amylase starts the digestion process, limit dextrans reach the intestine where they are degraded by enzymes, amaylase is inactivated in the stomach

59
Q

where are digestive carbohydrate enzymes located

A

intestinal brush border

60
Q

carbs transports with facilitated diffusion

A

fructose, mannose and glucose

61
Q

location of SGLT1 and2

A

1 is in the intestine, 2 is in the kidney

62
Q

transporter responsive to insulin

A

Glut4 (muscle, fat and white blood cell)

63
Q

GluT 2

A

takes up glucose in liver, pancreas and intestines

64
Q

hexokinase vs glucokinase

A

hexokinase is present in all tissues and has a low Km so it is not sensitive to glucose changes. Glucokinase is present in the liver and pancreas and high a high Km allowing it to regulate glucose uptake.

65
Q

MODY

A

has a defective glucokinase gene

66
Q

What cells depend solely on glycolysis for energy?

A

red blood cells, hemolytic anemias can result from defects in these enzymes

67
Q

Energy requiring enzymes in glycolysis

A

hexokinase and PFK1

68
Q

Energy producing steps in glycolysis

A

Phosphoglycerate kinase and pyruvate kinase

69
Q

regulation of PFK1

A

inhibited by ATP, citrate, and fatty acids. Activated by fructose 2,6 bisphosphate

70
Q

which enzyme of glycolysis shows negative cooperativity

A

glyceraldehyde 3P dehydrogenase, allows buffering of the enzyme to changes in substrate concentration

71
Q

which glycolytic enzyme requires an inorganic phosphate

A

glyceraldehyde 3 phosphate dehydrogenase, to form high energy phosphate bond

72
Q

regulation of pyruvate kinase

A

stimulated by fructose 1,6 bisphosphate. Inhibited by alanine, NADH, ATP, fatty acids and succinyl CoA. Pyruvate gets phosphorylated by PKA under high glucagon to inactivate it

73
Q

pellegra

A

niacin deficiency, leads to diarrhea, dementia, dermatitis and death

74
Q

serine comes from which glycolytic intermediate

A

3-phosphoglycerate

75
Q

2,3 BPG comes from which glycolytic intermediate

A

1,3 BPG using bisphosphoglycerate mutase

76
Q

2-F Deoxyglucose (PET) targets….

A

hexokinase

77
Q

arsenate targets……

A

G3P dehydrogenase

78
Q

fluoride targets…..

A

enolase

79
Q

Tauri’s disease

A

lacking muscle PFK1, leads to weakness, also calle glycogen storage disease VII

80
Q

explain PFK1 regulation by F2,6BP

A

F2,6BP is produced by PFK2. F2,6BP activates PFK1 to allow glycolysis to proceed. When PFK2 is unphosphorylated it promotes glycolysis and when it is phosphorylated to prevent glycolysis

81
Q

metabolism of fructose

A

fructokinase converts to fructose 1-P, aldolase B converts of glyceraldehyde and DHAP which then get converted to G3P

82
Q

deficiency in aldolase B (bid deal)

A

cant process fructose (or sorbitol or sucrose), leads to the depletion of phosphate and ATP

83
Q

hereditary fructosuria

A

deficiency in fructokinase, not a big deal due to not using up phosphate

84
Q

Whats up with sorbitol

A

can be converted between glucose and fructose, important in fuel for sperm in seminal vesicles and in the eye for retinopathy

85
Q

Mannose metabolism

A

hexokinase and phosphmannose isomerase convert it to M6P and then F6P to enter glycolysis

86
Q

Galactose metabolism

A

first converted to galactose 1-P via kinase. this is converted to UDP galactose then UDP glucose then glucose-1-P then glucose-6-P

87
Q

galactokinase deficiency

A

leads to minor problems, not really an issue, galactose can be reduced to galactitol

88
Q

Classic galactosemia

A

very serious, deficiency in galactose-1-P-uridylyl transferase, accumulation of galactose-1-P is very toxic. PAtients can still synthesize from UDP glucose and epimerase

89
Q

metabolism of alcohol

A

converted to acetylaldehyde (toxic) then to acetate and acetyl CoA

90
Q

problems with alcohol consumption

A

acidosis from high acetate, high NADH, lacking of gluconeogenesis (hypoglycemia), triglycerol production, vitamin deficiency

91
Q

antidote for methanol and ethylene glycol poisoning

A

ethanol

92
Q

explain the pyruvate dehydrogenase reaction

A

pyruvate reacts with pyruvate dehydrogenase (E1) releasing CO2, CoASH accepts the acyl group from lipolate (E2), which is then in the reduced form. Lipolate it oxidized using FADH and NADH

93
Q

CoASH

A

accepts the acyl group from lipolate, forming acetyl CoA

94
Q

thiamine pyrophosphate

A

formed from thiamine, binds to pyruvate leading to rapid decarboxylation

95
Q

disease of thiamine deficiency

A

beri-beri

96
Q

lipolate

A

part of E2 of pyruvate dehydrogenase, accepts the incoming pyruvate molecule and gets reduced to SH

97
Q

FAD

A

from riboflavin, acccepts electrons from the reduced lipoate and forms FADH2, deficiency cause glossitis

98
Q

E1, E2 and E3

A

E1 - decarboxylase
E2- lipoate
E3 - FAD

99
Q

pyruvate dehydrogenase regulation

A

inhibited by acetyl CoA and NADH, ADP and by phosphorylation of the enzyme. Activated by insulin, calcium and dephosphorylation. Calcium and insulin activate the phosphatase, everything else affects the kinase

100
Q

pyruvate dehydrogenase deficiency

A

can be caused by enzyme deficiency or trivalent arsenic poisoning, neurological symptoms, bad prognosis

101
Q

reaction of TCA that release CO2

A

isocitrate dehydrogenase and alpha-ketoglutarate dehydrogenase

102
Q

Where are glutamate and glutamine formed in TCA

A

from alpha-ketoglutarate

103
Q

Where does heme come from in TCA

A

succinyl-CoA

104
Q

where does aspartate come from in TCA

A

oxaloacetate

105
Q

What is special about aconitase in TCA

A

teaches lesson in sterospecificity

106
Q

What two enzymes are sensivite to arsenic

A

alpha-ketoglutarate dehydrogenase and pyruvate dehydrogenase

107
Q

What TCA enzyme form GTP

A

succinyl CoA synthetase, via substrate level phosphorylation

108
Q

anaplerotic reactions

A

reactions that maintain the levels of TCA intermediates

109
Q

What TCA enzymes can not be transported through mitochondria

A

acetyl CoA, NADH, oxaloacetate

110
Q

relative levels of NAD/NADP in cytoplasm

A

cells have high NAD+ levels and high NADPH levels

111
Q

what cell types use PPP

A

5-10% of liver glucose, higher in adipose

112
Q

Two PPP reactions that produce NADPH

A

G6P dehydrogenase and 6P gluconate dehydrogenase

113
Q

transketolase

A

converts ribose 5P and xylulose 5P in 3 and 7 caarbon sugars, TPP is a coenzyme

114
Q

meyloperoxidase

A

generates bleach (HOCl) for killing bacteria

Biochemistry (4 decks)

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