Biochem miscellaneous Flashcards Preview

STEP > Biochem miscellaneous > Flashcards

Flashcards in Biochem miscellaneous Deck (123):
1

exceptions to degeneracy of genetic code

methionine + tryptophan (each encoded by only 1 codon)

2

codon for methionine

AUG

3

codon for tryptophan

UGG

4

nucleotides methylated in replication

cytosine + adenine

5

how is uracil derived?

deamination of cytosine

6

what makes thymine unique?

Has a methyl grow.

7

when does NER occur?

G1

8

sequence of events in base excision repair

glycosylase removes altered base and creates AP site --> AP endonuclease cleaves 5' end --> lyase cleaves 3' end --> pol fills gap --> ligase seals it

9

significance of N-formylmethionine (fMET)

- initiates protein synthesis in bacteria.
- Nucleic acid coded by start codon.
- Stimulates neutrophil chemotaxis.

10

polyadenylation signal

AAUAAA

11

describe mRNA quality control

Occurs at cytoplasmic processing bodies (P-bodies), which contain exonucleases, decapping enzymes, and microRNAs. mRNAs may be stored in P-bodies for future translation.

12

what initiates protein synthesis?

GTP hydrolysis

13

describe trimming

removal of N- or C-terminal propeptides from zymogen to generate mature protein (eg trypsinogen --> trypsin).

14

labile cell types

bone marrow + gut epithelium + skin + hair follicles + germ cells

15

stable cell types

hepatocytes + lymphocytes

16

golgi functions

1) protein distribution
2) modifies N-oligosaccharides on asparagine
3) adds O-oligosaccharides on serine and threonine.
4) adds mannose-6-phosphate

17

Signal recognition particle (SRP)

abundant, cytosolic ribonucleoprotein that traffics proteins from the ribosome to the RER. Absent or dysfunctional SRP leads to protein accumulation in the cytosol.

18

examples of intermediate filaments

vimentin + desmin + cytokeratin + lamins + glial fibrillary acid proteins (GFAP) + neurofilaments

19

Vimentin

stains for mesenchymal tissue (eg., fibroblasts, endothelial cells, macrophages).

20

microvilli

microfilament

21

cilia structure

9+2 arrangement of microtubule doublets. Base (basal body) consists of 9 microtubule triplets with no central microtubules.

22

axonemal dynein

ATPase that links peripheral 9 doublets and causes bending of cilium by differential sliding of doublets.

23

frequency of an x-linked recessive disease in males

q

24

frequency of an x-linked recessive disease in females

q squared

25

what is wrong in prader willi vs. angelmans

codebook

26

2 rules for inheritance chart

1) look for recessive/dominance
2) who's passing it down (only moms --> mitochondrial inheritance)

27

gene mutated in myotonic dystrophy type 1

DMPK

28

myotonia

Delayed relaxation of skeletal muscles after voluntary contraction or electrical stimulation. Feature of myotonic dystrophy.

29

medical word for night blindness

nyctalopia

30

medical word for dry, scaly skin

xerosis cutis

31

medical word for corneal degeneration

keratomalacia

32

significance of flavins (FMN, FAD)

used as cofactors in redox reactions

33

relationship between isoniazid and pyridoxine deficiency

Pyroxidine’s active form is the cofactor for gamma-aminolevulinate synthase, the enzyme that catalyzes the rate-limiting step of heme synthesis

34

vitamins required for niacin synthesis

B2 + B6

35

pyridoxine used in synthesis of...

cystathionine, heme, niacin, histamine, serotonin, epinephrine, norepinephrine, dopamine, GABA

36

storage form of vitamin D

25-OH D3

37

active form of vitamin D

calcitriol, 1,25-(OH)2D3

38

ergocalciferol

D2, ingested from plants

39

cholecalciferol

D3, consumed in milk, formed in sun-exposed skin.

40

location of D3 synthesis

stratum basale

41

biochemistry of folate deficiency

Deficiency inhibits the formation of deoxythymidine monophosphate (dTMP), which limits DNA synthesis and promotes megaloblastosis and erythroid precursor cell apoptosis. Since thymidine supplementation can moderately increase dTMP levels, it can reduce erythroid precursor cell apoptosis, so need to give thymidine with folate deficiency.

42

other names for vitamin K

phytomenadione, phylloquinone, phytonadione

43

enzyme that metabolizes ethanol in microsome

CYP2E1

44

biochem explanation for hepatosteatosis in alcoholism

dihydroxyacetone phosphate --> glycerol-3-phosphate, which combines with fatty acids to make triglycerides leading to hepatosteatosis.

45

dehydrogenase action

catalyze oxidation-reduction reaction

46

ATP production

32 net ATP via malate-aspartate shuttle, 30 net ATP via glycerol-3-phosphate shuttle

47

glycerol-3-phosphate shuttle

ATP shuttle in muscle

48

malate-aspartate shuttle

ATP shuttle in heart and liver

49

what does CoA carry?

acyl groups

50

what does lipoamide carry?

acyl groups

51

What does TPP cary (thiamine pyrophosphate)?

aldehydes

52

glycolysis equation

FA pg 99

53

enzymes requiring ATP

1) hexokinase/glucokinase 2) PFK-1

54

where is ATP produced in glycolysis?

1) 1,3 BP --> 3-phosphoglycerate
2) PEP --> pyruvate

55

where is GTP produced

succinyl-CoA --> succinate

56

regulation by F-2-6-bisphosphate

FBP-ase (fructose bisphosphatase-2) and PFK-2 (phosphofrutokinase-2) are the same bifunctional enzyme whose function is reversed by phosphorylation by PKA.

57

regulation by F-2-6-bisphosphate in fasting state

increased glucagon --> increased cAMP --> increased PKA --> inceased FBPase-2 --> decreased PFK-2 --> less glycolysis, more gluconeogenesis

58

regulation by F-2-6-bisphosphate in fed state

increased insulin --> increased cAMP --> increased PKA --> decreased FBPase-2 --> increased PFK-2 --> more glycolysis + less gluconeogenesis

59

pyruvate dehydrogenase reaction

pyruvate + NAD+ + CoA --> acetyl-CoA + CO2 + NADH

60

positive regulation of pyruvate dehydrogenase complex

elevated NAD+/NADH, elevated ADP, elevated Ca2+

61

vitamins required by pyruvate dehydrogenase complex

B1-B5, except B4

62

tissues that rely on anaerobic glycolysis

RBCs, WBCs, kidney, medulla, lens, testes, and cornea

63

products of pyruvate --> acetyl-CoA

acetyl-CoA + 1 NADH + 1 CO2

64

products of TCA cycle

3 NADH + 1 FADH2 + 2CO2 + 1 GTP per acetyl-CoA. Thus 10 ATP/acetyl-CoA.

65

Where is NADH generated in TCA cycle?

1) isocitrate --> alpha-KG
2) alpha-KG --> succinyl-CoA
3) Malate --> oxaloacetate

66

Where is FADH2 generated in TCA cycle?

succinate --> fumarate

67

Where is GTP generated in TCA cycle?

succinyl-CoA --> succinate

68

irreversible enzymes in TCA cycle

1) PDH 2) citrate synthase 3) isocitrate dehydrogenase 4) a-KG dehydrogenase

69

ATP produced via ATP synthase

1 NADH --> 2.5 ATP
1 FADH2 --> 1.5 ATP

70

site of gluconeogenesis

primarily liver, enzymes also in kidney + intestinal epithelium.

71

nonoxidative reaction in HMP shunt --> enzymes required + cofactors + products

ribulose-5-P --> ribose-5-p + glyceraldehyde-3-phosphate + fructose-6-p
- via phosphopentose isomerase + transketolases
- requires B1

72

sucrose

glucose + fructose

73

treatment for hereditary fructose intolerance

decrease intake of both fructose + sucrose

74

triose kinase

Fructose pathway: enzyme that metabolizes glyceraldehyde --> glyceraldehyde-3-P

75

aldose reductase 1) action 2) where its expressed

1) galactose --> galactitol
2) glucose --> sorbitol (using NADPH)

76

4 epimerase

galactose metabolism: interconverts UDP-gal to UDP-Glu

77

sorbitol dehydrogenase

sorbitol --> sorbitol dehydrogenase (using NAD+)

78

pathophys of osmotic damage (cataracts, retinopathy, peripheral neuropathy) in diabetics

glucose converted to sorbitol

79

tissues that have both aldose reductase + sorbitol dehydrogenase

liver + ovaries + seminal vesicles

80

tissues that have only aldose reductase

schwann cells + retina + kidneys + lens (primarily)

81

essential amino acids

all amino acids coded as glucogenic + glucogenic/ketogenic + ketogenic

82

location of synthesis of norepinephrine, dopamine, epinephrine

NE + dopamine are produced in the CNS + PNS. Epinephrine produced predominately in the adrenal medulla.

83

phenylketones (detected in urine of PKU kids)

phenylacetate, phenyllactate, phenylpyruvate

84

describe biochem of homocystinuria

...

85

limit dextrin

1-4 residues remaining on a branch after glycogen phosphorlase has already shortened it.

86

deficiency vs. accumulated substrate in gaucher's

glucocerebrosidASE deficiency; glucocerebroside accumulation

87

explain why ketone bodies build up in DKA and prolonged starvation

oxaloacetate is depleted for gluconeogenesis. This causes a build-up of acetyl-CoA, which shunts glucose and FFA toward the production of ketone bodies.

88

explain why ketone bodies build up in alcoholism

excess NADH shunts oxaloacetate to malate. This causes a buildup of acetyl-CoA, which shunts glucose and FFA toward the production of ketone bodies.

89

energy source during fasting state

Glycogenolysis is the primary source; also gluconeogenesis + adipose release of FFA.

90

LCAT

lecithin-cholesterol acyltransferase. Esterifies 2/3 of plasma cholesterol into cholesteryl ester (more hydrophobic form that is then sequested into the core of a lipoprotein particle). This forces newly synthesized HDL spherical and forcing reaction to become unidrectional.

91

exonucleases vs. endonucleases

Exonucleases remove base pairs, endonucleases cleave phosphodiester bonds within polynucleotide chains.

92

Folate deficiency labs

Methmalonic acid normal + homocysteine elevated.

93

Mucopolysaccharidoses

Hurler's + hunters

94

Location of heme synthesis

1st 2 steps in mitochondria, 4 steps in cytosol, final 3 steps in mitochondria

95

heme synthesis pathway

succinyl-CoA + glycine --> delta-aminolevulinic acid --> porphobilinogen --> hydroxymethylbilane --> uroporphyrinogen --> coproporphyrinegen --> protoporphyrinogen --> protoporphyrin --> heme

96

polyadenylation vs. capping

5' end is capped, 3' end is cleaved off, then polyadenylated

97

ketogenesis.

Think of DKA. Body breaks down fatty acids to produce ketone bodies. This process supplies energy to certain organs (particularly the brain) under circumstances like fasting.

98

DM1 HLA association

DR3 and DR4

99

Insulin sensitivity in DM1

High

100

glucose intolerance in DM1

Severe

101

serum insulin level in DM1

low

102

Genetic predisposition in DM1

Relatively weak (50% concordance in identical twins), polygenic.

103

genetic predisposition of DM2 vs. DM1

DM2 relatively much stronger than DM1

104

genetic predisposition of DM2

Relatively strong (90% concordance in identical twins), polygenic.

105

HLA type DM association

None

106

Glucose intolerance in Type 2DM

Mild to moderate

107

Labs in DKA

Hyperglycemia + increased hydrogen ions + decreased HCO3 + increased blood ketone + leukocytosis + HYPERKALEMIA.

108

DKA treatment

IV fluids + IV insulin + K+ + glucose if necessary to prevent hypoglycemia.

109

Amino acids necessary for purine synthesis:

o Code: Spartin gagging out peter strand + fat sailor masturbating /GAG  glycine + aspartate + glutamine. Massive wooden cat overhead/purine synthesis.
o Location: entrance to pool area

110

Basic positively charged amino acids

o Code: giant cat + pirate with terrible head + Edward Norton on the couch/arginine + lysine + histidine. Huge pirate in middle/arginine is most basic. Cat floating in pool of water in front of TV/histidine has no charge at body pH.
o Location: TV area

111

Acidic negatively charged amino acids:

Code: Spartin doing acid + fat sailor doing acid/aspartic acid + glutamic acid. Electrical wires from ceiling zapping them/negatively charged at body pH.
Location: His bedroom

112

Hydrophobic amino acids

o Coded character: Alan in corner + val in middle around stripper pole + Lucy in a block of ice + methhead in right corner + mike O’connell /hydrophobic amino acids = valine, alanine, isoleucine, methionine, and phenylalanine. /these amino acids compose the transmembrane domains of signaling proteins.
o Location: Hottub

113

glycogenic and ketogenic amino acids

o Code: lucy in a block of ice + pale and pasty Mike O’connell on top + a big turkey + theon greyjoy feasting on the turkey/isoleucine + phenylalanine + threonine + tryptophan.
o Location: Area between ketogenic and glucogenic area

114

glycogenic amino acids

o Code: Cuppola made of candy/glucogenic amino acids. Val stripping around pole + meth head + cat dancing/methionine (Met) + valine (Val) + histidine (his).
o Location: Patio

115

Describe G protein mechanism

Ligand activates the receptor ---> inducing conformational change --> GDP exchanged for GTP --> Galpha subunit dissociates --> Galpha has downstream effects.
Termination --> Ga subunit hydrolyzes GTP to GDP, allowing it to re-associate with Gby and start a new cycle.

116

GTPase

hydrolase that binds and hydrolyzes GTP

117

G protein regulation

When they are bound to GTP, they are activated, and when bound to GDP, they are 'off.' Thus,

118

Amino acid type found in proteins...

Only L

119

Vimentin staining tumors?

Mesenchymal tumors + endometrial carcinoma + renal cell carcinoma + meningiomas.

120

Fuel use in exercise -- when do you deplete ATP by? creatine phosphate? anaerobic metabolism?

Stored ATP depleted in 2 seconds.
Creatine phosphate rises and is depleted by 10 secs.
Anaerobic metabolism depleted by 1 min.

121

Myotonic type 1 Muscular dystrophy pathophys

CTG trinucleotide repeat expansion in the DMPK gene leads to abnormal expression of myotonia protein kinase.

122

Permanent cell types

Neurons
Skeletal and cardiac muscles
*RBCs

123

stable vs permanent vs labile cell types

FA 58