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STEP > Biochem miscellaneous > Flashcards

Biochem miscellaneous Flashcards

1
Q

exceptions to degeneracy of genetic code

A

methionine + tryptophan (each encoded by only 1 codon)

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2
Q

codon for methionine

A

AUG

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3
Q

codon for tryptophan

A

UGG

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4
Q

nucleotides methylated in replication

A

cytosine + adenine

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5
Q

how is uracil derived?

A

deamination of cytosine

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6
Q

what makes thymine unique?

A

Has a methyl grow.

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7
Q

when does NER occur?

A

G1

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8
Q

sequence of events in base excision repair

A

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

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9
Q

significance of N-formylmethionine (fMET)

A
  • initiates protein synthesis in bacteria.
  • Nucleic acid coded by start codon.
  • Stimulates neutrophil chemotaxis.
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10
Q

polyadenylation signal

A

AAUAAA

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11
Q

describe mRNA quality control

A

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

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12
Q

what initiates protein synthesis?

A

GTP hydrolysis

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13
Q

describe trimming

A

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

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14
Q

labile cell types

A

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

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15
Q

stable cell types

A

hepatocytes + lymphocytes

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16
Q

golgi functions

A

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

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17
Q

Signal recognition particle (SRP)

A

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

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18
Q

examples of intermediate filaments

A

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

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19
Q

Vimentin

A

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

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20
Q

microvilli

A

microfilament

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21
Q

cilia structure

A

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

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22
Q

axonemal dynein

A

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

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23
Q

frequency of an x-linked recessive disease in males

A

q

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24
Q

frequency of an x-linked recessive disease in females

A

q squared

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25
Q

what is wrong in prader willi vs. angelmans

A

codebook

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26
Q

2 rules for inheritance chart

A

1) look for recessive/dominance

2) who’s passing it down (only moms –> mitochondrial inheritance)

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27
Q

gene mutated in myotonic dystrophy type 1

A

DMPK

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28
Q

myotonia

A

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

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29
Q

medical word for night blindness

A

nyctalopia

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30
Q

medical word for dry, scaly skin

A

xerosis cutis

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31
Q

medical word for corneal degeneration

A

keratomalacia

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32
Q

significance of flavins (FMN, FAD)

A

used as cofactors in redox reactions

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33
Q

relationship between isoniazid and pyridoxine deficiency

A

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

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34
Q

vitamins required for niacin synthesis

A

B2 + B6

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35
Q

pyridoxine used in synthesis of…

A

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

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36
Q

storage form of vitamin D

A

25-OH D3

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37
Q

active form of vitamin D

A

calcitriol, 1,25-(OH)2D3

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38
Q

ergocalciferol

A

D2, ingested from plants

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39
Q

cholecalciferol

A

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

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40
Q

location of D3 synthesis

A

stratum basale

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41
Q

biochemistry of folate deficiency

A

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.

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42
Q

other names for vitamin K

A

phytomenadione, phylloquinone, phytonadione

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43
Q

enzyme that metabolizes ethanol in microsome

A

CYP2E1

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44
Q

biochem explanation for hepatosteatosis in alcoholism

A

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

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45
Q

dehydrogenase action

A

catalyze oxidation-reduction reaction

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46
Q

ATP production

A

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

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47
Q

glycerol-3-phosphate shuttle

A

ATP shuttle in muscle

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48
Q

malate-aspartate shuttle

A

ATP shuttle in heart and liver

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49
Q

what does CoA carry?

A

acyl groups

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50
Q

what does lipoamide carry?

A

acyl groups

51
Q

What does TPP cary (thiamine pyrophosphate)?

A

aldehydes

52
Q

glycolysis equation

A

FA pg 99

53
Q

enzymes requiring ATP

A

1) hexokinase/glucokinase 2) PFK-1

54
Q

where is ATP produced in glycolysis?

A

1) 1,3 BP –> 3-phosphoglycerate

2) PEP –> pyruvate

55
Q

where is GTP produced

A

succinyl-CoA –> succinate

56
Q

regulation by F-2-6-bisphosphate

A

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

57
Q

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

A

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

58
Q

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

A

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

59
Q

pyruvate dehydrogenase reaction

A

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

60
Q

positive regulation of pyruvate dehydrogenase complex

A

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

61
Q

vitamins required by pyruvate dehydrogenase complex

A

B1-B5, except B4

62
Q

tissues that rely on anaerobic glycolysis

A

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

63
Q

products of pyruvate –> acetyl-CoA

A

acetyl-CoA + 1 NADH + 1 CO2

64
Q

products of TCA cycle

A

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

65
Q

Where is NADH generated in TCA cycle?

A

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

66
Q

Where is FADH2 generated in TCA cycle?

A

succinate –> fumarate

67
Q

Where is GTP generated in TCA cycle?

A

succinyl-CoA –> succinate

68
Q

irreversible enzymes in TCA cycle

A

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

69
Q

ATP produced via ATP synthase

A

1 NADH –> 2.5 ATP

1 FADH2 –> 1.5 ATP

70
Q

site of gluconeogenesis

A

primarily liver, enzymes also in kidney + intestinal epithelium.

71
Q

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

A

ribulose-5-P –> ribose-5-p + glyceraldehyde-3-phosphate + fructose-6-p

  • via phosphopentose isomerase + transketolases
  • requires B1
72
Q

sucrose

A

glucose + fructose

73
Q

treatment for hereditary fructose intolerance

A

decrease intake of both fructose + sucrose

74
Q

triose kinase

A

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

75
Q

aldose reductase 1) action 2) where its expressed

A

1) galactose –> galactitol

2) glucose –> sorbitol (using NADPH)

76
Q

4 epimerase

A

galactose metabolism: interconverts UDP-gal to UDP-Glu

77
Q

sorbitol dehydrogenase

A

sorbitol –> sorbitol dehydrogenase (using NAD+)

78
Q

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

A

glucose converted to sorbitol

79
Q

tissues that have both aldose reductase + sorbitol dehydrogenase

A

liver + ovaries + seminal vesicles

80
Q

tissues that have only aldose reductase

A

schwann cells + retina + kidneys + lens (primarily)

81
Q

essential amino acids

A

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

82
Q

location of synthesis of norepinephrine, dopamine, epinephrine

A

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

83
Q

phenylketones (detected in urine of PKU kids)

A

phenylacetate, phenyllactate, phenylpyruvate

84
Q

describe biochem of homocystinuria

A

…

85
Q

limit dextrin

A

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

86
Q

deficiency vs. accumulated substrate in gaucher’s

A

glucocerebrosidASE deficiency; glucocerebroside accumulation

87
Q

explain why ketone bodies build up in DKA and prolonged starvation

A

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
Q

explain why ketone bodies build up in alcoholism

A

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
Q

energy source during fasting state

A

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

90
Q

LCAT

A

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
Q

exonucleases vs. endonucleases

A

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

92
Q

Folate deficiency labs

A

Methmalonic acid normal + homocysteine elevated.

93
Q

Mucopolysaccharidoses

A

Hurler’s + hunters

94
Q

Location of heme synthesis

A

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

95
Q

heme synthesis pathway

A

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

96
Q

polyadenylation vs. capping

A

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

97
Q

ketogenesis.

A

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
Q

DM1 HLA association

A

DR3 and DR4

99
Q

Insulin sensitivity in DM1

A

High

100
Q

glucose intolerance in DM1

A

Severe

101
Q

serum insulin level in DM1

A

low

102
Q

Genetic predisposition in DM1

A

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

103
Q

genetic predisposition of DM2 vs. DM1

A

DM2 relatively much stronger than DM1

104
Q

genetic predisposition of DM2

A

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

105
Q

HLA type DM association

A

None

106
Q

Glucose intolerance in Type 2DM

A

Mild to moderate

107
Q

Labs in DKA

A

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

108
Q

DKA treatment

A

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

109
Q

Amino acids necessary for purine synthesis:

A

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
Q

Basic positively charged amino acids

A

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
Q

Acidic negatively charged amino acids:

A

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
Q

Hydrophobic amino acids

A

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
Q

glycogenic and ketogenic amino acids

A

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
Q

glycogenic amino acids

A

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
Q

Describe G protein mechanism

A

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
Q

GTPase

A

hydrolase that binds and hydrolyzes GTP

117
Q

G protein regulation

A

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

118
Q

Amino acid type found in proteins…

A

Only L

119
Q

Vimentin staining tumors?

A

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

120
Q

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

A

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

121
Q

Myotonic type 1 Muscular dystrophy pathophys

A

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

122
Q

Permanent cell types

A

Neurons
Skeletal and cardiac muscles
*RBCs

123
Q

stable vs permanent vs labile cell types

A

FA 58

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