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FA > Biochem > Flashcards

Biochem Flashcards

1
Q

Chromatin

A

histones: + charge, lysine, arginine, octamer
DNA: loops 2X around –>nucleosome
H1=stabilize

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2
Q

Heterochromatin

A

highly condensed

inactive

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3
Q

Euchromatin

A

less condensed

active

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4
Q

DNA methylation

A

CpG methylation silences DNA

template strand methylated to distinguish template strand

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5
Q

Histone methylation

A

represses transcription

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6
Q

Histone acetylation

A

relaxes DNA coiling allowing transcription

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7
Q

Nucleoside

A

base and sugar

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8
Q

Nucleotide

A

base and sugar and phophate

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9
Q

Purines

A

Adenine, Guanine
2 rings
Gly, Asp, Glu needed for synthesis

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10
Q

Pyrimidines

A

C, U, T
1 ring
deamination of cytosine makes uracil

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11
Q

Pyrimidine synthesis

A

Glu +CO2–>Carbamoyl phosphate +Asp–>Orotic Acid +PRPP–>UMP–>UDP–>dUDP etc

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12
Q

Leflunomide

A

inhibits dihydroorotate dehydrogenase

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13
Q

Methotrexate, Trimethoprim, Pyrimethamine

A

inhibit dihydrofolate reductase (decrease dTMP)

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14
Q

5-fluorouracil

A

forms 5-F-dUMP that inhibits thymidlate synthase (decrease dTMP)

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15
Q

Purine synthesis

A

de novo or salvage

Ribose5P–>PRPP–>IMP–>AMP or GMP

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16
Q

6-mercaptopurine

A

inhibit de novo purine synthesis

pro-drug=azathioprine

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17
Q

Mycophenolate, ribavirin

A

inhibit IMP dehydrogenase (IMP–>GMP)

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18
Q

Hydroxyurea

A

inhibits ribonucleotide reductase used in both purine and pyrimidine synthesis

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19
Q

Adenosine deaminase deficiency

A

required for degradation of adenosine so dATP increases–>lympho toxicity–>SCID

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20
Q

Lesch-Nyhan syndrome

A 
X-linked recessive
absent HGPRT which converts hypoxanthine to IMP and guanine to GMP
excess uric acid production and de novo purine synthesis
Hyperuricemia
Gout
Pissed Off
Retardation
dysTonia
Treat: allopurinol or febuxostat
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21
Q

DNA Pol III

A

Prokaryotic only
5–>3 synthesis
3–>5 exonuclease proofing

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22
Q

DNA Pol I

A

Prokaryotic only
5–>3 exonuclease so degrades RNA primer
5–>3 syn
3–>5 exonuclease

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23
Q

Lac operon

A

low glucose, high cAMP, activate CAP

high lactose unbinds repressor via allolactose

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24
Q

Nucleotide excision repair

A

Endonuclease release damaged nts and DNA pol and ligase fill and reseal
in G1
bulky lesions

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25
Q

Base excision repair

A 
gylocosylase removes base and creates AP side
AP-endonuclease cleaves 5 end
Lyase cleaves 3 end
DNA Pol B fills
throughout cycle
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26
Q

Mismatch repair

A

usually in G2

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27
Q

Nonhomologous end joining

A

some DNA may be lost

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28
Q

mRNA stop codons

A

UGA
UAA
UAG

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29
Q

Euk RNA Pols

A

RNA Pol I –> rRNA
RNA Pol II –>mRNA
RNA Pol III –>tRNA

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30
Q

a-amanitin

A

death cap mushrooms
inhibits RNA Pol II
hepatotoxicity

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31
Q

Prok RNA Pol

A

only one that makes all 3 kinds

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32
Q

Rifampin

A

inhibits prokaryotic RNA Pol

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33
Q

Actinomycin D

A

inhibits prok and euk RNA Pol

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34
Q

RNA processing

A

in eukaryotes only
5’ cap
3’ polyadenylation
Intron splicing

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35
Q

RNA splicing

A
  1. primary transcript combines with snRNPs to form spliceosome
  2. lariat intermediate
  3. lariat and intron released
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36
Q

miRNAs

A

small RNAs that bind to mRNA and degrade it

can be found in introns

37
Q

tRNA

A

T arm: contains TYC for ribosome binding
D arm: contains dihydrouridine for correct aminoacyl-tRNA synthetase
Acceptor stem: 5’-CCA-3’ is amino acid acceptor site

38
Q

Aminoacyl-tRNA synthetase

A

1 per amino acid

responsible for accuracy of aa selection

39
Q

Initiation

A

GTP hydrolysis
initiation factors assemble 40S with initiator tRNA
60S assembles

40
Q

Elongation

A

rRNA - ribozyme catalyzes peptide bond formation

41
Q

Termination

A

stop codon recog by release factor

42
Q

Ribosome

A 
Euk: 40S+60S=80S
Pro: 30S+50S=70S
A site: incoming aminoacyl-tRNA
P site: growing peptide
E site: empty tRNA
43
Q

Trimming

A

post-translational

removal of N or C terminal propeptides

44
Q

CDKs

A

constitutive

inactive

45
Q

Cyclins

A

phase specific

activate CDKs

46
Q

Cyclin-CDK complexes

A

phosphorylate other proteins

47
Q

Tumor suppressors

A

p53 induces p21 that inhibits CDKs–>activation of Rb–>inactivates E2F–>inhibit G1-S

48
Q

Golgi Mods

A

modifies N-oligosaccharides on Asn
adds O-oligosaccharides on Ser and Thr
adds Mannose-6-PO4 to traffic to lysosomes

49
Q

I-cell disease

A

defect in N-acetylglucosaminyl-1 phosphotransferase–>no PO4 on mannose0–>extracellular buildup

  • coarse facies
  • clouded cornea
  • joint restriction
50
Q

Signal Recognition Particle

A

traffic protein from ribosome to RER

51
Q

COPI

A

retrograde
Golgi->golgi
cis-Golgi–>ER

52
Q

COPII

A

anterograde

ER–>cis-Golgi

53
Q

Clathrin

A

trans-golgi–>lysosomes

PM–>endosomes (RME)

54
Q

Peroxisome

A

membrane-encloses

catabolism of long chain FA, branched FA, AA, ethanol

55
Q

Microfilaments

A

muscle contraction, cytokinesis

actin, microvilli

56
Q

Intermediate filaments

A

cell structure

57
Q

Vimentin

A

int. filament

IHC for mesenchymal tissue

58
Q

Desmin

A

int. filament

IHC for muscle

59
Q

Cytokeratin

A

int. filament

IHC for epithelial cells

60
Q

GFAP

A

int. filament

IHC for neuroglia

61
Q

Neurofilaments

A

int. filament

IHC for neurons

62
Q

Microtubules

A

movement, cell division
cilia, flagella, axon, spindle
-composed of helix of heterodimers of a and b-tubulin each with 2 GTP
-dynein and kinesin

63
Q

Dynein

A

retrograde mvmt

postive to negative

64
Q

kinesin

A

anterograde mvmt

negative to positive

65
Q

Microtubule drugs

A 
Mebendazole (anti-helminth)
Griseofulvin (anti-fungal)
Colchicine (anti-gout)
Vincas (anti-cancer)
Paclitaxel (anti-cancer)
66
Q

Cilia

A

9+2 arrangement of mt doublets
base is called the basal body with 9 mt triplets and no central mts
axonemal dynein-ATPase cause bending

67
Q

Kartagener Syndrome

Primary Ciliary Dyskinesia

A

immotile cilia due to defective dynein arm

  • male and female infertility
  • ectopic preg risk
  • bronchiectasis, sinusitis
  • situs inversus with dextrocardia
68
Q

Na+-K+-ATPase

A

For each ATP consumed, 3Na+ go out of the cell when the pump is phosphorylated and 2K+ come into the cell when the pump s dephosporylated

69
Q

Ouabain

A

Inhibits the Na-K pump by binding to K site

70
Q

Digoxin, digitoxin

A

cardiac glycosides
directly inhibit Na-K pump
leads to indirect inhibition of Na/Ca exchange–>increase in intracellular Ca–> increased cardiac contractility

71
Q

Type I Collagen

A

BONE, skin, tendon, dentin, fascia, cornea

72
Q

Type II Collagen

A

CARTILAGE, vitreous body, nucleus pulposus

73
Q

Type III Collagen

A

Reticulin - skin, BV, uterus, fetus, granulation tissue

74
Q

Type IV Collagen

A

Basement membrane, lens
defective in Alport syndrome
targeted by auto-Ab in Goodpasture syndrome

75
Q

Collagen Synthesis

A
  1. Pro a-chain (Gly-X-Y): usually proline or lysine
  2. Hydroxylaton of proline and lysine (need Vit C)
  3. Gycosylation of pro-a-chain hydroxylysine to form procollagen 3 helix
  4. Exocytosis into ECM
  5. Cleavage of terminal regions to make insoluble tropocollagen
  6. link between lysine-hydroxylysine to make collagen fibrils by lysyl oxidase (copper)
76
Q

Osteogenesis Imperfects

A 
COL1A1, COL1A2 defects
autosomal dominant
decreased production of type I collagen with issues making triple helix
-fractures
-blue sclerae
-hearing loss
-tooth issues
77
Q

Ehlers-Danlos Syndrome

A

faulty cross-linking in collagen

  • hypermobility type: hypermobie joints
  • classical type: joint and hyperextensible skin (type V collagen)
  • vascular type: easy bruising, aortic aneurysms, organ rupture (type III coll)
78
Q

Menkes disease

A

X-linked recessive
impaired copper absorption due to bad ATP7A
decreased activity of lysyl oxidase needed for crosslinks
-kinky hair
-growth retardation
-hypotonia

79
Q

Elastin

A

nonhydroxylated proline, glycine, and lysine
tropoelastin and fibrillin
broken down by elastase (normally inhibited by a1-antitrypsin)

80
Q

Marfan syndrome

A

defect in fibrillin

81
Q

Emphysema

A

a1-antitrypsin deficiency

82
Q

Southern blot

A

DNA

83
Q

Northern blot

A

RNA

84
Q

Western blot

A

protein

85
Q

Southwestern blot

A

DNA-binding proteins

86
Q

Microarrays

A

nucleic acid sequences on grids with DNA and RNA probes to detect amount of binding
detect SNPs, CNVs

87
Q

ELISA

A

detect antigen or antibody
use of an Ab linked to an enzyme
added substrate reacts with enzyme to get signal

88
Q

Cre-lox system

A

manipuate genes at specific developmental points

89
Q

RNAi

A

dsRNA promotes degradation of target mRNA –>knock-down

FA (2 decks)

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