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MCBM > Kandpal > Flashcards

Kandpal Flashcards

1
Q

Central dogma of molecular biology

A

DNA –> RNA –> protein

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2
Q

What are the constituents of DNA?

A

DNA is a polymer of 4 bases and a five carbon sugar (deoxyribose); alternating sugar and phosphodiester bonds create backbone; bound to other strands by hydrogen bonds

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3
Q

M phase

A

mitosis & cytokinesis

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4
Q

POLI

A 
low processivitiy (DNA repair);
for rRNA
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5
Q

POLII

A

somewhat high processivity;
involved in repair;
for mRNA

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6
Q

POLIII

A

DNA replication;

for tRNA

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7
Q

In what direction does replication occur?

A

5’ –> 3’

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8
Q

Topoisomerase I

A

only cuts one strand

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9
Q

Type II topoisomerase

A

relieves overwinding; ATP dependent

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10
Q

Primase

A

synthetsizes an RNA as a primer; absolute requirement for replication!

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11
Q

RNA is removed by

A

POLI

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12
Q

DNA ligase

A

seals the gap between okasaki fragments

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13
Q

Novobiocin

A

binds to the B subunit of gyrase

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14
Q

Rifiampin

A

binds to beta-subunit of Pol to block initiation

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15
Q

Actinomycin D

A

acts through blocking movement of RNA polymerase; ring gets stuck b/n 2 GC (minor groove of DNA)

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16
Q

Zidovudine (AZT)

A

analog of deoxy thymidine; prevents DNA chain elongation by reverse transcriptase

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17
Q

End replication problem

A

when the replication fork reaches the end there is no place for an RNA primer for the last Okazaki fragment

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18
Q

Telomere

A

piece of DNA which does not code for any protein but has repeating adenine base pairs; used to seal off ends of chromosomes and facilitate replication

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19
Q

Telomerase

A

extends the leading strand DNA synthesis into the telomere

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20
Q

Histone

A

highly alkaline proteins found in eukaryotic cell nuclei; package and order DNA

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21
Q

What is the fundamental subunit of chromatin?

A

nucleosomes

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22
Q

Heterochromatin

A

tightly wound, inaccessible

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23
Q

Euchromatin

A

loose, available

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24
Q

Genomic imprinting

A

certain genes are expressed in a parent-of-origin specific manner; ex: Prader-Willi and Angelman syndromes

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25
Q

Prader-Willi syndrome

A

paternal inheritance of a deletion of 15q11-13

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26
Q

Angelman syndrome

A

maternal inheritance of same deletion as Prader-Willi

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27
Q

Pyrimidine base

A

Cytosine, Thymine, Uracil; 6-membered ring; two N + 4 Cs

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28
Q

Purine base

A

Adenine, Guanine; 9-membraned double-ring system; 4 Ns + 5 Cs

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29
Q

Transitions

A

purine replaced with a purine or a pyrimidine replaced with a pyrimidine

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30
Q

Transversion

A

purine replaced with a pyrimidine or vice versa

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31
Q

Uracil glycosylase

A

eukaryotes don’t want uracil in their DNA so this recognizes and cleave it

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32
Q

Misincorporation

A

creates a distortion in the structure; strand directed mismatch repair decides which strand is correct

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33
Q

Base excision repair

A

specific base is removed and repaired

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34
Q

Nulceotide excision repair

A

stretch of DNA strand is removed and new strand with correct base is synthesized

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35
Q

Hereditary nonpolyposis colon cancer (HNPCC)

A

due to a mismatch repair deficiency; if there is an inherited mutation in one copy of mismatch repair gene, there is a predisposition to this; second copy of gene is spontaneously mutated

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36
Q

DNA polymerase

A

moves from 3’ - 5’ (same direction as RNA synth); the replicate strand is building in the opposite direction

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37
Q

Promotors of prokaryotes have 3 characteristics:

A
  1. -10 sequence
  2. -35 sequence
  3. separation between two above
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38
Q

Promotors of eukaryotes are one of 3 types:

A
  1. TATA containing: TATA is at -25 and -35
  2. Initiator containing: initiator is a consensus sequence surrounding the start site of transcription
  3. TATA-less and initiator-less promotors: GC rich island of about 100 nucleotides upstream of the initiation start site
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39
Q

Ribosomal RNA (rRNA)

A

transcribed by RNA polymerase I; rRNA + protein combine to form a ribosome that serves as the site of protein synth

40
Q

Messenger RNA (mRNA

A

transcribed by RNA polymerase II; carries the genetic code from the nucleus to the cytoplasm where protein synth occurs

41
Q

Transfer RNA (tRNA)

A

transcribed by RNA polymerase III; reads the genetic code from the mRNA and carries the amino acids needed to be incorporated into the developing protein

42
Q

Prokaryotic mRNA

A

unmodified ends; several proteins made from one mRNA

43
Q

Eukaryotic mRNA

A

uncoupling of transcription and translation by the nuclear membrane

44
Q

What carries out transcription?

A

RNA Polymerase

45
Q

Where does RNA polymerase bind?

A

promoter region

46
Q

Promoter

A

region of nucleotides that promotes transcription

47
Q

RNA polymerase

A

made up of 5 subunits; sigma subunit recognizes promoter

48
Q

Transcription factors

A

regulate initiation

49
Q

Rifampin

A

inhibits E Coli RNA polymerase thereby blocking new RNA from synth

50
Q

Alpha-amantin

A

inhibits E Coli, Pol II and Pol III

51
Q

Pit-1

A

transcription factor specific for pituitary development essential to human growth hormone

52
Q

Silent mutation

A

a mutation in the codon that does not lead to a change

53
Q

Missense mutation

A

a substation of one amino acid for another

54
Q

Nonsense mutation

A

replacement of a sense codon with a stop codon

55
Q

Frameshift mutation

A

insertion of deletion of one of two bases

56
Q

Erythromycin

A

inhibits transcription by binding to the 50s ribosome

57
Q

Chloramphenicol

A

inhibits peptidyl transferase in prokaryotes

58
Q

Tetracycline

A

binds the 30s ribosome and prevent aminoacyl-tRNA binding

59
Q

Streptomycin

A

binds to the 30s bacterial ribosome to prevent initiation of protein synth

60
Q

Puromycin

A

causes premature chain termination in protein synth

61
Q

Kozak sequence

A

located 3 base pairs upstream from start codon; plays major role in initiation of translation process

62
Q

Translation

A

RNA –> proteins

63
Q

Transcription

A

DNA –> RNA

64
Q

Thrombopoeitin (TPO)

A

regulates the production of platelets

65
Q

Hereditary thrombocyotpenia

A

autosomal dominant disorder;
attributed to mutations in TPO genes
sx: high levels of TPO, high platelet counts;

66
Q

Specificity factors

A

enzymes that change the RNA poly specificity for promoters

67
Q

Transcription factors

A

complex of proteins that position the RNA pol onto the protein coding template

68
Q

Repressors

A

bind to non-coding sequences on the DNA strand that are close to or overlapping the promoter region

69
Q

Activators

A

enhance the binding between RNA pol and its promoter, encouraging the expression of a gene

70
Q

Enhancers

A

short regions of DNA that bind to activators in order to enhance transcription

71
Q

Exons

A

codes for a protein

72
Q

Introns

A

does not code for a protein; gets spliced out

73
Q

Alternative splicing

A

eons of the RNA produced by transcription are reconnected in multiple ways during RNA splicing resulting in different protein isoforms

74
Q

Receptor mediated endocytosis

A

uptake of soluble proteins and high mol weight material

75
Q

Coat-recruitment GTPases

A

control the assembly of clathrin, COPI and COPII coats

76
Q

Rab proteins

A

important for regulating flow of vesicles to correct target membrane

77
Q

SNAREs

A

proteins mediate fusion with the target membrane

78
Q

Zellweger syndrome

A

empty peroxisomes; won’t last long after bith

79
Q

I-Cell disease

A

phase-dense intracytoplasmic inclusions in the fibroblasts; won’t live long but will survive longer than Zellweger pts

80
Q

Hereditary emphysema

A

deficiency in a1-antitrypsin which normal inhibits trypsin; without this elastase is not inhibited and is then able to degrade fine lung tissue

81
Q

What does viagra inhibit?

A

The degradation of cGMP which is what causes relaxation of smooth muscle after being activated by GTP

82
Q

PKG

A

requires NO; activated cGMP

83
Q

What is HSP90 and what does it do?

A

inhibitory protein that is released upon ligand binding, freeing the COOH end to wrap around the ligan

84
Q

Olfactory signal transduction

A

activates adenylate cyclase, elevates cAMP

85
Q

Rhodopsin signal transduction

A

light activated and photon acts as ligand; activated cGMP PDE and lowers cGMP which –> closure of Na+ channels which –> hyper polarization which inhibit synaptic signaling

86
Q

Sanger method

A

for known and unknown mutations;
can detect SNPs/point mutations, deletions, insertions;
used in BRCA1/2 testing

87
Q

Alpha-thalassemia

A

Hg is a tetramer of 2 alpha and 2 beta parts; chrome 16 has 3 copies of normal alpha-globin genes

88
Q

Positional cloning

A

method of gene identification in which a gene for a specific phenotype or disease is identified; links the disease to a region of genome by using polymorphic markers

89
Q

Neurofibromatosis 1

A

autosomal dominant disease linked to chromosome 17 (determined through linkage mapping);
sx: brownish spots on skin, benign nodules on iris, neurofibromas

90
Q

Gene therapy

A

use of DNA as a pharmaceutical agent to treat diseases

91
Q

Ex vivo gene therapy

A

correct the defect in pt’s cells outside of the body and then inject the correct cells

92
Q

In vivo gene therapy

A

directly inject the cloned gene

93
Q

Hardy-Weinberg equilibrium

A

states that both allele and genotype frequencies in a population remain constant from generation to generation unless specific distributing influences are introduced;
p2 + 2pq + q2 = 1

94
Q

What are the 4 assumptions of the HW equilibrium?

A
  1. Mutation is not occurring
  2. Natural selection is not occurring
  3. Completely random mating
  4. There is no migration in or out of population
95
Q

Chromosomal mapping

A

linkage analysis that involves logarithm of likelihood ratios for a marker’s linkage to a gene vs no linkage

96
Q

Recombinant fraction

A

indicative of genetic distance that can be converted into an approximate physical distance

97
Q

LOD score

A

logarithm of ratio of likelihoods; likelihood of linkage b/n two loci at a specific recombination fraction :: likelihood that loci are unlinked

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