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Board Review - B - Biochemistry > Molecular II > Flashcards

Molecular II Flashcards

1
Q

nucleotide excision repair

A

endonuclease release damaged base

DNA polymerase and ligase fill and reseal

repair bulky lesions
occur in G1

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2
Q

defective nucleotide excision repair

A

xeroderma pigmentosa

prevent repair of pyrimidine dimers (UVB damage)

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3
Q

base excision repair

A

base specific glycosylase
-create site without pur or pyr

AP-endonuclease - remove one or more nucleotides - cleaves 5’ end

lyase cleaves 3’ end

DNA polymerase beta - fills gap and DIA ligase seals it

throughout cell cycle

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4
Q

mismatch repair

A

newly synthesized strand recognized
-mismatched nucleotides removed - gap filled and sealed

G2 phase of cell cycle

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5
Q

defective in hereditary nonpolyposis colorectal cancer

A

mismatch repair

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6
Q

nonhomologous end joining

A

bring together 2 ends of DNA fragments repair ds breaks

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7
Q

mRNA is read

A

5’ > 3’

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8
Q

direction DNA and RNA synthesis

A

DNA and RNA - both synthesized 5 > 3

5’ end - high energy bond - tri-P

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9
Q

protein synthesis direction

A

N-terminus to C-terminus

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10
Q

start codon

A

AUG

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11
Q

stop codon

A

UGA, UAA, UAG

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12
Q

fMet

A

prokaryote start codon

stimulate neutrophil chemotaxis

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13
Q

methionine

A

start codon - AUG - AA

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14
Q

promoter

A

site where RNA polymerase II and other transcription factors bind DNA upstream gene locus

AT rich - TATA box

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15
Q

enhancer

A

further upstream from promoter (TATA)

-alter gene expresion

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16
Q

silencer

A

site where gene repressor binds

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17
Q

RNA polymerse I

A

makes rRNA

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18
Q

RNA polymerase II

A

makes mRNA - largest RNA

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19
Q

RNA polymerase III

A

makes tRNA - smallest RNA

20
Q

a-amanitin

A

in amanita phalloides - death cap mushroom

inhibit RNA polymerase II - mRNA synthesis

severe hepatotoxicty

21
Q

rifampin MOA

A

inhibit RNA polymerase

22
Q

actinomycin D

A

inhibit RNA polymerase

23
Q

RNA processing - after transcription

A

occus in nucleus

1 - capping 5’ end - 7 methylguanosine cap
2 - polyadenylation 3’ end - 200 As
3 - splicing out introns

capped, tailed, spliced = mRNA

24
Q

cytoplasmic P-bodies

A

mRNA quality control

exonucleases, decapping enzymes, microRNAs

25
Q

snRNP

A

involved in splicing pre-mRNA

lariat shaped loop generated
-remove intron - join 2 exons

26
Q

anti-smith antibodies

A

Abs to spliceosomal snRNP

specific for SLE

27
Q

anti-U1 RNP Ab

A

associated with mixed CT disease

28
Q

alternative splicing

A

different exon combination of single mRNA

29
Q

beta-thalassemia

A

abnormal splicing variant

30
Q

tRNA

A

CCA at 3’ end opposite anticodon - binds the amino acid

anticodon loop

T-arm - contains thymine, pseudouracil, cytosine - for tRNA ribosome binding

D-arm - dihydrouracil residues - for tRNA recognition by correct aminoacyl tRNA synthetase

31
Q

charging of tRNA

A

aminoacyl tRNA synthetase uses ATP to bind amino acid to CCA 3’ end of tRNA

32
Q

wobble

A

accurate base pairing only required first 2 nucleotide positions of mRNA codon

codon difference position 3 “wobble” may code for same AA - degeneracy of code

33
Q

steps protein synthesis

A

initiation
elongation
termination

34
Q

initiation

A

by GTP hydrolysis

initiation factors assemble 40S ribosome subunit with initiator tRNA
-released when mRNA and 60S subunit assemble with complex

35
Q

eukaryote ribosomes

A

40S and 60S

36
Q

prokaryote ribosomes

A

30S and 50S

37
Q

elongation

A

aminoacyl tRNA binds to A site

rRNA catalyzes peptide bond formation - transfer growing polypeptide to AA in A site

ribosome advances 3 nucleotides toward 3’ end of mRNA - moving peptidyl tRNA to P site (translocation)

38
Q

A site

A

incoming aminoacyl-tRNA

39
Q

P site

A

accomodate growing peptide

40
Q

E site

A

holds empty tRNA as it exits

41
Q

termination

A

stop codon recognized by release factor

polypeptide released from ribosome

42
Q

protein synthesis ATP and GTP

A

ATP - activation - charging

GTP - translocation

43
Q

trimming

A

remove N or C terminal propeptide from zymogen

44
Q

covalent alterations of peptide

A 
phosphorylation
glycosylation
hydroxylation
methylation
acetylation
ubiquitination
45
Q

chaperone proteins

A

intracellular proteins involved in facilitating protein folding

yeast - Hsp60 - expressed at high temp - prevent protein denaturing/misfolding

Board Review - B - Biochemistry (13 decks)

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