Brainscape's Knowledge GenomeTM

Browse over 1 million classes created by top students, professors, publishers, and experts.


See full index

M2M wk 1 > M2M wk 1 > Flashcards

M2M wk 1 Flashcards

1
Q

High energy compounds

A

ATP, NADH, NADPH, FADH2

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
2
Q

first law of thermo

A

energy is always conserved

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
3
Q

second law of thermo

A

delta S(universe) always increasing

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
4
Q

Redox rxn related to gibbs free energy

A

G=nFE

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
5
Q

gibbs free energy eqn

A

G=RTlnKeq

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
6
Q

high energy bonds

A

Thioeseter bonds (acetyl CoA; P-O-P (ATP); P-N (phosphocreatine); C-O-P (phosphoenolpyruvate)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
7
Q

electron flow

A

glucose= major source of e-, O2 is the final acceptor; the circuit is a series of proteins including cytochromes with FeII/FeIII

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
8
Q

biological information transfer:

A

DNA transcription to RNA translation to Proteins

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
9
Q

Purine bases

A

adenine and guanine

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
10
Q

pyrimdine bases

A

Thymine (urain in RNA) and cystine

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
11
Q

nucleotide solubility

A

purines < pyrimidine; bases < nucleoside < nucleotide

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
12
Q

gout from Lesch-nyhan disease

A

accumulation of uric acid in joints due to a deficiency in phosphoribosyl transeferase which converts guanine to GMP (purine salvage pathway)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
13
Q

DNA convention

A

5’ to 3’ (phosphodiester bonds)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
14
Q

AZT

A

reversetranscriptase inhibitor (anti-retroviral therapy)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
15
Q

Avery, McCloud, and McCarty

A

DNA isolated from heat killed virulent bac turns live non-virulent bac to encapsulated virulent bacteria

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
16
Q

hershey-chase

A

radioactive labeled DNA or coat infecting bacteria

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
17
Q

chargaff’s rule

A

%G=%C and %A=%T but he ratios of the different pairs can be different

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
18
Q

DNA backbone

A

deoxyribose sugar backbone with phosphodiester bonds

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
19
Q

grooves

A

major and minor; bases in the major groove are more accessible than in the minor groove

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
20
Q

stacking energy

A

higher for more purine content (G-C stacked with G-C)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
21
Q

lower salt concentration (DNA effect)

A

less [salt] will decrease Tm because there is less cations to nutralize exposeed phosphate neg charges

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
22
Q

pH (DNA effect)

A

high pH (melts DNA but leaves phosphodiester bonds intact); low pH hydrolyzes phosphodiester bonds

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
23
Q

increased chain length (DNA Tm)

A

longer chains have higher Tm

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
24
Q

complementary sequences

A

good way to distinguish DNA mismatches

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
25
Q

5-methylcytosine

A

has consequences in gene regulation and mutagenesis

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
26
Q

deamination of nuc bases

A

can tun 5-MeCytosine into thymine, guanine into xanthine etc; nitrous acid or precursors can speed up this process

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
27
Q

depurination of deoxyribose by hydrolosis

A

leads to breakdown of phosphate backbone

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
28
Q

UV cross linking of DNA

A

thymin 2+2 rxn, leads to DNA kinks

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
29
Q

Hydroxyl radicals

A

can add hydroxyl groups to DNA bases

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
30
Q

alkylating agents

A

nucluophilic bases can get alkylated

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
31
Q

intercalating agents

A

disrupt base stacking screw up DNA structure; eg. actinomycin D or doxorubicin

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
32
Q

supercoiled DNA

A

+supercoiled DNA = like a knotted phone cord, -supercoil=like stretched cord

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
33
Q

topoisomerases

A

relaxes supercoils to normal DNA form which is necessary for DNA replication. Drugs inhibit topoisomerase to prevent cancer cells from raplicating

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
34
Q

nucleoside analogues do what?

A

mimic chemistry of natural nucleosides except they typically block transcription. Useful for antiviral therapies

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
35
Q

RNA vs DNA

A

RNA turns over faster, much more susceptible to hydrolysis (can hydrolyze itself), can have implications in gene expression; no double helix so can have different conformations and also act as enzymes

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
36
Q

puromycin

A

nucleotide analogue that binds to the 3’ end of tRNA and blocks translation

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
37
Q

rRNA

A

the business end od the small and large subunits (proteins hang off the RNA scaffold)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
38
Q

3 classes of RNA

A

structural RNA; Regulatory RNA, Information containing RNA

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
39
Q

Structural RNA

A

rRNA, tRNA, small nuclear RNA, small nucleolar RNA

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
40
Q

Regulatory RNA

A

microRNA, small interfering RNA

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
41
Q

Information containing RNA

A

mRNA

42
Q

transcription direction

A

unidirectional and processive, 3’ -OH group on the growing nucleophilically attacks the proximal phosphate of a new NTP molecule

43
Q

RNA transcription initiation

A

RNA pol binds to promoter sequence; pol melts DNA near transcription start site; Pol catalyzes first phosphodiester linkage between first two NTPs

44
Q

RNA transcription elongation

A

Polymerase advances from 3’ to 5’ down template DNA trand making the new 5’ to 3’ RNA

45
Q

RNA transcription termination

A

at transcription stop site, pol releases and the completed RNA releases and dissociates from DNA

46
Q

E.Coli RNA pol

A

makes mRNA, tRNA, and rRNA

47
Q

RNA pol I

A

makes rRNA

48
Q

RNA pol II

A

makes mRNA, snRNA, miRNA and lncRNA

49
Q

RNA Pol III

A

makes tRNA

50
Q

RNA pol promoters

A

promotor proximal elements, TATA box

51
Q

TATA box

A

at -30, TATA binding protein clamps onto DNA minor groove and directs assembly of the pre-initiation complex

52
Q

xeroderma pigmentosum

A

can be caused by a defect in TFIIH which functions in transcription and DNA repair

53
Q

5’ and 3’ UTR

A

parts of exons upstream or downstream of the ATG start site or the termination site

54
Q

alpha-amanitin

A

competitive inhibitor of pol II, blocks chain elongation by preventing translocation

55
Q

rifampicin

A

binds bacterial RNA pol and blocks the RNA exit channel

56
Q

3 ways pre mRNA’s are processed

A

capping, splicing, cleavage/polyadenylation

57
Q

mRNA Capping

A

happens on 5’ end: 1) cleave triphosphate (triphosphatase), 2)add a GMP (gyanylyltransferase) and then methylate the 7 position of the guanine (guanine-7-methyltransferase). Ultimately, the 5’ end will have a triphosphate linkage to the 5’ carbon of 7’methyl guanosine

58
Q

5’ cap function

A

protects from degradation by 5’ exonucleases; cap binding protein regulates nuclear exportation. CBC is replaced by eIF-4E in the cytoplasm

59
Q

overexpression of eIF4E

A

malignant transformation

60
Q

5’ splice site

A

GU

61
Q

3’ splice site

A

AG

62
Q

initiation codon

A

AUG (codes for Met)

63
Q

termination codon

A

UAG, UAA, UGA

64
Q

splicing

A

2’ OH of branchpoint attacks 3’ phosphate on the 5’ end, kicking off 3’ -OH. That 3’ -OH attacks the 5’ phosphate on the 3’ end. Lariat intron gets excised

65
Q

poly A consensus sequence

A

AAUAAA

66
Q

polyadenylation rxns

A

after the AAUAAA endonuclease cleaves subsequent nucleotides; then polyadenylate polymerase adds a bunch of adenosines

67
Q

thallasemia

A

defect in humoglobin production; caused by mutations in poly A consensus sequence

68
Q

alternative splicing

A

allows many different proteins to be encoded by a single gene

69
Q

U1 snRNA

A

recognizes the 5’ splice site

70
Q

U2 snRNA

A

recognizes the branch point

71
Q

genetic disorders caused by splicing defects

A

marfan syndrome disrupted splicing of the fibrilin gene

72
Q

AAUAAA and termination

A

when pol II reaches AAUAAA termination of transcription is signalled

73
Q

poly A tail function

A

protection, stabilization, enhanced translation

74
Q

example of different proteins from alternative polyA site choice

A

secreted form mRNA plasma cells and membrane form mRNA cells

75
Q

altered PolyA site and cancer

A

shortening of the 3’ UTR can activate cancer oncogenes

76
Q

Bidirectional DNA replication

A

replication begins from a site of origin and proceeds in both directions from there

77
Q

sites of origin

A

prokaryotes have one site on each chromosome; eukaryotes have multiple sites (humans have 100’s); usually multiple short repeats

78
Q

semiconservative DNA replicaiton

A

each new DNA strand has a parent and a daughter strand

79
Q

DNA synthesis

A

unidirectional polarity: proceeds in the 5’ to 3’ direction, is semi discontinuous.

80
Q

replication forks

A

site at which DNA synthesis occurs,

81
Q

origin binding proteins

A

recognize and bind origins of replication (tend to be A-T rich since they ar easier to melt; multiple short repeats too)

82
Q

helicases

A

separate and unwind DNA parent strands

83
Q

single strand binding proteins

A

bind to the single (parent) strands and prevents re-annealing to allow for stability and synthesis

84
Q

topoisomerases

A

relaxes supercoiling to relieve torsional stress ahead of the replication fork

85
Q

DNA Gyrase

A

a topoisomerase inhibited by quinolones, found mostly in prokaryotes

86
Q

RNA primer

A

DNA polymerase canno initiate de novo synthesis: needs RNA primer (~10 nucleotides)

87
Q

primase

A

catalyzes the reaction for synthesis of RNA primer

88
Q

DNA pol III

A

elogation of the new chain, it is the major replicative enzyme, has sliding clamp

89
Q

sliding clamp

A

part of DNA pol III; keeps the pol attached over a long distance, giving pol III a high processivity

90
Q

DNA pol I

A

removes RNA primer and copies it into DNA

91
Q

Eukaryotic DNA replication:

A

used pola, pold, and pole and is similar to prokaryotic. pola, serves as primase tho

92
Q

okazaki fragments

A

discontinuous fragments of the lagging strand, joined together by DNA ligase

93
Q

DNA ligase

A

forms phosphodiester bonds between okazaki fragment “nicks”

94
Q

5’-3’ exonuclease

A

removes RNA primer in eukaryotes (done by Pol I in prokaryotes)

95
Q

fidelity of replication

A

overall error rate of 10-9 to 10-10

96
Q

polymerase fidelity

A

hydrogen bonds and geometry of complementary base pairs allows for 1 error per 10k to 100k nucleotides

97
Q

proofreading

A

performed by 3’to5’ exonuclease increases fidelity by 100 to 1000x

98
Q

3’ to 5’ exonuclease

A

proofreading enzymes closely associated with polymerase complex, increased fidelity by 100-1000x; both polI and polIII have 3’to5’ exonuclease activity

99
Q

post replicational repair processes

A

eg. mismatch repair; further increase fidelity of repair

100
Q

reverse transcription

A

synthesis of DNA from an RNA template; catalyzed by reverse transcriptase (commonly in retroviruses), telomerases also have reverse transcriptase activity

M2M wk 1 (2 decks)

Brainscape helps you reach your goals faster, through stronger study habits.
© 2024 Bold Learning Solutions. Terms and Conditions