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molecular biology Flashcards

1
Q

Define a nucleoside

A

sugar + base

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2
Q

What is the linkage between a sugar & base?

A

B-N-glycosidic linkage (btw 1C of sugar and base)

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3
Q

Beta sugar linkage mnemonic

A

It’s better to B Up

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4
Q

The 3’ of DNA has what group

A

OH

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5
Q

The 5’ of DNA has what group

A

phosphate

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6
Q

Viral genomes are

A

circular or linear and can consist of DNA or RNA which can be single or double stranded

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7
Q

DNA gyrase is a

A

topoisomerase

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8
Q

what is the function of a topoisomerase?

A

cut one or both strands and unwrap the helix releasing excess tension created by the helicases

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9
Q

DNA gyrases is involved in

A

compacting prokaryotic genome; supercoils

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10
Q

Nucleosomes are composed of?

A

DNA wrapped around an octamer of histones

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11
Q

Ribosomes are composed of ?

A

protein + rRNA

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12
Q

The 3 stop codons are

A 
UGA = U Go Away
UAA = U Are Away
UAG = U Are Gone
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13
Q

Replication occurs in the

A

5 to 3 prime direction

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14
Q

Replication requires

A

a primer and a template

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15
Q

How many origins does replication have for eukaryotes and prokaryotes?

A

eukaryotes - multiple

prokaryotes - single (replication occurs bidirectionally)

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16
Q

Prokaryoties have how many DNA polymerases?

A

3

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17
Q

DNA Polymerase I

A

has 5–>3 exonuclease capability for the removal of RNA primers

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18
Q

Another name for the template strand

A

noncoding strand, antisense strand

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19
Q

The complementary strand of the template strand is the

A

coding, sense strand

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20
Q

How many RNA polymerases do prokaryotes have?

A

1

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21
Q

How many subunits does the prokaryote RNA polymerase have?

A

5

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22
Q

B-N-Glycosidic

A

linkage between the sugar and nitrogenous base in nucleic acids

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23
Q

is the B-N-Glycosidic up or down

A

up. remember “it is better to B up”

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24
Q

these amino acids are unusually abundant in histones

A

arginine and lysine

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25
Q

DNA is _____ and histones are ______

A

acidic; basic

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26
Q

telomere repeat

A

5’-TTAGGG-3’

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27
Q

prokaryotes have telomeres.

A

FALSE

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28
Q

In DNA replication, the parental strand is read in the

A

3 to 5 direction

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29
Q

In DNA replication, the daughter strand is written in the

A

5 to 3 direction

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30
Q

DNA polymerase I has ____ polymerase activity

A

5 to 3

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31
Q

DNA polymerase I has ____ exonuclease activity

A

3 to 5 and 5 to 3

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32
Q

DNA polymerase I is important for ________ repair

A

excision

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33
Q

3 to 5 exonuclease activity is also referred to as

A

proofreading

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34
Q

DNA polymerase III has high _______

A

processivity

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35
Q

processivity

A

catalyze consecutive reactions without releasing the substrate

36
Q

DNA polymerase III has _____ polymerase activity

A

5 to 3

37
Q

DNA polymerase III has _____ exonuclease activity

A

3 to 5 (proofreading function)

38
Q

DNA polymerase III is important for _______ repair

A

none; it has no known function in repair; therefore, is considered a replicative enzyme

39
Q

Compared to DNA, RNA has the following differences

A

is single stranded (DNA is double stranded)
has the base uracil (DNA has thymine)
sugar is ribose (DNA is deoxyribose)

40
Q

monocistronic

A

one gene one protein

41
Q

What is the significance of monocistronic when looking at experiments?

A

of unique proteins = # of mRNA

42
Q

Monocistronic applies to prokaryotes or eukaryotes?

A

eukaryotes

43
Q

Explain why deoxyribose is more stable than ribose

A

ribose has 2-OH which is nucleophilic and can attack the 5’-phosphate

44
Q

What is the driving force for replication and transcription in terms of energy?

A

the hydrolysis of pyrophosphate

45
Q

Holoenzyme

A

bound to sigma factor

46
Q

bacterial promoter sequence

A

pribriow box: -10 and -35 sequence

47
Q

when is the sigma factor released? where is it released from?

A

it is released after a few phosphodiester bonds have been formed (between RNA nucleotides).
from the RNA polymerase

48
Q

Prokaryotic Transcription is

A

rho / rho-independent (need to look up)

49
Q

anabolism

A

biosynthetic
repressible
only occurs when product is scarce

50
Q

catabolism

A

degradation

inducible

51
Q

Eukaryotes have how many DNA polymerases

A

1

52
Q

Eukaryotes have how many RNA polymerases

A

3

53
Q

RNA polymerase I

A

transcribes rRNA

54
Q

RNA polymerase II

A

transcribes mRNA

55
Q

RNA polymerase III

A

transcribes tRNA

56
Q

what is heterogeneous RNA (hnRNA)

A

applies to eukaryotes
before splicing
located in the nucleus
primary transcript

57
Q

Eukaryotic modifications to RNA

A
  1. Splicing
  2. 5’ Cap - Methylated Guanine
  3. Poly Adenine Tail
58
Q

What is the importance of the 5’ Cap - Methylated Guanine

A

essential for translation

59
Q

Eukaryotic promoter

A

TATA box (~25 bp from initiation site)

60
Q

Eukaryotic promoters contain regulatory sequence elements that are bound by _________ which result in an (increase/decrease) in transcription?

A

sequence specific transcription factors

either increase or decrease

61
Q

Enhancers are located where

A

upstream or downstream from the sequence

62
Q

Sequence specific transcription factors bind to

A

both to promoter and enhancer to regulate transcription

63
Q

what regulates the binding of factors to DNA?

A

extracellular signals

64
Q

what is the tertiary structure of tRNA? and how is it stabilized?

A

stem-and-loop

stabilized by hydrogen bonds between bases of neighboring atoms

65
Q

Does tRNA nucleotides

A

tRNA contains several modified nucleotides

66
Q

tRNA sites consist of

A
  1. Anticodon

2. AA receptor site

67
Q

peptide bond formation is (positive/negative) delta G and kinetics are _____

A

positive

slow

68
Q

tRNA loading is also called

A

AA activation

69
Q

What drives peptide bond formation?

A

breaking of the aminoacyl bond

70
Q

loading of tRNA

A

AA is attached to AMP + 2 high energy bonds are hydrolyzed

71
Q

Prokaryotic ribosomes

A

30s, 50s, 70s (odd)

72
Q

Eukaryotic ribosomes

A

40s, 60s, 80s (even)

73
Q

synthetase

A

use energy from ATP

74
Q

synthase

A

do not use energy from trinucleotide

75
Q

Prokaryotes translation:
upstream sequence
function of that sequence?

A

Shine-Dulgarno sequence

ribosomal binding site

76
Q

Prokaryotic Translation:

Initiation of translation

A

1 GTP required
f-met-tRNA
P-site
Initiation factor proteins involved

77
Q

Prokaryotic Translation:

A site versus P site

A

Aminoacyl-t-RNA site

Peptidyl-tRNA site

78
Q

Prokaryotic Translation:

elongation involves

A

several EF (proteins)

79
Q

Prokaryotic Translation:

Binding of tRNA in A site requires

A

1 GTP

80
Q

Prokaryotic Translation:

which ribosomal subunit has the peptidyl transferase

A 
Large subunit
function of transferase is to catalyze the peptide bond
81
Q

Prokaryotic Translation:

Transduction

A

1 GTP required

82
Q

Prokaryotic Translation:

Termination

A

Release Factor enters A site

83
Q

Eukaryotic Translation:

N terminal AA is ____

A

Methonine

84
Q

Ribosomal binding site

A

Kozak sequence

85
Q

Eukaryotic Translation:

Sequence of events in translation:

A
  1. tRNA binds to small subunit
  2. mRNA binds to small subunit
  3. lg subunit binds
86
Q

Prokaryotic Translation:

Sequence of events in translation:

A
  1. IF combine with small subunit
  2. mRNA binds to small subunit
  3. first aminoacyl-tRNA
  4. lg subunit binds
87
Q

Activation of each AA during translation requires

A

2 ATP

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