Unit 3 Flashcards Preview

Molecular Biology > Unit 3 > Flashcards

Flashcards in Unit 3 Deck (95):
1

reading a DNA template to synthesize a piece of RNA

transcription

2

transcription language

nucleic acid to nucleic acid language

3

translation language

nucleic acid language to amino acid

4

coding (non template) strand

sequence in this DNA strand will match the sequence in the resulting RNA strand

5

promoter region

contains DNA sequence required for transcription to start

6

sigma factor

protein/example of transcription factor that binds to DNA

7

initiation of transcription

sigma factor binds promoter sequence and recruits RNA poly to bind DNA and start transcription

8

elongation of transcription

proofreading mechanisms occur

9

proofreading mechanisms of transcription

1) kinetic
2) nucleolytic

10

kinetic

immediately after misincorporation
-activated when nucleotide can't base pair so it doesn't fit in active site

11

nucleolytic

after 3 to 5 nucleotides incorporated
-activated when nucleotide doesn't fit

12

2 mechanisms of termination

Rho Independent and Dependent

13

Rho Independent

-DNA terminator sequence = palindrome
-palindrome base pairs with itself to form hairpin and force RNA poly off DNA
-weak A:U base pairing occurs after hairpin sequence so it is easier for stalled mRNA to fall off

14

Rho Dependent

-hairpin forms in the RNA
-Rho protein helps the hairpin pull RNA poly off DNA/RNA
-Rut site: Rho utilization site for the Rho protein to bind

15

sigma factor 70

general sigma factor, most commonly used binds to -35/-10 promotor sequence

16

sigma factor 28

flagella structure

17

sigma factor 32

heat shock sigma factor (saves energy to only transcribe certain sets of genes when needed)

18

sigma factor 38

osmotic stress

19

How do we know that sigma 38 binds to osmy gene?

-EMSA
-CHIP
-DNase protection assay/foot printing (proteins bind to DNA, protects DNA from being degraded)

20

structure of mRNA

-5' untranslated region
-3' untranslated region
-start and stop codons

21

5' untranslated region

initiation of translation

22

monocistronic mRNA

one start and stop codon

23

polycistronic mRNA

multiple start and stop codons in one mRNA piece

24

tRNA

adaptor molecule

25

translation

mRNA nucleotide language to protein amino acid language

26

adaptor molecule experiment question

is tRNA made of nucleotides or protein?

27

adaptor molecule experiment

-used radio labeled Leu a.a
-allowed cells to use radio labeled for short or long time
-break open cells and centrifuge
-identify where radio labeled Leu a.a. were

28

adaptor molecule experiment conclusions

-adaptor molecule is a nucleotide (tRNA) because radio labeled Leu was in the nucleotide/supernatant layer after short time periods

29

tRNA structure

-encoded by DNA
-transcribed but not translated

30

Phenylalanine amino-acyl tRNA synthetase enzyme

-has active site that can bind Phe a.a. and the tRNA that base pairs with UUU or UCC

31

roles of aminoacyl-tRNA synthesis

-makes covalent bond between a.a. and tRNA
-determines specificity of genetic code
-active site fits an a.a. and the tRNA anticodon
-requires ATP

32

wobble base pairing

1) first two positions follow normal base pairing (A:U, C:G)
2) 3rd position only
G:U, I:U,A,C

33

ribosome structure

-protein + rRNA
-2 subunits (large and small)

34

small ribosomal subunit

21 individual (16S rRNA)

35

large ribosomal subunit

34 proteins individual (5S rRNA and 23s rRNA)

36

initiation

-large and small brought together
-mRNA bind ribosome
-1st tRNA bind mRNA (MET)

37

initiation factors

proteins that control initiation

38

steps in initiation

-IF 1 and 3 bind small subunit (prevent from bind too early)
-mRNA base at 5' untranslated region pairs with 16S rRNA in the small subunit
-TF2 brings tRNA with MET to ribosome
-tRNA bind mRNA = conformational change, IF fall off
-large bind to small

39

steps in elongation

1) proofreading
2) peptide bond formation
3) indexing/translocation

40

translation proofreading

1) EF-TU binds to a tRNA and a.a. and brings it to ribosome
2) ribosomal protein with GTP hydrolysis activity

41

proper base pairing during elongation

GTP on EF-TU gets hydrolyzed to GDP

42

not proper base pairing during elongation

GTP on EF-TU not hydrolyzed, EF-Tu floats away with tRNA and a.a.

43

peptide bond formation

50 S has enzymatic activity

44

translocation

EFG binds GTP, empty tRNA floats away with EFG, A site open for next tRNA and a.a.

45

translation termination

-EF-Gu and tRNAs will try to bind stop codons but no tRNA anti-codons can base pair with stop

46

Ribosome releasing factor

-can bind to stop codons
---last amino acyl chopped off tRNA
---RRF induces confirmation changes in ribosome and everything falls apart

47

what happens if the stop codon gets mutated?

translation stalls, no mRNA in A site, fail safe occurs

48

fail safe

tmRNA can bind to empty A site and unstall so the mutated protein becomes degraded by protease

49

mischarge tRNA has wrong amino acid...what happens?

aminoacyl tRNA synthetase mistake = no proofreading

50

operons

-control over which genes get expressed when

51

another way prokaryotes control gene expression

sigma factors

52

heat shock sigma factor protein

sigma factor turns on heat shock genes only when needed

53

lac operon

-genes needed to digest lactose
-lactose not usually present
-only on when lactose is present

54

lac operon off when E coli using glucose

B gal and permease levels are very very low

55

glactoside permease

transport lactose into e coli cell

56

beta galactosidase

-breaks galactoside down to simple sugars
-turns lactose into allocates

57

galactoside transacetylase

-neutralizes toxic galactosides

58

Lac R protein in relation to no lactose present

-binds promoter (Pzya)

59

lac operon has 3 proteins so it is an example of (BLANK) mRNA

polycistronic

60

during normal conditions (no lactose, glucose) lac i gets expressed at

consistently high levels

61

what happens if the Pzya promoter is bound?

prevents RNAP from binding so lac z, y, a are expressed at very very low levels

62

when lactose is present and glucose is absent what is the relationship between CRP, cAMP, and DNA

CRP and cAMP binds to DNA, help RNAP bind to Pzya

63

if lactose is present, lac R

can't bind to the DNA because some all-lactose leads to a conformational change

64

mechanism to determine if glucose is present or absent?

-cAMP levels are low when glucose levels are high because glucose inhibits cAMP production

65

relationship between CRP and cAMP

-CRP and cAMP bind DNA but CRP alone cannot bind
-CRP + cAMP enhances transcripton

66

lactose absent, glucose absent (Lac R)

on the DNA, no allolactose

67

lactose absent, glucose absent (CRP)

on DNA but Lac R overrides CRP ability to help with transcription because there is no room for RNAP

68

lactose absent, glucose absent (expression)

very very low levels

69

lactose present, glucose present (Lac R)

off DNA

70

lactose present, glucose present (CRP)

off DNA

71

lactose present, glucose present (expression)

very low levels

72

lactose absent, glucose present (Lac R)

on DNA, no allolactose

73

lactose absent, glucose present (CRP)

off DNA, no cAMP

74

lactose absent, glucose present (expression)

very very low levels

75

lactose present, glucose absent (Lac R)

off DNA
-some allolactose which prevents binding

76

lactose present, glucose absent (CRP)

high cAMP, binds CRP so it is able to bind

77

lactose present, glucose absent (expression)

very high

78

Ara operon

genes needed to metabolize arabinose

79

what protein controls the arabinose operon?

Ara C (dimer)

80

what are the genes needed for arabinose mechanism?

ara B, A, D

81

Ara present, glucose absent (Ara C- binding where)

I1 and I2 (no loop)

82

Ara absent, glucose present (Ara C- binding where)

I1 and O2 (loop)

83

Ara present, glucose present (Ara C- binding where)

I1 and I2 (no loop)

84

Ara absent, glucose absent (Ara C- binding where)

I1 and O2 (loop)

85

Ara present, glucose absent (CRP binding?)

yes

86

Ara absent, glucose present (CRP binding?)

no

87

Ara present, glucose absent (operon on/off, level of expression)

on (high levels)

88

Ara absent, glucose present (operon on/off, level of expression)

off (loop= RNAP can't bind PBAD, very very low)

89

Ara present, glucose present (CRP binding?)

No

90

Ara present, glucose present (operon on/off, level of expression)

Off (RNAP doesn't have CRP so low levels)

91

Ara absent, glucose absent (CRP binding?)

Yes

92

Ara absent, glucose absent (operon on/off, level of expression)

Off (very low because RNAP can't get in because looping)

93

wobble rules

only 3rd
G:U
I: A, U, C

94

is the binding required for gene z transcription?

Northern blot or qRT-PCR

95

ways to mess up the binding to determine if the sigma factor is required?

+/- sigma 25 protein and look at mRNA of gene z
+/- mutated version of sigma 25 that can't bind and look
wild type DNA vs mutated DNA and look