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Biochem BLOCK 3 > Transcription > Flashcards

Flashcards in Transcription Deck (79):
1

RNA polymerase action (general features of transcription)*

-begins transcription without a 'primer'
-reads the template strand from 3' to 5'
-synthesizes the RNA transcript 5' to 3' using ribonucleotides (NTPs)
-recognizes transcription termination signals

2

Transcription begins with

-RNA polymerase identifying a gene's promoter region
-interacting with the DNA template strand
-initiating synthesis of a complementary, antiparallel RNA transcript

3

When does transcription end

When a termination signal is reached

4

What strand is read during transcription?

Template strand

5

DNA coding strand sequence compared to RNA transcript sequence

Identical except RNA has Us instead of Ts

6

How are are base sequences (in DNA) numbered?

By giving the first base to be transcribed a +1 designation with +2, +3, etc. in the 3' direction (downstream to the right)

7

How are the upstream DNA bases to the left, in the 5' direction designated?

-1, -2, -3, etc

8

Holoenzyme

Core enzyme + sigma factor

9

Core enzyme

4 subunits
-two alpha subunits
-1 beta subunit
-1 beta-prime subunit
=a2BB

10

What kind of enzyme activity does core enzyme have?

RNA polymerase activity

11

What is sigma factor required for?

Recognizing and binding promoter sequences

12

Sigma factor

-different sigma factors recognize different types of promoter sequences
-recruits the core enzyme to the DNA promoter
-dissociates from the core enzyme after the transcription begins

13

Initiation of transcription in prokaryotes

-scanning and recognition of promoter sequence cues by the holoenzyme trigger transcription initiation

14

Promoters

Contain two consensus sequences that are recognized by sigma factor
-TATA box
- -35 sequence

15

TATA box in prok

Consensus sequence of 6 nucleotides (TATAAT) sometimes called the pribnow box, ~7 nucleotides upstream from the +1 transcriptional start site (~-7)

16

-35 sequence in prok

Second consensus sequence (TTGACA) ~ 35 bases upstream (-35) from the +1 transcriptional start site

17

Elongation in transcription of prok

Transcription beings at the +1 transcriptional start site, sigma factor is released and the core enzyme continues

18

What does elongation create in transcription of prok

A temporary 'melt' between the double stranded DNA-forming a transcription bubble
-supercoils may be relieved by the action of topoisomerases

19

Net reaction of prok RNA synthesis (transcription)

Addition of a ribonucleotide to the growing RNA chain, and the release of pyrophosphate

20

What is pyrophospate cleaved by?

Pyrophosphatase

21

Cleaving of pyrophosphate by pyrophosphatase

-irreversible coupled reaction
-2 high energy bonds are cleaved

22

2 termination mechanisms of prokaryotic RNA synthesis (transcription)

-Rho dependent termination
-Rho independent termination

23

Rho dependent termination

Requires an additional protein
-rho factor: displaces the DNA template strand from RNA polymerase

24

Rho factor

Displaces the DNA template strand from RNA polymerase

25

Rho independent termination

Requires G-C rich step loop followed by a poly-U stretch
-causes RNA polymerase to dissociate

26

Prokaryotic mRNA can be...

Polycistronic

27

Polycistronic

One mRNA can code for several proteins

28

Polycistronic mRNAs

Often code for multiple enzymes in the same biosynthetic pathway

29

Eukaryotic mRNAs are always

Monocistronic

30

Rifamipin (rifamyin)*

-antibiotic
-binds to prokaryotic RNA polymerase and prevents transcription initiation/elongation
-used to treat tuberculosis

31

Prokaryotic synthesis of tRNA and rRNA

Similar to the model for eukaryotes, except in prokaryotes the same RNA polymerase produces all types of RNA

32

Why is eukaryotic DNA highly condensed (chromatin)

To allow gene transcription the genes must be exposed

33

Euchromatin

-Less condensed
-more accessible to RNA polymerases

34

Acetlyation of histone H1

Causes the chromatin to revert to nucleosomes (bead on a string)

35

Heterochromatin

-appears more dense
-DNA is relatively inaccessible due to highly condensed structure

36

DNA in herterchomatin

Highly methylated

37

What is the foundation of epigenetics

DNA methylation
-twins with same genes, some mutations can result in the way its methylated in expressed between the twins

38

RNA polymerase I (euk)

Transcribes precursors to rRNA in the nucleolus

39

RNA polymerase II (euk)

Transcribes the precursor to mRNA (hnMRNA) in the nucleoplasm (some snRNAs as well)

40

RNA polymerase III (euk)

Transcribes tRNA precursors (also small rRNA and some snRNAs)

41

RNA pol II recognizes what two consensus sequences in eukaryotes

-TATA box (Hogness box)
-CAAT box

42

TATA box (Hogness box)

-similar yo prokaryotic TATA box
-approximately 25 nucleotides upstream (-25)

43

CAAT box

-eukaryotes
-appproximately 70 nucleotides upstream (-70)

44

Eukaryotic transcription elongation

Essentially the same as prokaryotic RNA syntheiss

45

Termination of euk transcription

Requires a signal not well understood in euk

46

rRNA synthesis and processing

-not actually expressing a gene
-three rRNAs are transcribed as a single larger precursor (by RNA pol I in the nucleolus)
-individual rRNAs cleaved apart by RNases
-prokaryotic rRNA synthesis is the same as in eukaryotes
-instrumental in making ribosomes

47

tRNA synthesis and processing

-RNA pol III in in the nucleoplasm

48

RNA polymerase III in tRNA synthesis and processing

-removal of intron loops
-trimming of the 5' and 3' ends
-base modifications
-addition of the 3'-CCA sequence***

49

Eukaryotic mRNA synthesis

Spatially and temporally separated from translation

50

Transcription takes place (euk)

In the nucleus

51

Translation takes place (euk)

In the cytoplasm

52

Eukaryotic mRNA processing

Processed extensively (hnRNA to mRNA)

53

When do prokaryotic mRNAs being translation?

Before transcription finishes

54

Shine Delgarno sequence

Tells ribosome to start translation in prok

55

Euk promoter regions

CAAT box (-70)
TATA box (Hogness box) (-25)

56

Prok promoter region

TATA box (Pridnow) (-10)
-35 sequence

57

Untranslated regions in prokaryotes and eukaryotes (UTRs)

Both have a 5' and 3' UTR

58

Coding region in eukaryotes and prokaryotes

Eukaryotes have introns and exons (monocistronic)
Prokaryotes don't have that

59

5' capping in eukaryotic mRNA

-Addition of a 7-methylguanosine to the 5' end of the mRNA-5' to 5' linkage
-serves as a ribosome recognition signal and stabilizes mRNA (protects from nuclease degradation)***

60

3' poly A tail in Euk mRNA

The 3' terminus contains a polyadenylation signal- a special enzyme (poly A polymerase) adds a variable stretch of adenin residues (~40-200)

61

What kind of signal does the 3' poly A tail of eukaryotic mRNA serve

Serves a signal for transport out of the nucleus, and stabilizes the mRNA from nuclease attack

62

Is the 3' poly A tail terminu encoded in the gene (of euk mRNA)

No, but the SIGNAL sequence is encoded, but the additional A's are not

63

Intervening sequences in euk RNA synthesis

Introns

64

Expressed sequences in euk RNA synthesis

Exons

65

Removal of introns

Must be removes from the coding region for proper translation

66

Splicing

The removal of introns and the jointing of exons by snRNPs

67

SnRNPs

Are composed of snRNAs and a group of proteins

68

What are the snRNPs combined with?

Primary transcript from the spliceosome
-this is the molecular machine that performs the splicing reaction

69

Lariat

Excised intron

70

Splice sites

Have very specific sequences (mutations at these sites can cause incorrect splicing)

71

Exons join together

During splicing to form mature mRNA

72

How many intron sequences can eukaryotes contain?

Between 0 and 50

73

Alternative splicing of hnRNAs

Joining of different exons together o form different mRNAs

74

What does alternative splicing permit?

The production of proteins with some common domains, but the over all function of the protein is different
-gene is same though

75

Systemic lupus erythematosus

Causes butterfly rash
-observed in late-teen females
-patient produces antibodies that recognize host proteins, including snRNPs

76

After all processing events, mature eukaryotic mRNA is transported where?

Cytoplasm

77

What mushroom genus accounts for 95% of all mushroom fatalities?

Genus amantia

78

Amanita phalloides

The death cap mushroom

79

Alpha-amanitin

From amanita phalloides mushroom
-binds to RNA polymerase II-inhibits mRNA synthesis