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Biochem Block 3 > Transcription > Flashcards

Flashcards in Transcription Deck (54):
1

RNA polymerase action in prokaryotes

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

2

What does transcription begin with?

-RNA polymerase identifying a genes promoter region
-interacts with DNA template strand
-initiates synthesis of a complementary, antiparallel RNA transcript

3

When does transcription end?

-when a termination signal is reached

4

what strand is read during synthesis?

-genes are described by the sequence of the CODING STRAND, but the TEMPLATE STRAND is the one read during synthesis by RNA polymerase

5

Coding strand of DNA and RNA transcript sequence

-they are the exact same, but there are U's instead of T's in the RNA transcript
-both are 5' to 3'

6

numbering and base sequence

-the first base to be transcribed is +1
-downstream(to the right in the 3' direction) goes up in plus direction
-upstream(to the left in the 5' direction) goes down in the negative direction

7

promoter

-always upstream of the +1 position

8

what direction does the template strand run?

3' to 5'

9

holoenzyme

-core enzyme+sigma factor
-prokaryotic RNA polymerase construction
-scanning and recognition or promoter sequence cues by holoenzyme initiate RNA transcription

10

core enzyme subunits

-2 alpha subunits
-1 beta subunit
-1 beta' subunit

11

core enzyme

-has RNA polymerase activity for nucleotide elongation

12

sigma factor

-required for recognizing and binding promoter sequences
-different sigma factors recognize different promoter sequences
-recruits core enzyme to DNA promoter
-dissociates from core enzyme after transcription begins

13

prokaryotic promoters

-2 consensus sequences
-TATA box
--35 sequence

14

prokaryotic TATA box

-prinbnow box
-sequence of 6 nucleotides
-7 nucleotides upstream from the +1 transcriptional start site

15

-35 sequence

-consensus sequence in prokaryotes
-35 bases upstream from +1 transcriptional start site

16

elongation in prokaryote RNA synthesis

-transcription begins at the +1 start site
-sigma factor must be released first, then core enzyme continues
-generated in the 5' to 3' direction
-creates a temporary "melt" of dsDNA to form transcription bubble
-results in supercoiling

17

Net reaction of prokaryote RNA synthesis

-addition of a ribonucleotide to the growing RNA chain
-release of a pyrophosphate

18

what do DNA polymerases and RNA polymerases have in common?

-both release a pyrophosphate which is further cleaved by pyrophosphatase
-provides energy to drive reaction
-makes reaction irreversible

19

What are the two termination mechanisms for prokaryotic RNA sequences?

-Rho-dependent termination
-Rho-independent termination

20

rho

-displaces the DNA template strand from RNA polymerase

21

rho-dependent termination

-requires an additional protein to displace DNA template from RNA pol

22

rho-independent termination

-requires a G-C rich stem loop followed by a poly-U stretch
-causes RNA pol to dissociate

23

Shine-dalgarno sequence

-translation
-right before a gene
-tells ribosome to begin at that point to start translation
-the next time you see a start codon, you should start translation
-new shine-dalgarno sequence right before each new gene

24

polycistronic

-only prokaryotes
-one mRNA codes for several proteins(multiple genes on one transcript
-code for multiple enzymes in the same biosynthetic pathway

25

rifampin

-antibiotic
-binds to prokaryotic RNA pol to prevent transcription
-used to treat TB
-interact with core enzyme and cause conformational change so it cannot read template strand
-ONLY PROKARYOTIC

26

prokaryotic RNA polymerase

-RNA pol I produces ALL types of RNA

27

Euchromatin

-less condensed DNA
-more accessible to RNA polymerase for transcription

28

Acetylation of histone H1

-causes chromatin to revert to nucleosomes,beads on a string, so it is more exposed

29

Heterochromatin

-appears more dense DNA
-DNA is relatively inaccessible due to its highly condensed structure
-highly methylated which determines epigenetics/phenotype

30

Eukaryotic RNA polymerase I

-transcribes precursors to rRNA in the nucleolus

31

RNA polymerase II

-transcribes precursor to hnRNA in nucleoplasm
-eventually hnRNA becomes mRNA

32

RNA polymerase III

-transcribes tRNA precursors

33

Eukaryotic consensus sequences

-TATA box
-CAAT box

34

Eukaryotic TATA box

-Hogness box
-25 nucleotides UPstream from start site
-recognized by RNA pol II

35

CAAT box

-70 nucleotides UP stream from start site
-recognized by RNA pol II

36

rRNA synthesis in Eukaryotes

-three rRNAs are transcribed as a single large precursor
-large precursor cut to three by RNA pol I
-individual rRNA are cleaved apart by RNases

37

tRNA synthesis in Eukaryotes

-RNA pol III
-removal of intron loops
-trimming of 5' and 3' ends
-base modifications at 3' end
-addition of 3'CCA sequence(important for adding amino acids)

38

where does eukaryotic transcription take place?

nucleus

39

Where does eukaryotic translation take place?

cytoplasm

40

Eukaryotic mRNA and prokarotic mRNA

Eukaryotic: extensively processed from hnRNA to mRNA
Prokaryotic: begin mRNA translation before transcription is over

41

5' capping

-addition of 7-methylguanosine to 5' end of eukaryotic mRNA
-ribosome recognition signal AND protect from nuclease degradation

42

3' poly-A tail

-3' terminus of eukaryotic mRNA contains a polyadenylation signal
-site for addition of adenine residues
-the additional A's are not encoded in the gene
-serves are a signal for transport out of the nucleus and stabilizes mRNA from nuclease degradation

43

introns

intervening sequences

44

exons

expressed sequences

45

Why must introns be removed?

-they are not exressed, so they must be removed for proper translation

46

Splicing

-the removal of introns and the joining of exons by snRNPs

47

snRNPs

-composed of snRNA and a group of proteins
-form lariot, clip it out, join exons

48

lariat

-the excised intron

49

alternative splicing

-joining of different exons together to form different mRNAs
-produces proteins with SOME common domains, but the overall function is different

50

Who is primarily affected by systemic lupus erythematosus?

-onset is in late-teen females

51

systemic lupus erythematosus

-produce antibodies that recognize host proteins, including snRNPs
-results in butterfly rash

52

where is mature mRNA transported after processing events are complete?

cytoplasm

53

Amanita phalloides

-death cap mushroom
-contains alpha-amanitin

54

alpha amanitin

-binds to RNA pol II and inhibits mRNA synthesis