Dna Transcription

Question 1

information flow in the central dogma

Answer 1

1. DNA replication (DNA -> DNA)
2. Transcription (DNA -> RNA)
3. Translation (RNA -> Protein)

Question 2

in all living organisms, genetic information flows…

Answer 2

…from DNA to RNA to Proteins in a unidirectional pathway

Question 3

exceptions to the central dogma

Answer 3

information between nucleic acids is flexible
1. RNA replication: RNA can make RNA (eg: RNA viruses)
2. reverse transcription: RNA can make DNA (eg: telomerase)

Question 4

is translation unidirectional

Answer 4

yes, translation has so far proven to be unidirectional

Question 5

RNA is the essential…

Answer 5

…intermediate between DNA and proteins

Question 6

RNA primary structure

Answer 6

1. four different nucleotides
2. each nucleotide contains one base, ribose, phosphate
3. joined through phosphodiester bonds
4. polarity from 5’ -> to 3’

Question 7

what are the consequences of the differences in primary structure between RNA and DNA

Answer 7

1. T (5-methyl-U) and U both base pair with A
2. the presence of 2’ OH makes RNA sugar-phosphate backbone more sensitive to hydrolysis

Question 8

RNA secondary structure

Answer 8

1. very different to DNA
2. contains only one strand which makes them very flexible
3. RNA molecules can make intramolecular base pairs on the same strands -> creating crazy structures like hairpins, stems etc due to palindromes

Question 9

base pairing rules in RNA

Answer 9

1. same as in DNA meaning Chargaffs rules apply here as well
2. A-U, G-C
3. The only exception is that G can technically base pair with U; they don’t contribute to stability

Question 10

stability of stems

Answer 10

depends on
1. length: long > short
2. sequence (number of hydrogen bonds): GC>AU>GU

Question 11

Palindromes

Answer 11

a word or a phrase that reads the same forwards and backwards

Question 12

palindromes in DNA sequence

Answer 12

sequences where the same sequence is found not on the same strand, but rather on the complementary strands

Question 13

complex 3d structures of RNA

Answer 13

1. can be stably folded into complex structures
2. this freedom allows RNA to develop catalytic abilities -> ribozymes
3. RNA catalyses some of the key reactions in RNA processing and translation

Question 14

transcription definition

Answer 14

synthesis of RNA from a DNA template

Question 15

RNA transcription requirements

Answer 15

1. ssDNA
2. activated (triphosphate) nucleotide precursors
3. transcription proteins (RNA polymerase)

Question 16

RNA polymerases

Answer 16

transcription protein in RNA transcription that can start new chains

Question 17

Biochemistry of polymerization

Answer 17

1. free 3’ OH attacks alpha phosphate
2. release of pyrophosphate (PPi)
3. Hydrolysis of PPi

Question 19

What is RNA catalyst

Answer 19

Is a ribozyme that catalyzes many key reactions during processing and translation

Question 20

Transcription in rna vs dna

Answer 20

Transcription is basically the same. However, rna polymerase unwinds dna helix itself, and always the same strand is transcribed for a gene

Question 21

What is required for transcription

Answer 21

1. Different accessory proteins
2. Transcription bubble
3. Does not require a primer

Question 22

Transcription in E.coli initiation

Answer 22

1. Sigma factor associates with core RNA polymerase
2. Holoenzyme binds to promoter
3. Sigma factor promotes melting of dna, which generates an open complex
4. First nucleotide binds to +1 position, and second one binds as well
5. Rna pol catalzys first phosphordiester bond
6. Core polymerase escapes from promoter, and only Sigma factor is left behind

Question 23

Promoter recognition in E.coli

Answer 23

The promoter has a consensus sequence that the holoenzyme binds to. Different sigma factors will recognise different consensus sequences

Question 24

What determines how well the holoenzyme binds to the promoter

Answer 24

Spacing between -35 and -10 sequence. If the sequence is further apart or closer together, it means that the dna helix made more or less of a full turn, and the holoenzyme can’t bind as efficiently

Question 25

Elongation in e.coli

Answer 25

Rna polymerase add s about 40 nucleotides per second. The transcription bubble is 18 nucleotides wide and moves with the rna polymerase. Rna stays base paired with template for 8bp

Question 26

Termination in E.coli

Answer 26

Can be either rho dependent or rho independent

Question 27

Rho independent termination

Answer 27

1. Hairpin structure causes the rna polymerase to slow down or pause 2. An Adenine rich stretch in template strand leads to a Uracil rich stretch in Rna. 3. This causes weak associations between rna and Dna 4. Rna polymerase falls off

Question 28

Rho dependent termination

Answer 28

1. Inverted repeats from hairpin slows down/ stop rna polymerase 2. Upstream from inverted repeats is a stretch of dna that won't form a secondary structure as rna 3. Unstructured rna allows rho to bind and once it catches up with rna pol it unwinds rna/dna hybrid 4. Release of rna

Question 29

Transcription in eukaryotes vs prokaryotes

Answer 29

Very similar just a bit more complicated. Rna polymerase have additional parts

Question 30

What does RNA pol I create

Answer 30

Large rRNA (ribosomal RNAs

Question 31

what does RNA pol II create

Answer 31

mRNAs some snRNAs miRNA precursors

Question 32

what does RNA pol III create

Answer 32

5s rRNA tRNAs some snRNAs RNAs

Question 33

what does core RNA polymerase consist of

Answer 33

multiple protein subunits, accessory proteins

Question 34

transcription initiation in eukaryotes

Answer 34

TBP and TFIID binds to TATA box TBP recruits RNA pol II and other TF to create PIC RNA pol II separates from the TFs (they stay at promoter so they can recruit the next polymerase) and starts transcription CTD of RPB1 subunit is phosphorlated

Question 35

what does rna pol II create

Question 36

what does rna pol III create

Question 37

Initiation in Eukaryotes (pol II)

Answer 37

- TBP and TFIID bind to TATA box - TBP recruits TFs and RNA pol II to create PIC - RNA pol II separates from the PIC - CTD of RPB1 subunit of RNA pol II is phoshporylated

Question 38

rna pol I promoter

Answer 38

- contains two dna sequences (core element and upstream element) - requires two factors (UBF binds to both elements and recruits SL1, SL1 contains TBP and recruits RNA pol 1)

Question 39

rna pol III promoter

Answer 39

- vary in structure (some look like RNA pol II promoters) - 5S rRNA and tRNA have internal promoters that bind RNA pol III specific TF

Question 40

termination rna pol I

Answer 40

- uses termination factor which binds to a DNA sequence downstream of termination site

Question 41

termination pol III

Answer 41

- terminates after string of U, no need for hairpin

Question 42

termination pol II

Answer 42

- tends to stop at random places in a region that can stretch several hundred bp - likely promoted once mRNA is cleaved and polyA tail is added