lecture 14- transcription

Question 1

central dogma

Answer 1

DNA —transcription–> RNA —translation–> protein

(DNA->mRNA–>protein–>function)

Question 2

majority of DNA is coding or non-coding?

Answer 2

non-coding

Question 3

what is the importance of non-coding DNA?

Answer 3

becomes ncRNA, can’t encode protein, but important for translation process and gene expression –> function

Question 4

describe RNA structure

Answer 4

• composed of nucleotides
• sugar = ribose
• presence of 2’ OH group
• nitrogenous bases = A, G, C, U
• nucleotides joined by phosphodiester bonds (5’ phosphate to 3’ hydroxyl)
• usually single-stranded
• secondary structure varies a lot- gives RNA diverse functions
• stability: easily degraded

Question 5

RNA ___ enables RNA molecules to fold into many different shapes that lend themselves to many functions

Answer 5

secondary structure

Question 6

RNA’s nucleotides are joined by ___ bonds, which is

Answer 6

phosphodiester
5’ phosphate to 3’ hydroxyl

Question 7

describe RNA secondary structure

Answer 7

• RNA’s have helical secondary structures- tRNA forms a cloverleaf with 4 helices
• double-helical characteristics of RNA:
  . right-handed helical conformation dominated by base-stacking conformations
  . internal loops where nucleotides don’t pair
  . hairpins
  . non-watson crick base pairing important to stabilize secondary structure
  . helical portions have overall geometry of A-form duplex

Question 8

name 4 interactions that contribute to stability of secondary 3D RNA structure

Answer 8

1- non- Watson Crick interactions
2- additional unusual interactions (base triples)
3- 2’ hydroxyl group
4- base stacking

Question 9

describe non- Watson Crick interactions

Answer 9

contribute to stability of RNA secondary structure
- adenine pairing with adenine by 2 hydrogen bonds
- guanine pairing with uracil

Question 10

describe additional unusual interactions that contribute to stability of RNA secondary structure

Answer 10

C:G:C base triple
U:A:U base triple
(purine in the middle)

Question 11

describe how 2’ hydroxyl group stabilizes secondary structure

Answer 11

2’ OH can form hydrogen bonds with the oxygen of the ribose on the following nucleotide
- also hydrogen bonding through a water molecule between 2’ hydroxyl and the phosphate oxygen

Question 12

how does base stacking contribute to stability of secondary structure

Answer 12

nucleotide bases stacked one on top of the other is favored

Question 13

___ is the entire set of RNA transcripts produced in a cell

Answer 13

transcriptome

Question 14

which DNA strand is transcribed to RNA

Answer 14

template (noncoding, antisense) strand
- RNA sequence will be exact same as nontemplate (coding, sense) strand but with uracil

Question 15

how does rate of transcription vary

Answer 15

very different for different genes
- genes that promote high rates of expression called housekeeping genes (usually genes of metabolic pathways- glycolysis, etc.)

Question 16

brief overview of transcription process

Answer 16

• RNA polymerases synthesize RNA
• RNA synthesis always in 5’ to 3’ direction, meaning DNA template copied from 3’ to 5’ because antiparallel
• use rNTP’s to synthesize RNA complementary to template
• add ribonucleotides to 3’ OH end only (same as DNA poly’s)
• no primer required
• product does not remain paired with template
• less accurate than DNA replication

Question 17

does RNA polymerase require primer

Answer 17

no

Question 18

how many RNA polymerases are needed in prokaryotes and eukaryotes

Answer 18

prokaryotes: a single RNA poly synthesizes all RNA’s
eukaryotes: have at least 3- RNA poly I, II, III

Question 19

what is a transcription unit

Answer 19

sequence of nucleotides in DNA that codes for a single RNA molecule, along with the sequences necessary for its transcription- normally contains a promoter, a RNA-coding sequence, and a terminator

Question 20

RNA polymerase attaches and initiates transcription at the ___, which is located where?

Answer 20

promoter
upstream of the information contained in the gene

Question 21

what signals the end of transcription?

Answer 21

terminator

Question 22

promoter is the RNA polymerase binding site on the DNA and determines…

Answer 22

which strand is going to be transcribed

Question 23

+1 and +10 sites

Answer 23

+1 site is the start site in the promoter
+10 is the 10th nucleotide downstream of the start side

Question 24

everything before the coding region in DNA is considered ___

Answer 24

upstream

Question 25

describe the general steps of transcription

Answer 25

• similar in prokaryotes and eukaryotes
• step 1: RNA polymerase binds at promoter of gene- this forms a closed complex
• step 2: promoter melting- double helix DNA melts in promoter region (not bound by hydrogen bonds anymore) - forms open complex
• step 3: transcription initiated within complex
• step 4: promoter clearance and elongation- RNA polymerase moves along DNA, leaving promoter (RNA polymerase bound to DNA so tightly, synthesizes RNA very fast)
• step 4: RNA polymerase finds terminator site, dissociates, and releases the new RNA, recycled

Question 26

describe the formation of transcription bubble in initiation

Answer 26

promoter melting- DNA duplex is unwound for about 17 bp, forming the open complex bubble, which enables RNA polymerase to access template strand
- DNA supercoiling occurs both in front and behind the bubble (pos supercoils ahead of RNA poly and neg supercoils behind in the DNA)

Question 27

the addition of an rNTP to a growing transcript is a ___ dependent reaction that produces a ___ linkage

Answer 27

Mg2+
5’-3’ phosphodiester linkage

Question 28

the presence of the 2’ OH makes RNA vulnerable to ___ but also allows additional ___ bonding between segments of molecule

Answer 28

hydrolysis
hydrogen

Question 29

base-paired segments of RNA generally adopt the compact geometry of ___ helices

Answer 29

A-form