Chapter 13

Question 1

How can you tell if a strand of RNA is single stranded?

Answer 1

If the A’s do not equal the U’s and the C’s do not equal the G’s

Question 2

How do you find the percentage of the DNA template strand from the percentage of an RNA template strand?

Answer 2

Take the complement of the bases and that is the same percentage

Question 3

Which direction does RNA polymerase run?

Answer 3

3’-5’ because it grows the RNA strand grows 5’-3’ meaning the DNA strand has to be opposite

Question 4

RNA polymerases carry out transcription at a much slower rate than that at which DNA polymerases carry out replication. Why is speed more important in replication than in transcription?

Answer 4

Much more DNA is copied per cell during DNA replication because the whole genome is copied. When carrying out transcription, only a small part of the genome is being transcribed, so it does not need to move as fast.

Question 5

What happens if there is a mutation in RNA polymerase I?

Answer 5

some ribosomal RNA not synthesized

Question 6

What happens if there is a mutation in RNA polymerase II?

Answer 6

pre-mRNA is not made

Question 7

What happens if there is a mutation in RNA polymerase III?

Answer 7

tRNA is not synthesized and some ribosomal RNA is not synthesized

Question 8

How do the DNA and RNA nucleotides differ?

Answer 8

DNA is composed of deoxyribose and RNA is made of ribose sugar. RNA has 2 OH groups while DNA only has one. DNA is a double helix with base pairs AGCT, and RNA is single stranded and has AGCU. DNA molecules are more stable than RNA molecules

Question 9

Where do transcription and translation take place?

Answer 9

transcription - inside the nucleus
translation - cytoplasm

Question 10

What are ribozymes?

Answer 10

catalytic RNAs - rRNA are ribosomes and they are part of a ribosome structure and are catalytic which is important in the creation of proteins

Question 11

Which RNA has a specific structure?

Answer 11

tRNA

Question 12

What are the three main types of RNA?

Answer 12

rRNA, mRNA, and tRNA

Question 13

What are the components of transcription?

Answer 13

1 DNA strand, RNA nucleotides, transcription apparatus (various proteins and enzymes that allow transcription to occur)

Question 14

What is the transcriptional unit?

Answer 14

a promoter, RNA coding sequence, and the terminator

Question 15

What is the non-template strand called?

Answer 15

the coding strand

Question 16

Describe upstream vs downstream

Answer 16

the promoter contains the upstream sequences, which are negatives. The first downstream sequence is +1 and it is not part of the RNA coding region or the promoter

Question 17

What are the functions of the promoter?

Answer 17

• serves as sequences to which the transcription apparatus binds
• determines the first nucleotide that is transcribed into RNA
• determines which DNA strand is template

Question 18

How are rNTPs added in transcription?

Answer 18

they are added to the 3’OH end of the growing RNA molecules and then 2 phosphates are removed and it becomes RMP

Question 19

What creates the secondary structure of proteins?

Answer 19

hydrogen bonds between amino acids

Question 20

What causes the tertiary structure of proteins?

Answer 20

folding due to hydrophobic and hydrophilic interactions

Question 21

What is the bacterial core of RNA polymerase made up of?

Answer 21

5 subunits:
- 2 copies of an alpha peptide
- single copy of beta gene
- single copy of beta prime gene
- stabilizing enzyme (omega gene)
- the sigma gene

Question 22

What does the sigma factor do?

Answer 22

aids in RNA polymerase binding to the promoter when transcription starts in bacteria

Question 23

What is not required for transcription?

Answer 23

RNA primers

Question 24

How many genes are need to form the holoenzyme?

Answer 24

five genes (six units)

Question 25

Define transcription vs. translation

Answer 25

transcription - copies the DNA from to RNA (deoxynucleotides to ribonucleotides) translation - ribonucleotides to amino acids

Question 26

What was the original genetic material?

Answer 26

RNA

Question 27

What is the title of the area between the promoter and the coding region of a transcriptional unit?

Answer 27

0 because it is between the upstream and downstream units

Question 28

What are the monomers used for transcription?

Answer 28

rNTPs aka NTPs and they are added to the 3'OH end of the growing RNA molecule

Question 29

Which protein structures are fiber like?

Answer 29

primary and secondary structure

Question 30

Which structures are globular proteins?

Answer 30

globular proteins

Question 31

What are consensus sequences?

Answer 31

sequences that are similar from one gene to another

Question 32

What is the Pribnow box (-10 consensus)?

Answer 32

10 bp upstream of start site (TATA box)

Question 33

What happens during initiation of transcription?

Answer 33

initial RNA synthesis, and the location of the consensus sequence determines the position of the start site (because the binding of the RNA polymerase will tell where transcription occurs)

Question 34

What happens during elongation of transcription?

Answer 34

RNA polymerase adds nucleotides

Question 35

When is the sigma factor released?

Answer 35

once the RNA polymerase moves past the promoter (+2 position)

Question 36

What is rho-independent termination?

Answer 36

does not use rho protein and creates a hairpin structure from a bunch of inverted repeats that is followed by a string of uracils. the base pairing is then destabilized by the hairpin and the RNA falls off the DNA (terminating)

Question 37

What is rho-dependent termination?

Answer 37

uses rho protein to aid in termination - rho binds to the rut site and moves towards the 3' end, then when RNA polymerase encounters a terminator sequences it pauses and rho catches up. Rho uses helicse to unwind the DNA-RNA hybrid, therefore terminating transcription

Question 38

What does RNA polymerase I transcribe?

Answer 38

large rRNAs

Question 39

What does RNA polymerase II transcribe?

Answer 39

pre-mRNAs

Question 40

What does RNA polymerase III transcribe?

Answer 40

tRNAs and small rRNAs

Question 41

What is the core promoter in eukaryotic transcription?

Answer 41

TATA box (25-30 bp and is bound by transcription factors)

Question 42

What does TBP (TATA binding protein) do?

Answer 42

allows RNA polymerase, transcription factors, and mediators to bind to the TATA box

Question 43

What is the transcriptional activator protein?

Answer 43

the enhancer and mediator to start transcription in eukaryotic cells

Question 44

What is the holoenzyme in eukaryotic cell transcription?

Answer 44

RNA polymerase II, TBP, and transcription factors

Question 45

Exons vs introns

Answer 45

exons - code for amino acids introns - remove by RNA splicing after transcription

Question 46

What is the difference between transcription factors and transcription activating proteins?

Answer 46

transcription factors - work with RNA polymerase to form the basal transcription apparatus that initiates minimal levels of transcription transcription activating proteins - bind to specific DNA sequences to being out higher levels of transcription