EC1: RNA, Transcription, and Promoters

Question 1

Where in the cell are genes found?

Answer 1

Nucleus

Question 2

Where are proteins made?

Answer 2

Cytoplasm of ribosomes

Question 3

What carries the ‘message’ from the nucelus (or wherever the genes are made) to the ribosome?

Answer 3

mRNA

Question 4

What do the arrows represent in this diagram?

Answer 4

The flow of information in a biological system

Question 5

What is transcription, and what enzyme is involved?

Answer 5

DNA-dependent mRNA synthesis; RNA polymerase

Question 6

What is translation, and what enzyme is involved?

Answer 6

mRNA-depended protein synthesis; ribosome

Question 7

What is this molecule and where is it found? What is the numbering system of carbons around this ring?

Answer 7

Ribose

Found in RNA

Question 8

What is this molecule and where is it found?

Answer 8

Deoxyribose

Found in DNA

Question 9

What are the four bases in RNA? Which ones are shared with DNA?

Answer 9

Adenine (A) – shared with DNA

Guanine (G) – shared with DNA

Cytosine – shared with DNA

Uracil (U) – unique to RNA

Question 10

What’s the difference between the RNA base uracil and the DNA base thymine?

Answer 10

Thymine is 5-methyl-U, i.e. has a methyl group on the fifth carbon of uracil

Question 11

Which bases (DNA and RNA) are purines and which are pyrimidines?

Answer 11

Purines: adenine, guanine

Pyrimidines: thymine, cytosine, uracil

Question 12

Is RNA in cells single- or double-stranded? What is the exception?

Answer 12

It is single-stranded, but some viruses have dsRNA

Question 13

Is there base equivalence in RNA?

Answer 13

No – the amounts of the four bases vary independently

Question 14

How does ssRNA form a secondary structure? What is the name of this structure?

Answer 14

It folds back on itself, forming non-standard pairs in step-loop structures, resulting in partial double-stranded regions

Question 15

How many base pairs have a folded piece of RNA and a folded piece of DNA per 360° turn?

Answer 15

RNA: 11 base pairs

DNA: 10 base pairs

Question 16

Are all enzymes proteins?

Answer 16

No – some can be made of RNA

Question 17

What are the major types of RNA and what is their approximate relative proportions in a cell?

Answer 17

messenger RNA (mRNA) – approx. 5%

ribosomal RNA (rRNA) – approx. 80%

transfer RNA (tRNA) – approx. 15%

Question 18

What are the purposes of mRNA?

Answer 18

It carries genetic information that is copied from the gene (DNA)

It is used as a template for translation by ribosomes

Question 19

Differentiate between bacterial and eukaryotic rRNA.

Answer 19

Bacterial:

3 x rRNAs; two large, one small; 50 proteins in bacterial ribosome

Eukaryotic:

4 x rRNAs; two large, two small; 80 proteins in eukaryotic ribosome

Question 20

How long is tRNA?

Answer 20

Approx. 76 nucleotides

Question 21

What is the role of tRNA?

Answer 21

It carries amino acids to the ribosomes for protein synthesis

Question 22

Define ‘proteinogenic amino acid’.

Answer 22

An amino acid that goes into a protein

Question 23

How many tRNAs are dedicated to each proteinogenic amino acid?

Answer 23

One

Question 24

What is the standard abbreviation for RNA polymerase?

Answer 24

RNAP

Question 25

What is the general equation for RNA synthesis (transcription)?

Answer 25

(RNA)_n + NTP ⇌ (RNA)_n+1 + PPi | (PPi → 2Pi)

Question 26

What catalyses RNA synthesis?

Answer 26

RNA polymerase

Question 27

What drives RNA synthesis?

Answer 27

Cleavage of inorganic pyrophosphate (PPi) by pyrophosphatase

Question 28

What does the synthesis of RNA require?

Answer 28

Nucleoside triphosphates (NTPs) Mg²⁺ dsDNA template

Question 29

In which direction are all nucelic acids made?

Answer 29

5' → 3'

Question 30

How processive is RNA synthesis?

Answer 30

Very

Question 31

How does RNA synthesis differ from DNA synthesis? (x4)

Answer 31

* No primers * Not semi-conservative, as the DNA template remains unchanged * No nuclease activities * Only one DNA strand copied in the complementary sense even though dsDNA is required

Question 32

Is transcribed RNA made parallel or anti-parallel to a DNA strand?

Answer 32

Anti-parallel

Question 33

How does RNAP know: 1. which strand to transcribe 2. where to start?

Answer 33

Using promoters: 1. The RNA polymerase looks for promoters 2. Promoter is directional

Question 34

What is a promoter?

Answer 34

A specific binding site for RNA polymerase

Question 35

How does a promoter work?

Answer 35

It is directional and 'catches' and 'orientates' the RNAP RNAP opens the promoter RNAP then transcribes the 3'→5' strand

Question 36

To which part of the DNA strand do the terms 'upstream' and 'downstream' refer?

Answer 36

The coding region

Question 37

Is the promotor upstream or downstream of the coding region?

Answer 37

Upstream

Question 38

Is the promoter transcribed in RNA transcription?

Answer 38

No

Question 39

How do we find promoters?

Answer 39

Footprinting: the sequences is protected from digestion by RNAP

Question 40

What are the benefits of having different sequences for promoters?

Answer 40

* **Regulation**: possibility of turning some promoters on and some off independently * **Some promoters will catch RNAP more efficiently** so functions more effectively than other promoters so more mRNA is made and more proteins are made

Question 41

What do promoters look like?

Answer 41

They all differ, but the best guess is a 'consensus sequence'.

Question 42

What is a strong promoter?

Answer 42

A promoter that generates more of their product