Gene Expression

Question 1

What is a gene?

Answer 1

Stretch of DNA, chromosomal locus
Code+regulation of protein 
2x 25,000 alleles per cell
"Unit of inheritance"
"Unit of transcription"

Question 2

Which direction is the antisense strand of DNA read during transcription?

Answer 2

3’ to 5’

Question 3

Which direction is mRNA synthesised during transcription?

Answer 3

5’ to 3’

Question 4

Which direction are proteins synthesised?

Answer 4

N to C

Question 5

What is needed to synthesise a polynucleotide or polypeptide?

Answer 5

Enzyme
Activated substrates
Needs a template

Question 6

What are the stages in making a polynucleotide or polypeptide?

Answer 6

Initiation
Elongation
Termination

Question 7

What is needed to synthesise RNA?

Answer 7

Enzyme - RNA polymerase
Activated substrates - NTPs
Templates - DNA

Question 8

What are the stages in making RNA?

Answer 8

Initiation
Elongation
Termination

Question 9

What is needed to make a polypeptide?

Answer 9

Enzyme - ribosome
Activated substrates - amino acids
Template - mRNA

Question 10

What are the 3 stages in making a polypeptide?

Answer 10

Initiation
Elongation
Termination

Question 11

Describe the 3 stages in DNA replication

Answer 11

Initiation - recognition origin of replication, initiation proteins, DNA polymerase

Elongation - 5’ to 3’ chain growth

Termination - when replication forks meet

Question 12

Describe the 3 stages in transcription

Answer 12

Initiation - promoter recognition, transcription initiation factors, RNA polymerase

Elongation - 5’ to 3’ chain growth

Termination - sequence dependent

Question 13

Give a general equation to denote making an mRNA polynucleotide

Answer 13

(rNMP)n + rNTP —-> (rNMP)n+1 + PPi

NMP = nucleotide monophosphate 
NTP = nucleotide triphosphate

Question 14

What is a promoter sequence?

Answer 14

Upstream sequence - regulates gene expression

Define where the transcription of a gene by RNA polymerase begins

Question 15

What is a TATA box?

Answer 15

A DNA sequence that indicates where a genetic sequence can be read and decoded. It is a type of promoter sequence which specifies to other molecules where transcription begins.

Question 16

Why is RNA processing necessary

Answer 16

Turn pre-mRNA into mature mRNA

mRNA is prone to degradation

Question 17

What is capping?

Answer 17

Cap added at the 5’ end - protection against degradation
A 5’ - 5’ linkage is created
Plays a role in translation

Question 18

What is tailing?

Answer 18

aka polyadenylation
PolyA tail added at the 3’ end - protection against degradation
Signal for termination is AAUAA. The mRNA is cut a but later
PolyA polymerase adds up to 200 A nucleotides to the 3’ end
This uses ATP

Question 19

What is splicing?

Answer 19

Introns in the middle removed, sequence dependent

Question 20

Describe prokaryotic ribosomes

Answer 20

3 rRNAs + 56 proteins
30S + 50S subunits
70S ribosome

Question 21

Describe eukaryotic ribosomes

Answer 21

4 rRNAs + 82 proteins
40S + 60S subunits
80S ribosome

Question 22

Name 5 types of RNA

Answer 22

• rRNA (ribosomal RNA) - RNA polymerase I - few kinds, many copies of each, >80%
• mRNA (messenger RNA) - RNA polymerase II - 100,000s of kinds, few copies of each, ~2%
• tRNA (transfer RNA) - RNA polymerase III - ~100 kinds, very many copies of each, ~15%
• miRNA (microRNA)
• noncoding RNA

Question 23

Briefly describe the genetic code

Answer 23

Triplet code, degenerate
Non-overlapping, no gaps
“Changing the language” from 4-letter DNA to 20 letter protein “language” results in 5’ to 3’ template producing N to C polypeptide chain extension
Adaptor molecule needed is tRNA

Question 24

What is needed for translation?

Answer 24

Enzyme - ribosome
Activated substrates - amino acids
Template - mRNA

Question 25

Describe the structure of tRNA

Answer 25

Clover model 3 stem loops - hydrogen bonds are formed between antiparallel complementary sequences Has an anticodon loop which binds to mRNA - e.g. tRNA 5'CAU recognises mRNA 5'AUG (methionyl tRNA) CCA terminus at 3' end (OH) which binds correct amino acid

Question 26

What are wobble bases?

Answer 26

5' base of anticodon has I base - this is the wobble position (3' base of codon) This allows a single tRNA to recognise more than one codon

Question 27

Describe the 3 steps in translation

Answer 27

Initiation - AUG codon recognition, "special" methionyl tRNA ribosome Elongation - N to C chain growth, aminoacyl tRNAs Termination - stop codons

Question 28

Describe initiation of translation

Answer 28

Cap recognised by cap binding proteins, initiation factors, methionyl tRNA binds, GTP needed Downstream, AUG recognised methionyl tRNA binds, initiation factors, cap binding proteins, GDP

Question 29

Describe elongation in translation

Answer 29

60S subunit 2 sites of ribosome, P site and A site Methionyl tRNA on P site, binding of aminoacyl-tRNA to A site Peptide bond formation between AAs (now attached to tRNA in A site)- peptidyl tRNA Translocation of this tRNA to P site using GTP (ribosome "moves along") - enzyme peptidyl transferase ensures peptide is transformed and growing chain on correct side A site now empty for another tRNA to bind

Question 30

Describe termination of translation

Answer 30

Stop codon reached, water added to peptidyl tRNA to give the peptide and tRNA