Gene Expression

Question 1

Basal transcription factors

Answer 1

Initiate transcription
Match RNA polymerase with appropriate DNA promoter region
Analogous to sigma function in bacteria

Question 2

Promoter

Answer 2

Contains a TATA box
5’-TATAAAA-3’
TATA box about 30bp from transcription START codon

Question 3

Transcription initiation complex

Answer 3

Distal control elements make up an enhancer on the DNA strand before the promoter region
Activator molecules bind the enhancer
The activator/enhancer complex allows a DNA bending protein to bind to the DNA and bend the strand over so the activators are close to the TATA box
A group of mediator proteins binds to the activators and promoter region
Transcription factors and RNA polymerase II join onto the mediator proteins and form a transcription initiation complex

Question 4

Transcription initiation

Answer 4

Upstream of the gene (5’ on non-template strand) is the promoter which includes a TATA box
After binding to the START codon, the RNA polymerase II moves 3’-5’ along template strand and manufactures new mRNA strand in 5’-3’ direction

Question 5

Transcription elongation

Answer 5

RNA polymerase II moves along DNA and unwinds about 10-20 base pairs at a time
mRNA is elongated and detaches from DNA

Question 6

Transcription termination

Answer 6

RNA polymerase II transcribes polyadenylation signal in DNA
10-35 base pairs downstream of signal mRNA transcript detaches from RNA polymerase II
5’ cap added to 5’ transcript end
3’ tail added to 3’ end

Question 7

5’ cap

Answer 7

Modified guanine residue
Protects from degradation
Aids stability
Promotes export of mRNA from nucleus
Assists with translation

Question 8

3’ tail

Answer 8

Poly-A tail
50-250 adenine nucleotides
The more adenine nucleotides means more stability and less degradation

Question 9

Splicing

Answer 9

Excision of introns and joining of exons
snRNPs - small nuclear RiboNuclear Proteins
snRNPs join with proteins to make a spliceosome
mRNA has splice sites which bind to complementary snRNA sequence
Spliceosome excises and degrades introns and joins exons together

Question 10

Aminoacyl tRNAs

Answer 10

Aminoacyl tRNA synthetases catalyse addition of amino acids to tRNAs
Active site on aminoacyl tRNA synthetase binds ATP and amino acid
AMP and amino acid bonding release two phosphate groups from the enzyme
Enzyme complex is activated
Activated amino acid transferred from synthetase to specific tRNA
Aminoacyl tRNA created

Question 11

Cloverleaf secondary structure

Answer 11

CCA sequence at 3’ end of tRNA is the amino acid binding site
Triplet loop at opposite end is the anticodon that pairs with mRNA codon
tRNA structure folds over to produce L shaped tertiary molecule

Question 12

Wobble hypothesis

Answer 12

tRNA anticodons can successfully bind codons whose third position requires a non-standard base pairing
e.g. CCG tRNA can bind GGA even though the third pairing is unorthodox
tRNAS can bind more than one type of codon

Question 13

Ribosomes

Answer 13

Separated into large and small subunit
Large subunit forms peptide bonds
Small subunit holds mRNA in place
tRNA is found at 3 sites: A, P and E

Question 14

‘A’ site of ribosome

Answer 14

Acceptor

tRNA binds mRNA codon

Question 15

‘P’ site of ribosome

Answer 15

Peptide bond

tRNA adds amino acids to polypeptide chain

Question 16

‘E’ site of ribosome

Answer 16

Exit

Formerly bound tRNAs leave ribosome

Question 17

Translation initiation

Answer 17

Small ribosomal subunit binds first amino acid tRNA which is carrying formyl methionine
Small ribosomal subunit scans downstream to translation START site in mRNA 5’-AUG-3’
Large ribosomal subunit binds
Translation begins

Question 18

Translation elongation

Answer 18

tRNA anticodon hydrogen bonds to mRNA codon in acceptor site
Large ribosomal subunit catalyses peptide bond formation
Growing polypeptide chain at C terminus transferred to tRNS in acceptor site

Question 19

Translation termination

Answer 19

Release factor binds at acceptor site, not tRNA
Polypeptide-tRNA bond in peptide bond site is hydrolysed
Polypeptide is released
2 GTP molecules are added

Question 20

Primary protein structure

Answer 20

Unbranched polypeptide chain held together by polypeptide bonds formed in the large subunit of the ribosomal canal

Question 21

Secondary structure

Answer 21

Hydrogen bonding between amino acid side chains forms alpha helices or bets sheets

Question 22

Alpha helix

Answer 22

Primary chain is coiled into a spiral structure and stabilised by hydrogen bonds

Question 23

Beta sheets

Answer 23

Primary chain zig zags back and forth to form a pleated sheet with adjacent strands held together by hydrogen bonds

Question 24

Tertiary protein structure

Answer 24

Hydrophobic collapse forms hydrophilic external faces
van der Waals interactions form between non-polar amino acid side chains
Hydrogen bonds form between polar amino acid side chains
Ionic bonds form between charged amino acid side chains
Disulphide bridges form between cysteine molecules

Question 25

Quartenary protein structure

Answer 25

Complex becomes a dimer, either hetero (different subunits) or homo (same subunits)
Intricate structure determines protein function
Alteration in amino acid sequence at binding groove can change which enzymes can bind or determine degradation efficiency

Question 26

3 models of quartenary protein structure

Answer 26

Ribbon
Spacefilling
Wireframe

Question 27

Proteins manufactured by free ribosomes

Answer 27

Cytosolic proteins

Post translational modifications added by other cytosolic proteins

Question 28

Proteins manufactured by attached ribosomes

Answer 28

Organelle specific
Secreted
Membrane bound
Post translational modifications added by proteins in the endomembrane system

Question 29

5 methods of post translational modification

Answer 29

Phosphorylation
Methylation
Acetylation
Carboxylation
Cleavage

Question 30

Method of post translational modification

Answer 30

Complex in cytosol consisting of ribosome, mRNA and signal peptide
SRP binds to complex
SRP on complex binds SRP receptor protein in ER membrane which forms a translocational complex
Signal peptide is removed which dissociates SRP
Protein forms in ER lumen
Ribosome complex dissociates