Block A

Question 1

Purine bases

Answer 1

Adenine, Guanine

Question 2

Pyrimidine Bases

Answer 2

Cytosine, Thymine (DNA), Uracil (RNA)

Question 3

What is a nucleoside?

Answer 3

a base conjugated to a sugar via a Beta-Glycosidic linkage (eg. deoxyadenosine)

Question 4

what is a nucleotide?

Answer 4

a base conjugated to one or more phosphoryl groups (eg. dATP, deoxyadenosine triphosphate)

Question 5

“ideal” DNA helix conditions

Answer 5

10 base pairs per turn
each aromatic base 3.4Å thickness
helix pitch of 34Å (rise per turn)

Question 6

Hydrolysis of PPi to 2Pi

Answer 6

PPi broken down to two molecules of inorganic Pi with addition of water
(DNA synthesis reaction 1)

Question 7

Strongly negative ΔG⁰’

Answer 7

Gibbs free energy change (ΔG⁰’) of reaction is very negative, indicates reaction is EXERGONIC
-releases energy, spontaneous under standard conditions
(DNA synthesis reaction 2)

Question 8

Messenger RNA

Answer 8

-Template for protein synthesis
-Transcribed by RNA polymerase II

Question 9

Ribosomal RNA

Answer 9

-major component of ribosomes
-synthesised by RNA polymerase I

Question 10

Transfer RNA

Answer 10

-carries activated amino acids to ribosomes
-synthesised by RNA polymerase III

Question 11

Steps of mRNA synthesis

Answer 11

1. Initiation
2. Elongation
3. Termination

Question 12

mRNA synthesis:
1. Initiation

Answer 12

Promoters contain CAAT, TATA, or GC boxes
CAAT and TATA boxes recruit RNA Pol II and initiate transcription

Question 13

mRNA synthesis:
2. Elongation

Answer 13

RNA Pol moves along DNA template to synthesise mRNA (3’-5’ direction)
Sequence of growing mRNA driven by base pairing to DNA strand - copy of DNA template produced

Question 14

mRNA synthesis;
3. Termination

Answer 14

Occurs at defined sites
mRNA very unstable, so processed by 1. a modified 5’ cap, 2. Poly A tail at 3’

Question 15

Transcription Factors

Answer 15

-turn gene expression on/off
-recognise specific DNA sequences near promoters
-characteristic DNA binding structures
-targets for signaling pathways
-activated by phosphorylation + movement to nucleus

Question 16

what is epigenetics?

Answer 16

Modifications to the genome that affect gene expression, but DONT alter DNA sequence
Can be reversible, therefore can be modulated

Question 17

DNA Methylation

Answer 17

-addition of methyl groups to nitrogen bases of nucleotides - mostly to CYTOSINE, sometimes adenine
-regulates gene expression (gene silencing) by recruitment of gene expression proteins or hindering binding of TFs to DNA
-modulates DNA structure

Question 18

CpG Islands

Answer 18

-G/C content of genome 42%, CpG should occur at 4.4% freq., observed at 1%
-5’-CpG-3’
(“p” represents phosphate residue)
-Methylation: gene silencing
-Methyl groups protrude into major grooves of DNA, prevents binding of TFs
-High density of CpGs = CpG islands
-Highest in promoter regions

Question 19

CpG methylation

Answer 19

-cytosine methylated by DNA methyltransferase (DNMT)
-DNMT1 actively maintains DNA methylation during cell replication

Question 20

Eurochromatin

Answer 20

-loosely packed form of Chromatin
-enriched in genes
-under active transcript

Question 21

Heterochromatin

Answer 21

-tightly packed form of Chromatin
-genetically active
-inaccessible to RNA Polymerase

Question 22

Histone Acetylation

Answer 22

-acetylated by histone acetyltransferases (HATs)
-reduce +ve charge of histones, neutralise +ve lysines, decrease attraction between histones(+) and DNA(-)
-deacetylated by histone deacetylases (HDACs)
-NOT AN EPIGENETIC MODIFICATION

Question 23

Histone Methylation

Answer 23

-can correlate to both transcriptional activity and inactivity

Question 24

Epigenetics in Worker Bees

Answer 24

-all methylation removed in Queen Bee, all genes active
-when new Queen needed, egg is fed royal jelly
-compound in jelly inhibits methyl transferase
-demethylation in egg -> egg becomes Queen