Translation, Genetic Code, Gene Regulation & Expression

Question 1

is genetic code overlapping?

Answer 1

no

because single base mutations only ever affect 1 a.a

Question 1

The genetic code is universal, although some organisms/organelles have slight variations

examples?

Answer 1

• mitochondria
• some flatworms, roundworms and tapeworms
• some protozoa
• candida sp of yeast (CUG → Ser)
• Bacteria & Archaèa (CUG & UUG also commonly used as start codons)

Question 2

translation steps

Answer 2

1. initiation -> binding of small subunit & progression up to start codon (AUG)
2. elongation
3. termination

Question 3

mutation

Answer 3

due to changes in DNA base seq

Question 4

transition vs. transversion

mutations

Answer 4

• transitions: interchanges of 2-ring purines
  (A G) / of 1-ring pyrimidines (C T)
  -> ∴ involve bases of similar shape
• transversions: interchanges of purine for pyrimidine bases
  -> ∴ involve exchange of 1-ring and 2-ring structures

Question 5

types of mutations introduced by single base substitutions

Answer 5

• silent
• neutral
• mis-sense
• nonsense

Question 6

examples of polyphenism

gene expression

Answer 6

1. Daphnia pulex -> can grow horn (armour) in prescence of predator (external stimuli)
2. Myzus persicae -> single mother can produce female baby with no wings (apterous) & female baby with wings (alate)

Question 7

remodelling proteins

Answer 7

• physically push apart nucleosomes
• to allow RNA pol. 2 & basal factors to bind to promoter

Question 8

nucleosomes

Answer 8

repeating units in chromatin

Question 9

operon

bacterial gene expression

Answer 9

• group of genes with related functions clustered together
• operon has 1 promoter
• all genes in operon transcribed together

Question 10

telomere

chromosome structure

Answer 10

• highly repetitive DNA that allow ends of chromosomes to be replicated
• also protects ends of chromosomes being mistaken as broken

Question 11

origin of replication

chromosome structure

Answer 11

• special seq where duplication of DNA begins
• each chromosome will have many origins

Question 12

mitosis stages

Answer 12

1. prophase -> chromosomes become visible
2. metaphase: chromosomes align at equator of cell
3. anaphase: chromosomes separate
4. telophase: 2 nuclei form

Question 13

RNAi

Answer 13

RNA interference

mechanism of silencing gene expression

Question 14

RNAi gene silencing in natural systems

Question 15

how does ↑ no. of copies of gene lead to ↓ mRNA?

Answer 15

• 1998 - Andrew Fire & Craig Mello working on gene expression in nematode C. elegans
• they found that when they injected sense & artisense RNA together (‘double stranded’ RNA or dsRNA) …
• they were able to ↓ expression of protein involved in movement

Question 16

in a series of experiments, what did Fire & Mello deduce?

Answer 16

• dsRNA silences genes by ↓ levels of mRNA with matching nucleotide seq.s
• RNAi is specific for gene with code that matches RNA injected
• RNAi can spread between cells & even be inherited

Question 17

Why do organisms contain all the elements of the RNAi pathway, such as ‘dicer’ ?

RNAi in nature

Answer 17

RNAi may represent a primitive immune system that could protect organisms against exogenous genetic elements eg. transposons / viruses whose lifecycle includes a dsRNA stage

1. viral dsRNA infects organism
2. host RNAi machinery breaks apart dsRNA
3. host siRNAs spread throughout organism so it’s resistant to virus next time it’s infected

Question 18

can viruses ‘fight back’ ?

Answer 18

In ongoing ‘arms race’ between host & pathogen, both plant & animal viruses have evolved proteins that suppress gene silencing (eg. p19 protein)

Question 19

Does RNAi gene silencing work in nature?

Answer 19

• MicroRNAs which act like RNAi…
• have been shown to be key regulators in many biological processes eg. development, cell birth & death, & cancer

Question 20

is there clinical potential for RNAi ?

Answer 20

• RNAi, with its potential to specifically target gene expression, has potential to fight almost every disease imaginable
• how close are we to seeing RNAi transform medicine? -> example: Macular degeneration
• also Hepatitis C -> In 2002 researchers at Stanford Uni announced their RNAi treatment had controlled Hepatitis C virus in lab mice

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Question 21

macular degeneration

example of RNAi in medicine

Answer 21

• protein called VEGF (Vascular Endothelial Growth Factor) promotes blood vessel growth that can destroy vision
• RNAi can be delivered directly to diseased tissue through injection
• 1st clinical trial of 24 patients in 2004 had promising results, with 25% of patients showing significantly clearer vision

BUT STEM CELL TRANSPLANTS ARE MORE SUCCESSFUL

Question 22

Nature Biotechnology June 2007

clinical potential of RNAi

Answer 22

Australia tackles ‘bird’ (avian) flu using RNAi

• Therapeutic -> deliver RNAi in drinking water, boost innate immune system
• Prophylactic -> use transgenes (stable genetic insertion) to introduce permanent protection to influenza virus

Question 23

can RNAi be used as new contraception?

(alternate to the pill & its side effects)

clinical potential of RNAi

Answer 23

• in fertilisation, sperm binds to specific protein ZP3, before acrosome reaction which leads to egg being fertilised
• so if we can block production of ZP3 => no fertilisation
• so RNAi ZP3 encoding gene => failure in fertilisation :)