Genetic Changes and Protein Function

Question 1

Brief overview of Translation

Answer 1

• Occurs in the cytoplasm
• Carried out by ribsomses
  
  • Ribosomes are complex structures made of protein and rRNA
  • Ribosomes work like enzymes to catalyse protein synthesis (peptide bond reaction)
• There are four unique nucleobases in DNA or RNA (DNA: t, RNA u)
• There are 20 unique AAs
  
  • the code of DNA has to be read in sets of threes known as codons to make an AA
• The codon system is common across all life and is known as the ‘universal genetic code’

Question 2

Describe the role of tRNA in translation

Answer 2

Codons in mRNA are ‘read’ by another RNA molecule called tRNA
- has an anti-codoc - the complementary sequence to the mRNA codon
- Has an amino acid attached
- every codon/anti-codon sequence has a particular amino acid that it pairs with
- the tRNA attaches to the amino acid, and only the amino acid that matches tRNA molecules’ anti-codon will be able to match
- ensures the same mRNA sequence is always translated the same way (always makes the same protein)

Question 3

Describe the three stages of translation

Answer 3

Initiation: the ribosome, mRNA and the first rRNA come together to form the translation initiation complex
- the first tRNA always codes for methionine (AUG codon/UAC anti-codon)
Elongation: the ribosome moves along the mRNA, adding amino acids to the growing peptide chain
Termination: a ‘stop codon’ indicates that peptide chain has all the necessary amino acids and causes the translation complex to break apart
- releases the newly formed peptide chain (ready for protein folding and post-translational modification)

Question 4

Describe codons and redundancy

Answer 4

There are 64 possible codons
- four bases, 3 per codon 4 to the 3 = 64
There are 20 AA’s (plus ‘stop’)
Each amino acid can be coded for by multiple codons
- except methionine (Met) and tryptophan (Trp)
Known as codon redundancy
- allows for some flexibility in gene sequence, without changing the protein

Question 5

Describe genetic variation

Answer 5

• Genetic variation refers to the differences between the DNA sequences of members of the same species
  
  • humans are 0.1% different to each other at the DNA sequence level
  • whole diploid human genome is made up of 6 million base pairs
• Genetic variation is important in any species (to determine who is who, helps species survive, helps organisms adapt to their environment)
• genetic variant refers to a specific difference between individuals
  
  • in the sae location in the DNA, different forms of a variant are called alleles

Question 6

Describe the types of genetic variant

Answer 6

Genetic variants can be classified based on:
- number of DNA bases involved
- style of DNA sequence involved (repetition of DNA sequence vs. one-off differences)
- location of the change

In BIOC192 we will focus on single-base variants or small insertion/deletion variants found inside genes
- SNP: single nucleotide polymorphism, a single base change in the DNA sequence
- InDel: insertion-deletion, the addition or removal of one or more bases

Question 7

Describe the consequences of genetic variants

Answer 7

• Most variants are neutral (have no consequences)
• Variants in a regulatory region (non-coding variants) may change the expression of a gene (this changes the amount of protein that is produced)
• Variants within the exon of a gene (coding variants) may change the amino acid sequence, and potentially the function, of a protein
• Coding variants can have no, minor or major consequences

Question 8

Describe the specific types of consequences of genetic variants (name and what it does)

Answer 8

SNPs:
- Synonymous: altered codon specifies the same amino acid
- Missense: altered codon specifies one different amino acid
- Non-sense: altered codon specifies a translation stop signal (protein is too short)

InDel: usually has serious consequences for the protein
- Inframe insertion and Inframe deletion: Gain/loss of one amino acid. all codons after variant are read correctly
- Frame shift insertion or frame shift deletion: Frameshift causes all codons after the variant to be read incorrectly

Question 9

Describe the consequences of a missense genetic variant to the proteins function

Answer 9

The consequences depend on:
- where in the protein the amino acid change occurs (in an enzyme active site or receptor ligand binding site)
- how chemically similar/different the two amino acids are (ie. polar changed to polar or if polar charged changed to non-polar would be much worse)
- whether the amino acid breaks an essential structure (proline is a helix breaker so if that’s added to alpha helix that’s bad or if cysteine is removed from one side of the disulphide bond)
- the original function of the protein

Question 10

Describe the types of proteins affected from genetic variants

Answer 10

Genetic variants are found in every gene
- every type of protein can be affected by a genetic variant
Every type of protein can have any type of genetic variant
- leads to the wide variety of differences between organisms
- Variations causing complete loss of function to a protein essential for life will be lethal
(could be storage, catalysis, defence, transport, signalling, structure, growth/maintenance)

Question 11

Briefly explain what the sonsequences of a missense variant to an organism depend on

Answer 11

The consequences of a mis sense variant to an organism depend on:
- how important the protein’s job is
- whether another protein can compensate for the changed proteins function
- whether the protein lost its function or gained a new function

Question 12

describe the haemoglobin variants

Answer 12

Haemoglobin (beta subunit): most recorded variants are synonymous or missense changes
- HBB V55I - valine changes to isoleucine at AA 55 (no known consequences)
- HBB E6V - glutamate changes to valine at AA 6 (sickle cell anemia - ‘sticky’ Hb proteins clog blood vessels)
- HBB H64Y - histamine changes to tyrosine at AA 64 (methaemoglobinaemia - Fe3+, unable to bind oxygen)