L5: Translation 2 (Mutations)

Question 1

At what point is there the highest chance of the genomic DNA sequence being changed?

Answer 1

During DNA replication

Question 2

What can happen to the DNA sequence if it is altered?

Answer 2

The DNA sequence can be altered or permanently altered so the mutations are inherited into the next cell generation

Question 3

What can happen to the DNA nucleotides in mutation?

Answer 3

Normal nucleotides can undergo a proton shift, whereby a rare form of the nucleotides will be produced. This will impact the complementary base pairing between nucleotides

Question 4

What can happen to the DNA double helix if there are rare forms of the nucleotides (caused by mutations) binding with the normal nucleotides?

Answer 4

• Changes the distance between bases in the hydrogen bonding
• Changes the stability of the hydrogen bonding and will take up a different spatial place within the nucleus
• Can change the genomic DNA sequence

Question 5

What term is used to describe the reduction in stability of the DNA double helix?

Answer 5

Strand slippage caused by a wobble in the bases of the nucleotides

Question 6

How many mistakes will the DNA polymerase make, without the wobble?

Answer 6

A mistake approximately every 100 000 nucleotides

Question 7

How many mistakes would the DNA polymerase make for the human genome, with 6 billion base pairs in each diploid cell?

Answer 7

Amount to 120 000 mistakes every time a cell divides

Question 8

What does DNA polymerase do to prevent so many mistakes?

Answer 8

Has a proof reading ability
Fixes around 99% of errors

Question 9

What direction does DNA polymerase normally run in?

Answer 9

5’ to 3’ direction

Question 10

Which forms of DNA polymerase are able to run in the 3’ to 5’ direction and have exonuclease activity?

Answer 10

Gamma and delta polymerase

Question 11

Why is it so important that gamma polymerase has a proof reading ability?

Answer 11

Only one that functions in the mitochondria
Has to do both functions and still give a replicated daughter cell which has a high fidelity to the parent cell

Question 12

What term is used to describe corrections after replication?

Answer 12

Mismatch repairs

Question 13

Define a mismatch repair

Answer 13

When an incorrect nucleotide is added to the growing strand, replication is STALLED by the fact that the nucleotide’s exposed 3’-OH group is in the “wrong” position
Cannot form the 3’5’ phosphodiester bond

Question 14

Why does replication take 8 hours to complete?

Answer 14

DNA polymerase has to come in a fix any replication errors, like mismatch repairs, before it allows the cell to divide

Question 15

What happens to incorrectly paired nucleotides that still remain following mismatch repairs?

Answer 15

Become PERMANENT mutations after the next cell division. This is because once a mistake is established in the gene, the cell no longer recognises them as errors. Recognised as the parent

Question 16

When can these permanent mutations occur?

Answer 16

• When a rare mutation in the nucleotide base occurs, and these complementary base pair with a normal nucleotide base
• Wobble induced replication errors that can lead to strand slippage

Question 17

What two scenarios can occur if mutations from rare nucleotides occurs in the next cell division?

Answer 17

1) Newly synthesised DNA can loop out and remain there, with one nucleotide added to the new DNA strand - one extra nucleotide
2) The template strand can loop out and come back again, leading to the deletion of one base on the new strand - missing one nucleotide

Question 18

Key sentence to remember about changes in the genomic DNA through rare mutations

Answer 18

We can get permanent changes in the genomic DNA due to wobble induced replication errors that leads to strand slippage

Question 19

What is the space called between one gene and the next?

Answer 19

Upstream intergenic region
Intergenic means non-coding for a gene

Question 20

Where can permanent mutations arise which may have a detrimental effect arise on a gene?

Answer 20

Highlighted by the red arrows

Question 21

Where may mutations happen which will have limited effect on the outcome, or on a protein?

Answer 21

Highlighted by the green arrows
The non-coding or untranslated regions

Question 22

Where on a coding gene can mutations have a very large effect on the expression of a particular gene?

Answer 22

Promoter region and specific sites between the exons and introns

Question 23

Where in the promoter region can there be minimal effect on the expression of the gene, if mutation was to occur?

Answer 23

The intergenic regions between elements

Question 24

When is there a 100% chance that the mutation will affect the gene expression?

Answer 24

At the transcriptional start site

Question 25

What effect can mutations at the exon-intron borders have?

Answer 25

Prevent the snRNPs (small nuclear ribonucleoprotein particles) from binding to specific sequences between exons and introns, meaning the introns can not be removed, because the spliceosome cannot be formed. Effects gene expression

Question 26

What other ways can mutations occur in the genome, other than through errors in replication?

Answer 26

Physical damage to DNA

Question 27

What are the two forms of physical DNA damage?

Answer 27

1) Induced = environmental agents - exposure to chemicals or UV rays
2) Spontaneous = without exposure to environmental agents - spontaneous biochemical reactions taking place within the cell - wobble induced/replication errors

Question 28

What types of point mutations can occur?

Answer 28

• Point mutations- single base pair
• Substitutions - happen in 2 ways:
• Transitions = replace purine with a purine and pyrimidine with pyrimidine
• Transversions = replace a purine with a pyrimidine and vice versa

Question 29

How do point mutations occur?

Answer 29

Mainly due to wobble induced errors

Question 30

What 3 types of mutations can occur from substitution point mutations?

Answer 30

• Silent mutations = no change in the protein sequence
• Missense mutations= change the amino acid sequence - protein can still be deciphered
• Nonsense mutations = Introduces a stop codon to early - stop codon introduced to early and the peptide is too short, so does not function

Question 31

Example of a substitution point mutation, where guanine is changed to adenine on the RNA sequence

Answer 31

• Adenine remains as adenine on the RNA
• Code is degenerate so GAG and GAA both code for glutamine
• Change resulted in the same amino acid being produced
• Silent mutation
• Transition point mutation

Question 32

Example of a substitution point mutation, where thymine is changed to guanine on the DNA sequence

Answer 32

• Uracil is replaced with guanine on the RNA sequence
• This produces the UAG stop codon instead of tyrosine
• Translation stopped early as a release point is introduced, and meaning a very short peptide
• A nonsense mutation - cannot fold into a protein from the peptide chain - no function
• Transversion point mutation

Question 33

Example of a substitution point mutation, where cytosine is changed to adenine on the DNA sequence

Answer 33

• Instead of cytosine there is adenine on the RNA sequence
• This changes the amino acid from serine to arginine
• Missense mutation - small change in the polypeptide sequence
• Transversion point mutation

Question 34

How do you know if a missense mutation will have a big or small impact on the way the protein is folded, and therefore its resulting function?

Answer 34

• Have to look at the biochemical grouping
  e.g. Arginine is a basic amino acid and serine is nucleophilic
• However as basic amino acids are also nucleophilic the change here is less likely to affect the overall function and structure of the protein

Question 35

What other types of point mutations are there other than substitution?

Answer 35

Insertion and deletion
These can all be up to multiple bases

Question 36

What happens in a point deletion? Use the example

Answer 36

• The adenine is deleted
• This results in a sequence of RNA which is one base shorter than the parent coding strand
• Results in a frameshift missense mutation - the codon being read has moved up by one
• Resulting peptide is different

Question 37

What results from a point deletion mutation?

Answer 37

Frameshift missense mutation

Question 38

What happens in a point deletion mutation? Use the example

Answer 38

• The thymine is deleted from the termination sequence
• Sequence of RNA has to continue until another stop codon is met
• Known as an X frameshift causing EXTENSIVE missense
• The resulting protein will be completely different from what was to be made

Question 39

What happens in a point addition mutation? Use the example

Answer 39

• Guanine added to RNA sequence
• Caused a frameshift causing nonsense - X frameshift nonsense
• Introduced a stop codon to early resulting in a loss of function as the peptide is too short

Question 40

What happens if 3 bases are added or deleted after the position 1 or 2 of the bases?

Answer 40

• Cause a frameshift causing EXTENSIVE missense or frameshift nonsense
• Profound effect on the protein

Question 41

What happens if 3 bases are added or deleted after position 3 of the bases?

Answer 41

• No frameshift causing missense
• No frameshift causing nonsense
• Just missense or nonsense
• Simply a codon straight after another codon - just adds another amino acid

Question 42

What is the rule for when frameshift occurs when adding or deleting bases in a coding gene?

Answer 42

• If the position is a multiple of 3 and goes in after a position 3 base it will have an effect dependent on how large the sequence of addition or deletion is.
• This will not cause a frameshift

Question 43

When can there be a greater exchange of information that may change the parental DNA that’s going from one cell generation to the next?

Answer 43

• Metaphase
• Chromatids come together and recombination occurs
• Lead to a change in the genetic information going from one cell generation to the next

Question 44

What are the two types of missense mutation?

Answer 44

Conservative changes
Non-conservative changes

Question 45

What is conservative missense change?

Answer 45

• Result in the substitution of similar (similar biochemical family) but not identical amino acids
• e.g. glutamate (acidic) being substituted for aspartate (acidic)

Question 46

What is a non-conservative missense change?

Answer 46

• Result in the substitution of a different amino acid with different biochemical properties
• e.g. glutamate (acidic) being substituted for valine (hydrophobic)

Question 47

How does location affect a mutation?

Answer 47

Depending on the location, this can affect the functional consequences of the mutation, whether it has a large or small effect, or no effect at all