Sequence alteration at the gene level: mutations and polymorphisms

Question 1

What is the structure of a eukaryotic gene?

Answer 1

Promotor
Exon 1
Intron 1 
Exon 2
Intron 2
Exon 3
etc

Question 2

Where is the transcription start site?

Answer 2

Upstream of exon 1 and goes through the last exon

Question 3

What do RNA processing enzymes do?

Answer 3

Trim the 3’ end of primary transcript, removing introns and splice together the exons to give mRNA which codes for the protein.

Question 4

What are some post-transcriptional processing?

Answer 4

Poly A tail added to 3’ end
7mG cap added to 5’ end

90% of transcript removed leaving about 10-20 exons per gene

Question 5

What is the number of base pairs in the haploid human genome and what is the total number of genes?

Answer 5

3x10^9 = haploid number

~22,000 genes

Question 6

How do gene mutations arise?

Answer 6

Copying errors during DNA replication.
Spontaneous depurination.
Exposure to background ionising radiation.

Question 7

What happens to a deaminated cytosine?

Answer 7

This causes a C=G to become a U=A

Question 8

What happens to a depurinated adenine?

Answer 8

This causes an A=T to become a C=G

Question 9

What is a non-synonymous mutation?

Answer 9

Alters the protein produce by altering the base.

Question 10

What will a frameshift mutation occur in?

Answer 10

This will result in a termination codon (TAA, TAG, TGA) downstream of the insertion or deletion.

Question 11

What is the consequence of a truncated mutation?

Answer 11

We would expect a reduction in protein coded for by a certain gene as shown by a western blot

Question 12

What causes sickle cell anaemia?

Answer 12

Single base change:

GAG –> GTG

Question 13

What causes cystic fibrosis?

Answer 13

Deletion of a phenylalanine residue (D508)

Question 14

What are transcriptional mutations?

Answer 14

Mutation affects the promotor region of the gene

Question 15

What effect would abolition of a splice site have?

Answer 15

can lead to insertion of intron sequence into mRNA resulting in a non-functioning protein

Question 16

What effect would the creation of a new splice site have?

Answer 16

May lead to insertion of intron sequence resulting in truncation of the protein.

Question 17

What are some larger mutations?

Answer 17

Loss of complete exons - leads to loss of protein function

large intron insertions - leads to loss of protein function

Chromosomal mutations - additional chromosomes (T21) or chromosome deletions

Question 18

What is mismatch repair?

Answer 18

Proof reading system which detects slippages during replication of repeated nucleotides.

Able to inserted accidentally removed bases

Question 19

What are satellites in the genome and how do they form?

Answer 19

large arrays of tandemly repeating, non-coding DNA

Smaller repeats are microsatellites

formed by slippage mutations

Question 20

What is microsatellite instability (MSI)?

Answer 20

Laboratory marker for a defect in mismatch repair.

The detection of MSI in tumour DNA is indicative of genetic instability resulting from mutation of DNA mismatch repair gene

Question 21

What are DNA sequence polymorphisms?

Answer 21

single base changes that may arise as inherited or de novo sequence changes.
There are ~10 million SNPs, one every 300 bases

Question 22

What effect may SNPs have on the body?

Answer 22

Some may influence responses to treatments of therapeutic toxicity.

May also be modifiers of breast cancer risk

Question 23

What are triplet repeat mutations?

Answer 23

Expansion of 3 amino acids.
Low numbers is harmless however when the expansions are in large numbers this can cause disease such as Huntingtons disease (CAG)

Question 24

what is the copy number variants?

Answer 24

CNVs
Variation in number of deleted or duplicated versions of
segments of the genome that result in a range of the number of copies among individuals.

Question 25

What is the cancer genome project?

Answer 25

All cancers occur due to DNA abnormalities

cancer genome project uses the human genome sequence and high throughput mutation detection techniques to identify somatically acquired sequence variants/mutations and hence identify genes critical in the development of human cancers.

Question 26

What are the main 6 types of mutation?

Answer 26

A)Missense-1 bp change= 1AA
B)Nonsense-1bp= inappropriate stop codon
C)Frameshift-Insertion/deletion of 1-2 bps
D)Transcriptional-affects gene promoter
E)Abolishing splice sites
F)Creation of new splice sites-may lead to insertion of an intron

Question 27

What are the main larger mutations?

Answer 27

a .Loss of complete exons

Leads to loss of protein function

b. Large intron insertions

Leads to loss of protein function

c. Chromosomal mutations

Additional chromosomes T21
Chromosome deletions

Question 28

what is the main oncogene mutated in cancer?

Answer 28

Ras oncogene mutated in 30% of cancers.

Question 29

How does the ras oncogene get mutated?

Answer 29

mutation of glycine to valine in exon 12 leading to the deregulation of proliferative signalling

Question 30

What is the process of normal epithelia turning into malignant cancer?

Answer 30

Normal epithelia
mutation in APC
Proliferative epithelia
k ras mutation
adenoma
p53 problems as a result of C18 allele loss
carcinoma 
metastatic cancer