SAQ 2018

Question 1

For each of the following components of the human genome provide a definition and one function

a) Heterochromatin
b) 5’UTR
c) Start codon
d) Intergenic regions
e) mtDNA

Answer 1

Heterochromatin

• Chromatin that is highly condensed and shows little/no evidence of active gene expression
• When located at centromeres important for correct chromosomal segregation

5’UTR

• The 5’ untranslated region is the region between the transcriptional and translational start sites
• Contain elements that may be bound by trans-acting factors and that regulate translation

Start codon

• The three base pairs that results in the initiation of ribosome translation
• Necessary for protein production

Intergenic regions

• Regions of the genome that do not encode protein-coding genes
• Involved in regulation of gene expression

mtDNA

• Mitochondrial DNA
• The mitochondrial genome encodes genes necessary for optimal mitochondrial function

Question 2

For each of the process below, describe briefly what is involved and what the starting material and product of the process is

a. Replication
b. Transcription
c. Splicing

Answer 2

replication
DNA template strand is unwound
copied by DNA polymerase in opposite directions, either continuously from leading strand or discontinuously using Okazaki fragments from the lagging strand, to produce an identical copy of double stranded DNA

transcription
RNA polymerase makes primary RNA transcript (pre-mRNA or heteronuclear RNA; hnRNA from the template DNA strand

splicing
Spliceosomal proteins bind to the pre-mRNA template
The intron is removed in the form of a lariat and the two exons are ligated to make a mature mRNA

Question 3

What is epigenetics and give two examples of epigenetic modifications

Answer 3

The reversible regulation of gene expression mediated principally through changes in DNA methylation and chromatin structure, occurring independently of the DNA sequence

• Histone modification
• CpG methylation of DNA

Question 4

What are the 5 stages of mitosis and what is happening within the cell at each stage?

Answer 4

Prophase
condensation of chromosomes occurs, spindle is formed, nuclear envelope and organelles disappear
Metaphase
chromosomes connect to spindle fibres and align on metaphase plate in centre of cell
Anaphase
centromeres split and chromosomes separate. Chromosomes move to opposite poles of cell
Telophase
chromosomes form clusters at opposite poles of cell. Nuclear envelope and organelles reform
Cytokinesis
cytoplasm divides into 2 parts following furrowing of plasma membrane. Cells divide, gain separate membranes and become independent

Question 5

Describe the process of Nonsense-mediated Decay (NMD) and indicate the events that are happening at each step

Answer 5

• The Exon Junction Complex (EJC) is deposited at the sites where splicing has occurred
• The UPF1, UPF2 and UPF3 proteins bind to the EJC
• The translation release factors associate with the ribosome at the site of premature termination
• The release factors interact with UPF1
• The mRNA is decapped, deadenylated and degraded

Question 6

Describe what a genome-wide association study is, how and when they are performed and one strength and one limitation of the approach

Answer 6

Genome wide association studies are hypothesis free methods to identify associations between genetic regions (loci) and traits (including diseases)

used to identify genetic variants that contribute to polygenic disease

performed by comprehensively scanning the genome using a SNP chip with 100’s of thousands of markers or through sequencing in large-numbers of patients

“hypothesis-free” so new biology, small effects sizes, not pinpointing the gene because of LD

Question 7

Whole exome and whole genome sequencing is increasingly being used to find the genetic basis of undiagnosed disease. Findings from these studies are classified as primary and secondary (incidental) findings

a) Describe what primary and a secondary findings are in this context
b) The American College of Medical Genetics (ACMG) have recently updated their list of secondary findings recommended for clinical action. What three characteristics do most of the hereditary disorders on this list share

Answer 7

a) Primary findings are those that are being sought as the primary target of testing, identification of a genetic change that is causing the disease being investigated

Secondary findings are findings which have been found incidentally – a mutation that could cause a disease unrelated that being investigated.

b)
a. Life threatening
b. Not readily diagnosable before the onset of symptoms
c. Preventable/treatable

Question 8

Describe the process of DNA replication

Answer 8

DNA helicase unwinds the DNA template

Single-stranded binding proteins stabilise the unwound DNA

The leading strand is synthesised in the 5’ to 3’ direction by DNA polymerase

RNA primase which adds an RNA primer, which is then extended by DNA polymerase to form an Okasaki fragment

DNA ligase joins the Okasaki fragments to make a continuous strand

Question 9

Protein production, both the amount and nature, is controlled solely at the level of transcription. Why is this statement incorrect? Give mechanisms that support your answer

Answer 9

The prevalence of alternative splicing means that the nature of the proteins produced is controlled a lot at the level of splicing, not transcription

Regulation at the level of translation can be important for cellular responses that need to be very quick.

Regulation of transcript levels by miRNAs or other RNA-binding proteins

Post-translational modification may alter the final protein