Structure and function of the Human Genome

Question 1

What are the 4 types of chromosomes?

Answer 1

Telocentric is not found in humans

Question 2

What is a nucelosome?

Answer 2

• DNA double helix binds to histones
• Octamer of histones form nucleosome
• H1 stabiilises this structure
• Histone tails have many + aa side chains which interact with - charged phosphates of the DNA helix. This electrostatic attraction constrains the DNA to wrap around the histone octamers.

Question 3

What is the difference between euchromatin and heterochromatin?

Answer 3

Euchromatin: Allows gene expression due to loosely compact nucleosomes

Heterochormatin: Highly condensed and wound tightly around the histone, genes not expressed

Euchromatin also stains differently to heterochromatin which gives rise to diff banding patterns

Question 4

What are centromeres and what is their function?

Answer 4

• Rich in heterochromatin
• Normally is a highly repetitive DNA sequence- characteristic of non geneic sequences
• Keep sister chromatids together
• Attach to microtubules during cell division

Question 5

What is the function of telomeres?

Answer 5

Protect the ends of the chromosome

Telomerase repairs telomeres but is only active in certain cell types

If telomerase is switched on in the wrong cells this can lead to cancer

Question 6

What is the nuclear genome and exome?

Answer 6

All the genetic material in a cell. 22 pairs of autosomes and pair of sex chromosomes. The actual DNA sequence and the transcribed units (genes) within the DNA. These are involved in:

• •Protein coding
• •RNA-only coding (non-coding transcripts; make RNA but not protein)

exome: just the parts of the genome which code for protein, i.e. all the coding exons

Question 7

Give definitions for: Exons, utr, introns, Promoter region

Answer 7

Exons: code for amino acids except for Untranslated Regions (5’UTR & 3’UTR)

UTR: contain regulatory elements (important for control of p.synthesis). Don’t code for any aa.

Introns: non-coding gene regions between exons

Promoter region: 5’ of gene; contains important regulatory elements for transcription

Question 8

What is mitochondrial genome?

Answer 8

Question 9

What is the epigenome?

Answer 9

Chemical compounds that attach to DNA or histones and can affect gene activity and expression E.g. DNA methylation, histone acetylation. How do they affect gene activity?

• Alter chromatin structure, recruit histone modifiers
• Repress transcription
• Responds to environmental cues (cellular and external)

Question 10

What are the different types of gene expression?

Answer 10

This is due to differential gene expression:

In time (temporal)

• Development (i.e. embryos versus adults a different set of genes need to be active)
• In response to hormones, infection, other signals

Spatially

• Diff tissues/cells express different genes (e.g. brain vs liver)

Question 11

Failure to regulate gene expression tightly may lead to…

Answer 11

Question 12

What is meant by the term central dogma?

Answer 12

You will always go from DNA to RNA to protein and never the other way round

Question 13

What is sense and antisense?

Answer 13

The sense strand has the same sequence as the mRNA molecule

The opposite, antisense strand is used as the template to generate this identical mRNA strand

This is important to make sure that the aa sequence is correct

Question 14

Describe transcription

Answer 14

DNA helicase unzips the DNA
RNA polymerase attaches to a non coding region in front of a gene.
Free RNA molecules form complimentary base pairs w/ DNA strand.
RNA polymerase joins nucleotides juntos to make mRNA
mRNA leaves the nucleus via a pore

Question 15

What is pre mRNA and what happens to it?

Answer 15

The molecule that’s directly made by transcription in a eukaryotic cell is pre-mRNA. To mature, necesita undergo:

Addition of a 5’ cap to the beginning of the RNA

Addition of a poly-A tail (tail of A nucleotides) to the end of the RNA

Chopping out of introns and pasting together remaining exons

Question 16

Describe the 5’ cap, the poly-A-tail and splicing process

Answer 16

The 5’ cap is added to the 1st nucleotide in transcription. The cap is a modified G nucleotide. It protects 5’ end from degradation, facilitates transport into cytoplasm

A polyadenylation signal in RNA during transcription causes an enzyme to half the RNA. Polyadenylation polymerase adds 50-200 A nucleotides to the cut end, forming a poly-A tail. The tail protects the 3’ end.

Finally hay intron removal and splicing juntos of exons

Question 17

What is the triplet code?

Answer 17

• RNA “read” in threes = codons
• 64 possible combinations of 4 bases
• Codon → specific amino acid
• 20 amino acids
• Degenerate = >1 codon can code for same amino acid

Question 18

What is meant by open reading frame?

Answer 18

Question 19

How is translation initiated?

Answer 19

The ribosomal binding site in the 5’ UTR is recognised. This binds to comp RNA in the small subunit of the ribosome.

Once that binds, initiator tRNA will look for AUG. This codes for methionine- the aa which starts every protein sequence.

Once that first tRNA molecule has bound to the start codon, the small and large ribosome subunit bind juntos

Question 20

Describe the next part of translation after initiation

Answer 20

So you have the full ribosome complex. This creates three sites: exit site, peptidyl site, aminoacyl site.

The 1st tRNA is in the peptidyl site. tRNA carries its attached aa residue and comes into the aminoacyl site. The bond between the tRNA and its aa in the peptidyl site breaks, a new bond forms between the tRNA and the a.acyl site. The same happens again, but this time the tRNA comes into the exit site.

This chain continues til a stop codon. A release factor triggers the end of translation, the release of the peptidyl chain, and the disassociation of the ribosomal complex.

Question 21

What is the cell cycle?

Answer 21

• G1 = Cell makes a variety of proteins needed for DNA replication
• S = synthesis; chromosomes are replicated so that each chromosome now consists of two sister, identical chromatids
• G2 – synthesis of proteins especially microtubules
• Some cells don’t replicate; some are senescent.
• Transcription and translation occurs throughout interphase

Question 22

What is mutation/variant?

Answer 22

Mutation/variant: a change in the genetic material

A pathogenic mutation (pathogenic variant) results in an alteration of the function of the gene product and can cause a disease phenotype

Question 23

What are the types of variants?

Answer 23

Question 24

Differentiate between synonymous and non synonymous variants

Answer 24

Synonymous base substitution: silent mutation

Non synonymous is categorised into missense and nonsense:

• Missense: substitution causes a change in the aa type produced. Effects are difficult to predict
• Nonsense: substitution introduces a premature stop codon.

Question 25

Indels can be…

Answer 25

In-frame (if the bases inserted/deleted are multiple of three) or frameshift (not multiple of three)

Question 26

How can variants cause loss of function?

Answer 26

• Variants reduce activity/decrease stability = hypomorph
• Variants which cause complete loss of gene product = null allele/amorph

Eg sickle cell, CF etc. These are recessive, so often 1 healthy copy of gene is sufficient to produce enough protein for a sub clinical individual

Dominant loss of function: Haploinsufficiency (loss of 1 allele is sufficient to cause problem). Full amount of protein product is required, if not disease occurs. Eg MonoMac syndrome, Marfan syndrome

Question 27

How can variants cause gain of function?

Answer 27

Mutant allele produces a mutant protein which is damaging (upregulated or different role). Mostly in dominant diseases

eg Achondroplasia (gain of function mutation in FGFR3 leads to decreased bone mass by altered regulation of osteoblast/clast activity). Due to overactive protein

Question 28

What is a dominant negative variant?

Answer 28

Protein produced by mutant allele interferes with role of wildtype (normal) allele. Examples:

• Mutation in transcription factor removes activation domain but still contains DNA binding domain. So it can bind to the DNA, but can’t trigger transcription; blocks wildtype from binding
• Mutation in a dimer protein means it lacks function but can still dimerise with wildtype protein. However the resulting dimer is non-functional (eg sodium channels)

Question 29

What is the difference between germline and somatic mutations?

Answer 29

Germline affects the gametes, so can be inherited and passed down through generations.

Somatic only affects non-germline cells so cannot be passed down: only affects that individual, not the gametes

Mosaic mutations can affect germline and somatic cells so still have the possibility to be passed down.