Module 2.1 - The genome

Question 1

What is a genome?

Answer 1

The totality of genetic information belonging to a cell or an organism: in particular, the DNA that carries this information or the entire complement of genetic material in a chromosome set

Question 2

What is meant by the C-paradox?

Answer 2

The lack of correlation between the total amount of DNA (C-value = genome size in kilobases) in a genome and the complexity of an organism

Question 3

What is a gene?

Answer 3

Region of DNA that is transcribed as a single unit and carries information for a discrete hereditary characteristic. Usually corresponds to: a single protein (i.e. polypeptide), a single functional RNA (e.g. ribosomal RNA, transfer RNA)

Question 4

What is a Polycistronic gene?

Answer 4

can produce more than one protein from a single gene (mainly found in prokaryotes) (lac operon example)

Question 5

What are exons?

Answer 5

(expressed sequences) - are the parts of a gene that are present in the final, mature RNA form

Question 6

What are introns?

Answer 6

(intervening sequences) - the parts of a gene that are removed by splicing.
mRNA is entirely composed of exons

Question 7

What is the 5’UTR?

Answer 7

region of mRNA before the start codon

Question 8

What is the 3’UTR?

Answer 8

region of mRNA after the stop codon

Question 9

Tandem repeats

Answer 9

repeated end-to-end copies of a short DNA sequence which are all next to each other, are found in non-coding DNA

Question 10

Transposons

Answer 10

also known as “jumping genes”, are parasitic DNA sequences that can move around within a genome - found interspersed throughout the genome. Diseases like haemophilia and muscular dystrophy caused by transposons.

Question 11

Microsatellites

Answer 11

tandem repeats of very short (i.e. 1-6 bp) DNA sequence total array size ~ 10-150 bp

Question 12

Minisatellites

Answer 12

also known as short tandem repeats (STRs) tandem repeats of short (i.e. 7-100 bp) DNA sequence total array size ~ 100 bp -20,000 bp

Question 13

What is conservative transposition?

Answer 13

(cut and paste) the transposon is excised from its original position (often leaving a characteristic mark) and inserted at a new location. DNA transposons move conservatively.

Question 14

What is replicative transposition?

Answer 14

(copy and paste) the transposon inserts at a new location but the original copy remains. Retrotransposons move replicatively.

Question 15

ITR

Answer 15

Inverted terminal repeat - palindromic sequence involved in movement

Question 16

TSD

Answer 16

Target site duplication - genomic sequence duplicated during insertion

Question 17

Transposase

Answer 17

an enzyme involved in the movement of a DNA transposon

Question 18

How do DNA transposons move?

Answer 18

1. The transposase gene is transcribed and translated to make the transposase protein
2. transposase enzyme binds to ITRs
3. The transposase enzyme catalyses the excision of the transposon from its original site
4. It then moves to another part of the genome
5. The transposase enzyme catalyses the insertion of the transposon into a new site

Question 19

How many Alu elements are in the human genome?

Answer 19

> 1 million

Question 20

How many L1 elements are in the human genome?

Answer 20

516,000

Question 21

How do retrotransposons move?

Answer 21

1. retrotransposon is transcribed
2. translation creates reverse transcriptase
3. reverse transcriptase synthesises reverse strand (in DNA) using RNA as a template
4. 2nd DNA strand is produced
5. retrotransposon inserts into new chromosomal position

Question 22

What is chromatin?

Answer 22

a complex of DNA and protein found in eukaryotic cells. The primary function is to package long DNA molecules into more compact, denser structures. consists of 33% DNA and 66% protein. The ‘beads’ are called nucleosomes. They represent DNA wrapped around an octamer of Histone proteins.

Question 23

Describe the ionic bond between histones and DNA

Answer 23

Histones are positively charged (>20% Lysines and Arginines) and DNA is negatively charged due to the phosphate groups which help DNA and histones bind very tightly

Question 24

Euchromatin

Answer 24

is open and accessible to other molecules e.g. for transcription

Question 25

heterochromatin

Answer 25

is highly compacted - and generally not transcribed. It is found in some regions of the chromosome like the centromeres and telomeres where there are few genes (structural elements) and where genes have been silenced.

Question 26

What does histone acetylation do?

Answer 26

changes the charge on the lysine residues which makes them less positive and DNA wraps around less tightly. Associated with active gene expression.

Question 27

H3K9me

Answer 27

- inactive locus - constitutive heterochromatin (a part of the chromosome that is always heterochromatin) - broad regions

Question 28

H3K4me

Answer 28

- active locus (gene expression) - euchromatin - found near promoter

Question 29

H3K27me

Answer 29

- inactive locus - facultative heterochromatin (can switch between open and condensed states to regulate genes) - spread over genes

Question 30

Telomeres

Answer 30

protective cap on the ends of linear chromosomes (must be maintained/extended after replication)

Question 31

Centromeres

Answer 31

point of attachment of microtubules during mitosis (microtubules attach to the centromeres during mitosis to separate the chromatids)

Question 32

Origins of replication

Answer 32

regions where DNA replication is initiated (replication begins at multiple origins of replication)

Question 33

Origin of replication

Answer 33

a location on a chromosome where DNA replication on each linear chromosome. AT-rich (easier to separate the two DNA strands, AT bonds are only 2 hydrogen bonds compared to 3 between C and G, therefore are easier to break). Enriched for H4K20me2 (binding site for ORC).

Question 34

Describe DNA replication initiation in eukaryotes

Answer 34

1. The ORC (origin recognition complex) binds to the origin 2. A DNA helicase then binds, to complete the pre-replicative complex. 3. S-Cdk phosphorylates many targets associated with DNA synthesis (ORC and helicase) 4. When helicase is phosphorylated it becomes active and can start its job unwinding the DNA. ORC is deactivated until the next cell cycle so that it doesn't recruit more helicase and the DNA molecule isn't copied several times over

Question 35

Explain why the DNA replication mechanism results in single-stranded overhangs, and why this can result in chromosomes becoming shorter with each cell division

Answer 35

The leading strand can be replicated right to the end but on the lagging strand the last part of the chromosome (where the final RNA-primer was placed) cannot be replicated with DNA. Exonucleases will remove this single-stranded overhang. Therefore after each cell cycle chromosomes will be shortened. This process is opposed by telomeres and telomerase.

Question 36

Telomere

Answer 36

A protective structure at both ends of a linear chromosome, consisting of a tandem repeat of the sequence GGGTTA and associated protein which serves to maintain the integrity of chromosomes. Chromosomes lacking telomeres are unstable and may be susceptible to chromosomal rearrangements such as fusion

Question 37

Telomerase

Answer 37

A ribonucleoprotein (i.e. protein and RNA) that elongates telomere sequences.

Question 38

What are the two key aspects of telomerase

Answer 38

The RNA portion of Telomerase has the sequence CUAACCCUAAC which is complementary to the telomere repeat. The telomerase also has a protein component (called TERT), which has reverse transcriptase activity

Question 39

How does telomerase function?

Answer 39

1. The telomerase extends the 3' end of the overhanging strand (doesn't fill in the existing gap) 2. Telomerase binds to the 3' end of the telomere that is complementary to the telomerase RNA 3. Bases are added by the TERT reverse transcriptase, using the RNA as a template 4. the telomerase relocates 5. DNA polymerase then complements the lagging strand

Question 40

Centromere

Answer 40

the heterochromatic region of a chromosome which joins sister chromatids during mitosis. It is the region to which microtubules attach, via the kinetochore

Question 41

Histone modification

Answer 41

CENP-A are specific to centromeres (H3 variant) and alternates with normal H3 histones. Cohesin is dissolved at anaphase.

Question 42

Acrocentric chromosome

Answer 42

a chromosome in which the centromere is located close to the end of the chromosome

Question 43

Robertsonian translocations

Answer 43

Two chromosomes joining at the centromere region (can lead to non-disjunction)

Question 44

Transcription

Answer 44

copying one strand of DNA into a complementary RNA sequence by the enzyme RNA polymerase

Question 45

RNA polymerase

Answer 45

enzyme that catalyses the synthesis of an RNA molecule on a DNA template from ribonucleoside triphosphate precursors

Question 46

What does RNA pol I transcribe?

Answer 46

Ribosomal RNA

Question 47

What does RNA pol II transcribe?

Answer 47

messenger RNA

Question 48

What does RNA pol III transcribe?

Answer 48

transfer RNA

Question 49

How does transcription begin in eukaryotes?

Answer 49

Eukaryotic promoters have a key recognition region called the TATA box which is A/T rich. Transcription begins when the TFIID binds to the TATA box via one of its components, the TBP (TATA binding protein). The TFIID complex also has 11 other proteins called TAFs (YBP-Associated Factor)