Nuclear Genome

Question 1

Approximately what percentage of human genes code for more than one protein?

Answer 1

60%

Question 2

What allows one gene to code for more than one protein?

Answer 2

Differences due to alternative splicing: different exons are used in different kinds of cell

Question 3

Different products of a gene have related but not identical functions; can be specific to a particular tissue or developmental stage. Give an example of this

Answer 3

The gene for alpha-tropomyosin, which:
.Helps to regulate muscle contraction
. Stabilises actin filaments in the cytoskeleton

Question 4

Different types of muscle and non-muscle cells have different forms of tropomyosin. There are at least 8 different tropomyosin mRNAs. How are they different?

Answer 4

Different by mixing up exons, can mean they are terminated in a different place/ substitute one exon for another

Question 5

Introns can contribute to variation in gene size. Give an example of this:

Answer 5

The Huntington gene in humans and Pufferfish. Gene codes for a very large protein (3143 amino acids in humans, 3148 amino acids in pufferfish) found in the brain. In humans mutations cause Huntington’s.
In both species they have 67 exons, so 66 introns but the introns are larger in humans

Question 6

What is repetitive DNA?

Answer 6

DNA that occurs in many copies (generally similar, not identical, to one another) in the genome

Question 7

Give an example of a very simple tandem repeat

Answer 7

AAGAG/AAGAG/AAGAG… in Drosophila melanogaster; this repeat makes up about 6% of the genome

Question 8

What do tandem repeats/ simple sequence repeats contribute to?

Answer 8

Contribute to the organisation of chromosome structure, including centromeres, telomeres

Question 9

Give an example of a tandem repeat that contributes to organisation of chromosome structure, including centromeres, telomeres

Answer 9

Alpha satellite (density of the DNA is different characteristic base composition) DNA: 171bp sequence repeated thousands of times (imperfectly) at centromeres of all human chromosomes. Make up at least 5%of human genome

Question 10

Much of repetitive DNA consists of mobile DNA elements (transposons). What are these?

Answer 10

. Essentially ‘molecular parasites’
. Can be duplicated and transpose/ move into new regions of the genome into new sits in the genome- very slowly (because it may cause mutation) 1 copy, then 2, then 3

Question 11

What are the major classes of transposons in the human genome?

Answer 11

. LINES: long interspersed element = 6kbp

. SINES: short interspersed elements = 100-400

Question 12

What is the mechanism of transposition?

Answer 12

LINES, SINES and retro viral-like elements all transpose via an RNA intermediate (DNA -> RNA -> DNA). The RNA is copies to DNA by reverse transcription (RNA binding protein, reverse transcriptase) then the DNA will insert itself into the genome

Question 13

What do LINES code for?

Answer 13

Code for enzymes requires for transposition. (RNA binding protein, reverse transcriptase). However, <100 out of >500,000 in the genome are active. Estimated current transposition rate in humans: 1 insertion for every 20 to 200 births

Question 14

Why are SINE elements controlled by LINE elements?

Answer 14

Because they are non-autonomous (they can’t transpose themselves): transposition depends on LINE elements (can transpose them), so SINE elements are controlled by the LINE elements.

Question 15

Describe Alu elements

Answer 15

Make up about 10% of human DNA. They are about 300 bp long- members of the SINE class. There are >1 million Alu elements in the human genome; any region of 5kbp is likely to have one

Question 16

Where did the alpha and beta subunits in haemoglobin diverge from?

Answer 16

From the original 1 about 500 million years ago (the genes for the whole and beta subunits are at different loci. Each locus has several genes)

Question 17

Describe the human beta-globin cluster

Answer 17

5 gene splus 1 non-functional pseudogene, spread over about 50 kbp

Question 18

How did the beta-globin cluster form?

Answer 18

Revolves by gene duplication, followed by change or loss of function

Question 19

What is the LINEs and SINEs arrangement in the beta-globin cluster in human and mice?

Answer 19

. Similar arrangement of genes

. Different arrangment of SINEs and LINEs

Question 20

Describe the yeast genome

Answer 20

Is compact:
. Approx 4% repetitive DNA
. Average of 2kbp per gene
. Almost 70% of genome consists of open reading frames
. Little spears between genes
. 96% of genes have no introns
. Remaining genes usually have only one intron

Question 21

Describe he human genome

Answer 21

. Less than 2% of the human genome codes for proteins
. >50% repetitive DNA
. Average of one gene per about every 90kb
. Genes commonly have multiple introns, which in many genes are longer than the exons
. The average primary transcript is about 30kb but the average coding sequence is about 1.4kb. Most of the human genome is transcribed; functions of many transcripts are unknown

Question 22

What is synteny?

Answer 22

Comparison of genomes of different organisms shows that the order of genes in chromosomes is partly conserved through evolution.
Comparison of whole chromosomes can show extensive conserved blocks, especially in relatively closely related organisms (e.g. humans and mice). Conservation can even be detected even between pufferfish and humans (corresponding large fragments of chromosome 2 of both species)

Question 23

Give the essential concepts of eukaryotic genomes

Answer 23

. Eukaryotic genomes are large and variable in size
. Number of genes varies less than genome size
. Variability comes from: introns and intervenor (including repetitive DNA)
. Alternative splicing can give >1 gene product per gene
. Order of genes is partly conserved among related organisms

Question 24

How many chromosomes do humans have?

Answer 24

46

Question 25

Describe a chromosome

Answer 25

Contains a single DNA molecule complexes with proteins to form chromatin

Question 26

Proximately how long is DNA in a human cell?

Answer 26

2m

Question 27

Give the essential sequences in chromosomes

Answer 27

1. Multiple replication origins, typically 30,000 to 250,000 bases apart
2. Because DNA is linear, ends must be protected: ends are telomeres, defined by specific repetitive DNA sequences to which specific proteins attach
3. Specific repetitive DNA sequences with specific proteins attached also define the centromeres, where sister chromatids are held together and then pulled apart during mitosis

Question 28

Describe nucleosomes

Answer 28

The nucleosome is the basic building block of chromatin:
. 8polypeptides: 2 copies each of his tones H2A, H2B, H3, H4 (positively charged)
. DNA forms 2 loops around the histones

Question 29

What is the standard for further levels of packaging DNA?

Answer 29

View has been that nucleosomes are packed by Huston’s H1 into 30nm fibres. However, recent evidence indicates that “chromatin is a flexible and disordered 5-to -24nm diameter granular chain that is packed together at different concentration densities in interphase nuclei and mitotic chromosomes”

Question 30

Describe further packaging of DNA

Answer 30

Most popular model suggests that chromosome is folded up into loops attached to central scaffold (which is protein in nature). DNA is probably attached to the scaffold via specific DNA sequences

Question 31

During mitosis and meiosis how are chromosomes densely packed together?

Answer 31

By further coiling of the chromosome scaffold