Lecture 1 Organisation of the Human Genome

Question 1

What are the different types of DNA?

Answer 1

Nuclear, mitochondrial, bacterial and viral

Question 2

What are the dimensions of nuclear DNA?

Answer 2

10bp per turn, with 3.4 nm per turn and 2.37 diameter

Question 3

How many genomes are present in a cell?

Answer 3

2 genomes

Question 4

How many base pairs are there in the nuclear genome and corresponding genes?

Answer 4

3 x 10^9, (3-3.3 billion) corresponding to 30,000-20,000 genes

Question 5

How much does mitochondrial DNA account for in the genome?

Answer 5

0.001%

Question 6

How many base pairs are there in the mitochondrial genome? How many genes and how many proteins?

Answer 6

16,569 bp,
37 genes
13 involved in respiratory chain (protein coding)
24 non-coding RNAs (2 rRNAs, 22 tRNAs

Question 7

Does the mitochondrial genome contain introns?

Answer 7

No

Question 8

What is a karyotype?

Answer 8

The characteristic number and size of chromosomes examined through staining chromosomes during metaphase.

Question 9

What is the composition of the human genome?

Answer 9

3200 Mb, 2000Mb is intergenic, 1200 is gene relates sequences.

Question 10

What are LINES?

Answer 10

Long INterspersed repeat Elements;
6-8kb in length, can copy themselves into the genome. They encode proteins required for their integration into the genome: 3 Line families (LIINE1/2/3) however only LINE1 is transcriptionally active.

Question 11

What are SINES?

Answer 11

Repeat elements shorter than 6kb in length that have lost the ability for retrotransposition.

Question 12

What are the SINE families?

Answer 12

ALUs and MIRs; only ALUs are active.

Question 13

Can ALUs be found throughout the animal kingdom?

Answer 13

No, they are only present in primates, with 1 approx every 3 kb. They also have their own subfamilies and are over 80 million years old - molecular clocks

Question 14

What percentage of the human genome is transposable?

Answer 14

Approx 50%; however they do not move much anymore

Question 15

What are LTRs?

Answer 15

Long Terminal Repeat elements, related to viruses. Originate from retrotransposons, related to retroviruses

Question 16

What percentage of the genome is composed of retroviral insertions?

Answer 16

8.3%

Question 17

What are microsatellites?

Answer 17

Short sequence (1-15bp) repeated in tandem many times (2-50). Dinucleotide repeats are the most frequent (unineucleotide repeats are found). Most common is 3-4 bp repeats.

Question 18

How do microsatellites affect genomic complexity?

Answer 18

The reduce the complexity (ACACACACAC or GGGGGGG) for example.
They are prone to expansion and contraction during replication due to polymerase slippage.

Question 19

Can microsatellite sequences be found in coding sequences?

Answer 19

Yes, but not very often, 3bp in length if found.

Question 20

What are the major classes of RNA sequences that do not contain open reading frames?

Answer 20

tRNA (25% in cluster on Chr6) 
rRNA (28S, 18S, 5.8S, 150-200 copies)
snoRNA (RNA processing/base modification, 97 different snoRNA)
snRNA (22snRNA, multiple copies of some)
Unknown function (mostly single copy)

Question 21

What are pseudogenes?

Answer 21

sequences related to coding or non-coding sequences that have become mutationally saturated so that the function is lost. They are evolutionary relics, derived from genes (both coding and non-coding) by duplication or retrotransposition.

Question 22

What are the different types of pseudogenes?

Answer 22

Gene fragments: single/ multiple exons.
Whole genes that include introns, mutated splice sites
Processed pseudogenes: mature mRNA from expressed gene reverse-transcribed and integrated into the genome: 4/5 exons that are inserted into the genome.

Question 23

What are the features of coding genes?

Answer 23

They make up 1-5% of the genome, producing proteins which perform cellular activities. Can be single copy or multiple copy. Can be grouped into families based upon sequence familiarity; often evolved by duplication and divergence. Superfamilies also exist

Question 24

What is the significance of gene overlap?

Answer 24

Numerous genes can be located on the same section of DNA. For example the BRCA1 (5’-3’) and Rho7 (3’-5)
Opposite strands can also code different genes

Question 25

Describe the general structure of coding genes.

Answer 25

Promoter: RNA pol binding site, TF sites, TATA vs TATA-less Introns and exons (coding must have exons - mitochondrial genes do no have introns) Must have a 5'-UTR, drives translation for tissue specific elements. Has regulatory functions Start codon (ATG); multiple ATGs present Polyadenylation sequences to end transcription Splice sites (AG/GT vs AT/AC) Splice enhancers; exonic and intronic Stop codon (TAA, TAG, TGA) Once transcribed, mature mRNA can also have polyA tails added to them.

Question 26

Describe the structure of the beta-globin gene.

Answer 26

It has three exons; at the beginning of the introns, GT at the beginning and AG at the end; this pattern can be found throughout the genome -- splice sites.

Question 27

Describe the alternative splicing methods.

Answer 27

Exon skipping. Intron retention Alternative 3' site Alternative initiation

Question 28

Describe the Average Human Gene.

Answer 28

It covers 10-15kb of genomic DNA Encodes a cDNA 1500-2000 bp, with the majority being intronic sequences (>85%) There is a large variation in gene size, dystrophin is 2Mb whereas some are

Question 29

Describe the genome's content.

Answer 29

50'000-100'000 genes were predicted in the genome; there are 30'000-35'000 genes: alternative splicing however can account for some differences in number.

Question 30

Describe the common features that can be identified in genes with a common function.

Answer 30

The leader sequence (which directs the protein to the cell surface) are approx 20 amino acids in length. Extracellular domains Stalk region Membrane anchoring/ transmembrane sequence intracellular domains (of different families) to deliver different sequences.

Question 31

Which processes account for the largest number of genes?

Answer 31

Metabolism, reproductive and expression processes. Gene number reflects this (metabolism has the greatest number of genes)