9.6 Genomic architecture and evolution

Question 1

how many genes does the human genome have?

Answer 1

25000

Question 2

What is the part of the genome that corresponds to the exons of all known genes?

Answer 2

exome

Question 3

Exons make up most of a genome. true or false?

Answer 3

false, it is introns that make up majority of a genome

Question 4

What are the four components that make up a genome?

Answer 4

1. Exomes (maked up of all extrons ) = about 2%
2. Introns (98%-99%)
3. Centromeres, telomeres, transposable elements
4. Simple repeating sequences

Question 5

True or false, Neighbouring genes can be transcibed in the same or opposite direction

Answer 5

true (both chromosomal strands are the template strand for some genes)

Question 6

The genome contains distinct types of gene organization:

Answer 6

1. Gene-rich regions:
   -Chromosomal regions that have many more genes than expected from average gene density over entire genome. Example n human genome-class III region of major histocompatibility complex
2. Gene deserts
   - Regions of >1 Mb that have no identifiable genes. 3% of the human genome is comprised of gene deserts.

Question 7

Why does the genome have gene deserts?

Answer 7

Gene deserts exist because they are large regions of the genome with low gene density, often containing regulatory elements, repetitive sequences, or structural DNA, which may play roles in genome organization and regulation.

Question 8

What is the biological significance of gene-rich regions and gene deserts?

Answer 8

It is unknown

Question 9

How does exon shuffling create new genes?

Answer 9

After exon shuffling, protein products have novel domain architechtures. (slide 52)

Question 9

Class III region of the human major histocompatibility (MHC) complex:

Answer 9

MHC complex contains 60 genes within a 700 kb region
GC content is much higher than the genome average

Question 10

Genomes undergo evolutionary change:

Answer 10

Exons often encode protein domains: sequences of amino acids that fold into functional units.

Question 11

The genome contains gene families, what are gene families?

Answer 11

are groups of genes that are closely related in sequence and function.

Question 12

What two processes evolve gene families? (also explain these two processes further)

Answer 12

Duplication followed by divergence from an ancestral gene.
The two DNA sequence products of a duplication event, which start out identical, eventually diverge as they accumulate different mutations
Additional rounds of duplication and divergence can further increase the number of related genes

Question 13

What are Pseudogenes?

Answer 13

They look like genes but do not function as genes. (slide 54)

Question 14

Gene family nomenclature:

Answer 14

Orthologous genes and Paralogous genes (slide 55)

Question 15

Explain orthologous genes

Answer 15

Genes are in two different species that arose from the same gene in the species’ common ancestor, usually but not always retaining the same function.

Question 16

Explain paralogous genes

Answer 16

Arise by duplication within the same species, often within the same chromosome, they also often constitute a multigene family.

Question 17

What is the interpretation of slide 56 of chromosomal rearrangment?

Answer 17

This describes- how certain segments of chromosomes, known as syntenic blocks, are conserved between humans and mice. Each block contains at least two genes in the same order in both species. However, due to chromosomal rearrangements over evolutionary time, these blocks have been moved to different locations in the mouse genome compared to the human genome.

Question 18

Combinatorial amplification(explain what it is) at the DNA level
results in greater complexity from fewer genes:

Answer 18

Combinatorial amplification: Building a large number of different entities by combining small sets of basic elements in different ways.
Human T-cell receptor family
* DNA rearrangement combines V, D, and J segments into a
gene.
* Result is about 1000 different combinations (slide 57)

Question 19

Combinatorial strategies at the RNA level may
lead to gene amplification and diversity:

Answer 19

Example – three neurexin genes
* Two alternative promoters, five sites for alternative splicing
* Can generate 2000 different mRNAs
(slide 58)

Question 20

Alterations in domain architecture:

Answer 20

Genes with multiple exons often encode proteins with multiple domain analogous
The shuffling, addition or deletion of exons during evolution can create new genes whose protein products have novel domain architectures and thus can assume new roles in cells and organisms
Exon shuffling over evolution has produced different transcription factors with differing domains that enable these proteins to recognize particular DNA sequences and also to interact uniquely with cofactors such as other proteins