Genomics and Genome Evolution

Question 1

Importance of sequence census assays

Answer 1

vastly increasing ability to understand genome function

Question 2

Genomics

Answer 2

the study of whole sets of genes, their products, and their interactions

Question 3

Bioinformatics

Answer 3

the application of computational methods to the storage and analysis of biological data

Question 4

Gene annotation

Answer 4

the process of identifying all protein-coding genes in a genome sequence and ultimately their functions

Question 5

Organization of the human genome

Answer 5

1. Repetitive DNA that includes transposable elements and related sequences: 44%
2. Repetitive DNA unrelated to transposable elements: 14%
3. Unique noncoding DNA: 15%
4. Introns: ~20%
5. Regulatory sequences: 5%
6. Exons: 1.5%

Question 6

What do sequencing and comparisons of genomes among organisms provide?

Answer 6

insights into evolution and other biological processes

Question 7

Genome size and # of genes of bacteria and archaea vs. eukaryotes

Answer 7

-Bacteria and archaea: 1-6 Mb genome size & 1500-7500 genes
-Eukaryotes: 12-670,000 Mb & 5000-40,000 genes

Question 8

Single nucleotide polymorphism

Answer 8

a substitution of a single nucleotide that occurs at a specific position in the genome, defined by requiring the substitution to occur at an appreciable degree within a population
-most have no phenotypes and do not cause disease
-some can directly cause disease

Question 9

Various types of chromosomal structural rearrangements

Answer 9

genetic rearrangements between different chromosomes, or within the same chromosomes
-balanced translocations usually harmless
-unbalanced have numerous health effects

Question 10

Copy number variants (CNVs)

Answer 10

genetic loci that, due to duplication and deletion, vary in their number of copies across individuals in a population
-range in size from 50 base pairs to whole chromosomes
-stem from segmental duplications
-cover a large part of human genome

Question 11

Four categories of repetitive DNA

Answer 11

1. Short tandem repeats
2. Tandem repeats
3. Interspersed repeats
4. Segmental duplications

Question 12

Short tandem repeats

Answer 12

Duplications of simple sets of DNA bases (typically 1-5 bp) such as A, CA, CGG, etc.

Question 13

Tandem repeats

Answer 13

Typically found at the centromeres and telomeres of chromosomes these are duplications of more complex sequences that are 100-200 bp long

Question 14

Interspersed repeats

Answer 14

1. DNA transposons
2. Retrotransposons

Question 15

Segmental duplications

Answer 15

large blocks of 10, 000-300,000 bp that have been copied to another region of the genome

Question 16

Phenotypic Effects of Simple and Tandem Repeats

Answer 16

STR- and TR-containing genes are directly involved in the generation of phenotypic variation
-morphological variation in domestic dogs
-In yeast, variation in the # of TR repeats in the FLO1 gene, which encodes for a cell surface antigen, can make yeast cells stick to each other or be loose in liquid culture

Question 17

DNA transposons

Answer 17

move through a DNA intermediate; “cut-and-paste” or “copy-and-paste”

Question 18

Retrotransposons

Answer 18

move through an RNA intermediate; always “copy-and-paste”; most abundant