Genomes and their evolution

Question 1

What is genomics?

Answer 1

Upon sequencing the genome of any species, scientists can study whole sets of genes and their interactions, an approach called genomics

Question 2

What is bioinformatics?

Answer 2

the application of computational methods to store and analyze biological data.

Question 3

Explain the Human Genome Project?

Answer 3

The sequencing of the human genome,

Question 4

What is a reference genome?

Answer 4

a full sequence that best represents the genome of a species. The human reference genome is continuously being revised and re-released.

Question 5

What is the whole-genome shotgun approach?

Answer 5

the cloning and sequencing of DNA fragments from randomly cut DNA. Powerful computer programs then assemble the resulting very large number of overlapping short sequences into a single continuous sequence. The whole-genome shotgun approach is widely used today.

Question 6

what is metagenomics?

Answer 6

DNA from an entire community of species (a metagenome) is collected from an environmental sample and sequenced.

Again, computer software sorts out the partial sequences and assembles them into the individual species’ partial of complete genomes.

Question 7

What is gene annotation?

Answer 7

Using available DNA sequences, geneticists can study genes directly, rather than taking the classical genetic approach, which requires determining the function of an unknown gene from the phenotype.

scientists aim to identify all protein-coding genes in the sequence and ultimately their functions. This process, called gene annotation

Question 8

explain the term proteomics?

Answer 8

The scientific progress resulting from sequencing genomes and studying large sets of genes has encouraged scientists to attempt similar systematic studies of sets of proteins and their properties (such as their abundance, chemical modifications, and interactions), an approach called proteomics

Question 9

What is a proteome?

Answer 9

the entire set of proteins expressed by a cell or group of cells.

Question 10

Explain what systems biology is?

Answer 10

to model the dynamic behavior of whole biological systems based on the study of the interactions among the system’s parts.

Question 11

see table 21.1 for genome size information (skip this if not applicable)

Question 12

see table 21.6 for types of dna in the human genome. (skip if not applicable)

Question 13

Explain the term pseudogenes?

Answer 13

former genes that have accumulated mutations over a long time and no longer produce functional proteins.

Question 14

What is repetitive DNA?

Answer 14

DNA that consists of sequences that are present in multiple copies in the genome.

Question 15

Explain transposable elements?

Answer 15

Both prokaryotes and eukaryotes have stretches of DNA that can move from one location to another within the genome. These stretches are known as transposable genetic elements, or simply transposable elements

Question 16

State the two types of Eukaryotic transposable elements and what they do?

Answer 16

1. transposons:move within a genome by means of a DNA intermediate. Transposons can move by a “cut-and-paste” mechanism, which removes the element from the original site, or by a “copy-and-paste” mechanism, which leaves a copy behind. These actions require the enzyme transposase, which is generally encoded by the transposon.
2. retrotransposonsmove by means of an RNA intermediate that is a transcript of the retrotransposon DNA. Thus, retrotransposons always leave a copy at the original site during transposition. To insert at another site, the RNA intermediate is first converted back to DNA by reverse transcriptase, an enzyme encoded by the retrotransposon.

Question 17

What is a simple sequence DNA?

Answer 17

DNA that contains many copies of tandemly repeated short sequences, as in the following example (showing one DNA strand only):

Question 18

Explain What is a short tandem repeat (STR)? How does it relate to a simple sequence DNA?

Answer 18

simple sequence DNA contain many copies of tandemly repeated short sequences, as in the following example (showing one DNA strand only):

. . . GTTACGTTACGTTACGTTACGTTACGTTAC. . .

In this case, the repeated unit (GTTAC) consists of 5 nucleotides, but the number can range from 2 to 500. When the unit contains 2–5 nucleotides, the series of repeats is called a short tandem repeat

Question 19

what are multigene families?

Answer 19

collections of two or more identical or very similar genes.

Question 20

Give an example of multigene families of nonidentical genes?

Answer 20

two related families of genes that encode globins, a group of proteins that include the a and b polypeptide subunits of hemoglobin.

One family, located on chromosome 16 in humans, encodes various forms of α-globin; the other, on chromosome 11, encodes forms of β-globin

Question 21

How does Rearrangements of Parts of Genes Happen?

Answer 21

By process of Exon Duplication and Exon Shuffling

Question 22

What is transposition?

Answer 22

The ability of genes to change position on chromosomes, a process in which a transposable element is removed from one site and inserted into a second site in the DNA.

Genetic transposition was the first type of genetic instability to be discovered.

Question 23

What is a homeobox?

Answer 23

any of a class of closely similar sequences which occur in various genes and are involved in regulating embryonic development in a wide range of species.

Homeobox codes for a 60-amino-acid homeodomain in the encoded proteins. An identical or very similar nucleotide sequence has been discovered in the homeotic genes of many invertebrates and vertebrates.

Question 24

What are HOX genes?

Answer 24

short for homeobox-containing genes.