Introduction to genomes, transposable elements

Question 1

What’s a genome?

Answer 1

The entirety of an organism’s hereditary information. Usually DNA (but some viruses have RNA genomes).

Question 2

What is the DNA content of the genome measured in?

Answer 2

measured in base pairs (bp)

Question 3

Is there a correlation between DNA content and organism complexity?

Answer 3

No

Question 4

What is a gene?

Answer 4

the entire nucleic acid sequence that is necessary for the synthesis of a functional product (polypeptide or RNA)

Question 5

What is the difference between exons and introns?

Answer 5

Exons contain the coding region or Open Reading Frame (ORF), while introns separate the exons and are spliced out during mRNA processing.

Question 6

What is the function of control regions in a gene?

Answer 6

Control regions include the promoter and cis-regulatory factors and regulate gene expression.

Question 7

What is BLAST?

Answer 7

A tool used to find nucleic acid and protein sequence similarities

Question 8

Proteins with ________ functions often contain similar
____________ sequences that encode functional domains

Answer 8

similar
amino acid

Question 9

What is the main reason for differences in genome
size among species?

Answer 9

Differences in genome size among species are mostly due to different amounts of non-coding DNA and transposable elements.

Question 10

What is the difference in gene density between lower and more complex eukaryotes?

Answer 10

Gene density is much greater in lower eukaryotes than in more complex eukaryotes.

Question 11

What is a pseudogene?

Answer 11

A pseudogene is a non-functional DNA sequence that resembles a functional gene but cannot produce a functional protein or RNA product.

Question 12

What is an Alu site?

Answer 12

Alu sites are just repetitive elements of DNA and they’re called Alu sites because they include a recognition site for a restriction enzyme called Alu 1.

Question 13

What is the difference between orthologs and paralogs?

Answer 13

Orthologs are the same protein in different species, while paralogs are closely related proteins in the same species.

Question 14

What are called genes that are represented once in the genome?

Answer 14

solitary or single-copy genes

Question 15

What is the difference between solitary genes and duplicate genes?

Answer 15

Solitary genes are represented once in the genome, while duplicate genes occur in multiple copies.

Question 16

A set of related genes formed by duplication of an original single-copy gene make up a:

Answer 16

gene family

Question 17

What is DNA fingerprinting?

Answer 17

DNA fingerprinting compares individual differences in simple-sequence tandem arrays.

Question 18

What is the difference between microsatellite DNA
and minisatellite DNA?

Answer 18

Microsatellite DNA repeat units are typically 1 to 4 bp (shorter and more abundant) in length and found in arrays of up to ≈600 bp in length, while minisatellite DNA repeat units are ≈14 to 100 bp in length (longer and less abundant) and found in arrays of 1 to 5 kbp in length.

Question 19

What are transposable DNA elements?

Answer 19

DNA elements that move within genomes by different mechanisms.

Question 20

What is the percentage of the human genome that consists of DNA transposons?

Answer 20

3%.

Question 21

What is the percentage of the human genome that consists of retro-transposons?

Answer 21

40%.

Question 22

How does a transposon increase its copy number?

Answer 22

If it moves from a replicated region to a non-replicated region, copy number will increase by one in one of the daughter chromosomes.

Question 23

What are the two major classes of transposons?

Answer 23

DNA transposons
Retrotransposons

Question 24

What is the meaning of LTR in eukaryotic LTR retrotransposons?

Answer 24

Long terminal repeats.

Question 25

What does the protein coding region of eukaryotic LTR retrotransposons encode?

Answer 25

Reverse transcriptase, integrase, and other proteins.

Question 26

What is the mechanism for generating retroviral genomic RNA from integrated retroviral DNA?

Answer 26

RNA polymerase II transcribes the integrated retroviral DNA into a full-length RNA molecule.
This primary transcript is then processed by enzymes, including polyadenylation (addition of a poly-A tail) by poly(A) polymerase, to create mature retroviral genomic RNA for packaging and translation.

Question 27

What are LINEs?

Answer 27

nonviral DNA retrotransposons (Long interspersed nuclear element)

Question 28

What does LINEs code for ?

Answer 28

2 proteins:
ORF1: encodes an RNA binding protein involved in nuclear transport of LINE RNA.
ORF2: encodes a reverse transcriptase and a nuclease.

Question 29

How can recombination between repeated elements impact genes?

Answer 29

Recombination between repeated elements can shuffle exons and produce new genes with new combinations of existing exons.

Question 30

What is a notable characteristic of the sequences carried by DNA transposons and LINEs during their movement?

Answer 30

DNA transposons and LINEs can carry unrelated flanking sequences with them when they move.