Oct 4 Genes and genomes, transposable elements

Question 1

what is the genome?

Answer 1

the entirety of an organism’s hereditary information
usually DNA, but some viruses have RNA genomes

Question 2

how is double stranded DNA length measured?

Answer 2

measured in base pairs (bp)
100bp=1kbp or kb
1000000bp=1mbp=mb

Question 3

how is biological complexity related to the size of DNA content in the genome?

Answer 3

it is NOT related

Question 4

what is the largest sequenced genome?

Answer 4

the australian lungfish xiphophorus, 43Gb (14x human genome)
doesn’t have more genes but has lots of transposable elements

Question 5

what is a gene?

Answer 5

the entire nucleic acid sequence that is necessary for the synthesis of a functional product (polypeptide or RNA)
can be considered as transcription units

Question 6

what do exons contain?

Answer 6

the coding region or open reading frame (ORF)

Question 7

what are control regions?

Answer 7

promoter and cis-regulatory factors

Question 8

what are introns?

Answer 8

separate the exons
spliced out during mRNA processing

Question 9

what do proteins with similar functions have?

Answer 9

proteins with similar functions often contain similar amino acid sequences that encode functional domains

Question 10

how can nucleic acid and protein sequence similarity be found?

Answer 10

BLAST

Question 11

how does protein number vary among species relative to DNA content?

Answer 11

varies much less

Question 12

what is the difference in genome size mostly due to?

Answer 12

mostly due to different amounts of non-coding DNA and transposable elements

Question 13

what are orthologs?

Answer 13

the same protein in different species (alpha tubulin in humans and flies)

Question 14

what are paralogs?

Answer 14

closely related proteins in the same species (alpha tubulin and beta tubulin in humans)

Question 15

what are solitary/single copy genes?

Answer 15

protein coding genes that are represented once in the genome
there is only one gene that looks like that, if you do the BLAST search of a protein it makes, there will be no paralogy

Question 16

what is a gene family?

Answer 16

a set of related genes formed by duplication of an original single copy gene

Question 17

what proportion of protein coding genes do solitary genes represent?

Answer 17

25-50%
the remainder occurs as duplicates or in multiple copies

Question 18

what gene density do multicellular animals and plant genomes have?

Answer 18

lower gene density
noncoding introns and other noncoding sequences
long tandem arrays of repeated short sequences (larger genomes, but fewer genes)

Question 19

what does DNA fingerprinting compare?

Answer 19

compares individual differences in simple sequence tandem arrays

Question 20

what some characteristics of microsatellite DNA?

Answer 20

1. repeat units are typically 1 to 4bp in length
2. arrays of up to 600bp in length and are composed of tandem repeat units
3. are sometimes found in transcription units
4. expansion underlie several neuromuscular diseases like myotonic dystrophy and spinocerebellar ataxia

Question 21

how can short repeated sequences be generated?

Answer 21

by backward slippage during replication or
one unit is looped out (first replication produces n+1 and second replication makes duplex with extra repeat unit)

Question 22

what are some characteristics of minisatellite DNA?

Answer 22

1. repeat units are 14 to 100bp in length
2. 20-50 tandem repeat units
3. arrays of 1 to 5 kbp in length
4. often in centromeres and telomeres

Question 23

how are repeated sequences used in testing and identification?

Answer 23

they vary extensively in length among individuals
used for paternity determination and to identify criminals

Question 24

what are transposable (mobile) DNA elements?

Answer 24

non coding
transposable DNA elements move within genomes by different mechanisms
mobile DNA elements influenced evolution and can cause mutations leading to disease

Question 25

what does recombination between repeated elements do?

Answer 25

can shuffle exons and produce new genes with new combinations of existing exons

Question 26

what is stable transfection?

Answer 26

the plasmid has the gene that provides antibiotic resistance can select for the cells that have the gene with drug resistance selectable marker

Question 27

how can retroviral vectors be used to integrate cloned genes into mammalian genomes?

Answer 27

retroviral vectors can target living cells can infect particular tissue types can introduce a gene into a living organism tissue culture cells are transiently transfected with 3 different plasmids 1. vector plasmid with the gene of interest 2. packaging plasmid which encodes a lot of viral proteins 3. viral coat plasmid which encodes a gene for VSV G protein cells that have all 3 of the plasmids can make functional virus particles that have the gene of interest integrated in the viral genome

Question 28

what do some genes encode (that are not proteins)?

Answer 28

can encode RNA that has a function ribosomal RNA, tRNA, small RNA involved in splicing those RNA do not encode proteins but they are functional

Question 29

what is included in a gene?

Answer 29

what codes for mRNA but that is not linear, interrupted by introns

Question 30

what region lies upstream of the 5' end on a gene?

Answer 30

regions that control the expression of the gene (in what cell type, at what developmental time, and how it responds to stimulus)

Question 31

what region lies on the 3' end?

Answer 31

the Poly(A) site (polyadenilation) A residues are enzymatically added to the RNA at the 3' end this Poly(A) site determines where the transcript terminates and where the A will be added

Question 31

what happens to those regions during transcription?

Answer 31

not transcribed, do not become mRNA, but they are part of the gene

Question 31

how does BLAST work?

Answer 31

BLAST makes the best possible alignment between two or more sequences -> can see the similarities

Question 31

how can short repeated sequences be generated during replication?

Answer 31

can be generated by backwards slippage when DNA polymerase hits one of the sequences it can get confused and sometimes it will slip over one of them and keep going if that happens, in the next replication, one of the strands has an extra repeat, and that can expand because of the errors polymerase makes the more it expands the worse the disease is protein is not functional anymore or has altered functions

Question 32

what is the mechanism for increasing the copy number of DNA transposons?

Answer 32

if a transposon moves from a region that has been replicated to a region that hasn't been replicated yet (jumps ahead of the replication fork) then its copy number will increase by 1 in one of the daughter chromosomes (will be replicated twice)

Question 33

what are the two major classes of transposons and the difference?

Answer 33

DNA transposon: move as pieces of DNA and are part of DNA replication (3% of human genome) retrotransposon: have an RNA intermediate involved in the movement 40% of the human genome

Question 33

what is the general structure of eukaryotic LTR (long terminal repeat) retrotransposons?

Answer 33

whatever was a one end gets replicated at the other the protein coding regions encodes enzymes that are needed for transposition: reverse transcriptase (take RNA back to DNA), integrase (allows DNA copy to get integrated into a new chromosomal site) and others

Question 34

what is a retrovirus?

Answer 34

a virus whose genome resembles a retro transposon

Question 35

what are LINEs?

Answer 35

nonviral DNA retrotransposons (cannot be packaged into a virus) has one open reading frame that encodes RNA binding protein and another ORF that encodes protein that is both reverse transcriptase and DNA nuclease linked to some diseases if inserted in the wrong place

Question 36

what can recombination between repeated elements do?

Answer 36

can shuffle exons and produce new genes with new combinations of existing exons

Question 37

what can DNA transposons and LINEs do when they move?

Answer 37

they can carry unrelated flanking sequences (neighbouring DNA) with them when they move