Lecture RR5. Genes and genomes transposable elements

Question 1

what is a genome?

Answer 1

The entirety of an organism’s hereditary information

Usually DNA (some viruses = RNA)

Eukaryotes → composed of coding (islands) and non-coding DNA (open ocean)

Question 2

what is the difference in genome size attributed to?

Answer 2

the amount of non-coding DNA

Question 3

What is a gene?

Answer 3

Definition of a gene = the entire nucleic acid sequence that is necessary for the synthesis of a functional product (polypeptide [Protein] or RNA)

Genes are transcribed

Question 4

what is an Open Reading Frame (ORF)

Answer 4

it defines the coding sequence, it starts with a start codon and ends with a termination codon

Question 5

what is a control region?

Answer 5

typically present upstream of the gene, contains promoters (sequences that recruit RNA polymerase) and other regulatory factors that will control the activity of the RNA polymerase.

Question 6

what are ORF and control regions needed for?

Answer 6

so that transcription can start in the chain

Question 7

what is the role of introns ?

Answer 7

separate the exons and are spliced out during mRNA processing

another benefits of introns is that with a single gene we can generate different versions of a protein, with the process of splicing (the removal of introns) can vary

Alternative splicing !

Question 8

what is a transcription unit?

Answer 8

A region in DNA, bounded by an initiation (start) site and termination site, that is transcribed into a single primary transcript

Question 9

what is the effect of alternative splicing?

Answer 9

with a single gene we can generate different versions of a protein, with the process of splicing (the removal of introns)

Question 10

what are solitary or single-copy genes?

Answer 10

with a single gene we can generate different versions of a protein, with the process of splicing (the removal of introns)

Question 11

what is a gene family?

Answer 11

the remainder (75%) occur as duplicated or in multiple copies. A set of related genes formed by duplication of an original single-copy gene make up a gene family

Question 12

T or F, Proteins with similar functions often contain similar amino acid sequences that encode functional domains

Answer 12

True, these similarities can be observed with BLAST (Basic Local Alignment Search Tool) and other techniques

Question 13

what can happen to gene functions as they are copied? (2)

Answer 13

1. New gene copies can either evolve a new function or
2. alternatively, degenerate over time losing their function (pseudogenes, they look like genes but dont have function)

Question 14

what are paralogs?

Answer 14

closely related proteins in the same species (a-tubulin and b-tubulin in humans) but that have different functions

Question 15

Give 3 examples of Non-Coding DNA

Answer 15

• Intragenic Noncoding DNA
• Introns
• UTRs (UnTranslated Regions) will not be removed in the process of splicing

Question 15

what are orthologs?

Answer 15

the same protein, serving the same function, in different species (a-tubulin in humans and flies)

Question 16

what are the 2 types of simple sequence repeats (SSR)

Answer 16

sequences that are outside of genes,
there are 2 types:
Minisatellite DNA and Microsatellite DNA

Question 17

what is Minisatellite DNA ?

Answer 17

• repeat units are =14 to 100bp in length
• 20-50 tandem repeat units
• arrays of 1 to 5 kbp in length
• often in centromeres and telomeres

some of them seem to have a function because they are positioned at particular places like important places of our genome

Question 18

What is Microsatellite DNA?

Answer 18

• Repeat units are typically 1 to 4 bp in length
• Arrays of up to =600 bp in length and composed of tandem repeat units
• sometimes found in transcription units (this is what is important about them), they sometimes appear in coding sequences
• expansion underlie several neuromuscular diseases like myotonic dystrophy and spinocerebellar ataxia

DNA polymerase slips during the replication of repeats

Question 19

how can SSRs be used for DNA fingerprinting protocols?

Answer 19

each of us has a different amount of repeats in our genomes,

so then we do PCR fragments
and the lengths will be different from person to person

Question 20

what are transposable (mobile) DNA elements?

Answer 20

• transposable DNA elements move within genomes by different mechanisms
• Mobile DNA elements influenced evolution and can cause mutations leading to disease
• Originally identified by Barbara McClintock by studying the color pattern formation in maize caused by the production of the pigment anthocyanin

Question 21

what are the 2 types of repeated DNA sequences?

Answer 21

• Simple Sequence repeats (SSR)
• Transposable elements (TE) (also called jumping genes)

Question 22

what are the 2 major classes of Transposable elements (TE) ?

Answer 22

transposons and retrotransposons

Question 23

what is the enzyme needed for DNA transposons

Answer 23

transposase

Question 24

what are transposons?

Answer 24

3% of the human genome consists of DNA transposons

cut and paste mechanism

for them to increase their numbers, the transposition has to occur during DNA replication

Question 25

what are retro-transposons?

Answer 25

40% of the human genome consists of retro-transposons

first gets transcribed into RNA

generates DNA by reverse transcription

inserted into target sequence

there is an amplification in number!

Question 26

what are the 2 types of retrotransposons ?

Answer 26

1. Long Terminal Repeat (LTR)

8% of our genome
very similar to retroviruses
lacks the proteins that would envelope the virus and help it escape the cell
in the coding region, they code reverse transcriptase, converting the RNA into DNA
also coding an integrase that will take the DNA and paste in on another site

2. LINE and SINE

LINEs have only 2 ORFs , ORF2 is the one for reverse transcriptase
SINEs don’t code for any protein and are even shorter than LINEs
they use the proteins from LINEs to move around
most abundant in our genome

Question 27

why are transposons important for evolution?

Answer 27

1. they help shuffle genes and exons around
2. shuffle things in the genome