5. Genome Structure

Question 1

Features of DNA in three dimension

Answer 1

• Two antiparallel strands of DNA
• Bases “stacked”
•Two grooves
  - Major
  - Minor

Question 2

DNA packing levels

Answer 2

DNA double helix -> Nucleosomes -> Chromatin fibre - > Extended section of chromosome -> Loops o chromatin fibre -> Metaphase chromosome

Question 3

Briefly describe the structure of nucelosomes

Answer 3

• Basic proteins that bind DNA
• Eight histones form the nucleosome
• Histone 1 binds the linker DNA

Question 4

Describe the 3 types of chromosome structure

Answer 4

1) Metacentric ~ the centromere is in the middle of the chromosome and the arms of the chromatids are the same length
2) Submetacentric ~ centromere is off centre and produces a short and a long arm
3) Acrocentric ~ causes a very short arm (satelites)

Question 5

Function of the primary DNA

Answer 5

• The primary DNA sequence encodes all the gene products necessary for an organism
• The primary DNA sequence also includes a large number of regulatory signals
• Much of the DNA sequence does not have an assigned function as yet

Question 6

What is the exome?

Answer 6

• The sum of all the gene sequences

* aka the whole genome

Question 7

What is a gene?

Answer 7

• All of the DNA that is transcribed into RNA plus all of the cis-linked (physically local) control regions that are required to ensure quantitatively appropriate tissue-specific expression of the final protein
- (not just the bits that code for the protein - the regulation of the gene is also every important)
•Genes are often very different in size

Question 8

What are intergenic regions?

Answer 8

•Intergenic regions contain sequences of no known function, such as repetitive DNA, endogenous retroviruses, pseudogenes

Question 9

Why do genes often cluster in families? e.g. globin clusters

Answer 9

• Allows for co-ordinate gene regulation

* May just reflect evolutionary history

Question 10

What structures are found in genes?

Answer 10

Promoters, UTRS, inrons and exons

Question 11

What do promoters consist of? and what is the function?

Answer 11

• They contain regulatory element (CAAT box) - needed to regulate recruitment of RNA polymerase
• And TATA box - needed to recruit general transcription factors and RNA polymerase
• Eukaryotic RNA polymerases are unable to recognise promoters efficiently without help

Question 12

What are the three eukaryotic RNA polymerases? and what is the function of each?

Answer 12

• RNA polymerase I - needed to transcribe rRNA genes
• RNA polymerase II - needed to transcribe mRNA
• RNA polymerase III - needed to transcribe tRNA and other small RNAs

Question 13

Briefly describe the process of transcription.

Answer 13

1) RNA polymerase is recruited. DNA is a closed complex.
2) DNA helix locally unwound. (open complex).
3) RNA Synthesis begins
4) Elongation
5) Termination
6) RNA Polymerase dissociates

Question 14

What are introns?

Answer 14

• spliced out
• vary in size and number
• some contain other genes

Question 15

What are the other regulatory regions besides promoters?

Answer 15

• ENHANCERS - upregulate gene expression – they are short sequences that can be in the gene or many kilobases distant. They are targets for transcription factors (activators).
• SILENCERS - downregulate gene expression. They are also position-independent and are also targets for transcription factors (repressors).
• INSULATORS - short sequences that act to prevent enhancers/silencers influencing other genes

Question 16

Post-transcription modifications

Answer 16

1) Capped at 5’ end - Soon after RNA polymerase begins transcription a methylated cap is added to the 5’ end.
2) Polyadenylated at 3’ end - When transcription finishes, the G/U rich region is cleaved off and polyA tail (250 As) is added by polyadenylate polymerase (PAP)
3) Introns are spliced out - the end of the intron forms a 2’-5’ linkage with a region of the intron. - the exons on either end then join together and release the intron in a lariat like shape.

Question 17

What is alternative splicing?

Answer 17

Exons can be skipped or added so variations of a protein (called isoforms) can be produced from the same gene.

Question 18

What are the other structures found on the mRNA prior to nuclear export, besides the cap and the polyA tail?

Answer 18

• TREX export complex (TRanscription-EXport) ~ enhanced by EJC
• Exon junction complex (EJC) - bound to the message

Question 19

What are pseudogenes?

Answer 19

• These are genes that have been at least partially inactivated by the loss or gain of sequence that disrupt their correct transcription and/or translation
• Processed pseudogenes have no promoter or introns as they are copied from mRNA by retrotransposition (the reverse transposition of an RNA intermediate)