genome structure

Question 1

Why does DNA have a negative charge?

Answer 1

The phosphate group is negatively charged
everything else (sugar and bases) are neutral

Question 2

major groove

Answer 2

backbones are far apart

Question 3

minor groove

Answer 3

backbones are close together

Question 4

structure of dna

Answer 4

nitrogenous base - composed of Nitrogen and C
pentose sugar - 5 carbons form cyclical structure with O bridge between C1 and C4
nitrogenous base at C1
phosphate group at C5 w ester bond
hydroxyl at C3

Question 5

arrangement of DNA

Answer 5

bases stacked with major and minor groove

Question 6

how does 2 metres of DNA fit into a cell?!

Answer 6

DNA is bound to histone proteins to form nucleosomes (contains 8 histones)
Nucleosomes are wound further into chromatin and then into extended chromosomes
chromatin fibre then forms loops

they are then compressed and folded to form the most condensed form of DNA, the chromosome

Question 7

Describe the histone structure DNA wraps around

Answer 7

Eight histones form the nucleosome
2A,2B, 3 & 4 (2 copies of each)

Histone 1 binds the linker DNA (piece of DNA between nucleosomes)

Question 8

tightness of DNA packing and expression

Answer 8

DNA tightly packed = less accessible so less gene expression

DNA more loosely = more accessible so more gene expression

Question 9

types of chromosomes

Answer 9

Metacentric - centromere in middle and chromosome arms almost equal

Subcentric - centromere located near middle (sub median) resulting in slightly unequal lengths of chromosomal arms

Acrocentric - centromere located near the end of the chromosome (has little satellites)

Question 10

genome size and complexity

Answer 10

genome size is not related complexity of organism

Question 11

what is exome

Answer 11

The coding Genome
sum of all the gene sequences is called the exome

Some definitions just use the coding sequences
Some definitions use the whole gene sequences

Question 12

what do intergenic regions contain

Answer 12

sequence of no known function, such as repetitive DNA, pseudogenes and may contain regulatory elements

Question 13

what is gene cluster

Answer 13

two or more genes that code for the same or similar products, found close together in genome

Question 14

when do genes cluster and why - organisation of genes

Answer 14

in families ie, globin clusters

• allows for coordinated gene regulation
• may just reflect evolutionary history

Question 15

what are promoter regions

Answer 15

recruit RNA polymerase to DNA template

also binds transcription factors to regulate gene expression

Question 16

what are the different regulatory regions which affect gene expression

Answer 16

they are position independent
- enhancer sequences: short sequences in gene which are targets for transcription factors (activators) to up regulate expression

• silencer sequences: targets for transcription factors (repressors) to down regulate expression
• insulator sequences: short sequences that prevent enhancers/silencers influencing other genes outside of tehri target ones

Question 17

what are the diff modifications done to pre mrna to make it mature?

Answer 17

capping
splicing
polyadenilation

Question 18

capping

Answer 18

methylated guanosine cap added to 5’ end of euk RNAs

5’ cap protects mRNA from degradation

Question 19

splicing

Answer 19

spliceosome interacts w 3’ ed of exon and 5’ end of the next and breaks the link between intron to first exon
spliced exons are joined together and intron becomes lariat structure

Question 20

why is splicing needed

Answer 20

so other proteins (exon junction complex and TREX) target spliced mRNA for translation

Question 21

polyadenylation

Answer 21

addition of many adenine nucleotides to 3’ end of newly synthesized mrna to protect the end from degradation

Question 22

What are pseudogenes?

Answer 22

genes that have been at least partially inactivated by the loss or gain of sequence that disrupt their correct transcription and/or translation

Question 23

How does the spliceosome remove introns?

Answer 23

Spliceosome brings the ends of the exons together and cleaves the intron from in between then joining the adjacent exons together.

Lariat structure is then degraded

Question 24

What is alternative splicing?

Answer 24

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

Question 25

What is the role of RNA Polymerase during transcription?

Answer 25

RNA polymerase binds asymmetrically and can only move 5’ to 3’

Question 26

What two sequences form the gene promoter?

Answer 26

Regulatory CAAT box

Recruiting TATA box

Question 27

What is the role of the CAAT box?

Answer 27

Regulatory element

regulates the recruitment of RNA Polymerase

Question 28

What is the role of the TATA box?

Answer 28

Needed to recruit general Transcription factors and RNA polymerase

Question 29

Outline the process of transcription

Answer 29

1. promoter recruist RNA pol 2
2. DNA helix locally unwound
3. RNA synthesis begins in 5’ to 3’
4. RNA poly moves along - elongation occurs
5. RNA pol reaches a termination signal and stops
6. RNA polymerase dissociates, carrying the pre mRNA with it

Question 30

What export signals bind to the spliced mRNA?

Answer 30

Exon Junction Complex
TREX export complex

These all signal the compound out of the nucleus and into the ER ready for translation by the ribosomes