Genome Structure

Question 1

What is DNA?

Answer 1

→ Deoxyribonucleic acid

Question 2

In what direction does DNA run?

Answer 2

→ 5’ to 3’

Question 3

How are the bases bound to each other?

Answer 3

→ Hydrogen bonds

Question 4

How do the two strands run in double stranded DNA?

Answer 4

→ antiparallel

Question 5

What are the grooves in 3D DNA?

Answer 5

→ Major

→ Minor

Question 6

What are the bases like in 3D DNA?

Answer 6

→ Stacked

Question 7

How much DNA is in a nucleated cell?

Answer 7

→ 2m

Question 8

How wide is the average cell?

Answer 8

→ 50 micrometers

Question 9

What are the 6 levels of DNA packing?

Answer 9

→ DNA helix
→ Nucleosomes
→ Chromatin Fibres
→ Chromatin loops
→ Loops of condensed chromatin
→ Chromosome

Question 10

What are histones?

Answer 10

→ basic proteins that bind DNA

Question 11

How many histones form the nucleosome?

Answer 11

→ 8

→ 2A, 2B, 3, 4

Question 12

What histone binds Linker DNA?

Answer 12

→ Histone 1

Question 13

What is linker DNA?

Answer 13

→ piece of DNA that is between nucleosomes

Question 14

What is an acrocentric chromosome?

Answer 14

→ They don’t have the short arms

Question 15

What does the primary DNA sequence encode?

Answer 15

→ All the gene products necessary for an organism

→ Regulatory signals

Question 16

What is the exome?

Answer 16

→ Sum of all the gene sequences

Question 17

What do the two definitions of the exome include?

Answer 17

→ Coding sequences

→ whole gene sequences

Question 18

What is a gene?

Answer 18

→ All of the DNA that is transcribed into RNA

→ All control regions

Question 19

What is the size of the human genome?

Answer 19

→ Upto 2 Giga base pairs

Question 20

What % of the DNA is genes?

Answer 20

→ Less than 2%

Question 21

What is the general trend linking genes and organism complexity?

Answer 21

→ The more genes the more complex

Question 22

Why does the number of genes not necessarily correlate to complexity?

Answer 22

→ A marbled lungfish has 130Gbp

→ Paris Japonica (flower) has 149Gbp ( biggest genome)

Question 23

What is an example of gene size variation?

Answer 23

→ globin gene 1.8kb

→ dystrophin gene 2.4mb

Question 24

What do intergenic regions or pseudogenes contain?

Answer 24

→ Remnants of retroviruses

Question 25

How do genes often cluster and give an example?

Answer 25

→ In families | → Globin clusters

Question 26

What does gene clustering allow for?

Answer 26

→ Co-ordinate gene regulation | → Reflect evolutionary history

Question 27

What is the transcription unit divided into?

Answer 27

→ Exons | → Introns

Question 28

Where are introns found?

Answer 28

→ Between exons

Question 29

What does the promoter do?

Answer 29

→ Recruits RNA polymerase to a DNA template

Question 30

How does RNA polymerase bind and in what direction does it go?

Answer 30

→ Asymmetrically | → 5' to 3'

Question 31

What are 2 regulatory signals?

Answer 31

→ CAAT | → TATA

Question 32

What are the 5 components of a gene?

Answer 32

→ exons and introns → regulatory signals CAAT and TATA → Signals that allow to start transcription and translation → Signals to stop transcription and translation → 3' and 5' UTR

Question 33

What is the TATA box for?

Answer 33

→ recruit general transcription factors and RNA polymerase

Question 34

How many polymerases are there in eukaryotes and what are they?

Answer 34

→RNA pol I → RNA pol II → RNA pol III

Question 35

What are the RNA polymerases for in eukaryotes?

Answer 35

→ RNA pol I → transcribe rRNA genes → RNA pol II → transcribe mRNA → RNA pol III → Transcribe tRNA and other small RNAs

Question 36

What do co-factors do?

Answer 36

→ Regulate how much and when transcription is occurring

Question 37

What are the steps for transcription?

Answer 37

1) RNA polymerase is recruited (closed) 2) DNA helix is locally unwound (open) 3) RNA synthesis begins 4) Elongation 5) Termination 6) RNA polymerase dissociates

Question 38

What do some introns contain?

Answer 38

→ Other genes

Question 39

What are enhancers?

Answer 39

→ Short sequences that can be in the gene → or many Kb distant → Targets for transcription factors that activate expression

Question 40

What do enhancers do?

Answer 40

→ upregulate gene expression

Question 41

What are silencers?

Answer 41

→ Targets for transcription factors (repressors) | → position independent

Question 42

What do silencers do?

Answer 42

→ Downregulate gene expression

Question 43

What are insulators?

Answer 43

→ Short sequences that act to prevent enhancers/silencers influencing other genes

Question 44

How is eukaryotic mRNA modified after transcription?

Answer 44

→ Capped at 5' end → Polyadenylated at 3' end → Introns are removed

Question 45

When is the 5' cap added?

Answer 45

→ After RNA polymerase begins transcription

Question 46

What are the two termination signals?

Answer 46

→ AAUAAA | → G/U rich region

Question 47

What happens when the termination signal is reached?

Answer 47

→ G/U rich region and everything after it is removed | →polyadenylate polymerase adds lots of As to the end of the sequence

Question 48

Why is polyadenylation required?

Answer 48

→ Protects the end from degradation and targets it to leave the nucleus

Question 49

How does splicing work?

Answer 49

→ Protein complex called a spliceosome → brings the ends of the exons together and removes the intron inbetween → joins exons together → Lariat is degraded

Question 50

What is alternative splicing?

Answer 50

→ Exons can be skipped or added so variations of proteins (isoforms) can be made from the same gene

Question 51

What targets mRNA for nuclear export?

Answer 51

→ TREX is bound to the cap | → It is enhanced by the exon junction complex

Question 52

What are pseudogenes?

Answer 52

→ Genes that have been at least partially inactivated by loss or gain of sequence that disrupt their transcription or translation

Question 53

What is an example of a pseudogene?

Answer 53

→ glucocerebrosidase has an adjacent pseudogene | → it differs in the coding region by one 55bp deletion

Question 54

How are pseudogenes copied from mRNA?

Answer 54

→ retrotransposition