Genes, genomes and genomics

Question 1

What was the first genome to be sequenced?

Answer 1

Phi X 174

Question 2

What are plectonemes?

Answer 2

The result of over- and underwinding of RNA and DNA polymerases

Question 3

What is supercoiling maintained by?

Answer 3

• DNA gyrase
• DNA topoisomerases
• NAPs

Question 4

What is the purpose of a topoisomerase?

Answer 4

Causes a transient break to allow rotation of the strands

Question 5

What is euchromatin?

Answer 5

the fraction of the nuclear genome that contains transcriptionally active DNA and adopts a relatively extended conformation

Question 6

What is heterochromatin?

Answer 6

highly condensed chromatin that shows little or no active gene expression

constitutive - remains condensed
facultative - condensation is reversibel

Question 7

What is meant by the epigenome?

Answer 7

the set of chemical modifications to the DNA which alter gene expression and are heritable

Question 8

Describe the inactivation of the X chromosomes in female cells

Answer 8

1. one of the two copies of the X-linked Xist gene is transcribed
2. Xist RNA is processed and then binds to the X chromosome from which it was transcribed
3. X chromosome becomes coated in Xist RNA - recruits methylases, histone deacetylases and DNA-binding proteins

Question 9

What is the C value?

Answer 9

amount of haploid DNA per nucleus, usually in picograms

Question 10

What is the C value paradox?

Answer 10

genome size is not proportional to the apparent complexity of an organism

Question 11

What is meant by an open reading frame?

Answer 11

a region of the genome that is transcribed and has a defined start and stop codons

Question 12

What is meant by polycistronic?

Answer 12

multiple ORFs under the control of the same regulatory sequences

Question 13

What is meant by the Shine-Dalgarno sequence?

Answer 13

helps align ribosome to start codon (AGGAGG)

Question 14

What is the sequence of the pribnow box?

Answer 14

TATAAT

Question 15

List the start and stop codons

Answer 15

Start - ATG
Stop - TAG, TAA, TGA

Question 16

What recognises the terminator sequence?

Answer 16

Rho (p) factor

Question 17

What is the Kozac sequence?

Answer 17

the 5’ untranslated region (ACCATGG)

Question 18

What is the TATA box?

Answer 18

• the core promoter in archaea and eukaryotes
• recognised by TBP

Question 19

List some transcription factors

Answer 19

• zinc finger
• helix-turn-helix
• leucine zipper

Question 20

What is meant by the term analogues?

Answer 20

genes that share a function but not a common ancestor

Question 21

What is meant by the term homologous

Answer 21

genes that share a common ancestor

Question 22

What is meant by the term orthologues

Answer 22

two homologous genes arising as a result of species divergence

Question 23

What is meant by the term paralogues?

Answer 23

two homologous genes arising due to gene duplication

Question 24

What is meant by satellite DNA?

Answer 24

clusters of short repeated sequences - remain condensed throughout the cell cycle

Question 25

What are teleomeres?

Answer 25

repetitive sequences at the end of linear chromosomes that protect the ends from degradation or tangling

Question 26

List the types of chromosomes

Answer 26

- telocentric - one arm (telomere next to centromere) - acrocentric - p shorter than q - metacentric - p and q are equal length

Question 27

What is the difference between minisatellites and microsatellites?

Answer 27

minisatellites - occur at the ends of the genome (10-100bp) microsatellites - occur throughout the genome (2-6bp)

Question 28

What are transposons?

Answer 28

genes that can change their position in the genome (are called interspersed repeats if no longer active)

Question 29

List the two types of transposons

Answer 29

- non-replicative --> class II-DNA transposons - replicative --> class I-retrotransposons

Question 30

What is the difference between LINEs and SINEs

Answer 30

LINEs- transpose via an RNA intermediate which is then reverse transcribed SINEs - use LINE machinery to retrotranspose

Question 31

What is a pseudogene?

Answer 31

a fragment of DNA that resembles a protein-coding gene but does not actually encode a protein