genes and DNA replication

Question 1

what bond is between base & sugar in DNA

Answer 1

glycosidic bond

Question 2

what is the short & long arm called in chromosomes

Answer 2

long - q

short - p

Question 3

enhancer

Answer 3

short region of DNA that also binds proteins that enhance transcription of gene

Question 4

promoter

Answer 4

DNA sequences that are kept & expressed in mature RNA

Question 5

exons

Answer 5

gene sequences that are kept & expressed in the mature RNA

Question 6

introns

Answer 6

intragenic sequences occur between exons. noncodong. removed from mature RNA

Question 7

untranslated regions (UTRs)

Answer 7

sequences at end of a gene. these sequences are kept in mRNA but not translated into protein

Question 8

Topoisomerase

Answer 8

• prevents over-winding of DNA double helix ahead of replication fork
• make a transient single nick in DNA backbone to relax the overwinding & then reseals the nick

Question 9

what way does DNA replicate

Answer 9

5’ to 3’ direction

- it extends 3’OH ends

Question 10

okazaki fragments define

Answer 10

the short stretches of the lagging strand that are synthesised at a time = discontinuous fragments of new DNA

Question 11

DNA polymerase a-primase

Answer 11

initiates synthesis of DNA

• synthesises short RNA primers complementary to unwound DNA strands
• does not need a free 3’OH to create RNA primer can make without pre-exisiting

Question 12

replication fork

Answer 12

junction at which nucleotides added to growing DNA chain - resembles ‘y’

Question 13

semi-conservative

Answer 13

every new DNA double helix consists of an original & new strand joined together

Question 14

Steps in unwinding of DNA replication

Answer 14

1. ORC recruits Cdc6
2. Cdt1-MCM2-7 complex loads onto DNA (surrounding it) –> called a double hexamer
3. other factors recruited to the hexamer
4. active MCM circles leading strand at each replication fork
5. MCM, Cdc45, GINS complex acts as a helicase moves along the leading strand unwind the 2 strands
6. recruits DNA polymerase epsilon
7. primase creates the RNA primer
8. DNA polymerase a starts to elongate the primer with around 20 nucleotides

Question 15

role of Replication Protein A in DNA unwinding

Answer 15

binds & coats single stranded DNA to prevent DNA damage, activation & prevent strand rejoining
- dislodged by DNA polymerase delta

Question 16

ORC

Answer 16

origins of recognition complex which recognises origin of replication - a complex of 6 proteins

Question 17

define DNA polymerases

Answer 17

• synthesise DNA from deoxyribonucleotides
• only extend pre-existing primers
• adds free nucleotides to the 3’ prime end of the growing DNA strand
• uses energy from hydrolysis (chemical breakdown of compound due to reaction with water) of free DNTP into dNMP + Ppi
• high processive enzymes
• multi-subunit enzymes
• can have 3’ exonuclease activity (excises incorrect terminal nucleotides - useful for proofreading errors)

Question 18

role of DNA polymerase alpha

Answer 18

RNA primer synthesis & extension

- no proofreading –> low fidelity –> lots of mistakes

Question 19

role of DNA polymerase delta

Answer 19

lagging strand synthesis
- new primer is needed every 100-200 nucleotides

• proofreading –> high fidelity –> no mistakes

Question 20

role of DNA polymerase epsilon

Answer 20

leading strand synthesis
- has intrinsic 3’ exonuclease activity to proof read its own replication errors = clips off the wrong bases before resuming replication

• proof reading –> high fidelity –> low mistakes

Question 21

how does the lagging DNA replication work

Answer 21

1. when pol delta reaches the 5’ end of the proceeding Okazaki fragment it initiates strand displacement synthesis
2. flap structures are subsequently cleaved by FEN1 endonuclease (cleaves DNA backbone) & DNA gap sealed by DNA ligase
   3.

Question 22

role of the sliding clamp on lagging and leading strand

Answer 22

polymerases are clamped to DNA with a homotrimetric protein (PCNA) = forms a large ring around DNA, binds to DNA polymerase & slides along DNA as polymerase moves

lagging strand = each time the polymerase reaches 5’ end of the preceding Okazaki fragment, the polymerase is released

= prevent dissociation & provide high processivity

Question 23

PCNA stands for

Answer 23

proliferating cell nuclear antigen

Question 24

3 enzymes that contribute to DNA termination

Answer 24

RNA primers are removed & then replaced by DNA chain growth

1. FEN1 endonuclease = dominant pathway to remove RNA primers = by cleaving single stranded FLAP
2. RNAse H endonuclease = also contributes by removing the RNA portion of the RNA:DNA hybrid
3. DNA ligase = joins the adjacent fragments by catalysing the formation of phosphodiester bond between 3’ OH & 5’ phosphate groups of adjacent nucleotides

Question 25

DNA ligase

Answer 25

enzyme responsible for sealing breaks in DNA strands. responsible for patching together Okazaki fragments

Question 26

are introns, promoters and UTrs kept in DNA replication

Answer 26

yes