Exam

Question 1

central dogma

Answer 1

replication, transcription, translation - DNA, RNA, protein

Question 2

AT bonds

Answer 2

2

Question 3

GC bonds

Answer 3

3 bonds

Question 4

ten base pairs

Answer 4

0.34nm between stacked bases, 3.4nm per helical turns

Question 5

semi conservative replication

Answer 5

each strand is template for new strand, new DNA has 1 parental and one new strand

Question 6

conservative model

Answer 6

whole strand is conserved, whole new strand is made

Question 7

dispersive model

Answer 7

bits of old and new in both

Question 8

theta replication

Answer 8

most circular DNA like bacteria, bi and unidirectional, produces 2 circular molecules, does not break nucleotide strand

Question 9

rolling circle replication

Answer 9

F factor of E.coli and some viruses, unidirectional, breaks nucleotide strand, produces 1 circular molecule and 1 linear molecule that may circularize

Question 10

linear chromosome replication

Answer 10

eukaryotic, bidirectional, does not break strand, many replicons, produces 2 linear molecules

Question 11

DNA replication requirements

Answer 11

DNA polymerase, 4dNTPs, single stranded template, RNA primer

Question 12

DNA replication features

Answer 12

synthesized 5’-3’, strands held together by H bonds between bases

Question 13

leading strand

Answer 13

add nucleotides 3’-5’ continuously, same direction as unwinding towards helicase

Question 14

lagging strand

Answer 14

adds nucleotides 5’-3’ discontinuously, Okazaki fragments, opposite direction

Question 15

okazaki fragments

Answer 15

1-2kb in prokaryotes, 0.1-0.2kb in eukaryotes

Question 16

oriC

Answer 16

DNA replication origin in E.coli, AT bond rich, requires less energy to break

Question 17

proteins in prokaryotic DNA replication

Answer 17

initiator proteins, DNA helicase, SSBP, DNA gyrase

Question 18

DNA helicase

Answer 18

binds to replication fork and unwinds 5’-3’, breaks H bonds, travels on lagging strand ahead of replication machinery

Question 19

single stranded binding protein (SSBP)

Answer 19

binds to unwound stands and prevent parent strands from annealing (hairpins), protects from nucleases

Question 20

nucleases

Answer 20

want to break phosphodiester bonds

Question 21

DNA gyrase

Answer 21

topoisomerase that makes double stranded breaks in DNA to relieve torsional strain, moves ahead of DNA helicase, Type 1-2

Question 22

replication initiation prokaryotic

Answer 22

1. initiator proteins bind to oriC and opens up to DNA
2. DNA helicase binds to lagging strand to unwind DNA
3. SSBP bind to unwound strands to keep DNA apart
4. DNA gyrase binds upstream to replication fork

Question 23

primase/RNA polymerase

Answer 23

synthesizes short RNA primer (~10) that provides 3’ OH end for DNA polymerase to begin synthesis

Question 24

replication elongation prokaryotic

Answer 24

1. 5’-3’ direction
2. leading strand continuously synthesized by DNA polymerase III
3. lagging strand synthesized in fragments

Question 25

DNA polymerase III

Answer 25

elongates 5’-3’, requires recognition of RNA polymerase, 3’-5’ exonuclease, can back up to correct mistakes

Question 26

DNA polymerase I

Answer 26

removes and replaces primers, 5’-3’ exonuclease activity to remove RNA primer

Question 27

DNA ligase

Answer 27

joins Okazaki fragments together through phosphodiester bonds between 5’-phosphate group and 3’-OH group

Question 28

lagging strand process

Answer 28

1. when DNA pol.III reached 5’ end of RNA primer, pol.III swapped for pol.I
2. pol.I removes RNA primer and re-synthesizes short tract of DNA
3. DNA ligase makes phosphodiester bond between 5’-3’ group to become continuous

Question 29

replication termination prokaryotic

Answer 29

occurs when helicase/replication forks meet, stops unwinding

Question 30

unique aspects of eukaryotic chromosome replication

Answer 30

replication begins at AT rich replicating sequences, DNA helicase binds to initiator protein of double strands, shorter RNA primers/okazaki fragments

Question 31

DNA polymerase alpha

Answer 31

generates RNA primer

Question 32

DNA polymerase epsilon

Answer 32

performs leading strand replication

Question 33

DNA polymerase delta

Answer 33

performs lagging strand replication

Question 34

origin licensing

Answer 34

origins prepared for replication of G1 phase, begins in S phase, can replicate genome only once

Question 35

basic features of RNA

Answer 35

ribose sugar and unstable 2’OH group, single stranded, many structure types for different functions

Question 36

non-coding RNA/small ncRNA

Answer 36

small nucleolar RNA (snoRNA), small interfering RNA (siRNA), small nuclear RNA (snRNA)