DNA Replication

Question 1

What is the CENTRAL DOGMA?

Answer 1

DNA replication –> transcription (mRNA) –> translation (proteins)

Question 2

describe the structure of DNA.

Answer 2

made out of NUCLEOTIDES
–> A with T (double bond)
—> C with G (triple bond)
Right Handed Double Helix
–> 10 bp/turn
–> 0.34nm between stacked bases
–> 3.4 nm/helical turn

REMEMBER: C and G rhyme with THREE

Question 3

what does it mean that DNA is semi conservative?

Answer 3

each parent strand serves as a TEMPLATE for a COMPLIMENTARY daughter strand
after one round of replication, each helix contains one new strand and one old strand

Question 4

what were the other proposed models for DNA replication?

Answer 4

conservative (one completely old strand, one completely new)
dispersive (old and new scattered in daughter DNA)

Question 5

how is DNA read? synthesized?

Answer 5

read: 3’ to 5’
synthesized 5’ to 3’

Question 6

describe THETA replication

Answer 6

occurs in most CIRCULAR DNA
ONE origin of replication in AT rich area
replication fork opens and DNA is synthesized, BIDIRECTIONALLY
TWO circular strands of DNA produced
does NOT BREAK DNA

Question 7

describe the ROLLING CIRCLE replication

Answer 7

occurs in F factor of e coli
initiated by a BREAK in a strand
synthesis begins on the 3’ end of the BROKEN strand
CLEAVAGE releases a single stranded linear DNA and double stranded circular DNA
linear DNA can recirculize and replicate
liner DNA can go into another bacteria
replication is UNIDIRECTIONAL

Question 8

describe LINEAR chromosome replication

Answer 8

many origins of replication
a replication bubble produces at each origin
synthesis is BIDIRECTIONAL
adjacent fork FUSE
produce two IDENTICAL LINEAR DNA molecules
EUKARYOTES

Question 9

what does DNA replication require?

Answer 9

DNA polymerase
four dNTPs
template DNA
RNA primer (provides 3’ OH)

Question 10

what holds two strands of DNA together?

Answer 10

hydrogen bonds

Question 11

describe the directionality of the daughter strand

Answer 11

complementary and anti-parallel

Question 12

how is a new base added to the growing chain?

Answer 12

2 phosphates are cleaved off the end of the 3’ nucleotide
a new base is added to the 3’ end
phosphodiester bond formed between nucleotides

Question 13

how big are okazaki fragments?

Answer 13

prokaryotes: 1kb-2kb
eukaryotes: 0.1kb-0.2kb

Question 14

what type of replication does NOT have a lagging strand?

Answer 14

rolling circle

Question 15

what nucleotides are found in the origin of replication?

Answer 15

A&T –> two H bonds, easier to bread

Question 16

what is the origin of replication called in e. coli?

Answer 16

oriC

Question 17

what proteins are involved in the initiation of prokaryotic DNA replication?

Answer 17

DnaA –> bind or oriC, initiate unwinding
SSBP –> attach to one strand of DNA, keep linear, avoid hairpins
HELICASE –> unzips genes, binds to LAGGING strand
GYRASE/TOPOISOMERASE –> makes double stranded nicks, relieves torsion

Question 18

what proteins are involved in the synthesis of prokaryotic DNA replication?

Answer 18

PRIMASE –> synthesizes a short RNA primer, provides the 3’ OH end for polymerase, one primer on leading strand, multiple on lagging
DNA polymerase III. –> 5’ to 3’ polymerase activity (ELONGATES strand), 3’ to 5’ exonuclease activity (moves backwards to proofread)
DNA polymerase I –> 5’ to 3’ exonuclease activity, removes RNA primers

Question 19

what proteins are involved in the synthesis of prokaryotic DNA replication in the LAGGING strand?

Answer 19

once polymerase III reaches the 5’ end of a primer, it’s swapped for polymerase I
polymerase I removes primer and synthesizes short tract of DNA
LIGASE joins OKAZAKI fragments

Question 20

how does DNA replication differ in EUKARYOTES?

Answer 20

BIDIRECTIONAL from multiple origins of replication
HELICASE binds to initiator proteins, involves MCM complex
DNA replication occurs during the S phase
MCM complex attaches to origin during G1 phase
replication of entire genome ONCE and only once
shorter RNA primers and Okazaki fragments

Question 21

what are the four polymerases in eukaryotes?

Answer 21

alpha –> generates RNA primers
epsilon –> leading strand replication
delta –> lagging strand replication
translesion –> substitutes in to corrects mistakes from E or D

REMEMBER: epsilon starts with an e, leading has an E in it

Question 22

what happens to the nucleosomes?

Answer 22

histones need to be doubled and their modifications need to be replicated
new nucleosomes consist of old and new histones
facilitated by CHROMATIN ASSEMBLY FACTORS
H2A, H2B, H3, H4, H1 (there’s 2 twos)

Question 23

what happens to telomeres?

Answer 23

SHORTEN after each round of replication
only found in LINEAR DNA (has ends)
terminal primer positioned 70-100 NTs from the end of the chromosome

Question 24

how does TELOMERASE work?

Answer 24

RNA part of telomerase is complementary to G-rich telomere of chromosome
NTs added to G-rich strand
primer moves along the strand, more NTs added
the primer is cleaved off and synthesis on the complementary strand fills in the gap
present in HIGHLY dividing cells, LACK of enzyme in slowly dividing cells –> associated with AGING

Question 25

what diseases are associated with telomers?

Answer 25

PROGERIA and WERNER’S syndrome –> short telomeres

cancer cells –> high telomerase activity, promotes their growth