Chapter 30 DNA Structure, Replication, and Repair

Question 1

DNA structure

Define the structure of DNA
How is DNA situated in Eukaryotes and Prokaryotes

Answer 1

DNA is a polymer of deoxyribonucleoside monophosphates (dNMP))
DNA exist as double stranded (dsDNA)
two strands: double helix

Eukaryotes: associated w/ various types of proteins in the nucleus ( present in the nucleus
Prokaryotes: non- membrane bound (nucleoid)

dNMP is the primary structure of DNA
dsDNA is the secondary structure of DNA

Question 2

**3’ to 5’ phosphodiester bonds **

which end has a free phosephate ?
unbranched chain shows ?
which end of the strand has a free hydroxyl group ?
conventional direction of the strand reads from and to what end ?

Answer 2

5’ end
polarity
3’ end
from the 5’ end of the chain to the 3’end

conventional: reads from 5 to 3

Question 3

**Base-pairing **
1. Adenine is always paired with what ?
2. Cystosine is always paired with ?
3. These base pairs are held by what type of bonds ?
4. in simple terms define chargaff rule ?

Dna bases are always complement to each other

Answer 3

Thymine
Guanine
hydrogen bonds
states that in any sample of DOUBLE stranded DNA, the number/amount of A must equal the amount/number of T, and the amount of G must equal the amount of C.
Total amount of purines must be:
(A+G) = (T+C)

A = T
C = G

Key mnemonic”:
Anne=Tiangco
Connie=Gardiola

Question 4

**Prokaryotic DNA Replication **
where was the prokaryotic dna replication studied from ?
complimentary strand separation in prokaryotes ?
what is the site of replication called ?
what does the oriC site (replication site) consist of ?
How about in eukaryotes, where does the replication site start ?

only important points to know

Answer 4

1. E.coli bacteria
2. polymerase only use single starnd DNA as template and begins at a single nucleotide sequence
3. oriC
4. A-T rich segemnts
5. on multiple site along the DNA helix

Question 5

Unwinding supercoils:
1. define positive and negative supercoils on DNA starnds:
2. Topoisomerases enumerate twp types ?
3. DNA type I topoisomerase and DNA type II ? define

Answer 5

1.Positive coil: region of DNA ahead of the replication fork
Negative coil: region found behind the replication fork
2.Reversibly cleave one strand of the double helix (does NOT require ATP)
Releives and relaxes super coils

3. Top I and Top II

Type I Topoisomerase: relaxes coils, do not require ATP, stores energy (reuses it) Relaxes NEGATIVE coils

Type II Topoisiomerase: (gyrase)
breaks strands, reseals strands
relieves BOTH negative and positive supecoils
REQUIRE ATP !!!
+++ negative coils into

Anti cancer agents: target human Topoisomerase type II and Type I drugs can be specific to either targeting topo I or topo II

Fluproquinolones (ABX) targets DNA Gyrase

Question 6

Helicase

Answer 6

Unwinds DNA remplate at the replication fork

Question 7

Describe in a few words
“The Origin of Replication”

Answer 7

A-T rich site (sequences on the strand)
example TATA box regions found on “promoter” and origin = of replication

Question 8

Role of Primase in DNA

Answer 8

makes an RNA primer for DNA ploymerase III to continue to intiatiate its action (replication)

DNA polymerase III needs a “GO” signal from RNA primer
for exaple before finishing up on full glam make up (we need a primer) lol

Question 9

DNA polymerase I

Answer 9

Degrades RNA primer, replaces it with DNA.

Same functions as DNA pol III, excises RNA primer with 5’ to 3’ exonuclease

Question 10

DNA Ligase I

Answer 10

joins Okazaki fragments

Question 11

RNA primer

Answer 11

so DNA polymerase cannot initiate its activity in replication with out RNA primer !!! remeber this

RNA primer is a **short **piece of RNA base paired to the DNA template, there by forming a double stranded DNA-RNA hybrid.

Question 12

RNA PRIMER

what is the difference between a primase and primosome ?

Answer 12

**Primase: **a particular kind RNA polymerase (DnaG)
makes short stretches of RNA ( 10 nucleotides)
(this primase is antiparallel and complementary to the DNA template.

**Primosome **protein complex responsible for creating RNA primers on single stranded DNA during DNA replication. (required for the leading-strand)) synthesis and intiates formation

Direction of primer in DNA synthesis: 5 to 3

Keyword short stretch of nucleotides acts as an intiator for DNA pol III.
RNA primers are later removed.

Question 13

Elongation Process: Important enzyme
1. DNA polymerase III

Answer 13

uses 3’ end hydroxyl of the RNA primer as an acceptor to “start” the process

Remains bound onto the template strand as it moves along and does its job of replication

Action: adds nucleotides along the single stranded DNA

Polymerase III consist of a holoenzyme forming a ring that encircles and moves along the template serves as a SLIDING CLAMP

Question 14

RNA PRIMER EXCISION

what is the role of EXONUCLEASE ?
endonuclease ?
Exonuclease ?

get familiar with the difference of DNA pol I and DNA pol III

Answer 14

removes RNA primer !
removes nucleotides from the end of the DNA chain can be 5 to 3 direction or 3 to 5 direction

Endonucleases: cut out from “with in” the chain

Exonucleases: cut out from the end of the chain

Question 15

DNA LIGASE

Answer 15

glues the strand together
joins two stretches together
requires energy

Question 16

Proof reading:

which one does the proof reading of newly synthesized nucleotides ?

review foot notes on specific diferneces in the activities of these enzymes and the direction in which they work on the strand

5 to 3 = polymerase (polymerization, forming eg synthesizing chain)
3 to 5 = exonuclease (editing, checking for errors)
BOTH are called DNA polymerase but is labelled either Polymerase I or II depending on their responsibilities

Answer 16

DNA polymerase III
direction (3’ to 5’ exonuclease activity)
in addition to its job repliacting from 5’ to 3’ direction)

DNA pol III makes sure that the base of the newly added nucleotide correct !!! Now if it is not paired correctly the (3’ to 5’ exonuclease) removes the error/mistake in the direction opposite to the polymerization

Question 17

Nucleic Acids

Answer 17

Required for the storage and expression of genetic information

DNA is made out of nucleic acids