Chapter 6 Conceps

Question 1

What is meant by the term complementary strands of DNA?

Answer 1

At each and every position the other strand has the complimentary basepair, so where there is an A on one strand there will be a T on the other, and where there is a C on one strand, on the other strand there will be a G

Question 2

What is meant by the term semi-conservative replication?

Answer 2

each of the daughter DNA double helices ends up with one of the original strands plus one strand that is completely new.

Question 3

What types of bonds link the 2 DNA strands together?

Answer 3

hydrogen bonds

Question 4

After 1000 cell divisions, are the original molecules of DNA somewhere among those cells?

Answer 4

Yes

Question 5

Where does DNA synthesis begin?

Answer 5

In the nucleus

Question 6

Do bacteria have more than one origin of replication?

Answer 6

1 origin of replication (generally)

Question 7

Replication origins are generally easy to unwind, so they are rich in A-T basepairs or G-C basepairs?

Answer 7

easy to unwind, so A-T because A-T only has 2 H bonds while G-C has 3 H bonds

Question 8

DNA synthesis proceeds always in the same direction and that is?

Answer 8

5’ to 3’ ALWAYS

Question 9

How are nucleotides linked together on the growing leading or lagging strand?

Answer 9

Nucleotides are linked by covalent phosphoanhydride bonds (also called phosphodiester bonds)

Question 10

What provides the energy for DNA polymerization?

Answer 10

Incoming deoxyribonucleoside triphoshate is hydrolyzed and the energy is given from breaking the strong phosphoanhydride bond (had 3 phosphates and broke off 2 of them)-pyrophosphate goes on to be hydrolyzed by water molecule and this releases more energy making the reaction basically irreversible

Question 11

At the replication fork, are both strands polymerized in the 5’-to-3’ direction?

Answer 11

Yes

Question 12

At a replication fork, is the leading strand synthesized continuously?

What about the lagging strand?

Answer 12

Yes, the leading strand is synthesized continuously.

No, the lagging strand is synthesized discontinuously

Question 13

What is an Okazaki fragment?

Answer 13

Short pieces of DNA that are added 5’ to 3’ on the lagging strand then are later ligated together to make a continuous DNA strand.

Question 14

What is primase?

Answer 14

Type of RNA polymerase that synthesizes RNA primer on the lagging strand (also synthesizes a single primer to begin the leading strand)

Question 15

What is the RNA primer and where does it occur?

Answer 15

tiny strand of RNA (~10 nucleotides) added to single stranded DNA in the lagging strand so the polymerase can come in and have a 3’ end to add on to. (RNA primase also lays down a single RNA primer to begin the leading strand)

Question 16

What do single stranded DNA binding proteins do?

Answer 16

bind to the single-stranded DNA exposed by the helicase, transiently preventing it from re-forming base pairs and keeping it in an elongated form so that it can readily serve as a template for DNA polymerase.

Question 17

How often does DNA polymerase make an error?

Answer 17

The DNA polymerase with 3’ to 5’ proofreading and without strand mismatch repair makes one error per 1*10^7 nucleotides copied

Question 18

How often does DNA polymerase make an error if you add in the strand mismatch repair system?

Answer 18

1*10^9 nucleotides copied (99% corrected) (1 mistake in a billion; humans it is 1 mistake in 10 billion actually)

Question 19

How often does DNA polymerase make an error if you add in the strand mismatch repair system on top of the DNA polymerase and it’s 3’-to-5’ exonuclease (proofreading) activity?

Answer 19

1*10^9 nucleotides copied (99% corrected)

Question 20

Is proofreading and DNA polymerizing located in the same molecule?

Answer 20

DNA polymerase has two separate sites: one for synthesis (polymerizing) and one for proofreading

Question 21

Are they in distinct sites in the same molecule?

Answer 21

Yes

Question 22

What direction does proofreading occur? (5’-to-3’ or 3’-to-5’)

Answer 22

3’ to 5’

Question 23

Can DNA polymerase initiate a new strand from scratch or does it require a primer?

What kind of primer?

Answer 23

leading strand only needs a primer at the replication origin, but the lagging strand needs an RNA primer to begin each okazaki fragment.

An RNA primer

Question 24

How many primers for the leading strand?

Answer 24

Just 1 for the leading strand

Question 25

How many primers for the lagging strand?

Answer 25

1 for every okazaki fragment

Question 26

What is a primer?

Answer 26

a short segment of RNA or DNA about 10 nucleotides long

Question 27

Where does helicase that opens up the DNA at the replication fork get its energy to do this?

Answer 27

ATP hydrolysis to pry open the DNA by the replication fork

Question 28

What is the function of the sliding clamp?

Answer 28

replication protein; keeps the polymerase firmly attached to the template while it is synthesizing new strands of DNA (this phenomenon is referred to as processivity)

Question 29

Does a single nucleotide substitution always result in a mutation in a protein encoding gene?

Answer 29

NO only 1-2% of the genome codes for proteins so a single mutation will most likely not result in a mutation in a protein (in the exons that encode a protein)

Question 30

How much of the genome of humans codes for proteins?

Answer 30

~2 percent

Question 31

How does DNA mismatch repair identify the parental/template strand versus the newly synthesized strand?

Answer 31

There is a nick (single-stranded break) that provides a signal that directs the mismatch repair machinery to the appropriate strand

Important because it would not know which strand was the parental and which strand was the template strand–this is critical to not introduce new mutations

Question 32

What does depurination refer to and how does it occur?

Answer 32

Causes lesions that look like missing teeth; it is when the base is hydrolyzed leaving the deoxyribose sugar and phosphate backbone intact

Question 33

How often does deupruination occur?

Answer 33

1*10^12 depurinations of adenosine & guanine occurs in the body every few seconds (remember you are made of trillions of cells so probably less than one depurination occurring in each cell per second or so)

Question 34

How does UV irradiation affect the DNA?

Answer 34

Can cause pyrimidine dimers like thymine dimers

Question 35

What are thymine dimers?

Answer 35

promotes covalent linkage between two adjacent pyrimidine bases, usually thymines

Question 36

What does cytosine become when it is deaminated?

Answer 36

Cytosine when deaminated chemically is the nucleotide uracil

Question 37

What repair machinery repairs thymine dimers?

Answer 37

Strand mismatch repair, endonuclease recognizes distortion in DNA helix, nicks DNA on either side (approximately 25 basepairs around distortion) and then endonuclease removes this strand completely and DNA polymerase I repairs this and DNA ligase seals nick

Question 38

What are the 3 steps to DNA repair?

Answer 38

1. Excision of damaged region (by DNA glycosylase)
2. DNA polymerase makes new top strand using bottom strand as a template
3. DNA ligase seals nick

Question 39

What is DNA glycosylase and what does it do?

Answer 39

enzyme that removes damaged or incorrect base; is able to scan along the DNA molecule at incredible speed and identify distortions

Question 40

What is DNA ligase and what does it do?

Answer 40

enzyme that seals the nicks in the phosphodiester bonds in DNA molecule (phosphodiester bonds are covalent bonds)

Question 41

How fast does the replication fork move in a bacteria?

Answer 41

500-1000 nucleotide pairs per second

Question 42

How fast does the replication fork move In a eucarytoic cell?

Answer 42

50-100 nucleotide pairs per second; so 10-fold slower than in bacteria

Question 43

What enzyme deals with positive supercoiling ahead of the replication fork and removes these supercoils?

Answer 43

topoisomerase “untwisting enzyme”; introduces nicks in the DNA then unwinds supercoils one at a time and then reseals nicks (some topoisomerases make one nick (break one strand) and some nick both strands of the DNA backbone, and then after removing supercoils religates them together

Question 44

Does topoisomerases break the strands of DNA to accomplish its job?

Answer 44

it cuts either one or both of the DNA strands to relieve tension then they are religated back together.