Week 4_DNA structure/replication/repair

Question 1

what are the components of a nucleotide?

Answer 1

phosphate group

nitrogenous base

ribose sugar (in RNA)

deoxyribose sugar (in DNA)

Question 2

how do nucleotides join together to form DNA?

(what direction?)

Answer 2

phosphodiester bonds are formed between the existing nucleotide and the new nucleotide to be added

DNA is only is synthesized in the 5’ to 3’ direction by the enzyme DNA polymerase III

Question 3

what is the backbone of DNA held together by?

Answer 3

covalent phosphodiester bonds

Question 4

how many bp are in 1 complete turn?

Answer 4

10

Question 5

what is the 5’ and 3’ end of a nucleotide?

Answer 5

5’ == phosphate group

3’ == OH group on the ribose/deoxyribose sugar

Question 6

what is at the 5’ end of DNA?

Answer 6

has a free phosphate group attached to the 5’-carbon

Question 7

what is at the 3’ end of the DNA?

Answer 7

has a free hydroxyl (-OH) group at the 3’-carbon

Question 8

what does it mean if DNA is antiparallel?

Answer 8

DNA strands are in opposite directions

Question 9

what are the 3 phases of DNA replication?

Answer 9

initiation

elongation

termination

Question 10

describe initiation stage of DNA replication

Answer 10

starting of the process

bringing together all the necessary enzymes to replicate DNA

Question 11

describe elongation stage of DNA replication

Answer 11

actual process of replicating the DNA

Question 12

describe termination stage of DNA replication

Answer 12

make sure the process is appropriately stopped

Question 13

what does semiconservative replication mean?

Answer 13

(1) old DNA strands are separated (hydrogen bonds are broken)

(2) each old DNA strand is used as a template for a new DNA strand (semiconservative replication)

(3) the new DNA molecules are 1/2 old strand and 1/2 new strand

Question 14

what is the replication complex (RC)?

Answer 14

a large complex containing the enzymes needed to replicate DNA, interacts with the DNA

Question 15

where do RCs bind to the DNA to begin replication?

Answer 15

origin of replication (ori) == particular sequences of DNA where replication begins

Question 16

eukaryotic chromosomes have thousands of ori’s. Why?

Answer 16

eukaryotic chromosomes are very big

multiple ori’s allow for a much faster replication process

Question 17

describe how chromosomes get copied beginning at several ORI’s simultaneously

Answer 17

(1) the replication complexes bind to the ORI’s

(2) DNA strands are separated (by helicase) –> forms replication forks

(3) DNA replication proceeds bidirectionally

Question 18

DNA strands are separated at the ___ by helicase

Answer 18

replication forks

Question 19

what is the function of helicase?

Answer 19

breaks the hydrogen bonds between strands

Question 20

on the leading strand, new DNA is synthesized ___ in the ___ direction (by ___)

Answer 20

continuously

5’ –> 3’ direction

DNA Pol III

Question 21

on the lagging strand, new DNA is synthesized in ___ in the ___ direction (occurs more ___)

Answer 21

discontinuous fragments

opposite directions

occurs more slowly

Question 22

what are the 4 nitrogenous bases?

what do each of them bind to?

what bonds hold them together?

Answer 22

adenine

thymine

cytosine

guanine

adenine –> thymine
cytosine –> guanine

hydrogen bonds hold the nitrogenous bases together –> hold the two strands of DNA together

Question 23

what direction does DNA Pol III add nucleotides?

Answer 23

5’ –> 3’ direction

Question 24

what does DNA Pol III need in order to attach a new nucleotide?

Answer 24

needs a 3’-OH to attach a new nucleotide to

Question 25

is DNA Pol III able to add the first nucleotide in DNA replication?

Answer 25

no

Question 26

how does DNA replication get started?

Answer 26

through RNA polymerase enzyme

primase (an RNA polymerase) begins the DNA replication process

Question 27

DNA replication occurs ___ in the leading strand and ___ in the lagging strand

Answer 27

faster in leading

slower in lagging

Question 28

what enzyme removes the RNA?

Answer 28

DNA polymerase I removes and replaces the RNA nucleotides with DAN nucleotides

Question 29

what are nicks?

Answer 29

missing phosphodiester bonds in between Okazaki fragments

Question 30

what does DNA Pol I do?

Answer 30

1) removes RNA nucleotides

2) and replaces them with DNA nucleotides

3) can’t form the last phosphodiester bond –> leaves a ‘nick’ in the DNA backbone

Question 31

what does DNA ligase do?

Answer 31

1) enzyme that restores the missing phosphodiester bonds ‘nick repair’

Question 32

DNA polymerases are enzymes with high ___

Answer 32

processivity

Question 33

describe why DNA has high processivity

Answer 33

they can add thousands fo nucleotides without falling off the DNA (very stable)

Question 34

why are DNA polymerases so stable?

Answer 34

Sliding clamp protein helps DNA polymerases remain attached to the DNA

Question 35

if DNA polymerase adds an incorrect nucleotide, it can…

in other words, DNA polymerase has a ___ function

Answer 35

it can replace it with the correct nucleotide

proofreading

Question 36

what other proteins also scan DNA for errors and damage?

Answer 36

excision repair enzymes

Question 37

what do excision repair enzymes do?

Answer 37

detect and repair mismatches and DNA damage

Question 38

our DNA repair enzymes are constantly at work ___

Answer 38

repairing our DNA

Question 39

what happens when you have a deficiency in DNA repair enzymes?

Answer 39

xeroderma pigmentosum (XP) –> rare genetic disorder –> excision repair enzymes have significantly reduced ability to repair DNA damage

leads to development of cancers frequently and at young age

ER enzymes are critical for survival