DNA

Question 1

A polymer of deoxyribonucloside mono-phosphates covalently linked by a 3’⇢5’

1. Hydrogen bond
2. Phosphodiester bond
3. Peptide bond

Answer 1

Phosphodiester bond

Question 2

The structure of DNA has the following, which is not an answer

1. Double helix with antiparallel chains
2. Major groove which binds regulatory proteins
3. minor grove which binds drugs
4. sugar ribose backbone

Answer 2

sugar ribose backbone, because it is a sugar phosphate backbone

Question 3

Which DNA base pairing will need a lot of heat to separate them

1. AT
2. GC

Answer 3

GC - because it has 3 hydrogen bonds vs AT with 2 hydrogen bonds

Question 4

What is the temperature at which ½ of the helical structure is lost

1. heating temperature hm
2. melting temperature Tm
3. Vaporization temperature

Answer 4

Melting temperature Tm

At temperatures above Tm, DNA is present as a single strand.

Graph: vertical ( absorbance of UV), horizontal (temperature). More UV absorbed to break helical structure= high temperature

Question 5

Which structural form of the double helix of DNA is the most common?

1. B-DNA
2. Z-DNA
3. A-DNA

Answer 5

B-DNA

A-DNA; right handed helix usually present with non physiological conditions

Z-DNA; left handed helix. Present with methylation and modification of DNA

Question 6

Eukaryotes have the following characteristics, which one is incorrect?

1. Single stranded, circular chromosome associated with non-histone proteins
2. linear double stranded DNA molecule associated with histone and non histone proteins
3. closed circular DNA in mitochondria of eukaryotes
4. All the above

Answer 6

ingle stranded, circular chromosome associated with non-histone proteins. This is a prokaryote

Question 7

Small circular extra chromosomal DNA molecules are called

1. Histones
2. Plasmids
3. Prions
4. Myloid linkage

Answer 7

Plasmids

Question 8

Enzymes used for DNA synthesis are called

1. Ribonucleases
2. DNA polymerases
3. deoxyribonucleases
4. All the above

Answer 8

DNA polymerases

Question 9

What are the order of the steps in prokaryotic DNA synthesis

1. RNA primer
2. Separation of the two complementary strands
3. DNA ligase
4. Chain elongation
5. Excision of RNA primers and replacement by DNA
6. Formation of the replication fork
7. Direction of DNA replication

Answer 9

1. Separation of the two complementary strands
2. Formation of the replication fork
3. Direction of DNA replication
4. RNA primer
5. Chain elongation
6. Excision of RNA primers and replacement by DNA
7. DNA ligase

Question 10

What base pairs are at the origin of replacement site

1. AC pairs
2. AT pairs
3. GC pairs
4. GA pairs

Answer 10

AT pairs because they are easier to melt

Question 11

True or False

Eukaryotes have multiple origin site of replication for rapid replication because they have bigger DNA, prokaryotes have one origin site or replication because it has smaller DNA

Answer 11

True

Question 12

These 2 things happen at this step of prokaryotic DNA synthesis

1. As the 2 strands unwind and separate they form a V where active synthesis occurs
2. Replication of dsDNA is bidirectional generating a replication bubble

Answer 12

Formation of the replication fork

Question 13

Binds to origin and causes the AT rich regions to melt

Answer 13

DnaA protein

Question 14

unwinds the double helix

Answer 14

DNA helicases

Question 15

ssDNA binding proteins

Answer 15

keeps the strands apart and protect DNA from nucleases that degrade ssDNA

Question 16

Cut and rejoin one strand of double helix to remove supercoils

Answer 16

Topoisomerase I

Question 17

cuts and rejoins both strands e.g. DNA gyrase

Answer 17

Topoisomerase II

Question 18

The strand that is being copied in the direction of the advancing replication fork which is synthesized continuously

Answer 18

Leading strand

Question 19

Strand being copied in the opposite direction to the direction of the replication fork, it is synthesized discontinuously

Answer 19

lagging strand

this has okazaki strands

Question 20

True or False

DNA polymerases read the parental strand in the 3’⇢5’ direction therefore synthesis happens in the 5’⇢3” direction

Answer 20

True

Question 21

T/F

DNA polymerases require and RNA primer (`10nucleotide) with a free OH on the 3’ end

Answer 21

True

• RNA primer is catalyzed by primase
• RNA polymerases do not need a primer

Question 22

Which polymerase is responsible for chain elongation during the prokaryotic DNA synthesis

1. DNA polymerase III
2. DNA Polymerase I
3. RNA polymerase IV
4. DNA Polymerase II

Answer 22

DNA Polymerase III

• highly processive, it remains bound to template by its beta subunit as it moves along
• it has 3’to5’ exonuclease activity to correct mismatching bases. Goes backwards and corrects mis-matches

Question 23

Which polymerase is responsible for excising RNA primers and filing the gap during the prokaryotic DNA synthesis

1. DNA polymerase III
2. DNA Polymerase I
3. RNA Polymerase IV
4. DNA Polymerase II

Answer 23

DNA Polymerase I

Question 24

This makes the final phosphodiester linkage between the 5’ phosphate on the DNA chain synthesized by DNA pol III and the 3’ OH on the chain made by DNA pol I

Answer 24

DNA Ligase

Question 25

**True or False** In eukaryotic DNA replication, RNA primers are removed by RNase rather than DNA polymerase I

Answer 25

True

Question 26

Stage in interphase where a cell prepares to initiate DNA synthesis, biosynthesis also occurs here

Answer 26

G1

Question 27

Stage in interphase where a cell DNA content doubles, DNA synthesis occurs here

Answer 27

S phase

Question 28

Stage in interphase where a cell where biosynthesis for mitosis occurs, more DNA synthesis happens here

Answer 28

G2

Question 29

* If you remove growth factors, cells will end up in this phase of interphase * this is where cells are sent to reactivate * Nerve cells exit this cell cycle stage permanently * Cells that have ceased division

Answer 29

G0

Question 30

Phase of the cell cycle where cell division happends

Answer 30

mitosis

Question 31

* DNA polymerase that contains primase * initiates DNA synthesis

Answer 31

Polymerase Alpha

Question 32

DNA polymerase that elongates the okazaki fragments of the lagging strand

Answer 32

DNA Polymerase delta

Question 33

DNA polymerase that elongates the leading strand

Answer 33

DNA polymerase epsilon

Question 34

* complexes of noncoding DNA plus proteins located at the ends of linear chromosomes * maintain structural integrity of the chromosomes, preventing attach by nucleases * Allow repair enzymes to distinguish between a true end from a break in dsDNA * Consist of several thousand tandem repeats of noncoding AGGGTT paired with a complementary region of Cs and As * Shorten with every successive division

Answer 34

Telomeres

Question 35

This enzyme maintains telomeric length in stem cells and cancer cells

Answer 35

telomerase - keeps replacing the telomere region

Question 36

Enzyme that synthesizes DNA from RNA

Answer 36

Reverse Transcriptase

Question 37

* Basic proteins abundant in lysine and arginine residues that are found in eukaryotic cell nuclei. They act as spools around which DNA winds to create structural units called nucleosomes * Eukaryotic DNA is associated with these tightly bound basic proteins

Answer 37

Histones

Question 38

Histones + DNA

Answer 38

**Nucleosomes** ## Footnote Each chromosome contains a long molecule of DNA, which must fit into the cell nucleus. To do that, the DNA wraps around complexes of histone proteins, giving the chromosome a more compact shape

Question 39

DNA damage can happen by the following which is not correct? 1. Hydrolysis - lose amino group and get H2O 2. Oxidation - loss of electrons 3. Methylation - different parts of bases can be methylated 4. UV light 5. Ionizing radiation 6. All the above

Answer 39

All the above

Question 40

This DNA damage leads to the formation of pyrimidine dimers & thymine dimers ( thymines bond together)

Answer 40

UV light

Question 41

This type of DNA damage leads to strand breaks in the DNA

Answer 41

Ionizing radiation