Chapter 6: DNA and Biotechnology

Question 1

End Replication Problem

Answer 1

• The DNA at the very end of eukaryotic chromosomes can NOT be fully copied in each round of replication
• Results in shortening of chromosome
• A short stretch of DNA does not get an Okazaki fragment b/c primer would fall beyond the chromosome end
• The last RNA primer of the Okazaki fragment of the lagging strand is not converted to DNA
• Primer is degraded
• Each successive DNA copy is shorter than the previous one.

Question 2

What feature indicates higher stability of a DNA strand?

Answer 2

High GC content

*Higher # of hydrogen bonds (3)

Question 3

In what directions does DNA replication read the template and synthesizes?

Answer 3

Reads template: 3’ -> 5’

Synthesizes template: 5’ -> 3’

Question 4

Steps of Replication

Answer 4

1. Lay down RNA primer
2. DNA polymerase III (prokaryotes) or DNA polymerases alpha, delta, epsilon (eukaryotes) qill begin synthesizing the daughter strands of DNA in the 5’ -> 3’ direction.
3. Incoming nucleotides are dATP, dTTP, dCTP, and dGTP. As new phosphodiester bond forms a free pyrophosphate (PPi).
4. RNA primer removed by DNA polymerase I (prokaryotes) or RNase H (eukaryotes).
5. DNA nucleotides are added in place of RNA primer by DNA polymerase I (prokaryotes) or DNA polymerase delta (eukaryotes).
6. DNA ligase seals the ends of the DNA molecules together, creating one continuous strand of DNA.

Question 5

Primase

Answer 5

• Synthesizes a short primer (roughly 10 nucleotides) in the 5’ to 3’ direction to start replication on each strand
• RNA primers constantly added to lagging strand because not synthesized continuously and each Okazaki fragment needs new RNA primer
• Leading strand only needs 1 RNA primer

Question 6

Telomerase

Answer 6

• It replaces the telomeric sequence at the end of the DNA that is lost in each round of replication
• Highly expressed in rapidly dividing cells.

Question 7

What is the repeating unit at the telomere end?

Answer 7

TTAGGG

Question 8

What are the 5 classes of DNA polymerases in eukaryotic cells?

Answer 8

Alpha, Beta, Gamma, Delta, Epsilon

Question 9

Which eukaryotic DNA polymerases work together to synthesize both the leading and lagging strands?

Answer 9

Alpha, Delta, Epsilon

Question 10

Which eukaryotic DNA polymerase fills in the gaps left behind when RNA primers are removed?

Answer 10

Delta

Question 11

Which eukaryotic DNA polymerase replicates mitochondrial DNA?

Answer 11

Gamma

Question 12

Which eukaryotic DNA polymerases are important for DNA repair?

Answer 12

Beta and Epsilon

Question 13

Which eukaryotic DNA polymerases are assisted by the PCNA protein?

Answer 13

Delta and Epsilon

Question 14

Sliding clamp

Answer 14

• Formed by the trimer of PCNA protein

* It helps strengthen the interaction between DNA polymerases delta and epsilon and the template strand.

Question 15

How many origins of replication in eukaryotes?

Answer 15

Multiple per chromosome

Question 16

How many origins of replication in prokaryotes?

Answer 16

One per chromosome

Question 17

What bonds link nitrogenous bases?

Answer 17

Hydrogen Bonds

Question 18

How many hydrogen bonds are between adenine and thymine

Answer 18

2 Hydrogen Bonds

Question 19

How many hydrogen bonds are between guanine and cytosine?

Answer 19

3 Hydrogen Bonds

Question 20

What bonds link the nucleotides in the backbone?

Answer 20

Phosphodiester bonds

Question 21

Are phosphodiester bonds covalent or noncovalent?

Answer 21

Covalent

Question 22

Are hydrogen bonds covalent or noncovalent?

Answer 22

Noncovalent

Question 23

Operon

Answer 23

A unit of DNA containing a cluster of genes under control of a promoter and a repressor

Question 24

Conservative Mutation

Answer 24

A change in a DNA or RNA sequence that leads to the replacement of one amino acid with a biochemically similar one. It is conservative in the sense that it is not a radical change that might, for example, stop all protein production.

Question 25

Transition mutation

Answer 25

Purine -> Purine

or

Pyrimidine -> Pyrimidine

Question 26

Transversion

Answer 26

Purine -> Pyrimidine

or

Pyrimidine -> Purine

Question 27

Large-scale deletions

Answer 27

• More fatal since more genetic material is lost
• Large deletions could potentially reduce the methylation of important oncogenes
• Can affect epigenetic mechanisms associated with genes

Question 28

Endogenous compound

Answer 28

Produced by the body

Question 29

Antioxidants

Answer 29

Counteracts the effect of free-radicals in the cell

Question 30

Effect of Ethidium Bromide

Answer 30

Ethidium bromide’s intercalation into DNA causes conformational changes that can be oncogenic.

Question 31

What is a palindromic DNA sequence?

Answer 31

Nucleic acid sequence in a double stranded DNA molecule wherein reading in a certain direction (e.g. 5’ -> 3’) on one strand matches the sequence reading in the same direction (e.g. 5’ -> 3’) on the complementary strand.

Question 32

DNA Polymerase

Answer 32

Builds DNA from a DNA template

Question 33

RNA Polymerase

Answer 33

Builds RNA from a DNA template

Question 34

Reverse transcriptase

Answer 34

Builds DNA from a RNA template

Question 35

Why are antibiotics used in transfection?

Answer 35

To selectively grow only the bacteria that carry the antibiotic-resistant gene that was transfected into them.

Question 36

Why are antibiotics used in transfection?

Answer 36

To selectively grow only the bacteria that carry the antibiotic-resistant gene that was transfected into them.