Biochemistry 6: DNA and Biotechnology

Question 1

nucleosides

Answer 1

pentose sugar + nitrogenous base

Question 2

nucleotide

Answer 2

pentose sugar + nitrogenous base + phosphate group

Question 3

what is the difference between ribose and deoxyribose?

Answer 3

ribose has OH group on 2’ and 3’ carbons

deoxyribose only has OH group on 2’ carbon

Question 4

rules of aromatic rings

Answer 4

1. cyclic
2. planar
3. conjugated
4. Huckel’s rule: the compound has 4n + 2 π electrons

Question 5

B-DNA

Answer 5

right-handed DNA helix

turns every 3.4 nm and has 10 bases within each turn

major and minor grooves are the site of protein binding

Question 6

Z-DNA

Answer 6

left-handed DNA helix

turn every 4.6 nm, 12 bases within the turn

high GC content

no biological activity, very unstable

Question 7

DNA polymerases alpha, beta, epsilon

Answer 7

eukaryote polymerases responsible for synthesizing the leading and lagging strands

Question 8

DNA polymerase gamma

Answer 8

eukaryotic polymerase responsible for replicating mitochondrial DNA

Question 9

which eukaryotic DNA polymerases are important for DNA repair?

Answer 9

DNA polymerases beta and epsilon

Question 10

sliding clamp

Answer 10

PCNA protein + delta + epsilon

helps to strengthen the interaction between these DNA polymerases and the template strand

Question 11

oncogenes

Answer 11

mutated genes that cause cancer

Question 12

precursors to oncogenes

Answer 12

proto-oncogenes

Question 13

tumor suppressor genes

Answer 13

ex. p53

encode proteins that inhibit the cell cycle or participate in DNA repair sequences

sometimes called antioncogenes

Question 14

genes MSH2 and MLH1

Answer 14

involved in mismatch repair

detect and remove errors introduced in replication that were missing during the S phase of the cell cycle

Question 15

nucleotide excision repair

Answer 15

fixes helix-deforming lesions of DNA (such as adjacent thymine dimers) through a cut-and-patch process that requires an excision endonuclease to remove the incorrect nucleotide

DNA polymerase can then replace it with the correct nucleotide from 5’ to 3’

the nick in the strand is sealed by ligase

Question 16

base excision repair

Answer 16

fixes nondeforming lesions of the DNA helix (like cytosine deamination to form uracil) by removing the base, leaving an apurinic/apyrimidinic (AP) site

AP endonuclease required to remove the damaged sequence

DNA polymerase and ligase fill the gap and seal the strand

Question 17

DNA cloning

Answer 17

introduces a fragment of DNA into a vector plasmid that can be transferred into a host bacterium for proliferation

the fragment can be removed from the vector using restriction enzymes

Question 18

restriction enzymes

Answer 18

enzymes that recognize specific double-stranded DNA sequences

are palindromic

sometimes produce uneven, offset cuts (sticky ends) that are good for recombination with a vector DNA

can also create blunt ends that are straight across the DNA helix

Question 19

DNA libraries

Answer 19

large collections of known DNA sequences

could equate to the entire genome of the organism

can consist of either genomic or complementary DNA

Question 20

genomic libraries

Answer 20

DNA libraries that contain large fragments of DNA and include both exons and introns of the genome

cannot be used to make recombinant proteins or for gene therapy because genes can by chance be split into multiple vectors

Question 21

complementary DNA libraries

Answer 21

DNA libraries that contain only the coding sequences

made from reverse transcription of mRNA

can be used to reliably sequence specific genes, produce recombinant proteins, or make transgenic animal

Question 22

Southern blotting

Answer 22

blotting technique that can be used to detect the presence and quantity of DNA in a sample