final exam (second part)

Question 1

modification of minor nucleosides in DNA is before or after DNA synthesis

Answer 1

after

Question 2

is 5-methycytosine in eukaryotes, bacteria, or both?

Answer 2

both

Question 3

is N6-methyladenosine in eukaryotes, bacteria, or both?

Answer 3

bacteria only

Question 4

what is an epigenetic marker in prokaryotes?

Answer 4

way to mark own DNA so that cells can degrade foreign DNA

Question 5

what is an epigenetic marker in eukaryotes?

Answer 5

way to mark which genes should be active

Question 6

what is messenger RNA?

Answer 6

code carrier for the sequence of proteins

Question 7

messenger RNA contains ________ instead of deoxyribose and uracil instead of _________

Answer 7

ribose; thymine

Question 8

mRNA with tRNA does what?

Answer 8

transfers genetic information from DNA to proteins

Question 9

define palindromes and how does it relate to biochem?

Answer 9

palindrome’s: words or phrases that are the same when read backward or forward; they can form hairpins and cruciforms

Question 10

factors affecting DNA denaturation: the midpoint of Tm (the melting temperature of a nucleic acid duplex (double-stranded molecule)) depends on what? high comp does what to Tm?

Answer 10

depends on base composition; it increases Tm

Question 11

factors affecting DNA denaturation: Tm depends on DNA length, so longer DNA has (higher/ lower) Tm and shorter DNA has (higher/ lower) Tm?

Answer 11

higher; lower

Question 12

factors affecting DNA denaturation: Tm depends on pH and ionic strength. high salt does what to Tm?

Answer 12

increases Tm

Question 13

what kind of DNA is most susceptible to oxidative damage? Amino Acid?

Answer 13

mitochondrial DNA; guanine- the hydroxylation of guanine

Question 14

what AA is most susceptible to chemical alkylation?

Answer 14

guanine- methylation of guanine

Question 15

UV light induces…?

Answer 15

dimerization of pyrimidines causing skin cancer

Question 16

Ionizing radiation causes…?

Answer 16

ring opening and strand breaking

Question 17

what does chromatin consist of?

Answer 17

fibers of protein and DNA and small amount of RNA

Question 18

DNA associates tightly with proteins called _______, which can be defined as?

Answer 18

histones; small proteins with lots of basic (Lys, Arg) residues

Question 19

DNA and protein are packed into discrete untis called ______

Answer 19

nucleosomes

Question 20

nucleosomes consist of ________ wrapped around _________

Answer 20

DNA; histones

Question 21

“beads on a string” consist of DNA wrapped around 8 histones, with the amino-terminal tails of histones sticking out that forms what?

Answer 21

sites for covalent modification, and form important contacts between nucleosomes

Question 22

the lagging strand is made discontinuously in short pieces (Okazaki fragments) that are spliced together via _______

Answer 22

DNA Ligase

Question 23

DNA is degraded by _______

Answer 23

nucleases

Question 24

what cleaves bonds that remove nucleotides from the ends of DNA

Answer 24

EXOnucleases

Question 25

what cleaves bonds within a DNA sequence?

Answer 25

ENDOnucleases

Question 26

in DNA elongation, what serves as substrates in strand synthesis?

Answer 26

nucleoside triphosphates

Question 27

why is a primer important?

Answer 27

the newly formed base pair migrates to make an active site available to the next pair to be formed

Question 28

What are the two pocket regions of DNA polymerase?

Answer 28

insertion site (where incoming nuc binds) and post- insertion site (where newly made base pair resides when polymerase moves forward)

Question 29

the number of nucleotides added before dissociation is called...?

Answer 29

processivity

Question 30

to correct an error, what kind of exonuclease activity is used?

Answer 30

3' --> 5' exonuclease activity

Question 31

DNA polymerases 5' --> 3' exonuclease activity are in what fragment?

Answer 31

klenow fragment

Question 32

what is the klenow fragment

Answer 32

a distinct domain that can be separated by protease treatment