EXAM 2

Question 1

semiconservative DNA replication

Answer 1

during DNA replication the two strands of the parent DNA double helix separate –> each strand then forms a template for free nucleotides to bind to –> thus creating two identical daughter strands

each daughter stand winds up with a strand from the original parent and a new strand (thus, semi)

Question 2

DNA polymerase

Answer 2

has 3’ –> 5’ exonuclease activity (known as proofreading)

Question 3

proofreading

Answer 3

exonuclease activity used by DNA polymerase

when a wrong nucleotide is input during 5’ –> 3’ DNA synthesis, DNA polymerase can remove it using this technique in a 3’ –> 5’ fashion; the nucleotide can then be replaced, resuming 5’ –> 3’ polymerase activity

Question 4

nucleotide mismatch

Answer 4

if left unrepaired by DNA polymerase BEFORE the next round of DNA synthesis, this action could result in permanent changes

Question 5

sickle-cell anemia

Answer 5

consequence of a point mutation in the beta-globin gene

glutamic acid in the beta-globin protein is replaced with a valine (non-polar) due to a single nucleotide substitution in the DNA

Question 6

nicks

Answer 6

breaks in recently synthesized stands

Question 7

Okazaki fragments

Answer 7

short fragments due to the discontinuous synthesis of the lagging strand during DNA replication

these fragments polymerize 5’ –> 3’ and need to be amended via nick repair

Question 7

DNA mismatch repair proteins

Answer 7

(in eukaryotes)

these proteins recognize a mismatched pair because of the topological disturbance and take the change to bind to it

Question 8

mismatch repair

Answer 8

(in eukaryotes)

1) DNA mismatch repair proteins recognize the mismatch pair and bind to it
2) the DNA is scanned for any nicks in the DNA
3) the nicked strand is digested all the way from the nick back to the mismatch site
4) DNA polymerase and DNA ligase complete the rapair

Question 9

cytosine deamination

Answer 9

a deaminated C is a mismatch in which G is paired with a U (C–>U)

after DNA replication, one strand will be mutated & contains the U that will code for an A (G–>A)

the G containing strand of the parent will go unchanged

main point: cytosine pairs with guanine and uracil pairs with adenine

Question 10

adenine deamination

Answer 10

main point: adenine pairs with thymine and hypoxanthine pairs with cytosine

Question 11

depurination

Answer 11

results in a depurated sugar and no base pairing

a depurinated A in the parent strand has no A paired with the respective T

after DNA replication, the mutated strand is distorted by deletion of the A-T nucleotide pair

the new strand with the parent strand containing the T will go unchanged after DNA replication

Question 12

direct reversal (direct repair)

Answer 12

a general category of repair mechanisms for spontaneous mutations

this action fixes the altered molecular by reversing the chemical transformation occurring

it requires specific enzymes for each individual lesion (i.e. some organisms reverse thymine dimers by using a specific photo reactivating enzyme)

Question 13

base excision repair

Answer 13

is a general mechanism for repairing nucleotide mismatches caused by spontaneous mutations

chemical transformation is not reversed, but the damaged base(s) are replaced instead

the unpaired base is recognized and replaced before DNA replication occurs

Question 14

spontaneous mutation

Answer 14

these mutations introduce things that don’t belong in the DNA and are easily recognizable by the cell for repair

Question 15

base excision repair mechanism

Answer 15

1) DNA glycosylase removes the damaged base leaving only the sugar and phosphate backbone to remain); an endonuclease recognizes the site and cleaves the phosphodiester bond; a deozyribosephosphodiesterase removes the remaining sugar and phosphate

2) DNA polymerase places a new nucleotide (5’–>3’)

3) DNA ligase seals the nick (3’–>5’?)

Question 16

DNA rearrangements

Answer 16

recombination events that alter the arrangement of genes within the genome

Question 17

site-specific recombination

Answer 17

occurs between specific DNA sequences that share partial sequence homology (similarity)

this rearrangement doesn’t depend on DNA sequence recognition between chromosomes but instead, specific proteins recognize the homologous sequences and mediate somatic recombination

Question 18

lytic lifestyle

Answer 18

free circular DNA in host bacterial cell

Question 18

immunoglobulins

Answer 18

antibodies

Question 18

bacteriophage (phage)

Answer 18

a virus that infects bacteria

Question 19

lysogenic lifestyle

Answer 19

linear DNA integrated in host DNA (a prophage)

Question 19

attP (phage)

Answer 19

(before insertion) a common core sequence (O) is flanked by two gamma-specific sequences (P and P’)

P-O-P’

after insertion attL: B-O-P’

Question 19

attachment sites

Answer 19

include the attP site in phage DNA and the attB site in the host bacterial DNA

insertion resulting in two new sites attL and attR

Question 20

attB (bacteria)

Answer 20

(before insertion) same common core sequence (O) flanked by two bacterial specific sequences (B and B’)

B-O-B’

after insertion attR: P-O-B’

Question 20

transposable element

Answer 20

chromosome segment that can move

Question 21

insertion sequences

Answer 21

simple bacterial transposons

Question 22

non replicative transposition

Answer 22

“cut and paste”

the insertion sequence is cut from the donor site and pasted into the target site, resulting in the insertion sequence moving from one site of the genome to another

Question 23

replicative translation

Answer 23

“copy and paste”

a copy of the insertion sequence is made by local DNA replication and pasted into the target site, resulting in a new copy of the insertion sequence appearing at the target site

Question 24

retrotransposition

Answer 24

requires the synthesis of a copy of a retrotransposon that is catalyzed by the enzyme reverse transcriptase

Question 25

multipotent

Answer 25

stem cells that have the ability to differentiate into all cell types within one particular lineage (think of blood stem cells)

Question 26

pluripotent

Answer 26

cells that can become ANY cell in the entire body

Question 27

epigenetics

Answer 27

the study of changes and variations in phenotypes that are potentially heritable, but are not caused by permanent changes in DNA base sequences

Question 28

transcription regulatory proteins

Answer 28

function is to activate the transcription of DNA by binding to specific DNA sequences

Question 29

transcription initiation complex

Answer 29

formed by transcription regulators, general transcription factors, and RNA polymerase

Question 30

MyoD

Answer 30

a single transcription regulator that commits cells to become myoblasts (muscle cell precursors that then form into multinucleate myotubes that become muscle fibers)

*** the combinatorial control of the muscle cell fate

Question 31

induced pluripotent stem cells (iPS cells)

Answer 31

in the case of mice, cultured fibroblasts can be programmed to become these types of cells by the artificial expression of three transcription regulators (oct4, Sox2, klf4)

Question 32

epimorphic regeneration

Answer 32

(in salamanders)

adult cells dedifferentiation becoming neoblasts that undergo rapid cell division and become re-specified to form the missing adult structure

Question 33

epigenetic inheritance

Answer 33

involve heritable changes in gene expression that are not caused by changes in the DNA sequence

examples:
1) feedback loop circuits involving transcription regulators
2) preservation of covalent histone modifications and chromatin condensation patterns
3) preservation of DNA methylation patterns

Question 34

nucleosome core particle

Answer 34

a cluster of 8 histone proteins

Question 35

histone modifying enzyme

Answer 35

is preserved throughout the cell division and passed on to daughter cells

Question 36

DNA methylation

Answer 36

may occur on CG sequences and only at specific sites depending on the needs of the cell in relation to gene expression

these methylated sites turn OFF gene expression by attracting proteins that block transcription

Question 37

maintenance methyltransferase

Answer 37

an enzyme that recognizes only already methylated CG sequences and catalyzes the methylation of the corresponding Cis in the new, complementary strand

this enzyme is preserved through division and passed onto daughter cells to preserve the pattern

Question 38

de novo methyltransferases

Answer 38

establish new DNA methylation patterns during development or in response to external cues such as the environment, behavior, or diet