DNA 6

Question 1

proteins and other molecules need a specific recognition site in order to

Answer 1

bind to a given target

Question 2

all phosphates look

Answer 2

alike

Question 3

the grooves in DNA have specific

Answer 3

h-bond potential and shape

Question 4

to add more … it is often the case that nature uses precisely spaced units at … distances, a turn or more away

Answer 4

specificity
larger

Question 5

what is specificity (delta delta G)

Answer 5

the difference in affinity, delta G, etc. between a perfect match and a mismatch

Question 6

types of DNA patterns

Answer 6

random
symmetry (palendrome and mirror)

Question 7

the study of sequences is

Answer 7

informatics

Question 8

to take a meter of DNA and put it in a micron vessel requires

Answer 8

coiling it up

Question 9

to coil DNA the repulsions must

Answer 9

be overcome in this dense state

Question 10

the proteins at the core of a nucleosome are

Answer 10

histones

Question 11

how many histones are in each complex

Answer 11

8

Question 12

what are the names of the histones in each complex

Answer 12

H2A
H2B
H3
H2

Question 13

which histone binds to the linker DNA

Answer 13

H1

Question 14

two turns of DNA around each histone creates a

Answer 14

nucleosome

Question 15

the histones wrap around each other to form a

Answer 15

rosette and chromosomes

Question 16

how is DNA unpacked

Answer 16

epigenetics
the second code

Question 17

epigenetic markers

Answer 17

acetylation
methylation
phosphorylation
ubiquitination

Question 18

a more realistic version of DNA packing is

Answer 18

goo!
topologically associated domains come close to each other and sqeeze themseves into the nucleus like goo

Question 19

if we have 4 bases and a sequence n long then we have a total of

Answer 19

4^n possible sequences
exponential explosion

Question 20

so identifying a random sequence of … can be unique for the human genome of 3 billion bases

Answer 20

16

Question 21

viruses are more random than humans because

Answer 21

they need to be able to adapt their genome to evade the immune system

Question 22

certain drugs recognize specific

Answer 22

subsequences

Question 23

what recognize and stretch DNA vertically by slipping in and pi stacking with the bases

Answer 23

intercalators
ethidium bromide

Question 24

intercalation is often a means to

Answer 24

stop replication

Question 25

pi stacking is very specific so what is attatched to drugs

Answer 25

tails

Question 26

the DNA in any cell must be replicated with

Answer 26

efficiency and accuracy

Question 27

how many mistakes in human division

Answer 27

<1 mistake per billion in synthesis

Question 28

first step in replication

Answer 28

DNA must be read by separating one strand from another by heating or mechanical stress

Question 29

heat melting is unsatusfactory for replicating a

Answer 29

megabase

Question 30

twisting can lead to

Answer 30

strand separation

Question 31

what can mechanically twist DNA open

Answer 31

gyrase
topoisomerase
helicase

Question 32

DNA is replicated in which direction

Answer 32

5’ to 3’

Question 33

synthesis starts with a template and a small RNA primer synthesized by

Answer 33

primase

Question 34

once binding proteins hold the primer to the strand, DNA polymerase

Answer 34

synthesizes the DNA

Question 35

the original RNA primer is easily hydrolized and then

Answer 35

the site is treated as a repair

Question 36

the parent strand is

Answer 36

methylated

Question 37

methylation determines

Answer 37

which strand needs to be repaired

Question 38

the polymerase complex includes the ability to proofread and remove incorrectly synthesized bases. this is known as

Answer 38

nucleases
endo or exo

Question 39

small fragment in polymerase complex

Answer 39

5’ to 3’ exonuclease

Question 40

large fragment or klenow fragment in polymerase complex

Answer 40

3’ to 5’ exonuclease
polymerase

Question 41

the klenow fragment binds DNA when

Answer 41

the 3’ terminus of the primer is in the exonuclease active site

Question 42

polymerization proceeds by

Answer 42

nucleophilic attack

Question 43

exonucleases cut

Answer 43

from the end

Question 44

endonucleases cut

Answer 44

from the middle but can be specific about the strand direction and placement

Question 45

mistakes in replication and damage must be

Answer 45

fixed or repaired

Question 46

mistakes could be

Answer 46

lethal mutations

Question 47

mutations could also be causes by damage induced chemically or physically such as

Answer 47

radiation, fields, UV

Question 48

UV radiation causes

Answer 48

dimerization of T

Question 49

PU to PU or PY to PY is a

Answer 49

transition mutation

Question 50

Pu to Py is a

Answer 50

transversion mutation

Question 51

a simple tautonomer can lead to

Answer 51

favorable mispairing and a transition mutation

Question 52

sequence adjacent thymines can be dimerized by UV and lead to

Answer 52

a kink and a spot which cannot be replicated

Question 53

dimerization must be excised using a

Answer 53

nuclease

Question 54

deamination can also lead to a

Answer 54

lesion in the DNA

Question 55

polymerase must be

Answer 55

self correcting

Question 56

genes can jump from one strand to another during replication. this is a process known as

Answer 56

recombination by holiday junction.