DNA RNA lect

Question 1

refers to the single units within nucleotides

Answer 1

nucleoside monophosphates

Question 1

it serves as the precursor molecule during nucleic acid synthesis within the cell

Answer 1

triphosphate form

Question 2

two long polynucleotide chains are coiled around central axis forming a __

Answer 2

right handed double helix

Question 3

x-ray diffraction data shows that the DNA is a regular helix and the repeat distance is __

Answer 3

34 A*

Question 4

average structure should be __

Answer 4

10 base pairs

Question 5

• more base pairs refer as ___
• fewer base pairs refer as ___

Answer 5

more base pairs = overwound
fewer base pairs = underwound

Question 6

denaturing agents

Answer 6

formamide or urea

Question 7

site of interaction with many proteins that will bind to the specific nucleotides

Answer 7

binding or recognition sites

Question 8

DNA molecule that exists in a very high relative humidity environment (92%)

Answer 8

B-DNA

Watson-Crick DNA

Question 9

how many base pairs in each turn for B-DNA and the length of one turn of helix

Answer 9

10 base pairs
34A

Question 10

DNA is dehydrated or under high salt conditions

Answer 10

A-DNA

Question 11

which is short and thicker form of DNA?

Answer 11

A-DNA

Question 12

how many base pairs in each turn for A-DNA and the repeat double helix

Answer 12

11 base pairs
24.6 A

Question 13

a left handed, longer and narrower form of DNA in which it is known to occur in nature when there is a sequence of alternating purinepyrimidine

Answer 13

Z-DNA

Question 14

how many base pairs in each helical turn for Z-DNA and the repeat helix

Answer 14

12 base pairs
45.6 A

Question 15

Z-DNA is formed under conditions of __

Answer 15

high salt / presence of alcohol

Question 16

DNA is duplicated __ cell division

Answer 16

before cell division

Question 17

a stage in the cell cycle in which the replication undergo

Answer 17

S phase

Question 18

structure that unwind the double helix in opposite directions

Answer 18

replication fork

Question 19

phase in which the replication machinery moves along the parent dna strands and forms the daughter strands

adding of nucleotides

Answer 19

elongation phase

Question 20

what phase does the two replication forks moving in opposite directions meet

Answer 20

termination phase

Question 21

sites at which single stranded DNA is exposed and at which DNA synthesis occurs

Answer 21

replication forks

Question 22

an enzyme that synthesize the short RNA sequences that are complementary to a single stranded piece of DNA which serves as its templates

Answer 22

primase

Question 23

why there is a primase?

Answer 23

DNA polymerase cannot synthesize nucleotide without a based template

Question 24

protein complex that serves as a processivity-promoting factor in DNA replication.

Answer 24

sliding clamp (beta clamp)

Question 25

these protein binds DNA polymerase and prevents this enzyme from dissociating from the template DNA strand

Answer 25

sliding clamp

Question 26

major enzyme that is the one that polymerize the nucleic acid chain.

Answer 26

DNA polymerase

Question 27

enzyme responsible for sealing the nick between the new strands and the synthesized by polymerase III and polymerase I.

Answer 27

ligases

Question 28

these will proposed the semidiscontinuous replication mechanism

Answer 28

okazaki fragments

Question 29

okazaki fragments will linked this enzyme to form the second daughter strand

Answer 29

DNA ligase

Question 30

enzyme that harnesses the chemical energy from the ATP hydrolysis to separate the two DNA strands at the replication fork

Answer 30

helicase

Question 31

these proteins will bind selectively to single-stranded DNA as soon as it forms

Answer 31

Single-strand binding protein

Question 32

it allows enzymes to attach to the newly opened single strand and initiate elongation and these proteins are removed as DNA synthesis proceeds

Answer 32

Single-strand binding protein

Question 33

essential bacterial enzyme that catalyzes the ATP-dependent negative super-coiling of double-stranded closed- circular DNA

Answer 33

gyrase (topoisomerase TYPE 2)

Question 34

responsible for copying a short stretch of the DNA template strand to produce the RNA primer sequence

Answer 34

primase

Question 35

bind in a complex with the DNA polymerase

Answer 35

primases and alpha catalytic subunit

Question 36

subunits for eukaryotic primase

Answer 36

- alpha catalytic subunit - accessary subunit

Question 37

synthesizes a stretch of 10–30 nucleotides of RNA.

Answer 37

polymerase-α subunit-primase complex

Question 38

broad class of enzymes that cleave off nucleotides one at a time from the three prime or five prime ends of DNA and RNA chains; it also functions to protect the sequence of nucleotides, which must be faithfully copied

Answer 38

**exonucleases** exonuclease function gives the enzyme the capacity to proofread newly synthesized DNA

Question 39

First polymerase enzyme to direct during the initial synthesis

Answer 39

DNA polymerases III

Question 40

this is so called okazaki maturation process

Answer 40

DNA polymerase I

Question 41

uses its polymerase activity to fill in the gap left by the RNA with new DNA.

Answer 41

DNA polymerase I

Question 42

mass and number of subunits for the DNA polymerase I of E coli

Answer 42

mass: **103 kDa** subunits: 1

Question 43

mass and number of subunits for the DNA polymerase II of E coli

Answer 43

mass: **90** subunits: >4

Question 44

mass and number of subunits for the DNA polymerase III of E coli

Answer 44

mass: **830** subunits: >10

Question 45

This enzyme will add nucleotides to the end of a DNA strand in the *absence of hydrogen base pairing with a template*. it can synthesize polynucleotide chains without a template

Answer 45

terminal transferase

Question 46

the only dna polymerase that has 5' - 3' exonuclease activity

Answer 46

DNA Pol I

Question 47

often used in vitro as a method to introduce labeled nucleotides into DNA molecules. The resulting labeled products are used for DNA detection in hybridization analyses.

Answer 47

cut-and-patch **nick translation**

Question 48

responsible for the coupling of DNA replication. this is composed of DNA polymerase, sliding clamp, and clamp loader.

Answer 48

replisome

Question 49

responsible for holding catalytic cores onto their template strands.

Answer 49

sliding clamp

Question 50

recruiting DNA polymerase to the appropriate location on the DNA template. They localize specifically at the region where DNA synthesis needs to commence.

Answer 50

clamp loader and sliding clamp

Question 51

associated with the clamp loader and links this polymerases-clamp loader complex to the helicase.

Answer 51

Tau protein

Question 52

enzymes that modulate in the degree of DNA supercoiling. They can also convert one isomer of DNA to another

Answer 52

topoisomerases

Question 53

a topoisomerase enzymes transiently cleave and reseal one strand of duplex DNA in the absence of ATP

Answer 53

TP 1

Question 54

topoisomerase enzymes will cleave and relegate both DNA strands in the presence of ATP.

Answer 54

TP 2

Question 55

- TTGGGG - TTAGGG

Answer 55

- protozoans - vertebrates

Question 56

endonucleases that recognize specific base sequences and *break or restrict the DNA polymer at the sugar-phosphate backbone*

Answer 56

restriction enzymes

Question 57

most frequently used restriction enzyme in the lab

Answer 57

RE type II - cleave the DNA directly at the binding site, producing fragments of predictable size.

Question 58

- Analysis of gene rearrangements - Mutation detection - DNA recombination in vitro - Mapping a DNA fragment

Answer 58

uses of restriction enzymes

Question 59

the targets for several anticancer drugs. These __ inhibitors bring about cell death by interfering with the breaking and joining activities of the enzymes, in some cases trapping unfinished and broken intermediates

Answer 59

topoisomerase

Question 59

catalyze the addition of methyl groups to nitrogen bases, usually adenines and cytosines in DNA strands

Answer 59

methylation

Question 60

slipped structures, cruciform, and triple-helix

Answer 60

secondary structures

Question 60

the middle point of a temperature range where 50% of your DNA strands are denatured and the amount of denatured DNA is measured at an absorbance of __ nanometer.

Answer 60

**melting temperature** 260 nm

Question 61

DNA supercoiling is the __ winding of DNA helix axis that occurs when the double helix is under or over wound.

Answer 61

tertiary