Cell Biology Test 2

Front 1

______ is the main enzyme in DNA replication.

Back 1

DNA polymerase

Front 2

DNA Polymerase catalyzes the joining of ______

Back 2

deoxyribonucleoside 5′-triphosphates (dNTPs)

Front 3

______ was first identified in 1956. It provided a biochemical basis for the mode of DNA replication that was initially proposed by Watson and Crick.

Back 3

DNA polymerase

Front 4

All DNA polymerases share two fundamental properties:______

Back 4

All polymerases synthesize DNA only in the 5′ to 3′ direction

DNA polymerases can add a new deoxyribonucleotide only to a preformed primer strand that is hydrogen-bonded to the template; they cannot initiate DNA synthesis from free dNTPs.

Front 5

DNA replication was first analyzed by growing _____ in the presence of radioactive ______, which allowed visualization by _____.

Back 5

E. coli; thymidine; autoradiography

Front 6

Since the two strands of DNA run in opposite (antiparallel) directions, only one strand of DNA is synthesized in a continuous manner in the 5′ to 3′ direction. What is this strand called?

Back 6

The leading strand.

Front 7

The other (lagging strand) is formed from short (1–3 kb), discontinuous pieces of DNA that are synthesized backwards. These small pieces (Okazaki fragments) are joined by ______.

Back 7

DNA ligase

Front 8

Short fragments of _____ serve as primers for the synthesis of Okazaki fragments.

Back 8

RNA

Front 9

RNA synthesis can initiate ____.

Back 9

de novo

Front 10

An enzyme called _____ synthesizes short fragments of RNA that act as primers.

Back 10

primase

Front 11

The primers must then be removed and replaced with ____

Back 11

DNA

Front 12

In prokaryotes, RNA primers are removed by ______.

Back 12

polymerase I

Front 13

Polymerase acts as an _____ that can hydrolyze DNA in either direction.

Back 13

exonuclease

Front 14

In eukaryotic cells, RNA primers are removed by _____, which degrades the RNA strand of RNA-DNA hybrids and 5′ to 3′ exonucleases.

Back 14

RNase H

Front 15

Polymerase _____ is found in a complex with primase

Back 15

alpha

Front 16

_______ load polymerase onto the primer and maintain its stable association with the template and clamp-loading proteins

Back 16

Sliding-clamp proteins

Front 17

_____ catalyzes the unwinding of parental DNA, coupled to ATP hydrolysis, ahead of the replication fork.

Back 17

Helicase

Front 18

______ then stabilize the unwound template DNA so that it can be copied by the polymerase

Back 18

Single-stranded DNA-binding proteins

Front 19

_______ catalyze reversible breaking and rejoining of DNA strands. The transient breaks serve as swivels that allow the two strands to rotate freely around each other

Back 19

Topoisomerases

Front 20

Mutation rates indicate that the frequency of errors during replication is less than one incorrect base per ____ nucleotides. This is much lower than would be predicted simply on the basis of complementary base pairing.

Back 20

10^9

Front 21

_____ helps select the correct bases for insertion.

Back 21

DNA polymerase

Front 22

Binding of correctly matched ___ induces conformational changes in DNA polymerase that lead to the incorporation of the _____. This increases fidelity of replication about a thousandfold.

Back 22

dNTPs nucleotide

Front 23

DNA polymerases require primers and catalyze the growth of DNA strands only in the 5′ to 3′ direction, which ensures accurate DNA duplication. This is an example of ____.

Back 23

Proofreading

Front 24

Replicative DNA polymerases also have ______ that can hydrolyze DNA in the 3′ to 5′ direction. When an incorrect base is incorporated, it is removed by ______.

Back 24

exonuclease activity

Front 25

_____ are binding sites for proteins that initiate the replication process.

Back 25

Origins of replication

Front 26

In E. coli, an _____ binds to specific DNA sequences within the origin.

Back 26

initiator protein.
It begins to unwind the DNA and recruits the other proteins involved in DNA synthesis

Front 27

Eukaryotic origins of replication were first studied in ____

Back 27

yeast S. cerevisiae.
They were identified as sequences that can support replication of plasmids in transformed cells

Front 28

The terminal sequences of linear DNA molecules ,_______, consist of tandem repeats of simple-sequence DNA.

Back 28

telomeres

Front 29

______ catalyzes the synthesis of telomeres in the absence of a DNA template.

Back 29

telomerase

Front 30

Telomerase is a _____

Back 30

reverse transcriptase.
It carries its own template RNA, which is complementary to the telomere repeat sequences, as part of the enzyme complex.

Front 31

The synthesis of Okazaki fragments is initiated by ______.

Back 31

primase

Front 32

The mechanism of telomerase action was determined in 1985 in studies of______.

Back 32

protozoan Tetrahymena

Front 33

The RNA template allows telomerase to extend the _____ end by one repeat unit beyond its original length.

Back 33

3′

Front 34

The complementary strand can then be synthesized by the_______

Back 34

polymerase alpha-primase complex.

Front 35

Removal of the RNA primer leaves an overhanging ____ end, which can form loops at the ends of eukaryotic chromosomes.

Back 35

3'

Front 36

Telomerase activity maintains telomeres at their ____

Back 36

normal length

Front 37

Two categories of DNA repair mechanisms.

Back 37

Direct reversal of the chemical reaction responsible for DNA damage AND removal of damaged bases followed by replacement with newly synthesized DNA.

Front 38

Exposure to UV light forms _____, which distort the structure of the DNA and block transcription or replication past the site of damage

Back 38

pyrimidine dimers

Front 39

________ is one mechanism of repairing UV-induced pyrimidine dimers. Energy from visible light is used to break the cyclobutane ring structure, reversing the dimerization reaction

Back 39

Photoreactivation

Front 40

Many types of cells use photoreactivation but it is not universal; ______ lack this mechanism of DNA repair.

Back 40

placental mammals

Front 41

DNA damage can also result from ______—reactive compounds that can transfer methyl or ethyl groups to a DNA base.

Back 41

alkylating agents

Front 42

In _______, single damaged bases are recognized and removed.

Back 42

base-excision repair

Front 43

uracil can arise in DNA when ___ is incorporated in place of thymine.

Back 43

dUTP

Front 44

uracil can be formed in DNA by the deamination of ____.

Back 44

cytosine

Front 45

Excision of uracil in DNA is catalyzed by _____.

Back 45

DNA glycosylase, , which cleaves the bond between the uracil and the deoxyribose of the DNA. DNA glycosylases also recognize and remove other abnormal bases.

Front 46

_____, a sugar with no base attached is formed by excision of a base. (Purine bases can also be lost spontaneously.)

Back 46

An apyrimidinic or apurinic site (AP site)

Front 47

These sites are repaired by _____.

Back 47

AP endonuclease. The deoxyribose is removed and the resulting gap is filled by DNA polymerase and ligase.

Front 48

______ removes the damaged bases as part of an oligonucleotide

Back 48

Nucleotide-excision repair

Front 49

An _____ is an enzyme complex that can directly excise an oligonucleotide.

Back 49

excinuclease

Front 50

People with xeroderma pigmentosum (XP) are extremely sensitive to UV radiation and develop multiple skin cancers; XP results from lack of the ______.

Back 50

nucleotide-excision repair mechanism

Front 51

______ are used as an experimental system to identify DNA repair genes

Back 51

XP cells

Front 52

Repair genes mutated in XP are designated ____ through _____.

Back 52

XPA XPG

Front 53

Disrupted base pairing is recognized by ____.

Back 53

XPC

Front 54

followed by the cooperative binding of ____, ____, and a transcription factor called ____.

Back 54

XPA, RPA, TFIIH

Front 55

Two subunits of TFIIH are the _____ and ____ proteins

Back 55

XPB and XPD proteins, which act as helicases to unwind about 25 base pairs around the site of damage.

Front 56

The ____ protein is then recruited to the complex

Back 56

XPG, followed by XPF/ERCC1 (another repair protein).

Front 57

______ are endonucleases that cleave DNA on the 5′ and 3′ sides of the damaged region.

Back 57

XPG AND XPF/ERCC1

Front 58

_____ is nucleotide-excision repair during transcription.

Back 58

Transcription-coupled repair

Front 59

When RNA polymerase is stalled by DNA damage in mammalian cells, it is recognized by two proteins ___ and ____ that then recruit other proteins to repair the damage

Back 59

CSA and CSB

Front 60

In patients with Cockayne’s syndrome, genes for CSA and CSB are mutated, and they are defective in transcription-coupled repair.

Back 60

Cockayne’s syndrome

Front 61

The ______ system scans newly replicated DNA, and enzymes excise and replace mismatched bases.

Back 61

mismatch repair

Front 62

In E. coli, the newly synthesized DNA is not yet modified by methylation, allowing recognition of new versus parental strands.The protein ______ recognizes the mismatch

Back 62

MutS

Front 63

and forms a complex with _____ and _____.

Back 63

MutL and MutH.

Front 64

The MutH endonuclease then cleaves the unmethylated DNA strand at a GATC sequence. The DNA is then unwound and repaired.

Back 64

GATC

Front 65

Mutations in the human homologs of MutS and MutL cause ______, one of the most common inherited diseases.

Back 65

inherited colon cancer (HNPCC)

Front 66

Pyrimidine dimers and other types of lesions cannot be copied by normal DNA polymerases, so replication is blocked..Specialized DNA polymerases can replicate across a site of DNA damage—This is an example of _____

Back 66

translesion DNA synthesis.

Front 67

______ in E. coli is induced in response to extensive UV irradiation and can synthesize a new DNA strand across from a thymine dimer.

Back 67

Polymerase V

Front 68

____ and ____ are similarly induced by DNA damage.
(Eukaryotic cells also have specialized polymerases for translesion synthesis.)

Back 68

Polymerases II and IV

Front 69

______ are a particularly dangerous form of DNA damage because the continuity of the DNA molecule is disrupted. They can occur naturally, or can be caused by ionizing radiation or chemicals.

Back 69

Double-strand breaks

Front 70

______ can rejoin the broken strands by recombination with homologous DNA sequences on an undamaged chromosome.

Back 70

Recombinational repair

Front 71

Recombinational Repair only occurs following _______, when the newly replicated sister chromatids remain associated.

Back 71

DNA replication

Front 72

Double-strand breaks can also be repaired by rejoining the broken ends, but this leads to a high frequency of errors resulting from deletion of bases around the site of damage.

Back 72

Double-strand breaks can also be repaired by rejoining the broken ends, but this leads to a high frequency of errors resulting from deletion of bases around the site of damage.

Front 73

One of the genes responsible for inherited breast cancer (BRCA2) encodes a protein involved in repair of double-strand breaks by homologous recombination. Defects in this type of DNA repair can lead to the development of breast cancer.

Back 73

One of the genes responsible for inherited breast cancer (BRCA2) encodes a protein involved in repair of double-strand breaks by homologous recombination. Defects in this type of DNA repair can lead to the development of breast cancer.

Front 74

_____ is also the key to generating genetic diversity.
Genetic differences between individuals provide the essential starting material of natural selection.

Back 74

Recombination. Recombination allows genes to be reassorted into different combinations.

Front 75

_______ is the exchange of information between DNA molecules that share sequence homology over hundreds of bases.

Back 75

Homologous recombination

Front 76

Homologous recombination occurs during both _______.

Back 76

meiosis and DNA repair

Front 77

______ results from the breakage and rejoining of two parental DNA molecules.

Back 77

recombination

Front 78

The ______ is a molecular model for recombination.

Back 78

Holliday model

Front 79

Ligation of the broken strands then produces a crossed-strand intermediate, known as a ______.

Back 79

Holliday junction

Front 80

A Holliday junction can be resolved by cutting and rejoining the crossed strands to yield _____.

Back 80

recombinant molecules.

Front 81

A Holliday junction can form two different isomers, resulting in _____ or nonrecombinant heteroduplexes

Back 81

recombinant; nonrecombinant heteroduplexes

Front 82

It now appears that recombination is generally initiated at _____.

Back 82

double-strand breaks

Front 83

The key protein in E. coli is _____, which promotes the exchange of strands between homologous DNAs

Back 83

RecA

Front 84

RecA binds to single-stranded DNA to form a _____

Back 84

protein-DNA filament

Front 85

RecA then binds a second, double-stranded DNA molecule.

Back 85

RecA then binds a second, double-stranded DNA molecule.

Front 86

n eukaryotic cells, two closely related proteins, ____ and ___, function similarly to RecA.

Back 86

Rad51, Dmc1.
Rad51 is ubiquitously expressed, whereas Dmc1 is only expressed during meiosis.

Front 87

In E. coli, Holliday junctions are resolved by a complex of three proteins: ___,____,___

Back 87

RuvA, RuvB, and RuvC. RuvA recognizes the Holliday junction and recruits RuvB. They act as a motor to drive migration of the site at which the DNA strands are crossed, thereby varying the extent of the heteroduplex region. RuvC then cleaves the crossed DNA strands, which are rejoined by ligation.

Front 88

The discovery that genes can move to different chromosomal locations came from Barbara McClintock’s studies of corn in the 1940s.

Back 88

The discovery that genes can move to different chromosomal locations came from Barbara McClintock’s studies of corn in the 1940s.

Front 89

_____ occurs between specific DNA sequences, usually homologous over short stretches of DNA. This process is mediated by proteins that recognize specific DNA target sequences rather than by complementary base pairing.

Back 89

Site-specific recombination

Front 90

there are two major classes of vertebrate immune responses: B lymphocytes secrete antibodies (immunoglobulins) that react with soluble antigens; T lymphocytes express cell surface proteins (T cell receptors) that react with antigens expressed on the surfaces of other cells.

Back 90

there are two major classes of vertebrate immune responses: B lymphocytes secrete antibodies (immunoglobulins) that react with soluble antigens; T lymphocytes express cell surface proteins (T cell receptors) that react with antigens expressed on the surfaces of other cells.

Front 91

The key feature of both immunoglobulins and T cell receptors is their enormous diversity. One individual is capable of producing more than 1011 different antibody molecules.

Back 91

The key feature of both immunoglobulins and T cell receptors is their enormous diversity. One individual is capable of producing more than 1011 different antibody molecules.

Front 92

Immunoglobulins consist of pairs of identical heavy and light polypeptide chains, with C-terminal constant regions and N-terminal variable regions.

Back 92

Immunoglobulins consist of pairs of identical heavy and light polypeptide chains, with C-terminal constant regions and N-terminal variable regions.