Use LEFT and RIGHT arrow keys to navigate between flashcards;
Use UP and DOWN arrow keys to flip the card;
H to show hint;
A reads text to speech;
92 Cards in this Set
- Front
- Back
______ is the main enzyme in DNA replication.
|
DNA polymerase
|
|
DNA Polymerase catalyzes the joining of ______
|
deoxyribonucleoside 5′-triphosphates (dNTPs)
|
|
______ was first identified in 1956. It provided a biochemical basis for the mode of DNA replication that was initially proposed by Watson and Crick.
|
DNA polymerase
|
|
All DNA polymerases share two fundamental properties:______
|
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. |
|
DNA replication was first analyzed by growing _____ in the presence of radioactive ______, which allowed visualization by _____.
|
E. coli; thymidine; autoradiography
|
|
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?
|
The leading strand.
|
|
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 ______.
|
DNA ligase
|
|
Short fragments of _____ serve as primers for the synthesis of Okazaki fragments.
|
RNA
|
|
RNA synthesis can initiate ____.
|
de novo
|
|
An enzyme called _____ synthesizes short fragments of RNA that act as primers.
|
primase
|
|
The primers must then be removed and replaced with ____
|
DNA
|
|
In prokaryotes, RNA primers are removed by ______.
|
polymerase I
|
|
Polymerase acts as an _____ that can hydrolyze DNA in either direction.
|
exonuclease
|
|
In eukaryotic cells, RNA primers are removed by _____, which degrades the RNA strand of RNA-DNA hybrids and 5′ to 3′ exonucleases.
|
RNase H
|
|
Polymerase _____ is found in a complex with primase
|
alpha
|
|
_______ load polymerase onto the primer and maintain its stable association with the template and clamp-loading proteins
|
Sliding-clamp proteins
|
|
_____ catalyzes the unwinding of parental DNA, coupled to ATP hydrolysis, ahead of the replication fork.
|
Helicase
|
|
______ then stabilize the unwound template DNA so that it can be copied by the polymerase
|
Single-stranded DNA-binding proteins
|
|
_______ 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
|
Topoisomerases
|
|
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.
|
10^9
|
|
_____ helps select the correct bases for insertion.
|
DNA polymerase
|
|
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.
|
dNTPs nucleotide
|
|
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 ____.
|
Proofreading
|
|
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 ______.
|
exonuclease activity
|
|
_____ are binding sites for proteins that initiate the replication process.
|
Origins of replication
|
|
In E. coli, an _____ binds to specific DNA sequences within the origin.
|
initiator protein.
It begins to unwind the DNA and recruits the other proteins involved in DNA synthesis |
|
Eukaryotic origins of replication were first studied in ____
|
yeast S. cerevisiae.
They were identified as sequences that can support replication of plasmids in transformed cells |
|
The terminal sequences of linear DNA molecules ,_______, consist of tandem repeats of simple-sequence DNA.
|
telomeres
|
|
______ catalyzes the synthesis of telomeres in the absence of a DNA template.
|
telomerase
|
|
Telomerase is a _____
|
reverse transcriptase.
It carries its own template RNA, which is complementary to the telomere repeat sequences, as part of the enzyme complex. |
|
The synthesis of Okazaki fragments is initiated by ______.
|
primase
|
|
The mechanism of telomerase action was determined in 1985 in studies of______.
|
protozoan Tetrahymena
|
|
The RNA template allows telomerase to extend the _____ end by one repeat unit beyond its original length.
|
3′
|
|
The complementary strand can then be synthesized by the_______
|
polymerase alpha-primase complex.
|
|
Removal of the RNA primer leaves an overhanging ____ end, which can form loops at the ends of eukaryotic chromosomes.
|
3'
|
|
Telomerase activity maintains telomeres at their ____
|
normal length
|
|
Two categories of DNA repair mechanisms.
|
Direct reversal of the chemical reaction responsible for DNA damage AND removal of damaged bases followed by replacement with newly synthesized DNA.
|
|
Exposure to UV light forms _____, which distort the structure of the DNA and block transcription or replication past the site of damage
|
pyrimidine dimers
|
|
________ 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
|
Photoreactivation
|
|
Many types of cells use photoreactivation but it is not universal; ______ lack this mechanism of DNA repair.
|
placental mammals
|
|
DNA damage can also result from ______—reactive compounds that can transfer methyl or ethyl groups to a DNA base.
|
alkylating agents
|
|
In _______, single damaged bases are recognized and removed.
|
base-excision repair
|
|
uracil can arise in DNA when ___ is incorporated in place of thymine.
|
dUTP
|
|
uracil can be formed in DNA by the deamination of ____.
|
cytosine
|
|
Excision of uracil in DNA is catalyzed by _____.
|
DNA glycosylase, , which cleaves the bond between the uracil and the deoxyribose of the DNA. DNA glycosylases also recognize and remove other abnormal bases.
|
|
_____, a sugar with no base attached is formed by excision of a base. (Purine bases can also be lost spontaneously.)
|
An apyrimidinic or apurinic site (AP site)
|
|
These sites are repaired by _____.
|
AP endonuclease. The deoxyribose is removed and the resulting gap is filled by DNA polymerase and ligase.
|
|
______ removes the damaged bases as part of an oligonucleotide
|
Nucleotide-excision repair
|
|
An _____ is an enzyme complex that can directly excise an oligonucleotide.
|
excinuclease
|
|
People with xeroderma pigmentosum (XP) are extremely sensitive to UV radiation and develop multiple skin cancers; XP results from lack of the ______.
|
nucleotide-excision repair mechanism
|
|
______ are used as an experimental system to identify DNA repair genes
|
XP cells
|
|
Repair genes mutated in XP are designated ____ through _____.
|
XPA XPG
|
|
Disrupted base pairing is recognized by ____.
|
XPC
|
|
followed by the cooperative binding of ____, ____, and a transcription factor called ____.
|
XPA, RPA, TFIIH
|
|
Two subunits of TFIIH are the _____ and ____ proteins
|
XPB and XPD proteins, which act as helicases to unwind about 25 base pairs around the site of damage.
|
|
The ____ protein is then recruited to the complex
|
XPG, followed by XPF/ERCC1 (another repair protein).
|
|
______ are endonucleases that cleave DNA on the 5′ and 3′ sides of the damaged region.
|
XPG AND XPF/ERCC1
|
|
_____ is nucleotide-excision repair during transcription.
|
Transcription-coupled repair
|
|
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
|
CSA and CSB
|
|
In patients with Cockayne’s syndrome, genes for CSA and CSB are mutated, and they are defective in transcription-coupled repair.
|
Cockayne’s syndrome
|
|
The ______ system scans newly replicated DNA, and enzymes excise and replace mismatched bases.
|
mismatch repair
|
|
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
|
MutS
|
|
and forms a complex with _____ and _____.
|
MutL and MutH.
|
|
The MutH endonuclease then cleaves the unmethylated DNA strand at a GATC sequence. The DNA is then unwound and repaired.
|
GATC
|
|
Mutations in the human homologs of MutS and MutL cause ______, one of the most common inherited diseases.
|
inherited colon cancer (HNPCC)
|
|
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 _____
|
translesion DNA synthesis.
|
|
______ in E. coli is induced in response to extensive UV irradiation and can synthesize a new DNA strand across from a thymine dimer.
|
Polymerase V
|
|
____ and ____ are similarly induced by DNA damage.
(Eukaryotic cells also have specialized polymerases for translesion synthesis.) |
Polymerases II and IV
|
|
______ 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.
|
Double-strand breaks
|
|
______ can rejoin the broken strands by recombination with homologous DNA sequences on an undamaged chromosome.
|
Recombinational repair
|
|
Recombinational Repair only occurs following _______, when the newly replicated sister chromatids remain associated.
|
DNA replication
|
|
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.
|
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.
|
|
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.
|
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.
|
|
_____ is also the key to generating genetic diversity.
Genetic differences between individuals provide the essential starting material of natural selection. |
Recombination. Recombination allows genes to be reassorted into different combinations.
|
|
_______ is the exchange of information between DNA molecules that share sequence homology over hundreds of bases.
|
Homologous recombination
|
|
Homologous recombination occurs during both _______.
|
meiosis and DNA repair
|
|
______ results from the breakage and rejoining of two parental DNA molecules.
|
recombination
|
|
The ______ is a molecular model for recombination.
|
Holliday model
|
|
Ligation of the broken strands then produces a crossed-strand intermediate, known as a ______.
|
Holliday junction
|
|
A Holliday junction can be resolved by cutting and rejoining the crossed strands to yield _____.
|
recombinant molecules.
|
|
A Holliday junction can form two different isomers, resulting in _____ or nonrecombinant heteroduplexes
|
recombinant; nonrecombinant heteroduplexes
|
|
It now appears that recombination is generally initiated at _____.
|
double-strand breaks
|
|
The key protein in E. coli is _____, which promotes the exchange of strands between homologous DNAs
|
RecA
|
|
RecA binds to single-stranded DNA to form a _____
|
protein-DNA filament
|
|
RecA then binds a second, double-stranded DNA molecule.
|
RecA then binds a second, double-stranded DNA molecule.
|
|
n eukaryotic cells, two closely related proteins, ____ and ___, function similarly to RecA.
|
Rad51, Dmc1.
Rad51 is ubiquitously expressed, whereas Dmc1 is only expressed during meiosis. |
|
In E. coli, Holliday junctions are resolved by a complex of three proteins: ___,____,___
|
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.
|
|
The discovery that genes can move to different chromosomal locations came from Barbara McClintock’s studies of corn in the 1940s.
|
The discovery that genes can move to different chromosomal locations came from Barbara McClintock’s studies of corn in the 1940s.
|
|
_____ 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.
|
Site-specific recombination
|
|
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.
|
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.
|
|
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.
|
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.
|
|
Immunoglobulins consist of pairs of identical heavy and light polypeptide chains, with C-terminal constant regions and N-terminal variable regions.
|
Immunoglobulins consist of pairs of identical heavy and light polypeptide chains, with C-terminal constant regions and N-terminal variable regions.
|