Category - Definitions

Query - What definition best describes the term below?

Reversal

Category - Term Recognition

Query - What term does the description below refer to?

(Terms are shown on left, descriptions in middle, figures on right)

5,10-methenyltetrahydrofolate | A molecule that acts like 8-hydroxy-5-deazaflavin in DNA photolyases. It acts as a light harvesting factor. |  | 5-methylcytosine | The only methylated base found in eukaryotic DNA |  | 6-4 Photoproduct | A structure in DNA of a covalent link made between carbon #4 of the 3' pyrimidine and carbon #6 of an adjacent 5' pyrimidine. It occurs as a result of exposure to UV light. It can lead to mutation during replication. | Figure 25.9 | 8-hydroxy-5-deazaflavin | A molecule that acts like 5,10-methenyltetrahydrofolate in DNA photolyases. It acts as a light harvesting factor. |  | 8-oxoguanine | An oxidized form of guanine arising from oxidative damage. |  | attB | A locus in the E. coli chromosome targeted by the bacteriophage for site-specific recombination. | Figure 25.31 | attP | The site on the chromosome involved in site-specific recombination with the E. coli chromosome. | Figure 25.31 | Base Excision Repair | Cellular DNA repair system cleaves the glycosidic bond connecting a damaged base to the DNA sugar-phosphate backbone. |  | BRCA-1 | A gene associated with an increased risk of breast and ovarian cancer that is involved in transcription-coupled excision repair. |  | Chi | An octanucleotide sequence in E. coli (5'-GCTGGTCC-3') | Figure 25.28 | Chromophore | A structural moiety that absorbs light of characteristic wavelengths. | Figure 25.10 | Clonal Expansion | A mechanism by which large-scale production of specific antibodies occurs. The B and T cells produced by the body have randomly generated antigen specificities. When a particular antigen enters the body, it induces proliferation only in B and T cells that happen to be specific for it. Thus, the antigen selects the cells that will mount an immune response against it and stimulates them to undergo clonal proliferation. |  | Cyclobutane Pyrimidine Dimers | A structure in DNA of two covalent links made between adjacent pyrimidine residues as a result of exposure to UV light. The two new bonds form a four-membered ring and can lead to mutation during replication if not repaired. | Figure 25.9 | DNA Photolyase | An enzyme that repairs cyclobutane pyrimidine dimers in the presence of visible light. | Figure 25.10 | Excinuclease | A term used to describe the enzymatic cutting of DNA by the uvrABC system. |  | Exonuclease V (also called RecBCD nuclease) | A protein in E. coli recombination that binds at a double-strand break on duplex DNA and uses a helicase activity to unwind and partially degrade the DNA. It helps to load RecA to a 3' end. | Figure 25.28 | Gene Amplification | Selective amplification of a specific region of a genome |  | Heteroduplex | A double stranded DNA in which the two strands were not made from each other and came from other molecules. | Figure 25.19 | Holliday Junction | An intermediate during homologous recombination; a four-armed structure in which each of the participating DNA duplexes has exchanged one strand with the other duplex. | Figure 25.20 | Holliday Model | A model for homologous recombination involving alignment of homologous sequences, nicking, strand invasion, ligation, migration of the cross point (Holliday Junction), isomerization, breaking of strands, and rejoining. A variation of the model was proposed by Meselson and Radding. | Figure 25.20 | Homogeneously Staining Region | A region of a chromosome that lacks the typical chromosome banding pattern. It can be produced by gene amplification. |  | Homologous Recombination | Genetic recombination that requires extensive sequence homology between the recombining DNA molecules. Meiotic recombination by crossing over in eukaryotes is an example. |  | Illegitimate Recombination | An extremely rare type of recombination that possibly occurs by chance. It involves neither sequence homology nor the action of any known protein. |  | Immunoglobulin G (IgG) | An antibody of class 'G' containing two heavy chains and two light chains. |  | Maintenance Methylase | A eukaryotic enzyme that ensures that all of the methylated sites in the parental DNA are also methylated in the progeny DNA. | Figure 25.3 | Meselson -Radding Model | A proposed model for homologous recombination involving alignment of homologous sequences, nicking, strand displacement synthesis, strand invasion, loop cleavage, ligation of the displaced strand, isomerization, branch migration and ligation of the invading 'A' strand, and resolution as in the Holliday model. | Figure 25.22 | Microsatellite Instability | Mutations consisting of repeats of single, double, and triple-nucleotide sequences which probably arise by 'slipping' of strands during DNA polymerization. |  | Mismatch Repair | Cellular DNA repair system that recognizes DNA mismatches created either by replication errors, non-homologous recombination, or damage to one DNA base, and corrects the error. |  | Mutagenesis | The process of creating mutations. |  | mutT | An E. coli gene that catalyzes the following reaction: 8-oxo-dGTP + H2O <=> 8-oxo-dGMP + Ppi |  | Nucleotide Excision Repair | A process whereby a damaged section of a DNA chain is cut out, or excised, followed by the action of DNA polymerase and then DNA ligase to regenerate a covalently closed duplex at the site of the original damage. |  | O6-Alkylguanine Alkyltransferase | An unusual repair enzyme that transfers a methyl or ethyl group from an O6-methylguanine or O6-ethylguanine to a cysteine residue in the active site of the protein. It can thus only function once. |  | Oncogenic Transformation | Conversion of a normal cell to a cancerous one. |  | Photoproducts | The products that result when light energy causes a chemical reaction to occur in a substance. With respect to DNA, the term refers to the types of damaged DNA that can be caused by uv irradiation. | Figure 25.9 | Plaque | A cleared area on a Petri dish on a plate of bacteria arising from growth of a bacteriophage in that region. |  | Postreplication Repair | Processes that attempt to fix mismatches, gaps, or damage to DNA that escapes the repair process that occur during replication |  | Prophage | The integrated, inactive chromosome in the E. coli genome. |  | Provirus | With respect to a retrovirus, a virus integrated into the host genome. |  | RecA | A multifunctional protein with Mr of about 38,000. In recombination it promotes the pairing of homologous strands. In the SOS response it also plays a role in gene activation. | Figure | Recombination | A process in an organism in which two parent DNA molecules give rise to daughter DNA that combines segments from both parent molecules. It may involve the integration of one DNA molecule into another, the substitution of a DNA segment for a homologous segment on another DNA molecule, or the exchange of homologous segments between two DNA molecules. |  | Recombinational Repair | Cellular DNA repair system in which newly replicated DNA duplexes undergo genetic recombination, with ultimate removal of the damaged DNA segment. |  | Resolvase | An enzyme found in class II and class III type transposons that catalyzes site-specific recombination between the two elements of the transposon created by replicative transposition. |  | Restriction Endonucleases | Enzymes that catalyze the double-strand cleavage of DNA at specific base sequences. |  | Restriction/Modification | A defense system common in bacteria involving a restriction endonuclease and a site-specific methylase that methylates the same sequence the restriction endonuclease cuts at. Normally, the host DNA is methylated, which protects against the action of the restriction endonuclease, but invading viral DNA is not methylated, and is cut. | Figure 25.5 | Retrotransposon | A transposable element which goes through an RNA stage. |  | Retroviruses | A family of RNA viruses that possess reverse transcriptase. After the virus infects a cell, this enzyme transcribes the RNA genome into a double-strand DNA version, which integrates into a host chromosome. Human immunodeficiency virus (HIV) is an example. |  | ruvA | A protein involved in E. coli recombination. It is a DNA binding protein, whose specificity directs it toward the four-stranded Holliday structure |  | ruvB | A protein involved in E. coli recombination. It is an ATP-requiring "motor protein," which binds to two opposed arms of the Holliday junction and rotates them in opposite directions, forcing branch migration by driving the rotational movement of the other two strands toward the junction. |  | ruvC | A protein involved in E. coli recombination. It begins resolution of the Holliday structure by nicking two strands. |  | Site-specific Recombination | Recombination that involves only limited sequence homology between recombining partners. Sites of breaking and joining are determined by specific DNA - protein interactions. | Figure 25.17 | Somatic Mutations | Mutations that occur in non-germline cells. |  | SOS Response | A bacterial response to various potentially lethal stresses, including severe UV irradiation. It involves the coordinated expression of a set of proteins that carry out survival maneuvers, including an error-prone type of repair for thymine dimers in DNA. |  | Strand Invasion | A process that is postulated to occur in homologous recombination in which an unpaired part of a strand of DNA invades a duplex region of another DNA. |  | Thymine glycol | An oxidized form of thymine arising from oxidative damage. |  | Transition Mutation | A mutation that changes a purine-pyrimidine base pair to a different purine-pyrimidine base pair. An example is a transition from G-C to A-T. |  | Transposable Genetic Elements | DNA fragments containing genes that do not have a fixed location in a genome but can move from place to place within the genome, albeit with low frequency. | Figure 25.34 | Transposase | An enzyme involved in movement of a transposon from one DNA to another. It can make a staggered cut in a specific sequence in a target DNA into which the transposon moves. |  | Transposition | A type of recombination which involves neither sequence homology nor the RecA protein (in E. coli) but does require a special sequence on the donor DNA. |  | Tranverse Mutation | A mutation that changes a purine-pyrimidine base pair to a different pyrimidine-purine base pair. An example is a transition from G-C to T-A. |  | Unequal Crossing Over | A recombinational process that can lead to multiple copies of a gene. It may be important in gene amplification. |  | uvrD | A helicase component of the E. coli nucleotide excision repair system. |  | Xis | A protein required in addition to Int and Ihf to reverse the process by which was integrated into the genome. |

Category - General

Query - Is contained in the left column below, solution in middle, figure on right

Reversal - there is no reversal

After uvrAB in E. coli identifies a damaged site, what happens? | The DNA is bent, uvrA dissociates and is replaced by uvrC. The BC complex cuts on both sides of the dimer. | Figure 25.12 | At what level is cytosine methylated in most animal DNA? | 3%-5%. |  | Explain how the regulation of O6-alkylguanine alkyltransferase may be important in repairing damaged DNA | In bacteria, the enzyme regulates its own expression and that of DNA-N-glycosylase. There is evidence that the alkylated form of the enzyme is the specific form of the transcriptional activator. |  | For which of the three 'mut' proteins in E. coli is there no known eukaryotic equivalent? | mutH |  | How are cyclobutane thymine dimers removed from UV-irradiated DNA? | By photoreactivation. |  | How are different mismatches handled in eukaryotic cells? | By different dimerizations of MSH2, MSH3, and MSH6 proteins. |  | How are the sites of site-specific recombination determined? | By specific DNA - protein interactions |  | How can a retrovirus become oncogenic? | If it somehow acquires and mutates a cellular protooncogene or if the virus integrates next to a cellular proto-oncogene and stimulates its transcription uncontrollably. |  | How close to the site of damage does the E. coli uvrABC complex act? | Eight nucleotides to the 5' side of the damaged site and 4-5 nucleotides to the 3' side. |  | How does a bacterial methylase modify bases? | Bases undergoing methylation rotate completely out of the DNA duplex and into a catalytic pocket within the enzyme structure |  | How is diversity of immunoglobulin V sequences increased by DNA replication? | The DNA has a high rate of mutation. |  | How many possible light chain sequences can be created by shuffling V and J sequences in recombination for antibody production? | About 3000 |  | In coding for antibodies, how many different J sequences are there? | 4 |  | In coding for antibodies, how many different V sequences are there? | 300 |  | In repairing incorrectly paired DNA, how does E. coli identify the correct strand to repair? | By the methylation pattern. The most newly synthesized strand will be lacking methylation of the sequence GATC. This strand is therefore repaired, because the mismatch most likely arose during the replication process. |  | Integration of which bacteriophage occurs by a site-specific recombination process that is independent of RecA? | Lamda Phage | Figure 25.17 | Mutations in mismatch repair genes have been identified in what inherited cancer predisposition | Heritable Non-Polyposis Colon Cancer (HNPCC) |  | What are the chromophores in DNA photolyases | FADH2 and 5,10-methenyltetrahydrofolate or 8-hydroxy-5-deazaflavin |  | What are the effects of the SOS response? | They include mutagenesis, filamentation (in which cells elongate by growth but don't divide), and activated excision repair. |  | What are the possible types of ends left after cutting by restriction endonucleases? | 5' overhang, 3' overhang, or blunt ends (no overhang) |  | What are the primary methylated bases found in prokaryotic DNA? | N6-methyladenine and to a lesser extent N4-methylcytosine |  | What are the sequences found to the 3' side of each V sequence in antibody coding and to the 5' side of each J sequence called? | Recognition Signal Sequences |  | What bacterial genes are implicated in error prone repair? | umuC and umuD |  | What base analog is used to treat -thalassemia? | 5-azacytidine |  | What biological effect arises apparently from the lack of methylation where 5-azacytidine is incorporated into DNA? | Gene expression patterns can change. For example, bone marrow cells can reactivate the synthesis of fetal hemoglobin in adults. |  | What classes of DNA sequences making up antibodies are recombined to produce new combinations for production of the kappa light chains of IgG? | V, J, and C | Figure 25.32, Figure 25.33 | What does the E. coli uvrA-uvrB complex recognize in DNA? | Structural distortion created by a thymine dimer or damaged strand. | Figure 25.12 | What does the human disease xeroderma pigmentosum arise from? | Deficiency of one or more enzymes of the excision repair pathway for DNA. |  | What E. coli genes are involved in the nucleotide excision repair system? | uvrA, uvrB, uvrC, and uvrD | Figure 25.12 | What E. coli genes participate in mismatch repair? | mutH, mutL, mutS, DNA helicase II, single strand DNA binding protein. |  | What E. coli proteins with a role in DNA replication probably also function in homologous recombination? | DNA polymerase, DNA ligase, single strand DNA-binding protein |  | What E. coli repair protein is needed for both recombinational repair and SOS repair? | RecA |  | What function do the LTRs of retroviruses perform with respect to gene expression? | They are strong promoters |  | What gene found in class II and III bacterial transposons is not found in class I bacterial transposons? | Resolvase |  | What happens when 5-azacytidine is incorporated into DNA? | The cytosines that it replaces cannot be methylated. |  | What happens when DNA polymerase encounters an unrepaired thymine dimer during replication? | The first deoxyadenylate is incorporated opposite the first thymine base, but the enzyme stalls at the second base. An Okazaki fragment is synthesized on the other side of the damage. |  | What important biological processes involve DNA methylation? | Restriction/modification, mismatcherror correction, control of gene expression |  | What is a common feature of composite transposons? | Antibiotic resistance genes |  | What is a major distinction between transposition in eukaryotes and prokaryotes? | Integration and excision are distinct processes in eukaryotes |  | What is a topological requirement for site-specific integration of bacteriophage into the E. coli chromosome? | It must be supercoiled. | Figure 25.31 | What is the electron-carrying material in DNA photolyases? | FADH2 | Figure 25.10 | What is the enzyme that bacteriophage uses for site-specific integration? | Integrase |  | What is the methylation pattern in animal DNA? | Primarily in C residues that are immediately 5' to G residues, that is, in a sequence CpG. When such a C is methylated, so is the corresponding C in the complementary strand. |  | What is the methylation pattern in plant DNA? | The methylated sequence is the C of CpNpGp, where N can be any base |  | What is the most common type of mutation in tumor cells? | GC changing to AT |  | What is the most widely used type of restriction endonucleases used in biotechnology? | Type II restriction endonucleases |  | What is the retroviral reverse transcriptase gene called? | pol |  | What is the total number of possible IgG heavy chains? | 5000 |  | What modified forms of guanine are primary products of the treatment of DNA with methylating or ethylating reagents? | 6-methyguanine and O6-ethylguanine |  | What molecule is the methyl donor in methylation of DNA and RNA? | S-adenosylmethionine (AdoMet) |  | What non-recombinational 'shuffling' process is used to join the C and J segments in antibody production? | Splicing |  | What process is found in the development of resistance to the drug methotrexate? | Gene amplificaton of the dehydrofolate reductase gene, the target of methotrexate. |  | What retrovirus gene encodes the major glycoprotein of the viral envelope? | env |  | What role does FADH2 play in DNA photolyases? | It acts like a photochemical reaction center, translating light energy to facilitate the transfer of an electron to the photodimer, and breaking the pyrimidine-pyrimidine bonds by a free radical mechanism | Figure 25.10 | What role does methylation play in Neurospora? | Preventing inappropriate recombination between duplicated gene segments. |  | What sequence is commonly methylated in E. coli? | A residues in the sequence 5´-GATC-3´ |  | What sequences are assembled to make immunoglobulin heavy chains? | V, J, C, and D |  | What structural feature is found at the ends of retroviral genomes? | Long terminal repeated sequences | Figure 25.38 | What three genes are commonly found in retroviruses? | gag, pol, and env |  | What two proteins are required for site-specific integration by into the E. coli genome? | Phage integrase (int) and Integration Host Factor (Ihf), which is an E. coli protein. | Figure 25.31 | What type of recombination in E. coli involves the RecA protein? | Homologous recombination |  | What type of transposition is performed by class I transposons? | Simple transposition |  | What type of transposition is performed by class II and class III transposons? | Replicative transposition |  | What types of recombination in E. coli use sequence-specific enzymes? | Site-specific recombination and transposition |  | What wavelength of UV light is most effective in mutating DNA? | 260nm, which is the part of the spectrum where DNA light absorption is maximal. |  | Where do class III bacterial transposable elements insert their DNA in the host chromosome? | At random sites. |  | Which eukaryotic repair proteins are related to mutS of E. coli? | MSH2, MSH3, and MSH6 |  | Which genes are the preferred substrates for excision repair? | Ones actively undergoing transcription. |  | Which retrovirus gene encodes a polyprotein that contains virion core proteins? | gag |  | Whose work in the 1940s on maize genetics led to important discoveries about mobile genetic elements? | Barbara McClintock |  | Why are GC to AT mutations more frequent than other mutations? | Probably because deamination of a methyl-cytosine leaves a G-T base pair. |  | Why is it more important for DNA to maintain integrity during replication more than proteins or RNA? | Effects of changes in most biopolymers are minimized by turnover and replacement of altered molecules. DNA cannot be discarded or replaced in this manner. |  | Why is microsatellite instability a problem for HNPCC patients? | The mutations, which arise from slipping of a DNA strand during replication, would normally be repaired by a mismatch repair gene missing in these individuals. |

What two mechanisms are used by cells to maintain the stability of DNA sequences? | 1. A replication process of very high accuracy that prevents errors from occurring. 2. Mechanisms for correcting genetic information when DNA suffers damage. |  | What are five systems cells use to correct errors in DNA? | 1. Direct repair, in which a damaged DNA base is chemically altered to restore the original structure. 2. Nucleotide excision repair, in which a section of DNA that contains a damaged site is excised and replaced with normal DNA. 3. Base excision repair, which starts with cleavage of the glycosidic bond connecting a damaged base to the DNA sugar-phosphate backbone.

4. Recombinational repair, in which newly replicated DNA duplexes undergo genetic recombination, with ultimate removal of the damaged DNA segment.

5. Mismatch repair, a process that recognizes DNA mismatches created either by replication errors, non-homologous recombination, or damage to one DNA base, and corrects the error.

What are the two repair processes in E. coli that can repair the gap arising from replication of a site containing an unrepaired thymine dimer?

1. Recombinational repair, or daughter-strand gap repair.

2. SOS repair, or error-prone repair.

Figure 25.15
What are the functions of RecA?

1. Strand pairing - joining of two different DNAs by homologous base pairing with each other.

2. Genetic Regulation - activation of the synthesis of many proteins, including DNA repair proteins.

How does recombinational repair of gaps created by unrepaired thymine dimers function?

1. The uninvolved parental strand, which is complementary to the damaged parental strand, recombines into the gap, opposite the damaged site.

2. A gap now exists in the previously undamaged arm, but because it lies opposite an undamaged template, it can be filled by action of DNA polymerase and DNA ligase.

3. The thymine dimer itself is not repaired in this process, but the process allows time for the excision system to come in later and repair this damage.

Figure 25.15
What are common mechanisms of forming mismatches in DNA?

1. Replication errors

2. Through deamination of 5-methylcytosine in DNA to yield thymine

3. Through recombination between DNA segments that are not completely homologous.

By what mechanisms can recombination occur in the cell?

1. Integration of one DNA molecule into another

2. Substitution of a DNA segment for a homologous segment on another DNA molecule

3. Exchange of homologous segments between two DNA molecules.

What are four types of genetic recombination in E. coli?

Homologous Recombination

Site-Specific Recombination

Transposition

Illegitimate Recombination

How does exonuclease V work in recombination?

1. The protein binds at a double-strand break on duplex DNA.

2. It uses a helicase activity to unwind and partially degrade the DNA.

3. The 3' end is displaced as a loop, which is coated with single strand binding protein.

4. When the enzyme reaches Chi, a sequence-specific interaction causes the complex to switch strands and switch its preferred polarity of DNA degradation. These changes facilitate the loading of RecA to a free 3' end, and this initiates strand invasion of a nearby duplex

What are the three different classes of transposable elements in bacteria?

1. Class I elements encode a transposase but not a resolvase.

2. Class II transposons contain only one set of short flanking direct repeat sequences.

3. Class III - a small group of bacteriophages, of which the best-known is phage Mu. This phage is known to insert its chromosome at random in the host chromosome by a transpositional mechanism and also to replicate its genome by a transpositional mechanism, similar to that of type II elements.

Figure 25.35

Category - General

Query - What sequence is recognized and cut by the following restriction enzyme?

Reversal - there is no reversal

(restriction enzyme on left, sequence in middle, figure on right)

BamHI | GGATCC |  | BglII | AGATCT |  | EcoRI | GAATTC |  | EcoRII | CCGG |  | HaeIII | GGCC |  | HgaI | GACGCNNNNN |  | HhaI | GCGC |  | HindIII | AAGCTT |  | HinfI | GANTC |  | HpaI | GTTAAC |  | HpaII | CCGG |  | MspI | CCGG |  | NotI | GCGGCCGC |  | PleI | GAGTCNNNN |  | PstI | CTGCAG |  | SalI | GTCGAC |  | SmaI | CCCGGG |  | XbaI | TCTAGA |

Category - General

Query - What are the characteristics of the restriction endonculease type below?

Reversal - there is no reversal

(restriction endonuclease type on left, characteristics in middle, figure on right)

Type I | Cleaves DNA up to 10,000 nucleotides away from the recognition site, has the nuclease and restriction endonuclease in the same enzyme, requires ATP and AdoMet for cleavage. |  | Type II | Cuts within or very near to the sequenced recognized, is separate from the nuclease, does not require ATP or AdoMet |  | Type III | Cuts near the recognition site (within 100 bases), has the nuclease and restriction endonuclease in the same enzyme, does not require ATP, but does require AdoMet for cleavage. |