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)

Aphidicolin | A fungal product with a steroidlike structure that inhibits replicative DNA synthesis specifically in eukaryotes |

Allele | A specific version of a gene that occupies a particular location in the genome. It is distinguished from other alleles of the same gene by differences in nucleotide sequence. |  | Antiparallel | Arrangement of DNA strands, such that a strand running 5' to 3' forms base pairs with a strand of the opposite polarity (3' to 5'). |  | Apyrimidinic Endonuclease | An enzyme that recognizes an apyrimidinic site in DNA and cleaves the phosphodiester bond on the 5' side of the deoxyribose. | Figure 24.35 | Apyrimidinic Site | Within a DNA molecule, a sugar residue lacking an attached pyrimidine. Such sites can arise by action of uracil-DNA N-glycosylase. | Figure 24.35 | Bacteriocins | Proteins encoded by bacteria that are released by the organism and kill other bacteria. |  | -Lactamase | An enzyme coded for by a plasmid in bacteria that is capable of enzymatically degrading penicillin. Bacteria carrying this gene are resistant to penicillin. |  | Bidirectional Replication | The mechanism of E. coli replication in which replication starts at a single origin and proceeds in both directions away from it. |  | Cohesive Ends | Short oligonucleotide sequences at the end of a DNA fragment that are complementary to oligonucleotide sequences at the end of another DNA fragment. |  | Concatemer | In replication of the T4 and T7 linear genomes, end-to-end linear aggregates of the genome that are made during replication | Figure 24.41 | Conjugation | A form of sexual reproduction in bacteria in which DNA from a donor cell is transferred to a recipient cell. | Figure 24.7 | Copy Number | Number of copies per cell of a gene or DNA sequence. |  | Diploid | For a cell or an organism, the possession of two homologous sets of chromosomes per nucleus (with the possible exception of sex chromosomes, which may be present in only one copy). |  | DNA Gyrase | A type II topoisomerase from E. coli that can both relax a supercoiled DNA molecule and introduce negative superhelical turns into it. | Figure 24.31 | DNA Ligase | An enzyme catalyzing covalent joining of the 5' end of one strand to the 3' end of another. The enzyme catalyes formation of phosphodiester bonds between the ends and is important for joining Okazaki fragments together. | Figure 24.4, Figure 24.24 | DNA Polymerase I | A DNA polymerase in E. coli with a 5' -> 3' exonuclease activity (useful for removing Okazaki fragments), a 3' -> 5' exonuclease activity (good for proofreading), and a 5' to 3' DNA polymerase activity. | Table 24.2 | DNA Polymerase II | A DNA polymerase in E. coli that probably plays a role in DNA repair and the SOS response | Table 24.2 | DNA Polymerase III | The DNA polymerase in E. coli responsible for most DNA synthesis. It is found at the replication fork in active E. coli DNA synthesis. | Table 24.2 | DNA Polymerase III Holoenzyme | A multiprotein aggregate that includes DNA polymerase III and is involved in replicating DNA in vivo. | Figure | DNA Replication | The process whereby a DNA duplex is copied by DNA polymerase and accessory proteins to make two copies where one existed originally. |  | dnaA | The E. coli protein that binds to oric to initiate the process of DNA replication. |  | dnaB | A helicase that binds to the oric complex during initiation of DNA replication in E. coli. |  | dnaC | An initiation protein in E. coli that binds with dnaB during initiation. |  | dnaG | The E. coli primase protein that binds at the oric complex during initiation. |  | dUTPase | An enzyme which cleaves dUTP to dUMP plus PPi. It is important in reducing the amount of dUTP in the cell so that less is available for DNA polymerase during DNA replication. |  | Gap | A single-strand interruption in duplex DNA, in which nucleotides are missing, as distinguished from a nick, a similar interruption with no missing nucleotides. |  | Genetic Map | A map that identifies the relative positions of genes on chromosomes | Figure 24.8 | Genome | The total genetic information contained in a cell, an organism, or a virus. |  | Genotype | The genetic constitution of an individual organism. |  | Hairpin (stem loop) | A structure in DNA (or RNA) arising from pairing of complementary sequences within a single strand. |  | Haploid | For a cell or an organism, the possession of only one copy of each chromosome per nucleus (or cell). |  | Helicases | Enzyme that catalyze the unwinding of duplex DNA strands. | Figure 24.6 | Integration | Insertion of one molecue of DNA into another. |  | Klenow fragment | A proteolytic cleavage fragment of DNA polymerase I of E. coli that contains the DNA polymerase and 3' ->5' exonuclease activities of the enzyme. | Figure 24.16 | Lagging Strand | The daughter strand during DNA replication that is extended in the direction away from the replication fork in a discontinuous manner. This strand contains the Okazaki fragments. | Figure 24.3 | Leading Strand | The daughter strand during DNA replication that is extended in the same direction as the replication fork and in a continuous manner. | Figure 24.3 | Linkage Map | A map of the genes of a genome made by measuring recombination frequencies of the genes. |  | Long Terminal Repeats | A feature of the retrovirus genome in which the sequence at one end of the linear chromosome is repeated at the other end. |  | Mismatch Repair Systems | Cellular repair system that works by scanning the newly replicated DNA, excising any residues that are not properly base-paired and replacing them with the correct nucleotides. |  | Nick | A single-strand interruption in duplex DNA, in which no nucleotides are missing, as distinguished from a gap, a similar interruption with one or more missing nucleotides. |  | Nick Translation | A process in which nucleotides in one strand of a nucleic acid duplex are replaced one by one with nucleotides complementary to the other strand. The process starts at a nick in the strand and causes the location of the nick to migrate. | Figure 24.5 | Okazaki Fragments | The discontinuous stretches in which the lagging strand is initially synthesized during DNA replication; these fragments are later joined to form a continuous strand. | Figure 24.3, Figure 24.6 | oric | The replication origin on the E. coli chromosome. |  | Phenotype | The appearance and other measurable characteristics of an organism; it results from the interaction of the organism's genetic makeup with the environment. |  | Physical Map | A map which shows the physical locations of genes on a chromosome. |  | Plasmid | Small, extrachromosomal circular DNA molecules found in many bacteria. They replicate independently of the main chromosome and may occur in multiple copies per cell. |  | polA | The name of the structural gene for DNA polymerase I in E. coli. |  | polB | The name of the structural gene for DNA polymerase II in E. coli. |  | polC | The name of the structural gene for DNA polymerase III in E. coli. |  | Primase | An enzyme essential for initiating DNA replication in most cells. It is an RNA polymerase and creates a short RNA primer, which is elongated by DNA polymerase. | Figure 24.4 | Primer Strand | The strand being elongated in DNA replication. |  | Primosome | An enzyme complex that is located in the replication fork during DNA replication. It synthesizes the RNA primers on the lagging strand and also participates in unwinding the parental DNA helix. |  | Processivity | For a DNA or an RNA polymerase, the average number of nucleotides incorporated per event of binding between the polymerase and a 3' primer terminus. It describes the tendency of a polymerase to remain bound to a template. |  | Proofreading | A process in DNA replication that occurs when the 3' to 5' exonuclease activity of a DNA polymerase recognizes and excises mispaired bases in the newly replicated DNA. Such a process probably contributes to the surprisingly low error rates of DNA replication in vivo. | Figure 24.44 | Reconstitution | A method of studying an enzymatic process in which the individual proteins for a process are purified separately and then added back together in a test tube to perform the reaction they catalyze in vivo. |  | Replicase | An RNA-dependent RNA polymerase found in RNA viruses that do not go through a DNA intermediate in their life cycle. |  | Replication Fork | A structure occurring in DNA replication. It is the point at which replication is actually occurring. | Figure 24.1 | Replication Origin | A region in a DNA molecule defined by a specific nucleotide sequence where replication of DNA begins. |  | Replicative Form (RF) | In bacteriophages, the circular duplex form of DNA. |  | Replicon | The cluster of DNA that includes the sequence of nucleotides at which DNA replication begins and the structural genes for proteins whose action on the origin sequence inititates replication at that point. |  | Replisome | The multiprotein DNA replication complex. |  | Retrovirus | An RNA virus that goes through a DNA intermediate as part of its life cycle. It contains an enzyme called reverse transcriptase. | Figure 24.45 | Reverse Transcriptase | An enzyme, found in retroviruses, that uses RNA as a template to make DNA. | Figure 24.45 | Reversion | A mutation in a mutated gene which restores the wild-type genotype (and phenotype). |  | RFI | In bacteriophages, a covalently closed circular duplex of DNA. | Figure 24.36 | RFII | In bacteriophage DNA, a nicked circular form of the DNA | Figure 24.36 | RNAse H | An enzyme that degrades RNA paired to DNA. Reverse transcriptase has an activity like this. | Figure 24.45 | Second-site Reversion (Suppression) | A mutation in a mutated gene that restores the wild-type phenotype, but which occurs at a location other than the original mutation. |  | Semiconservative DNA Replication | A mode of DNA replication in which each daughter duplex contains one strand from the parent duplex and one newly synthesized strand. |  | Silent Mutation | A mutation which occurs that does not affect the phenotype of the organism. |  | Single-strand DNA-binding Protein (SSB - also called Helix Destabilizing protein) | An E. coli protein that binds to DNA so as to stabilize a structure in which hydrogen-bonding surfaces of the DNA bases are spatially oriented toward the incoming nucleotides. | Figure 24.6, Figure 24.26 | Strand Displacement | A phenomenon that occurs when replication of one DNA strand displaces a previously made DNA strand during the replication process. | Figure 24.15 | Telomerase | An enzyme capable of elongating the termini of eukaryotic linear chromosomes. |  | Template Strand | The strand being copied in DNA replication. |  | Terminal protein | In adenovirus and the phi29 bacteriophage, a protein covalently attached to the 5' terminus of each strand of the linear genome that serves to initiate DNA replication. |  | Terminal Redundancy | Duplication of a small part of the genome at the end of a linear chromosome. Is employed by bacteriophages T4 and T7. |  | Structure | The appearance of the E. coli chromosome during bidirectional replication, as viewed by electron microscopy. | Figure 24.11a | Topoisomerases | Enzymes that change the supercoiling of DNA helices by either allowing the superhelical torsion to relax (thus reducing the supercoiling) or adding more twists (thus increasing the supercoiling). | Figure 24.6 | Transcription | The synthesis of an RNA molecule complementary to a DNA strand. The information encoded in the base sequence of the DNA is thus "transcribed" into the RNA version of the same code. |  | Translation | The synthesis of a polypeptide under the direction of an mRNA, so that the nucleotide sequence of the mRNA is "translated" into the amino acid sequence of the protein. |  | Virion | A virus particle. |  | Wild Type | An unaltered, unmutated form of a gene in an organism. |

Category - General

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

Reversal - there is no reversal

How are the E. coli topoisomerases classified? | Topoisomerases I and III are type I topos, whereas Topoisomerases II (also known as DNA gyrase) and IV are type II topos. |  | How does DNA polymerase manage to copy the strand opposite the one running 5' to 3'? | In E. coli, the replicative polymerase operates as a dimer. One copy of the polymerase works on one strand continuously in the 5' to 3' direction (making one continuous strand) and the other polymerase of the dimer copies the complementary strand discontinuously, but still only in the 5' to 3' direction. |  | How does replication of the bacteriophage X174 differ from that of bacteriophages G4 and M13? | X174 assembles a complete E. coli primosome during replication. The others do not. |  | How does the free energy of formation of a Watson-Crick base pair affect the fidelity of DNA replication? | It contributes only about 100-100 fold difference in binding energy compared to an incorrectly paired set of bases. This is insufficient to explain the actual fidelity of replication, which is thousands of times more accurate. |  | How does uracil-DNA N-glycosylase act on DNA to remove uracil? | It hydrolytically cleaves the glycosidic bond between N-1 of uracil and C-1 of deoxyribose, yielding free uracil and DNA with an apyrimidinic site (a sugar residue lacking an attached pyrimidine). | Figure 24.35 | How fast does E. coli replicate its entire chromosome? | 40 minutes |  | How is HIV classified as a virus? | It is a retrovirus |  | How long is oric? | 245 base pairs. |  | How many different helicases are present at the E. coli replication fork? | At least two - one that acts on the lagging strand template, as part of the primosome, and one that acts upon the leading strand template. |  | How many molecules per cell are there of DNA polymerases I, II, and III of E. coli? | 400, 100, and 10, respectively | Table 24.2 | How many origins of replication are found in the E. coli chromosome? | One |  | How many topoisomerases are known in E. coli? | Four |  | How much accuracy does the mismatch repair system contribute to replication fidelity? | 100 fold |  | In single strand bacteriophages, which strand is the plus strand and which is the minus strand? | The plus strand is the one originally injected into the bacterium and is the strand copied during replication. It is the product of a round of replication. The minus strand is simply copied from the plus strand. | Figure 24.36 | Uracil-DNA N-Glycosylase | An E. coli enzyme which removes any dUMP residues that make it into DNA | Figure 24.35 | What activity of E. coli DNA polymerase I is essential for replication in the organism? | The 5' -> 3' exonuclease activity. |  | What are the basic proteins that bind to the dnaA-oric complex in inititiation of E. coli DNA replication? | HU and IHF |  | What are the five distinct DNA polymerases in eukarytic cells? | , , , , | Table 24.3 | What are the structural requirements of most DNA ligases? | A 3' hydroxyl group and 5' phosporyl terminus on the two ends to be joined. |  | What are the three enzymatic activities of E. coli DNA Polymerase I? | 5'-> 3' DNA polymerase, 3' -> 5' exonuclease, 5' -> 3' exonuclease. |  | What are the two known roles of the 5' to 3' exonuclease activity of DNA polymerase I of E. coli? | 1. Excision of RNA primers from primase 2. An ability to cleave deoxyribonucleotides in damaged DNA enabling repair. |  | What are the types of topological interconversions catalyzed by type II topoisomerases? | 1. Relaxation 2. Catenation/decatenation 3. Knotting/unknotting | Figure 24.33 | What common feature of DNA replication systems are missing in RNA polymerases? | Proofreading |  | What complex of E. coli DNA polymerase III holoenzyme serves as the clamp loader? | The complex |  | What effect does nalidixic acid have on E. coli? | It inhibits DNA replication by inhibiting DNA gyrase. |  | What energy source is used by helicases to unwind DNA? | ATP hydrolysis |  | What enzyme catalyzes the chemical reactions of DNA synthesis? | DNA Polymerase | Figure 24.2 | What enzyme helps reduce the amount of dUTP used by DNA polymerase in synthesis of DNA? | dUTPase |  | What enzyme removes the apyrimidinic site in a DNA molecule after action by apyrimidinic endonuclease? | DNA polymerase I | Figure 24.35 | What function do HU and IHF perform in initiating E. coli DNA replication? | Bend the DNA. |  | What inherited diseases in humans arise from defects in DNA helicase genes? | Werner's syndrome and Bloom's syndrome |  | What initiation protein binds to oric to initiate E. coli DNA replication? | dnaA |  | What is a difference in the mechanisms of action of type I and type II topoisomerases? | Type I topoisomerases break one strand of a double-stranded helix. Type II topoisomerases break two strands of a double stranded helix. | Figure 24.30, Figure 24.31 | What is a problem that must be overcome in replication of liinear genomes? | At the 5' terminus of a linear chromosome, an RNA primer will exist (if no other mechanism of initiation is available) that, when removed, cannot be filled in by DNA polymerase, since it is unable to initiation synthesis of DNA in the absence of a primer. |  | What is the 3' to 5' activity of DNA polymerases useful for? | Proofreading (error correction) |  | What is the bias in direction of DNA synthesis? | DNA synthesis occurs only in the 5' to 3' direction. |  | What is the chemical form of the primer in cellular DNA replication? | RNA | Figure 24.4 | What is the chemical reaction that occurs in DNA synthesis? | The 3' hydroxyl group at the end of a DNA chain reacts with the (innermost) phosphate of an incoming dNTP. The reaction involves nucleophilic attack by the 3' hydroxyl at the primer terminus upon the phosphorus atom of the phosphate of the dNTP substrate, with pyrophosphate as the leaving group, helping to drive the reaction energetically. | Figure 24.2 | What is the complex the helicase associated with the lagging strand is called? | Primosome |  | What is the difference between type I and type II topoisomerases? | Type I topoisomerases change the DNA linking number in units of 1, whereas type II enzymes change the linking number in units of 2. |  | What is the energy source for E. coli DNA ligase? | NAD+ |  | What is the energy source of T4 DNA ligase and eukaryotic DNA ligases? | ATP |  | What is the initial primer in replication of retrovirus RNA? | A molecule of tRNA |  | What is the phenotype of E. coli mutant in DNA Polymerase I? | They are abnormally sensitive to ultraviolet irradiation and to alkylating agents that react with DNA. |  | What is the phenotype of E. coli mutants lacking dUTPase? | They are hypermutable (are prone to mutation), probably because they incorporate a lot of uridine into the DNA during replication. |  | What is the rate of replicative chain growth in E. coli? | 800 nucleotides per second. |  | What process is the most accurate of known enzyme-catalyzed reactions? | DNA replication |  | What proteins are present at a DNA replication fork? | DNA polymerases, single-strand DNA binding proteins, helicases, primase, topoisomerases, and DNA ligase |  | What subunit of the DNA polymerase III holoenzyme is responsible for making the enzyme very processive? |  |  | What subunit of the E. coli DNA polymerase III holoenzyme complex is known as the clamp? |  |  | What three processes can DNA replication be divided into? | 1. Initiation 2. Elongation 3. Termination |  | What two cellular systems contribute significantly to increasing the fidelity of DNA replication? | 1. Proofreading 2. Mismatch repair |  | Which DNA polymerase in E. coli is useful for nick translation? | DNA Polymerase I |  | Which E. coli topoisomerase is inhibited by nalidixic acid? | DNA gyrase |  | Which E. coli topoisomerase plays a critical role in completion of a round of replication | Topoisomerase IV | Figure 24.34 | Which E. coli topoisomerase plays the predominant role during replicative chain elongation | DNA gyrase |  | Which eukaryotic DNA polymerase is likely involved in DNA replication? |  |  | Which eukaryotic DNA polymerase is located in the mitochondrion? |  |  | Which eukaryotic DNA polymerase requires an additional protein, called proliferating cell nuclear antigen (PCNA), to carry out highly processive DNA synthesis in vitro? |  |  | Which eukaryotic DNA polymerases are more sensitive to aphidicolin? | , , and |  | Which of the eukaryotic DNA polymerases has a subunit with primase activity? |  |  | Which viruses integrate into the host genome as a normal part of their life cycle? | Retroviruses | Figure 24.45

What are the general features of DNA replication? | 1. DNA replication is semi-conservative. 2. DNA replication is ordered and sequential. 3. DNA replication uses activated substrates (dNTPs). 4. DNA replication is discontinuous. 5. DNA replication is far more accurate than any other enzyme-catalyzed process. |  | What must occur when a growing Okazaki fragment reaches the 5' terminus of the next Okazaki fragment? | 1. Removal of the RNA primer. 2. Replacement of the departed ribonucleotides with deoxyribonucleotides. 3. Covalent joining of the 3' end of the newly synthesized Okazaki fragment to the 5' end of the next Okazaki fragment. |  | What are the names and functions of the 10 polypeptides of the E. coli DNA Polymerase III Holoenzyme complex? | - PolC gene product. Has polymerase activity. Part of the core polymerase. - Contains a 3'-5' exonuclease activity comparable to the 3'-5' exonuclease domain of Polymerase I. Part of the core polymerase. - Unknown function. Part of the core polymerase.

- This dimeric protein dimerizes the holoenzyme, holding leading and lagging strand polymerases together so both DNA strands are elongated at the replication fork.

- Mediates the switch from making RNA primers (with Primase) to making DNA (with PolC).

- Functions as a sliding clamp to hold the holoenzyme complex to DNA, making the enzyme very processive.

, ', , , - This group of proteins is called the complex (also called clamp loader). Is composed of one copy of all proteins except , of which there are 2 or 3. Clamp loader functions to wrap the clamp onto the DNA.

Figure 24.24
What are the names and known functions of the eukaryotic DNA polymerases?

- is distinctive for containing a primase activity. It is also highly sensitive to aphidicolin. Functions in lagging strand synthesis.

- has low processivity (does not polymerize DNA for long periods of time). Functions in DNA repair. Low sensitivity to aphidicolin.

- Mitochondrial DNA polymerase. Low sensitivity to aphidicolin.

- May be principal leading strand polymerase. Requires a protein called proliferating cell nuclear antigen (PCNA) to carry out highly processive DNA synthesis in vitro. PCNA functions like the clamp of E. coli DNA Polymerase III.

- Function not completely clear.

What is the sequence of events in replication of single-strand bacteriophage DNA?

1. Minus strand synthesis.

2. Supercoiling.

3. Site-specific nick in the DNA by an initiation protein.

4. Extension (replication) of the plus strand from the 3' end of the nick.

5. Completion of the new plus strand.

6. A protein nicks and releases original plus strand and generates a new RFII.

What are the steps in oric-directed replication in E. coli?

1. Binding of 10-20 molecules of a dnaA/ATP complex. This causes the DNA to bend.

2. DnaC/DnaB protein complex binds to both forks of the opened loop. The helicase (DnaB) acts to open the structure further.

3. DnaG (primase) binds and synthesizes RNA primers. RNA polymerase may also synthesize some primers.

4. DNA Polymerase III holoenzyme extends both leading and lagging strands.

Figure 24.37
What are the sequence of events in replication of mitochondrial DNA?

1. Initiation occurs at a fixed origin on the L strand.

2. The heavy strand is displaced by replication on the L strand.

3. About 2/3 of the way around the circle, a second origin is exposed on the displaced H strand.

4. Unidirectional synthesis from this origin proceeds back in the other direction.

Category - General

Query - What mechanism do the following viral systems employ to replicate linear genomes?

Reversal - there is no reversal

(viral system on left, mechanism in center, figure on right)

T4 and T7 bacteriophages | End to end recombination at terminal redundancies | Figure 24.41 | Adenovirus and 29 | 5'-genome linked protein, which serves to initiate DNA replication. | Figure 24.41 | Poxviruses | Replication around hairpin loops at the termini, followed by two-strand cutting. | Figure 24.41