PCB 4522 Exam 1 Study Guide - Gurley

How many amino acids (out of 715) have changed in FOXP2 since humans split from mice?

The frequency of what types of mutations are used as a molecular clock?

Which of the pathways shown in the phylogenetic tree below has undergone the most positive selection?

Approximately how long ago did behaviorally modern humans appear?

Approximately how many years ago did anatomically modern humans probably first appear? (Note: "Anatomically Modern" defined here is only related to the position of the larynx and windpipe.)

How big was the parent population of modern humans immediately before the third exodus from Africa ca. 70,000-100,000 yrs ago?

Neanderthals are thought to have had the modern configuration of the larynx and windpipe.

What are some examples of mutations that suggest that evolution is continuing to change our species?

What transcription factor has undergone comparatively rapid evolution in the interval between chimps and humans, perhaps contributing to the capacity for complex language?

What two actions can all vertebrates, with the exception of adult Homo sapiens, perform simultaneously?

What's the difference between synonymous and nonsynonymous mutations?

Which of the answers below illustrates that the concept of an organism is a matter of definition?

Which of the answers below illustrates the concept that a species is somewhat arbitrary and relative?

Which two forms of archaic humans made the first exodus from Africa more than 200,000 yrs ago?

Which of the following proteins is perhaps the largest in the human genome and mutations of it have been implicated in autism, dyslexia, schizophrenia, intellectual disability, Tourette syndrome and language impairment?

Which enzyme methylates bacterial oriC?

What are the DNA sequence elements of oriC?

Under what circumstances can the replication fork be bidirectional?

What is the replication fork?

Which chemical reaction occurring at the bacterial origin of replication plays a role in the regulation of initiation?

The Bacterial origin of replication, oriC, can only initiate replication when _________________?

Which function is NOT regulated by the bacterial origin of replication?

Which statement is TRUE?

What is a replicon?

Which mechanism does NOT contribute to the control of reinitiation of bacterial replication?

Which statement is TRUE regarding replication control?

What is the function of ter sites in the genome?

Bacterial origin of replication oriC consists of ________________________?

Which statement is TRUE regarding replication control?

What is the function of Tus protein?

Which of the following is a transcription factor associated with the origin in yeast?

In yeast the ______________________ functions as the origin of DNA replication.

At which point in the cell cycle is Geminin degraded?

What is an average size of replicons found in eukaryotic genomes?

How long does the S phase last, and what fraction of the DNA is thought to replicate at any given time in a typical eukaryote?

During which cell cycle phase is DNA replicated in eukaryotes?

Which two Archaeal replication initiator proteins are thought to be same as in eukaryotes?

Phosphorylation of the ORC _____________________________.

What is the role of the Geminin protein in the initiation of eukaryotic DNA replication?

How does DNA replication terminate in yeast (fungus), Drosophila (insect) and Arabidopsis (plant)?

Which replicon machinery movement is the fastest?

The __________________________ is a complex containing 6 proteins that bind to the A and B1 domains of the yeast origin of replication and is required for replication of the chromosome.

How many replicons can be found in typical eukaryotic genomes?

Which of the following proteins or complexes leaves the origin and moves ahead of the DNA polymerase during replication?

Which two proteins are unstable in yeast, bind to the ORC, and are only synthesized during the G1 phase of the cell cycle?

Why does it take so long for the origin oriC to be able initiate a second round of replication?

Present day mitochondria do not have enough genes for them to survive as an independent organism. Where did all the missing genes go?

Which of the numbered molecules in the figure is (are) used to synthesize the new H strand under normal conditions? (mtDNA not depleted)

How are mitochondria inherited in humans (and most mammals)?

Which bacterial group is most closely related to mitochondria and is thought to represent the original endosymbiont that gave rise to this organelle?

Most of the protein encoding genes in mammalian mitochondrial DNA are located on the same strand that is displaced in the D-loop.

Identify the location designated "4" in the figure of mitochondrial DNA.

Which of the following would provide the best region, or gene, to use as a molecular clock to study the divergence of various species of monkey?

Which of the numbered molecules is (are) used to prime DNA synthesis when mitochondrial DNA is severely depleted?

Is mitochondrial DNA replication considered bi-directional or uni-directional and why?

Mitochondrial genes are pretty closely packed. What type of genes are located in between the protein-encoding genes?

What are the two major roles played by the Light Strand Promoter present in the mitochondrial genome? It serves as a promoter for ____________ and _____________.

How does Adenovirus use a single replication mechanism to replicate both strands?

Name three proteins needed to replicate the linear Adenovirus genome.

Linear templates: How do T4 and Lambda phage solve the problem of having linear double-stranded DNA templates?

Which of the following is primed in DNA replication by a single nucleotide (CTP) covalently linked to a protein?

PhiX174 replication: Which of the following is NOT a function of Protein A?

Plasmids are like phages in many respects. Which of the following is FALSE?

Adenovirus replication: What happens to the Terminal Protein after priming?

There are difficulties in replicating linear DNA. What are they?

Plasmid copy number: Why is a mechanism for segregation not important for high-copy plasmids?

In eukaryotes the chromosomes are linear DNAs. How is the problem of replication handled?

Tra locus: What is the name of the gene that regulates transcription, but does not encode a protein?

Tra locus: Which protein directs the TraY/I/M-DNA complex to the T4SS channel? (Note: It was not covered in the lectures, but TraT/Y complex also contains TraM.)

Tra locus: Which protein is the first protein translated on the long polycistronic transcript (RNA) and recognizes oriT?

Problem: An F plasmid contains an insertion sequence (IS element) that is identical to one found on the host chromosome. However, the IS element copy on the F plasmid contains a defective transposase coding region (a single bp mutation).

F plasmid: How are the donor and recipient cells drawn together for the transfer of DNA during conjugation?

Tra locus: Which protein(s) shares many of the activities of PHiX174 Protein A?

F plasmid: Where is the nic site located?

The F plasmid has three modes of DNA replication. Which one uses a rolling circle mechanism?

When the F plasmid integrates into the chromosome, which origin does it use to replicate?

When a portion of the bacterial chromosome is transferred to the donor cell from an Hfr donor, how does this DNA integrate into the recipient chromosome?

F plasmid immunity: Which inner membrane protein blocks the transfer of DNA between F positive cells?

Which term below signifies and free F plasmid containing a portion of the host chromosome?

If an insertion sequence (IS element) was located on the E. coli genome half-way around the circle from an integrated copy of the F plasmid, how long would it take for the insertion sequence to transfer to the recipient cell?

When Hfr cells are mixed with F minus cells the recipient cell acquire traits found in the Hfr strain. Why are the recipients usually still F minus?

How long would it take for an integrated copy of the F plasmid to replicate itself by conjugation under standard lab conditions?

Which term below signifies a cell containing a free F plasmid?

Why do Hfr cells promote a high level of recombination when added to a F minus population of bacteria?

Helicase activity: How fast does the TraY/I complex unwind DNA starting at oriT?

Tra locus: Which protein is called the "€œpilot protein" because it covalently links to the 5'€™-end of the transferred DNA and leads the DNA into the recipient cell?

Tra locus: Which protein(s) senses that a stable mating pair has formed and then allows TraI to nick at oriT?

F plasmid immunity: Which protein blocks contact between the Tip protein of the pilus between two F positive cells?

Tra locus: Which protein is a positive transcriptional regulator and controls expression of TraM and TraY/I?

The ____ protein of Agrobacterium contains two nuclear localization sequences (NLS's) and nicks the T-DNA at two sites. (In your answer include the full name of the protein: for example ChvX or VirX, instead of the X protein.)

Vir ____ binds to the single strand of the displaced T-DNA single-strand, and Vir _____binds to overdrive DNA.

In the Ti plasmid (pTi)-based Binary vector system, where are the vir genes located?

Which vir proteins perform an analogous function as TraY and TraI?

What entity transferred from Agrobacterium to the plant nucleus causes the production of the crown gall tumor?

In Agrobacterium, ___ and ___ comprise bacterial a two-component signaling system.

Which three proteins perform analogous functions in various models of replication? (functionally analogous, not necessarily structurally analogous)

The following genes are located on the Agrobacterium tumefaciens chromosome: chvA, chvB, chvE and pscA. Which of these genes encodes a protein that binds to simple sugars and to the extracellular domain of VirA?

Vir____ is a histidine kinase trans-membrane protein, which autophosphorylates when it binds an inducer.

Which protein is phosphorylated by VirA and then acts as a positive transcription factor?

The ____ protein is embedded in the membrane of Agrobacterium and senses the presence of acetosyringone from the wounded plant cell. (In your answer include the full name of the protein: for example ChvX or VirX, instead of the X protein.)

Which of the following proteins from the pTi are transferred to the plant cell?

The ____ and _____ proteins contain nuclear localization sequences (NLS) that target the T-DNA to the plant nucleus.

Why is it important for the Overdrive element to be located next to the Right Border instead of the Left Border? (Read the answers carefully.)

_____ activates the _______ response regulator by phosphate group transfer onto its receiver domain.

Which part of the Ti plasmid gets transferred and integrated into the plant genome?

Which two genes of the Vir region (Ti-plasmid) perform a similar function in the Tra region of the F plasmid?

The soil bacterium Agrobacterium tumefaciens infects plants at a wound site. What is the signal that activates the vir locus as a result of the wound?

What are the basic features of the miniTi vector plasmids?

Which statement is TRUE? (Read carefully)

Which vir genes recognize right border and nick it, thus generating the primer for DNA strand synthesis?

The ____ protein of Agrobacterium coats the surface of the T-strand and contains a nuclear localization sequence that facilitates the transport of the DNA to the plant nucleus. (In your answer include the full name of the protein: for example ChvX or VirX,

Which of the following statements is TRUE?

What would happen if the Left Border sequence was deleted from the pTi (Ti plasmid)?

Which vir genes are constitutively expressed?

Which answer is FALSE?

What two general classes of genes are found in the T-DNA region of the Ti plasmid? Hint: What are the two main characteristics of the tumor? Which two classes of genes are responsible?

Bacterial DNA replication can be divided into two processes: 1-DNA synthesis and 2-formation of the septum in preparation for the physical separation of the two daughter cells. Which of the following statements is FALSE?

Plasmid compatibility: In the case of ColE1 plasmids, mutations in which location near the origin are most likely to lead to the formation of new Compatibility Groups?

If a growing bacterial cell (E. coli) is 1.5 micons in length, it should have only one active origin.

Compatibility groups: Which of the following statements is TRUE?

When a bacterial cell replicates its genome (DNA), it soon divides. Which statement is FALSE?

ColE1 replication: What would happen if you over-expressed the first 600 base of RNA II by introducing a truncated copy of the RNA II primer gene into the plasmid? The ColE1 plasmid would have a second copy of the RNA II gene (including a strong promoter) that would only be comprised of nucleotides 1-600.

Which numbered arrow represents the promoter for RNA II. RNA II serves as the primer for DNA synthesis for plasmid replication. (The two fat arrows, blue and red, represent promoters.)

ColE1: Which of the following molecules enable, or facilitate, the negative regulation of DNA replication?

Coli E1 plasmid replication: Which of the following numbered arrows represents a protein?

ColE1 origins: There are two promoters that control synthesis of RNAs that act to prime DNA synthesis or act to inhibit that priming event. If you wanted to increase the copy number of the plasmid from 20/cell to 120/cell, what would be your strategy?

Which of the following is a transcript that forms a double-stranded duplex with RNA II in order to disrupt priming of DNA synthesis for replication?

The ____ protein of Agrobacterium is phosphorylated by VirA in the presence of wounded plant cells. (In your answer include the full name of the protein: for example ChvX or VirX, instead of the X protein.)

The ____ protein binds to the overdrive sequence at the right border of T-DNA to ensure that the nick occurs at there before the left border. (In your answer include the full name of the protein: for example ChvX or VirX, instead of the X protein.)

The ____ protein binds arabinose (and other simple sugars) and then interacts with the portion of VirA exposed in the periplasm to increase its affinity for acetosyringone. (In your answer include the full name of the protein: for example ChvX or VirX,