Exam 1 HQ

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

1 & 2 the two strands closest to the d-loop

Helicase activity: How fast does the TraY/I complex unwind DNA starting at oriT? 500 base pairs per second 500 base pairs (bp) per min 1,200 bp per second 1,200 bp per minute

1,200 bp per second

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

3

What is an average size of replicons found in eukaryotic genomes? 15 kb-35 kb 40 kb-200 kb 1 kb-240kb 200 kb-4,200 kb

40 kb-200 kb

How big was the parent population of modern humans immediately before the third exodus from Africa ca. 70,000-100,000 yrs ago? 1.2 million 150 5,000-10,000

5,000-10,000

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? a little more than 100 min 10 min 20 min 50 min

50 min

Approximately how long ago did behaviorally modern humans appear? 1.2 million 10,000 50,000-100,000 600,000

50,000-100,000

How many replicons can be found in typical eukaryotic genomes? 500-35,000 1-35,000 15,000-35,000 3,500-35,000

500-35,000

How long does the S phase last, and what fraction of the DNA is though to replicate at any given time in a typical eukaryote? 1 hr/100% 3 hr/50% 6 hr/15% 4 hr/80%

6 hr/15%

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.) 100,000-120,000 600,000-700,000 50,000-60,000 2,000,000-3,500,000

600,000-700,000

Which of the following is a transcription factor associated with the origin in yeast? HSF1 SRGAP2 FoxP2 ABF1

ABF1

Which of the following is primed in DNA replication by a single nucleotide (CTP) covalently linked to a protein? Lambda phage Adenovirus T4 phage PhiX174 phage

Adenovirus

Which replicon machinery movement is the fastest? Bacteria Leopard Plants Mouse

Bacteria

Plasmids are like phages in many respects. Which of the following is FALSE? Both produce infective particles. Both have immunity mechanisms to prevent reinfection. Both have members that can integrate into the host cell chromosome. Both use a rolling circle type mechanism in at least one form of replication. Plasmids are always double-stranded DNA. Phages can be double or single-stranded and either DNA or RNA. Both can acquire chromosomal DNA when they are excised (cut) by an imprecise mechanism. In other words, a mistake is made when they leave the chromosome.

Both produce infective particles.

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? SRGAP2 FOXP2 CNTNAP2 TATAAA binding protein (TBP)

CNTNAP2

Which two proteins are unstable in yeast, bind to the ORC, and are only synthesized during the G1 phase of the cell cycle? FoxP2, MCM Cdc6, Cdt1 SeqA, DnaB ABF1, SRGAP2

Cdc6, Cdt1

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? D-loop of mitochondrial DNA coding sequence for hemoglobin coding sequence for FoxP2 DNA encoding ribosomal RNA

D-loop of mitochondrial DNA

Which enzyme methylates bacterial oriC? Mec methylase EcoKI methylase Dam methylase Dcm methylase

Dam methylase

Which mechanism does NOT contribute to the control of reinitiation of bacterial replication? Delay in remethylation Physical sequestration of oriC Inhibition of DnaA binding and its transcription Delay in demethylation

Delay in demethylation

Which term below signifies a cell containing a free F plasmid? F positive Hfr F minus F prime

F positive

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

F prime

What transcription factor has undergone comparatively rapid evolution in the interval between chimps and humans, perhaps contributing to the capacity for complex language? TFIIB TBP COX2 FOXP2

FOXP2

What are the DNA sequence elements of oriC? Only GATC Dam methylation sites GATC Dam methylation sites, SeqA protein high and low affinity binding sites GATC Dam methylation sites, DnaA protein high and low affinity binding sites SeqA and DnA high- and low-affinity binding sites

GATC Dam methylation sites, DnaA protein high and low affinity binding sites

Which two forms of archaic humans made the first exodus from Africa more than 200,000 yrs ago? Homo erectus and Neanderthal Homo habilis and Australopithecus Homo ergaster and Homo sapiens

Homo erectus and Neanderthal

The Bacterial origin of replication, oriC, can only initiate replication when _________________? It is fully methylated on both strands at the adenines It is fully demethylated It is alkylated It is hemimethylated

It is fully methylated on both strands at the adenines

Adenovirus replication: What happens to the Terminal Protein after priming? It remains permanently covalently linked to the 5-terminus of each strand. It disassociates from the template after priming is complete. Its displaced by NF1. It is degraded.

It remains permanently covalently linked to the 5-terminus of each strand.

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? The TraS and T proteins block transfer of the F plasmid. The F plasmid is inactivated by the recombination machinery. Recombination inhibits the vegetative origin (oriV) of the F plasmid. It takes a long time to transfer the F plasmid, since the host chromosomal DNA is transferred first. Usually the mating is disrupted before F has a chance to transfer itself.

It takes a long time to transfer the F plasmid, since the host chromosomal DNA is transferred first. Usually the mating is disrupted before F has a chance to transfer itself.

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). It will use a double-strand break generated by the host IS element to integrate into the chromosome. It will using site-specific (not homologous) recombination to insert into the chromosome at the site of the IS element. It will not be able to integrate due to the defective IS element. It will use homologous recombination to integrate into the chromosome at the site of the IS element.

It will use homologous recombination to integrate into the chromosome at the site of the IS element.

Which of the following proteins or complexes leaves the origin and moves ahead of the DNA polymerase during replication? MCM 2-7 ORC ABF1 Cdt1

MCM 2-7

Present day mitochondria do not have enough genes for them to survive as an independent organism. Where did all the missing genes go? This is a trick question. Since the acquisition of mitochondria by eukaryotes occurred at least 2 billion years ago, the genomes of the original bacterial endosymbionts were much smaller than bacteria today. Most have migrated to the chloroplast genome. Most of the original mitochondrial genes are still present in the mitochondrial genome, but are no longer functional. Many have migrated to the eukaryotic nucleus.

Many have migrated to the eukaryotic nucleus.

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

Methylation

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. ORC Cdc6 ABF1 factor DnaB

ORC

What is the role of the Geminin protein in the initiation of eukaryotic DNA replication? It recruits the helicase to the origin. It constitutes Licensing Factor. It has to bind to the origin before the ORC can bind. Once bound to the Cdt1 protein, it blocks further binding of the helicase, MCM.

Once bound to the Cdt1 protein, it blocks further binding of the helicase, MCM.

Plasmid copy number: Why is a mechanism for segregation not important for high-copy plasmids? The RNA I regulatory molecule would prevent one of the daughters from retaining too many copies and, thereby, facilitate an equal distribution. This must be a trick question. It is important to have a segregation mechanism to prevent and unequal distribution of molecules. Once you have over 10 copies per cell (i.e. high copy), chances, based on simple probability, of getting at least one copy of the plasmid in each daughter cell is very high. The high-copy plasmids use the segregation machinery of the host cell to prevent unequal distribution into the daughter cells.

Once you have over 10 copies per cell (i.e. high copy), chances, based on simple probability, of getting at least one copy of the plasmid in each daughter cell is very high.

Which two Archaeal replication initiator proteins are thought to be same as in eukaryotes? Cdc6/Cdt1 Orc1/Cdc6 SeqA/DnaA DnaA/Orc1

Orc1/Cdc6

Which of the following statements is TRUE? Opines are synthesized in Agrobacterium and transported to the plant cell. The vir locus on the Ti plasmid encodes the genes required for bacterial conjugation. Opine catabolism genes are transferred from the pTi to the plant nucleus. Plants and most organisms are not able to metabolize opines as a nutrient source.

Plants and most organisms are not able to metabolize opines as a nutrient source.

What is the replication fork? Point at which replication is occurring Point in which RNA genome forms a hairpin Point in the genome where to replication eyes meet Point in the genome which consists of the ter sites

Point at which replication is occurring

During which cell cycle phase is DNA replicated in eukaryotes? M S G2 G1

S

What's the difference between synonymous and nonsynonymous mutations? Nonsynonymous mutations do not result in a change in the amino acid sequence of the coded protein. Synonymous mutations occur much less frequently than nonsynonymous mutations. Synonymous mutations do not result in a change in the amino acid sequence of the coded protein.

Synonymous mutations do not result in a change in the amino acid sequence of the coded protein.

Which statement is TRUE? (Read carefully) Double-stranded T-DNA produced by new synthesis at a nick is transferred to the plant nucleus. T-DNA is generated when a nick at the left boarder creates a primer for synthesis of a new DNA strand. T-DNA is transferred as a complex single stranded DNA with the virE2 single strand-binding protein and virD2 bound at the 5 terminus. Transfer of T-DNA is initiated when DNA synthesis reaches a nick at the right border.

T-DNA is transferred as a complex single stranded DNA with the virE2 single strand-binding protein and virD2 bound at the 5 terminus.

Which part of the Ti plasmid gets transferred and integrated into the plant genome? Tra locus Vir regulon T-DNA region only Opine catabolism locus

T-DNA region only

Name three proteins needed to replicate the linear Adenovirus genome. DNA polymerase (virus), NF1 (host); Protein A (virus) Terminal Protein (virus); NF1 (host); DNA polymerase (host) RNA polymerase from the virus; ATF1 (host); Terminal Protein (virus) Protein A (virus); NF1 (virus); DNA polymerase (host)

Terminal Protein (virus); NF1 (host); DNA polymerase (host)

Which function is NOT regulated by the bacterial origin of replication? Frequency of replication Initiation of replication Termination of replication Segregation

Termination of replication

Which statement is TRUE? The Mitochondrial genome is a single replicon. The Eukaryotic genome is a single replicon. The Chloroplast genome is a single replicon. The Bacterial chromosome is a single replicon.

The Bacterial chromosome is a single replicon.

How does DNA replication terminate in yeast (fungus), Drosophila (insect) and Arabidopsis (plant)? The DNA polymerases run into each other from opposing directions, which results in a fusion of the replication eyes. The eukaryotic ter sites control this process. Licensing factor is used up, which, in turn, causes DNA polymerase to terminate. Replication is only terminated by the polymerase reaching the end of the template.

The DNA polymerases run into each other from opposing directions, which results in a fusion of the replication eyes.

Which statement is TRUE regarding replication control? Chloroplast DNA displays single-copy control. The Eukaryotic chromosome must activate replication only once per cell cycle. Mitochondrial DNA displays single-copy control. The bacterial chromosome can replicate several times before cell division.

The Eukaryotic chromosome must activate replication only once per cell cycle.

Why do Hfr cells promote a high level of recombination when added to a F minus population of bacteria? The F plasmid transfers to the recipient and stimulates homologous recombination. During bacterial conjugation the F plasmid leaves the chromosome and stimulates homologous recombination in the recipient cell. The F plasmid often does not transfer to the recipient, but chromosomal DNA does. Homologous recombination occurs between this newly introduced DNA and the donor. The F plasmid transfers and stimulates mutation in the recipient which needs to be repaired.

The F plasmid often does not transfer to the recipient, but chromosomal DNA does. Homologous recombination occurs between this newly introduced DNA and the donor.

Which bacterial group is most closely related to mitochondria and is thought to represent the original endosymbiont that gave rise to this organelle? The SAR11 clade (a phylogenetic grouping), which is an Alpha-proteobacteria, a member of the Rickesettsiales. Agrobacterium tumefaciens, a member of the Rhizobium species Liberibacter asiaticus, a Gram negative bacteria in the Rhiboziaceae Pseudomonas aeruginosa, a Gram negative cocobacillus

The SAR11 clade (a phylogenetic grouping), which is an Alpha-proteobacteria, a member of the Rickesettsiales.

In eukaryotes the chromosomes are linear DNAs. How is the problem of replication handled? The centromeres contain highly repetitive sequences that allow for imprecise replication without losing genes. The chromosomes form circles during mitosis, allowing them to be easily replicated by the rolling circle mechanism. The ends of the chromosomes contain telomere repeat sequences that do not contain genes, so failing to replicate the complete 5-ends of the template has little consequence. Eukaryotes have evolved a special set of proteins, similar to Adenovirus, that allow the chromosomes to be fully replicated.

The ends of the chromosomes contain telomere repeat sequences that do not contain genes, so failing to replicate the complete 5-ends of the template has little consequence.

What would happen if the Left Border sequence was deleted from the pTi (Ti plasmid)? VirD1 would no longer be necessary for transfer of T-DNA to the plant. The direction of new strand synthesis of the T-DNA would be reversed. No transfer of T-DNA would occur due to faulty processing. The entire pTi would be transferred to the plant cell.

The entire pTi would be transferred to the plant cell.

How does Adenovirus use a single replication mechanism to replicate both strands? The second strand has direct repeats that provide the primer. The replication machinery starts at both linear ends simultaneously. Host RNA polymerase II provides the priming for both strands. The inverted repeats causes the displaced second strand to form a hairpin structure that mimics the end of a linear template.

The inverted repeats causes the displaced second strand to form a hairpin structure that mimics the end of a linear template.

There are difficulties in replicating linear DNA. What are they? Repeat sequences at the ends are hard to replicate with precision. The DNA polymerase runs off the end of the template causing a problem. The primer must be supplied. No place for the DNA polymerase to attach at the end. (No place to sit.) Priming of DNA polymerase occurs at random sites.

The primer must be supplied. No place for the DNA polymerase to attach at the end. (No place to sit.)

How are mitochondria inherited in humans (and most mammals)? Mitochondria are usually inherited randomly from either the male or the female parent, but not from both. Mitochondria usually show mixed inheritance, a variable percentage derived from the sperm cell and a variable percentage contributed by the egg. They are passed along only through the material line (female) to the offspring. Both male and female offspring receive their mitochondria from the mother. The mitochondria are only inherited through the sperm cells. If a father has no male offspring, then his mitochondrial line stops with him.

They are passed along only through the material line (female) to the offspring. Both male and female offspring receive their mitochondria from the mother.

Linear templates: How do T4 and Lambda phage solve the problem of having linear double-stranded DNA templates? Each has a special protein similar to Terminal Protein that primes DNA polymerase. Both contain disposable terminal repeats that reduce the consequences of imperfect replication. Protein A provides a single nucleotide primer. They dont. Instead, they both convert from a linear form to a circular form and then use the rolling cir

They dont. Instead, they both convert from a linear form to a circular form and then use the rolling cir

Whys is it important for the Overdrive element to be located next to the Right Border instead of the Left Border? (Read the answers carefully.) This location facilitates the recruitment of VirE2 to the newly replicated T-strand. This location ensures that the T-strand gets shipped to the plant nucleus. Overdrive ensures that the VirD1 nicks at the correct site. This ensures that the right border is cut first. Otherwise the entire T-DNA region would stay in the bacteria instead of being transferred.

This ensures that the right border is cut first. Otherwise the entire T-DNA region would stay in the bacteria instead of being transferred.

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.) TraT TraD TraM TraM

TraD

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? TraY TraI TraJ FinP

TraI

Tra locus: Which protein(s) shares many of the activities of PHiX174 Protein A? Tra M TraS/T TraI/Y TraJ

TraI/Y

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

TraJ

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

TraM

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

TraS

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

TraT

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

TraY

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

TraY

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

True

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

True

Is mitochondrial DNA replication considered bi-directional or uni-directional and why? Uni-directional: even though both stands get replicated, each uses a separate unidirectional origin. Bi-directional: DNA replication proceeds in both directions from the D-loop region of the genome. Bi-directional: since both strands are replicated, replication must be bi-directional Uni-directional: all DNA replication occurs at the D-loop, which is uni-directional.

Uni-directional: even though both stands get replicated, each uses a separate unidirectional origin.

Which answer is FALSE?: Vir genes of the Ti plasmid are located on the T-DNA and are transferred to the plant. Vir genes of the Ti plasmid are required for the T-DNA transfer process. Vir genes of the Ti plasmid are located outside of the transfer region. Some Vir genes are expressed constitutively and some are inducible.

Vir genes of the Ti plasmid are located on the T-DNA and are transferred to the plant.

Vir____ is a histidine kinase trans-membrane protein, which autophosphorylates when it binds an inducer. VirD2 VirC VirA VirG

VirA

Which vir proteins perform an analogous function as TraY and TraI? VirE and virC VirA and virG VirD1 and VirD2 VirB1-B11

VirD1 and VirD2

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.)

VirD2

Which of the following proteins from the pTi are transferred to the plant cell? octopine synthase VirD2 and VirE2 VirD2 and ChvE nopaline synthase

VirD2 and VirE2

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,

VirE2

Vir ____ binds to the single strand of the displaced T-DNA single-strand, and Vir _____binds to overdrive DNA. VirD1 and VirD2 VirA and VirG VirE2 and VirC VirB1-B11

VirE2 and VirC

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.)

VirG

Which protein is phosphorylated by VirA and then acts as a positive transcription factor? VirE2 VirG VirD2 VirD1

VirG

Under what circumstances can the replication fork be bidirectional? When a separate origin is used for each strand When the origin of replication creates two replication forks that move in opposite directions. When the origin of replication creates two replication forks that move in the same direction at different speeds When the origin of replication moves in one direction, and the replication eye in the opposite.

When the origin of replication creates two replication forks that move in opposite directions.

Which of the answers below illustrates that the concept of an organism is a matter of definition? a flock of seagulls a herd ofcows a large grove of elm trees in Utah

a large grove of elm trees in Utah

How long would it take for an integrated copy of the F plasmid to replicated itself by conjugation under standard lab conditions? more than 200 min a little more than 100 min 13 min 50 min

a little more than 100 min

Which of the answers below illustrates that the concept that a species is somewhat arbitrary and relative? the mycelium of mushroom a ring species a grove of elms in Utah

a ring species

Which of the pathways shown in the phylogenetic tree below has undergone the most positive selection? b to Macaque (15/5) the common ancestor between Gorilla and the Human/Chimp group before the split. (1/2 and 0/0) a to c (7.5/2.5) a to b (33/3)

a to b (33/3)

In yeast the ______________________ functions as the origin of DNA replication. autonomous replicating sequence OriC Tus recognition sequence origin of recognition complex

autonomous replicating sequence

The F plasmid has three modes of DNA replication. Which one uses a rolling circle mechanism? when integrated using oriC conjugation using oriT vegetative using oriC vegetative replication using oriV

conjugation using oriT

F plasmid: How are the donor and recipient cells drawn together for the transfer of DNA during conjugation? depolymerization of pilin protein in the donor activity of TraS and TraT embedded in the membrane of the donor activity of TraJ action of TraM

depolymerization of pilin protein in the donor

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? site-specific recombination involving IS elements (insertion sequences). double homologous recombination between the new fragment and the host chromosome. The newly introduced chromosomal DNA circularizes and forms a stable plasmid. The TraY/I complex nicks the host chromosome which triggers recombination.

double homologous recombination between the new fragment and the host chromosome.

Phosphorylation of the ORC _____________________________. triggers ubiquitination must occur before it can recruit the MCM causes it to be rapidly degraded either inhibits its binding to DNA, or blocks it from recruiting MCM

either inhibits its binding to DNA, or blocks it from recruiting MCM

Tra locus: What is the name of the gene that regulates transcription, but does not encode a protein? finP traS/T traJ traY/I

finP

F plasmid: Where is the nic site located? in oriT in the TraI encoding region in oriV in the finP gene

in oriT

What are the two major roles played by the Light Strand Promoter present in the mitochondrial genome? It serves as a promoter for ____________ and _____________. initiating DNA primers to make the D-loop; tRNA synthesis synthesis of the Tra genes; synthesis of the Vir locus synthesis of mitochondrial ribosomal genes; synthesis of DnaA initiating the RNA primers for DNA replication; for synthesis of mRNA to express mitochondrial genes

initiating the RNA primers for DNA replication; for synthesis of mRNA to express mitochondrial genes

What are some examples of mutations that suggest that evolution is continuing to change our species? lactose tolerance and various disease resistance genes hair on the backs of Bio majors a double line of eyebrows in a tribe located a little south of the Williston airport

lactose tolerance and various disease resistance genes

At which point in the cell cycle is Geminin degraded? early G2 late M and early G1 G2 early S

late M and early G1

PhiX174 replication: Which of the following is NOT a function of Protein A? covalently link to the 5-end of single-strand DNA recognition of the origin nuclear localization single-strand ligase helicase DNase (nicking)

nuclear localization

In the Ti plasmid (pTi)-based Binary vector system, where are the vir genes located? on the miniTi on the helper plasmid on the wild type Ti plasmid on the modified pTi

on the modified pTi

When the F plasmid integrates into the chromosome, which origin does it use to replicate? the BOM site oriC,and its own oriV is suppressed oriV oriT

oriC,and its own oriV is suppressed

What two actions can all vertebrates, with the exception of adult Homo sapiens, perform simultaneously? swallow and breathe breathe and hear swallow and hear chew gum and walk

swallow and breathe

The frequency of what types of mutations are used as a molecular clock? synonymous nonsynonymous asynchronous microdeletions

synonymous

Mitochondrial genes are pretty closely packed. What type of genes are located in between the protein-encoding genes? tRNAs T-DNA microRNA genes ribosomal genes

tRNAs

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

the light strand promoter (LSP), which is used to transcribe the genome and to provide the start nucleotides for the 7 S primers.

How many amino acids (out of 715) have changed in FOXP2 since humans split from mice? three seven two 136

three

Which vir genes recognize right border and nick it, thus generating the primer for DNA strand synthesis? virB1-B11 virE and virC virA and virG virD1 and D2

virD1 and D2