MY Exam 1 Study Guide

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

ABF1

F plasmid: Where is the nic site located?

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

At which point in the cell cycle is Geminin degraded?

late M and early G1

**Which replicon machinery movement is the fastest?

**Bacteria

**Which of the following regions of the brain expanded in humans compared to chimps and is strongly associated with language? It is located on the left side of the brain.

**Broca's area

**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?

**CNTNAP2

**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

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

**Homo erectus and Neanderthal

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

**Lactose tolerance and various disease resistance genes

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

**MCM 2-7

**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

**What is the replication fork?

**Point at which replication is occurring

**What is the function of ter sites in the genome?

**Serve as backup to prevent bacterial replication forks from going too far

**What is a replicon?

**Unit of DNA in derived from a specific origin

- HQ 1 -

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- HQ 2 -

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- HQ 3 -

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- HQ 4 -

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- HQ 5 -

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- HQ 6 -

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Adenovirus replication proteins & locations

-Virus: (1) TP (Terminal Protein) (2) DNA Polymerase (3) DNA Binding Protein (helicase) -Host: (1) NF1 (2) Oct-1

A genetic bottleneck occurred in the human genome around 50,000 to 90,000 years ago. This crisis in the population of Homo sapiens is thought to have occurred in response to the harsh conditions brought about due to climate change: expansion of the Sahara desert. As few as _____ mating pairs were thought to survive.

10,000

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

10,000 mating pairs *Genetic bottleneck right BEFORE 3rd exodus

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

3

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

3

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

40 kb-200 kb

Approximately how long ago did behaviorally modern humans appear?

50,000-100,000

How many replicons can be found in typical eukaryotic genomes?

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?

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.)

600,000-700,000

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

A Ring species

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

A large grove of elm trees in Utah

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

Adenovirus

DNA Binding Protein

Adenovirus-encoded helicase

DNA Polymerase

Adenovirus-encoded replication enzyme

Which replicon machinery movement is the fastest?

Bacteria

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

Because SeqA binds to hemimethylated DNA and sequesters it to the membrane

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

Both produce infective particles.

Which of the following regions of the brain expanded in humans compared to chimps and is strongly associated with language? It is located on the left side of the brain.

Broca's area

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?

CNTNAP2

What is a replicon?

Canvas: Unit of DNA in derived from a specific origin Actual: Unit of DNA in which individual acts of replication occur

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

Cdc6, Cdt1

Which enzyme methylates bacterial oriC?

Dam methylase

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

Delay in demethylation

Bacterial origin of replication oriC consists of ________________________?

Eleven GATC/CTAG repeats methylated on adenines in both strands interspersed among and between high and low affinity DnaA binding sites

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

FOXP2

What are the DNA sequence elements of oriC?

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

Which two forms of the genus Homo were already in Europe when Homo sapiens arrived?

Homo erectus and Neanderthal

Oct-1

Host-encoded transcription factor that assists in initiation by binding downstream of NF1

Nuclear Factor-1 (NF-1)

Host-encoded transcription factor that helps position the TP

What is the function of Tus protein?

It acts as a contrahelicase by unwinding DNA in the opposite direction from the replication helicase, DnaB.

How does the Terminal Protein make sure that 100% of the 3'-end of the template is replicated?

It first pairs the attached dCTP with the second G from the 3'-terminus of the bottom strand. It next "jumps" back to pair with the terminal G.

Why is it important for the displaced strand (top strand) to form a duplex with itself?

It forms a double-strand end that can be used by the Terminal Protein (and other components) to initiate DNA synthesis. This means that the same machinery used to initiate replication of the original linear form of the virus can also be used to replicate the displaced top strand.

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

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.

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

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?

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

Which of the following statements is NOT true regarding Mitochondrial DNA replication?

Mitochondrial DNA replication is bi-directional

Which of the following proteins is encoded by the Host?

NF1

ECP and EDN are two Ribonuclease enzymes that arose from a duplication 31 million years ago of the original gene. Which of the pathways shown in the phylogenetic tree below has undergone the most positive selection for ECP?

Node a to b (33/3)

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

Nuclear localization

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

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

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?

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?

Orc1/Cdc6

What is the replication fork?

Point at which replication is occurring

During which cell cycle phase is DNA replicated in eukaryotes?

S

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

Swallow and breathe

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

Synonymous

**What's the difference between synonymous and nonsynonymous mutations?

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

What's the difference between synonymous and nonsynonymous mutations?

Synonymous mutations do not result in a change in the amino acid sequence of the coded protein. *Synonymous = same (regardless of change, still same)

Name three proteins needed to replicate the linear Adenovirus genome.

Terminal Protein (virus); NF1 (host); DNA polymerase (virus) *Other proteins needed are DBP (DNA binding protein (virus) and Oct-1 (host))

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

Termination of replication

Which statement is TRUE?

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.

Which statement is TRUE regarding replication control?

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

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.

"Frying Pan" Structure

The duplex stem and loop formed by the displaced single strand ("top" strand)

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

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.

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

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

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.

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

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

What is the function of the "frying pan" structure?

The single-strand that is displaced during replication (top strand) forms a stem-loop structure that mimics the double-stranded terminus of the linear form of the genome before replication.

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

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?

They don't. Instead, they both convert from a linear form to a circular form and then use the rolling circle mechanism.

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

True

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

True

The Terminal Protein is permanently attached to the 5-end of each strand of the Adenovirus genome.

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.

Under what circumstances can the replication fork be bidirectional?

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

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

autonomous replicating sequence (ARS)

Terminal Protein (TP)

covalently bound to dCTP which acts as the primer

Phosphorylation of the ORC _____________________________.

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

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

molecules 1 and 2