Week 5: MMBIO Exam 1

In 2D PAGE, the second electrophoresis is done at a ______ degree angle relative to the firstelectrophoresis.

90

In Sanger dideoxy sequencing (or just Sanger sequencing for short), dideoxy nucleotides (dd for didexoy and thus the abbreviation is ddNTP's) are present in a DNA synthesis reaction. The DNA polymerase does not distinguish between a dNTP or a ddNTP - either one will act as a substrate as long as base pairing to the template is correct. A single stranded template is base paired to a primer and in the presence of DNA polymerase dNTP's and ddNTP's, DNA synthesis occurs. In the reaction, you start with 100 mMoles of dCTP and 0.5 mMoles of ddCTP. When a ddNTP is incorporated, DNA synthesis is terminated. At what frequency will DNA synthesis likely terminate when the template nucleotide is a G?

1 time in 200 incorporations of C into the growing polynucleotide

The band of what size most likely is the trypsin protein?

10 Kd

Which size is typical for a mammalian mitochondria?

16,000 base pairs

About what proportion of the human genome encodes proteins?

2%

A genome is....

A diploid set of chromosomes plus one copy of any organelle DNA present

Which of the following is an example of natural selection?

A flower that happens to more attractive to pollinators is more likely to have reproductive success.

Which assay would be most useful in testing whether or not CML1 transcription is increased in the CML patients?

A northern blot of neutrophils from normal and CML patients.

Which of the following statements regarding transcriptomes is INCORRECT? a. A transcriptome represents the entire rRNA content of a cell. b. RNA editing impacts the make-up of the transcriptome. c. Transcriptome analysis provides information on changes in gene expression patterns in cancerous cells. d. A transcriptome is influenced by both synthesis and degradation of RNA molecules. e. The composition of a transcriptome is influenced by alternative splicing pathways.

A transcriptome represents the entire rRNA content of a cell.

Genomics

Is the field dedicated to the study of DNA on a cellular

What kind of enzyme is the telomerase protein?

Reverse transcriptase

Supercoiling of double-stranded DNA is called its ____________________ structure.

Tertiary

Under the assumption that these trees are correctly rooted, how does this result support the inference that the South Carolina 1918 strain (the only exemplar from the 1918 flu pandemic) arose from recombination between a human and a swine virus?

The fact that the South Carolina 1918 strain is more closely related to the swine strains in tree A but to the human strains in tree B.

Although you are not told by the graduate student how the SDS-PAGE was performed, it is most reasonable to assume that you can see bands in the gel because

The gel was stained with coomasie blue.

The topoisomerase DNA gyrase will introduce negative supercoils into DNA. What effect will this enzyme have on relaxed, covalently closed DNA?

The treated DNA will migrate farther in an agarose gel than the relaxed DNA.

Prokaryotic cloning vector that can accommodate large pieces of DNA up to 1 million base pairs.

bacterial artificial chromosome (BAC)

The term X-linked is used for genes carried on the Y chromosome.

false

Supercoiling of DNA is NOT necessary for:

protein tertiary structure.

Telomerase is a _____________________.

reverse transcriptase

Which technique would best identify which band in lane A is the trypsin protein?

western blot

Which of the following techniques would you most likely use to obtain purified and active trypsin?

Affinity chromatography

Approximately 80 percent of the total RNA in eukaryote cells is ribosomal RNA (rRNA) and 15 percet is transfer RNA (tRNA); protein-coding mRNA thus constitutes only about 5% of the total RNA. THe rRNA and the tRNA genes are transcribed much more frequently than the protein coding genes. in RNA-seq, you must separate the mRNA from the rRNA/tRNA molecules in order to sequence just the mRNA - too much noise otherwise. Which of the following would be the best technique to separate mRNA from rRNA/tRNA molecules?

Affinity chromatography using beads with a TTTTTTTTTTTTTTTTT nucleotide sequence attached to the beads.

In a typical sequencing reaction the amount of dNTPs is much greater than of the ddNTPs. If equal amounts of both types of nucleotides were used in each reaction, how might that affect the outcome?

After gel electrophoresis and visualization of the results mostly short fragments would be present and only sequences very close to the primer could be read.

Which of the following does NOT affect the evolution of a group of organisms?

Allopatric drift

When 2-D protein gel electrophoresis is completed, proteins with a high molecular weight will be found where on the gel?

Along the top edge of the gel.

Centromeres

Are sequences on the eukaryotic chromosome that function during cell division as an attachment point for proteins that link the chromosome to the mitotic spindle.

Which of the following is a current approach for determining the last universal common ancestor(LUCA)? a. Assemble a list of genes and other features that are currently shared by every living creature. b. Assemble a list of genes and other features that are currently shared by animals. c. Assemble a list of genes and other features that are currently shared by plants. d. Define the minimum set of genes necessary to support an animal cell.

Assemble a list of genes and other features that are currently shared by every living creature.

The figure illustrates one interpretation of the origin of humans. The dotted lines indicate possible evolutionary relationships, and the vertical bars show the period from which fossils are known for each species. The data in the figure suggests that

Australopithecus species may have given rise to modern humans.

Which of the following is NOT a nucleic acid that needs compacting? Mitochondrial DNA of animals Mitochondrial DNA of plants Chloroplast DNA of plants Linear chromosomes of plants Chloroplast DNA of animals

Chloroplast DNA of animals

When the RNA seq data is aligned with genomic DNA sequences, the RNA-seq data will likely ONLY align with which region of the hypothetical gene shown below?

D (exon)

Which of the following tools of recombinant DNA technology is INCORRECTLY paired with one of itsuses? a. restriction endonuclease - production of DNA fragments for gene cloning. b. DNA ligase - enzyme that cuts DNA, creating sticky ends. c. DNA polymerase - copies DNA sequences in the polymerase chain reaction. d. reverse transcriptase - production of cDNA from mRNA. e. electrophoresis - RFLP analysis.

DNA ligase - enzyme that cuts DNA, creating sticky ends.

In the figure, total (nuclear and mitochondrial) DNA was isolated from the family members as shown. A single locus was sequenced for each person. The two women have a disease. The father does not have the disease and is homozgous at the locus. In the lanes marked A, which of the following reagents were added to perform the sequencing reaction?

DNA polymerase, dATP, dGTP, dCTP, dTTP, ddATP, DNA primer, buffer.

Which of the following is NOT true with regard to compacting nucleic acids? a. Some viral coat proteins are RNA-binding proteins that compact the RNA genome of the virus. b. There are enzymes that introduce and maintain coiling of double-stranded DNA molecules. c. There are DNA-binding proteins that maintain structural organization in eukaryotes. d. There are DNA-binding proteins that maintain structural organization in prokaryotes. e. DNA viruses don't need to compact their genomes significantly because the dimensions of their viral coats are much greater than those of RNA viruses.

DNA viruses don't need to compact their genomes significantly because the dimensions of their viral coats are much greater than those of RNA viruses.

DNA microarrays ... a. Can reveal protein-protein interactions. b. Demonstrate differential expression of genes. c. Can reveal protein-RNA interactions. d. Can be used to purify proteins that bind to epitope tags. e. Are somewhat large and unwieldy but give a great deal of information.

Demonstrate differential expression of genes.

A researcher compares the amino acid sequences of cytochrome c from four vertebrates shown below: sheep, dog, rabbit, and kangaroo. The amino acid differences among the four species are shown in the difference matrix below. Which of the following statements is true?

Dogs are more closely related to Sheep than Dogs are related to Rabbits.

Chromosomal defect in which individuals have three copies of chromosome 21:

Down syndrome

When performing automated DNA sequencing, why can all four sequencing reactions be analyzed together in the capillary gel?

Each ddNTP has a different fluorescent tag.

When performing automated Sanger dideoxy DNA sequencing, why can all four sequencing reactions be analyzed together during electrophoresis?

Each ddNTP has a different fluorescent tag.

Which one of the following would be the best technique to use to purify PolI from PolII?

Gel filtration chromatography

Consider the identical nucleotide position marked by a horizontal arrow in each of the three sequences. Both the mother and daughter have both a T and a C in the same position whilst the father only has a C. It is most likely that the mother and daughter are __________________ at the marked nucleotide position.

Heterozygous

Why is the human haplotype diversity greatest in Africa?

Human populations that migrated only took a subset of the variable human haplotypes.

Which of the following is NOT a Learning Objective for this discussion about proteomes, transcriptomes and genomes (Lesson 13)?

Interpret a polyphyletic tree.

In chemistry, a zwitterion is a molecule with two or more functional groups, of which at least one has a positive and one has a negative electrical charge and the net charge of the entire molecule is zero. Depending on the pH of a solution, an individual amino acid, or, a polypeptide (both an amino acid and a polypeptide have a potential positive charge (amino group) and a potential negative charge (carboxyl group)) can have an overall net charge of zero. The pH where the overall charge on a protein is zero is called the

Isoelectric Point

Mulek and his entourage left Jerusalem and made their way to the Americas. When they arrived, there were other humans living and thriving in the Americas, many of whom likely were descendants of hearty souls who entered the Americas thousands of years before from northeastern Asia and across Alaska and then south. The contribution of Mulek et al. and their genes to the existing gene pool in the Americas is an example of

Migration

Which of one of the following will have the greatest impact on the genetic change of a population over time?

Migration

Which of the following is true of supercoiling?

Most organisms maintain their DNA in a slightly underwound state in order to compact their DNA.

Which of the following is a substrate for topoisomerase I?

Negative supercoiled DNA

Which of the following allows detection of specific RNA fragments that have been separated by gel electrophoresis?

Northern blotting

The most common method for genotyping allelic SSRs is by:

PCR and gel electrophoresis

A scientist studies three populations of frog (populations A, B, and C) that live in the same rainforest. She notices some interesting similarities between the three groups. What would be the best evidence that A and B have a more recent common ancestor than A and C, or, B and C.

Populations A and B share similar mtDNA sequences, but differ in their nDNA sequences.

Which of the following is a correct comparison of prokaryotic and eukaryotic chromosomes? a. Both have a single replication origin. b. Only eukaryotes have specific sequences necessary for DNA distribution during cell division. c. Eukaryotic DNAs usually have circular chromosomes; prokaryotes have linear. d. Both have multiple origins. e. Prokaryotic chromosomes have circular chromosomes; eukaryotes have linear.

Prokaryotic chromosomes have circular chromosomes; eukaryotes have linear.

Comparison of two-dimensional gels from cells in stationary versus active growth phases reveals that one protein (A) has disappeared and a slightly larger protein (B) has appeared in the active cells. Mass spectrophotometry of the two spots indicates that the new larger protein (B) has sequences that match the smaller protein (A). Which of the following is not a reason for this result?

Proteins A and B are completely different proteins.

Which one of the following is the best explanation for the multiple bands seen in lane A?

Proteins other than trypsin are in Sample X.

Mass spectrometry is used in

Proteome analysis

The telomerase enzyme is made of

RNA and protein

Which of the following is an important tool in transcriptomics?

RNA-seq

The numbers on the branches of an evolutionary tree ...

Reflect the confidence the investigator has in the information contained in that branch.

Which of the following is true of the Sanger sequencing method?

Requires chain terminating ddNTPs which are lacking a 3'OH and are unable to form a bond with the next nucleotide.

Besides topoisomerase I and gyrase, which one of the following is an enzyme that interacts with or modifies DNA?

Restriction endonuclease

After IEF in 2D gel electrophoresis, ______ is added to the proteins to denature them and impartequal negative charges to the proteins.

SDS

Which of the following are most likely to contain the sequence GTAGTAGTAGTA?

SSR

Which one of the following would be least likely to provide data about the level of gene expression in a cell?

Sequencing the genome.

With proteomics, 2D electrophoresis is one approach to identify the different proteins. Are you thinking through the steps in SDS-PAGE electrophoresis as you work through 2D electrophoresis? (this is a rhetorical question. The real question follows.) Proteins vary greatly in their ionic charge. Before SDS PAGE electrophoresis, proteins are treated to ensure that all polypeptides have similar charge:mass ratios. What is the substance used for this treatment?

Sodium dodecyl sulfate

Mutations in the rhodopsin gene may lead to a disease called retinitis pigmentosa, leading to progressive vision loss in humans. A GC repeat is known to be within the first intron of the human rhodopsin gene. Genomic DNA is isolated from individuals and digested with restriction enzymes. A radiolabeled probe is made for the GC repeat. Using this isolated material and probe, which of the following techniques would be the most useful in detecting the inheritance of alleles of the rhodopsin gene in a given family?

Southern

Mutations in the rhodopsin gene may lead to a disease called retinitis pigmentosa, leading to progressive vision loss in humans. A GC repeat is known to be within the first intron of the human rhodopsin gene. Genomic DNA is isolated from individuals and digested with restriction enzymes. A radiolabeled probe is made for the GC repeat. Using this isolated material and probe, which of the following techniques would be the most useful in detecting the inheritance of alleles of the rhodopsin gene in a given family?

Southern blot

The gel pattern in Figure 5-18 was obtained in an attempt to sequence a DNA molecule using the Sanger method. What is the sequence of the DNA molecule in question?

TACCTTGAT read in opposite direction of migration (bottom to top)

Which of the following is the best evidence that supercoiling is an intrinsic property of double-stranded DNA molecules? a. That strand separation during transcription and replication introduce strain. b. Purified plasmid DNAs are supercoiled even though all proteins are removed. c. That when two strands of an entwined rubber band are pulled apart they will twist into supercoils. d. That linear fragments of double-stranded DNA are not supercoiled.

That strand separation during transcription and replication introduce strain.

After allowing for DNA synthesis and after denaturing the double strand DNA and after separating the single strand DNA by size in a polyacrylamide gel with the A, T, G, and C tube contents in separate lanes, and after performing autoradiography, you detect bands in the A, T, G, and C lanes. In which lane do you expect to see the smallest band?

The T Lane

Which of the following is NOT a benefit or advantage of using mass spectrophotometry? a. The activity of the protein can be determined directly from the sequence information generated. b. Even short sequences (fragments) of the protein are often enough to permit unambiguous association with its gene. c. Because very little material is needed for mass spectrophotometry, proteins extracted from a two-dimensional gel can be sequenced. d. Using mass spectrophotometry the mass of a protein can be determined, which is a critical parameter in determining the identification of the protein. e. The accuracy of the method allows measurement of changes in mass due to binding of cofactors, bound metal ions, and covalent modifications.

The activity of the protein can be determined directly from the sequence information generated.

In a separate experiment, you test the action of the enteric trypsin inhibitor (ETI) on the pancreas trypsin isolated from X. laevis. The elevated presence of this inhibitor in humans is associated with types of digestive disorders. ETI acts as a noncompetitive inhibitor. Which one of following statements about ETI is most probably true? a. The inhibitor acts at a site other than the substrate binding site. b. The inhibitor decreases KM but has no effect on Vmax. c. The inhibitor increases KM but has no effect on Vmax. d. The inhibitor has no impact on KM but lowers the maximum velocity of trypsin. e. The inhibitor has a greater specific activity than does trypsin.

The inhibitor has no impact on KM but lowers the maximum velocity of trypsin.

What is the root of an evolutionary tree?

The node at the base of the tree representing a common ancestor

The isoelectric point (pI) is ...

The pH at which a protein has a net charge of zero.

Which of the following is true about two-dimensional gel electrophoresis? a. The second dimension separates proteins based on their size. b. The second dimension separates proteins based on their charge. c. The first dimension separates proteins based on their size. d. The second dimension separates proteins based on their isoelectric point (pI). e. The first dimension separates proteins based on their density.

The second dimension separates proteins based on their size.

Which one of the following statements about the Km and specific activity of trypsin from these tissues would you correctly predict to be true. a. In measuring the Km of the muscle trypsin, you added an allosteric competitive inhibitor to the assay. b. The Km of pancreas trypsin will be measured in units of product/time. c. A double reciprocal plot of the pancreas trypsin Km will yield a hyperbolic plot. d. The specific activity of trypsin from muscle tissue will be less than the specific activity of trypsin from pancreas. e. The total amount of protein in an aliquot of muscle homogenate was measured by determining the amount of light absorbed at 260 nm.

The specific activity of trypsin from muscle tissue will be less than the specific activity of trypsin from pancreas.

Which of the following is a function of telomeres? a. Serve as an attachment site for the proteins of the kinetochore. b. They are sequences at the ends of the linear eukaryotic chromosome that protect the ends from nucleases. c. They are sequences of the eukaryotic chromosome that ensure proper distribution during mitosis. d. They are sequences of the prokaryotic chromosome that ensure proper distribution during mitosis. e They are the sites at which replication initiates.

They are sequences at the ends of the linear eukaryotic chromosome that protect the ends from nucleases.

In an assay, supercoiled DNA was incubated with a DNA replication related enzyme over a 5 minute time period. Aliquots were removed at 0, 0.25, 0.5, 1, 1.5, 2, 3 and 5 minutes. Each aliquot was electrophoresed in a 1% agarose gel and the DNA visualized by staining with ethidium bromide. The results are shown in the figure below. If the DNA used in this assay was positively supercoiled, which one of the following enzymes was most likely used in the assay?

Topoisomerase II

Which of the following subdisciplines is concerned with the expression of RNA molecules?

Transcriptomics

Which of the following is NOT affected by supercoiling of the DNA?

Translation

Which of the following is likely LEAST affected by supercoiling of the DNA?

Translation

Which of the following processes is likely LEAST directly affected by negative supercoiling of the DNA?

Translation

The human genome is mostly composed of ...

Transposons and retrotransposons that are mostly inactive.

What will heterozygous single nucleotide substitution look like on your Sanger dideoxy sequencing chromatogram?

Two peaks of equal height at the same position

Which of the following is NOT a Learning Objective for Lesson 12, Sequencing, Arrays and Genomes?

Using RT PCR, determine the gene expression levels of normal and tumor tissue.

The technique of DNA fingerprinting takes advantage of what genomic feature?

Variable number tandem repeats

The modern human BRCA1 gene contains the sequence,...ATAGATCATGCCGCCATGAATT.... When you sequence the neanderthal BRCA1 cDNA sequence using the Sanger approach with four separate reactions, you obtain the band pattern shown in the figure. Is there any evidence that the modern human and neanderthal sequences are different?

Yes, a purine in the modern sequence is a pyrimidine in the neanderthal sequence.

DNA from spores that are suspected to be the bacterium that causes anthrax is being tested using small, flat pieces of glass or silicon containing thousands of tiny spots of unique sequences of DNA from known bacteria. Matching DNA from a spore sample sticks to the corresponding anthrax DNA spots on the piece of glass or silicon and shows up as glowing spots when illuminated with a laser. This tool is called

a gene chip or micro array.

This figure illustrates: a method of separating DNA fragments by length. micro array or gene chip technology. gene therapy. a method of producing recombinant DNA plasmids. a method of producing many copies of a segment of DNA.

a method of separating DNA fragments by length.

Darwin analogized the effects of evolution as the above-ground portion of a many-branched tree, with extant species being the tips of the twigs. The common ancestor of two species is most analogous to which anatomical tree part?

a node where two twigs diverge

Which one amino acid is most likely to be found on the surface of the tertiary structure of trypsin?

asp

The field that is concerned with the management and analysis of biological data using computers

bioinformatics

A DNA clone of a DNA copy of an mRNA molecule.

cDNA clone

A mass spectrometer is used to:

determine a molecules mass by the migration of the ionized molecule in an electric field

How are the four different bases distinguished in automated sequencing systems?

each base has a distinctive fluorescent tag

virus or plasmid that carries a DNA sequence into a suitable host cell and there directs the abundant synthesis of the protein encoded by the sequence.

expression vector

Trypsin contains at least two polypeptides.

false

An abnormal human karyotype is shown in the figure. This particular karyotype is found in the cancer cells of more than 90% of patients with chronic myelogenous leukemia. Arrows indicate two abnormal chromosomes. Is this patient male or female?

female

The random loss of alleles in a population is called

genetic drift

Manipulation of DNA with precision in vitro or in vivo.

genetic engineering

A collection of clones that contain a variety of DNA segments from the genome of an organism.

genomic DNA library

The process whereby two complementary nucleic acid strands form a double helix.

hybridization

The molecular basis of microarray analysis is based upon _____. a hybridization between reverse-transcribed mRNAs and anchored single-stranded oligonucleotides representative of specific genes b. the relative fraction of total RNA that makes up the mRNA pool c. base pair complementarity between microRNA and mRNA d. the half-life of mRNAs in the cell undergoing investigation

hybridization between reverse-transcribed mRNAs and anchored single-stranded oligonucleotides representative of specific genes

Both Illumina and PacBio sequencing are examples of 2nd generation or next generation sequencing (NGS). Both involve DNA polymerase and the synthesis of a new DNA strand based on a template. Which technique removes unincorporated (unused) nucleotides before the next nucleotide is added to the growing polynucleotide?

illumina

The chromosome in the figure would most likely be found ________________.

in a yeast cell

Of the following, which one is present in the human genome at the greatest frequency?

introns

Comparison of sequences in mitochondrial DNA is often used to establish the degree ofrelatedness between organisms and thus to suggest evolutionary relationships, particularly incomplex, higher-level organisms. Mitochondrial DNA is used because it

is only inherited from one of the parents, the mother.

A ___________ shows an individual cell's metaphase chromosomes arranged in pairs and sorted by size.

karyotype

Positively supercoiled plasmid DNA is purified. A small amount of bacterial topoisomerase II, buffer, and ATP is added to an aliquot of the positively supercoiled plasmid DNA and the reaction is allowed to proceed for a short period of time. The reaction was stopped and the products subjected to electrophoresis in an agarose gel and the DNA visualized by ethidium bromide staining. Which lane in Figure 7.3 has the pattern most likely produced by DNA topoisomerase II in these conditions?

lane 2

What technology allows one to estimate the numbers and kinds of genes active in a given sample?

microarray technology

The centromere is the site of ___________ attachment.

microtubule

Which of the following factors is most likely to contribute to gene flow between populations?

migration

Lactase is an enzyme in humans which breaks down lactose, one of the sugars in milk. Milk is a safe and nutritious food which is readily available year-round. Although most adults around the world lose the ability to produce lactase as they mature, more than 90% of Europeans have a lactase-producing allele which remains active into adulthood. Analysis of DNA in bone samples from a number of Neolithic Europeans (dated between 5840 BC and 5000 BC) and found that none of them had the adult lactase allele. The most likely explanation for this data is that

modern Europeans are not descended from the Neolithic Europeans tested.

DNA that is positively supercoiled is the same thing as DNA that has _____.

more helical turns than it would normally have as B-DNA

Technique in which RNA fragments, separated by electrophoresis, are immobilized on a paper sheet and then detected by hybridization with a labeled nucleic acid probe.

northern blotting

The figure below depicts the current distribution of DNA sequences in human males and the possible routes by which those sequences may have distributed worldwide. The DNA sequences used in this study are most likely found _______________________.

on a linear double stranded DNA molecule.

After centrifugation in CsCl and fractionation as shown in the figure, supercoiled DNA will be found at peak A, B, or C?

peak c

A certain class of protein is found to exist in several different species. The amino acid sequence of this protein is compared between a large number of species. The greatest number of amino acid differences will be found between species of different

phyla

Small circular DNA molecule that replicates independently of the genome and can be used for DNA cloning.

plasmid vector

Technique for generating multiple copies of specific regions of DNA by the use of sequence-specific primers and multiple cycles of DNA synthesis.

polymerase chain reaction (PCR)

You would use Western, Northern, and Southern blots respectively to study the following (in correct order):

protein, RNA, DNA

The complete set of proteins present in a cell under a given set of conditions is a...

proteome

Any DNA molecule formed by joining DNA segments from different sources.

recombinant DNA

One of a large number of enzymes that can cleave a DNA molecule at any site where a specific short sequence of nucleotides occurs.

restriction nuclease

Non-denaturing PAGE has the disadvantage that it

separates on the basis of more than one property thus to some degree confusing the results.

The ___________, which is present at either end of the chromosome, is needed for stability.

telomere

Consider the manufacture of an artificial chromosome. Considering the minimal requirements for natural chromosomes, to be functional, artificial chromosomes for eukaryotes must have:

telomeres, centromeres, and replication origins.

The four-chambered hearts of birds and the four-chambered hearts of mammals evolved independently of each other. If one were unaware of this independence, then one might logically conclude that

the common ancestor of birds and mammals had a four-chambered heart.

The location of the centromere is most likely at what position on the chromosome shown in the figure?

the middle of the two C

Proteomics is:

the study of the entire collection of proteins expressed by an organism

The population of mRNA expressed in a single cell or cell type is called:

transcriptome

A transcriptome will not include intron sequences but a genome will include intron sequences.

true