Deck 16: Genome Analysis: DNA Typing, Genomics, and Beyond

Question 1

The majority of the human genome is

A) protein-coding gene exons
B) intergenic DNA
C) genes and gene-related sequences
D) interspersed elements

Answer 1

intergenic DNA

Question 2

What are minisatellites and microsatellites?

A) Small, extrachromosomal loops of DNA that are similar to plasmids.
B) Parts of viruses that have become integrated into the genome of an organism.
C) Incomplete or inactive remains of transposable elements in a host cell.
D) Short and simple repeated sequences in DNA.

Answer 2

Short and simple repeated sequences in DNA.

Question 3

The variable number of short tandem repeats in the human genome primarily results from

A) unequal crossing-over.
B) slippage during DNA replication.
C) alternative splicing.
D) movement of transposable elements.

Answer 3

slippage during DNA replication.

Question 4

The variable number of minisatellite repeats in the human genome primarily results from

A) unequal crossing-over.
B) slippage during DNA replication.
C) alternative splicing.
D) movement of transposable elements.

Question 5

Forensic DNA typing often involves recovery of very tiny amounts of DNA from a crime scene. What is a major concern in analyzing this DNA?

A) There is rarely enough DNA to allow PCR amplification.
B) Even with these minute amounts of DNA, there still may be too much DNA for efficient PCR.
C) It is important to avoid the introduction of contaminating human DNA into the sample.
D) Suspects may refuse to provide a sample of their DNA.

Question 6

In establishing paternity by DNA typing, how many short tandem repeat (STR) alleles in a child come from the father?

A) ¼
B) ½
C) ¾
D) none

Question 7

At approximately 2 PM; Ms. Smith, Ms. Taylor, and Ms. Jones each delivered a healthy baby girl at a local hospital. At 2:16 PM, the hospital's fire alarm sounded. Nurses and orderlies hurried to evacuate patients, and the three newborns were rushed to safety. After the danger had passed, the hospital staff discovered that in the confusion, they had forgotten which baby was which. Since the babies were moved before receiving their identification bracelets there was no easy way to identify them. The attending physician ordered that DNA typing be performed on the babies and their parents. Results of gel analysis are shown below. Your job is to decide to which set of parents Baby 1 belongs. ?

A) Baby 1 belongs to the Jones
B) Baby 1 belongs to the Taylors
C) Baby 1 belongs to the Smiths

Question 8

Multiplex PCR is

A) the simultaneous amplification of many target DNA sequences of interest in one reactionby using more than one pair of primers.
B) the amplification of one target DNA sequence of interest in one reaction by using morethan one pair of primers.
C) the amplification of many target DNA sequences of interest by performing multiplereactions with a different pair of primers in each reaction tube.
D) the amplification of one target DNA sequence of interest by performing multiple reactionswith a different pair of primers in each reaction tube.

Question 9

Following up on reports of a man who attacked an elderly lady (Victim Reference Sample) and spit in her face, the police went to the homes of Suspect 1 and Suspect 2, who each gave police a cheek swab. The electropherogram resulting from STR analysis is shown below. The Evidence Sample is spit from a handkerchief the elderly woman used to wipe her face. Your job is to decide which suspect committed the crime.

A) Suspect 1 committed the crime
B) Suspect 2 committed the crime

Question 10

Which statement is not correct?

A) Mitochondrial DNA (mtDNA) typing usually involves PCR plus DNA sequencing.
B) mtDNA typing is often used for analysis of ancient DNA samples.
C) mtDNA typing can be used to trace paternal lineages.
D) mtDNA typing can be used to trace maternal lineages.

Question 11

What distinguishes the field of genomics from genetics?

A) Genomics deals with genomes; genetics deals with gene products.
B) A goal of genomics is to understand how genes influence both genotype and phenotype; genetics only considers how genes influence phenotype.
C) Genomics is based almost solely on studies of human genome sequences; genetics is based on studies of organisms from bacteriophage to Arabidopsis.
D) Genomics is based on DNA sequence analysis and considers the sequence, function and interactions of many genes; genetics more often considers one or a small number of genes at a time and is generally involved in the passage of hereditary traits from one generation to the next.

Question 12

All of the following apply to the discipline of bioinformatics except:

A) Bioinformatics is a synonym for genomics.
B) The most commonly used bioinformatics tool is BLAST.
C) Bioinformatics is an area of computer science devoted to to collecting, organizing andanalyzing DNA and protein sequences.
D) Bioinformatics tools support high-throughput screening methods for both proteomic andgenomic research programs

Question 13

What is the difference between an open reading frame (ORF) and a gene?

A) There is no difference.
B) An ORF is a potential gene identified by a potential protein-coding segment in DNA bordered by start and stop codons; a gene is a DNA segment known to produce a product.
C) An ORF is a known gene-containing DNA segment that is shorter than a full-length gene.
D) An ORF may or may not have introns; a gene must have introns.

Question 14

Which best describes the logic behind shotgun sequencing?

A) Fragment the genome into short pieces. Sequence each piece. Use overlapping ends to assemble the pieces in the correct order.
B) Start with one end of each chromosome. Sequence straight through to the other end of the chromosome.
C) Use a variety of techniques to identify genes and open reading frames. Sequence these segments but not the noncoding and repeated sequences.
D) Fragment the genome into pieces. Map the location of each piece. Then sequence each piece.

Question 15

What evidence do molecular biologists use to infer that a gene is part of a gene family?

A) Its sequence is almost exactly identical to that of a gene in another organism.
B) Its structure (meaning its pattern of exons and introns) is identical to that of a gene found in another species.
C) Its composition, in terms of percentage of A-T and G-C pairs, is unique.
D) Its sequence, structure, and composition are similar to those of another gene in the same genome.

Question 16

What is a pseudogene?

A) A coding sequence that originated by DNA slippage during replication.
B) A gene whose sequence is similar to that of functioning genes but does not produce a functioning product.
C) A gene with more than two alleles present in a population.
D) An open reading frame (ORF) whose function has not yet been established.

Question 17

An expectation that has been borne out by comparative genomic analysis is that:

A) Increased degrees of complexity in multicellular organisms are closely correlated with increased genome sizes.
B) Increased genome size correlates with an increased number of genes.
C) All vertebrate genomes are roughly the same size.
D) Human and chimpanzee sequences are closely related.

Question 18

Like DNA microarrays, Northern blots can be used to analyze levels of gene expression. However, Northern blots are almost always prepared with a probe tagged with one label, whereas DNA microarrays almost always use two groups of probes, each one tagged with a different fluorescent label. What advantage is conferred by using two labels for the probes of microarrays?

A) The two labels increase the sensitivity of the microarray.
B) The two labels allow the analysis of the expression of more genes.
C) The two labels allow simultaneous comparison of gene expression between two samples.
D) The two labels allow simultaneous assay of levels of RNA and protein.

Question 19

To begin the process of DNA microarray, the following cellular component is extracted from sample tissues:

A) DNA
B) RNA
C) protein
D) A and B

Question 20

In a comparative gene expression analysis between two samples labeled with Cy3 (green) and Cy5 (red), if the two samples contained equivalent amounts of mRNA for a particular gene, the spot on the array corresponding to that gene would appear

A) red.
B) green
C) brown
D) yellow

Question 21

Which technique has almost eliminated the need to chemically sequence a polypeptide?

A) peptide mass fingerprinting using MALDI-TOF
B) functional protein array
C) DNA microarray
D) whole-genome shotgun sequencing

Question 22

You want to analyze the entire proteome of a particular organelle. Which technique would you use?

A) DNA microarray
B) tandem mass spectrometry
C) Western blot
D) analytical protein array

Question 23

Single nucleotide polymorphisms are

A) mutations that cause genetic diseases
B) the most common type of sequence variation in an individual
C) variable number tandem repetitive sequences

Question 24

Which two types of genomic variation have been commonly analyzed in genome-wide association studies?

A) copy number variation and small deletions
B) small deletions and single nucleotide polymorphisms
C) small deletions and small insertions
D) single nucleotide polymorphisms and copy number variation

Question 25

Genome-wide association studies are used for identifying the causes of

A) monogenic (single gene defect) diseases
B) diseases with multiple genetic components
C) diseases that do not have a genetic component
D) all of the above

Question 26

Compare and contrast the techniques of AFLP and RAPD analysis in DNA typing.

Question 27

About 60% of the human genome is composed of intergenic DNA. Describe two types of intergenic DNA that are used in DNA typing and how they are used.

Question 28

What type of analysis is currently the most widely used DNA typing procedure in forensic genetics - short tandem repeat (STR) analysis or minisatellite analysis? Which technique uses multiplex PCR? Which technique uses a Southern blot?

Question 29

"The power of DNA evidence lies in statistics." Explain the meaning of this statement.

Question 30

When is mitochondrial DNA analysis considered the method of choice in forensic analysis? Explain why it should not be used for paternity testing.

Question 31

Compare and contrast the terms "bioinformatics," "genomics," and "proteomics."

Question 32

When is a sequence considered a "rough draft" as opposed to a "finished" sequence? Does a genome sequence have to be 100% complete and accurate to be declared "finished"?

Question 33

The Japanese pufferfish (Takifugu rubripes) genome is approximately eight times smaller than the human genome, but contains just as many protein-coding genes. How can that be?

Question 34

What is the meaning of the term "synteny" in comparative genomics?

Question 35

Is it accurate to call a cDNA a gene? Why or why not?

Question 36

Describe the process of making a DNA "chip."

Question 37

Match each technique for high-throughput analysis of proteins with its possible application(s):
Technique
Analytical protein array
Peptide mass fingerprinting using MALDI-TOF
Shotgun proteomics using MS/MS
Application
Analysis of a single isolated protein from a protein gel
Analysis of an entire proteome
Analysis of ligand binding

Question 38

What kinds of questions can be better addressed using a protein microarray rather than a DNA microarray?

Question 39

Compare and contrast an analytical protein array with a functional array. What type of information can be obtained from each method?

Question 40

Diagram the process of peptide mass fingerprinting using MALDI-TOF. What type of information can be obtained from this method?

Question 41

Diagram the process of shotgun proteomics using tandem mass spectrometry. What type of information can be obtained from this method?

Question 42

Explain the key difference(s) between peptide mass fingerprinting using MALDI-TOF and shotgun proteomics using tandem mass spectrometry.

Question 43

You have characterized the entire proteome of a particular organelle. What further analysis would you do to confirm localization of the identified proteins to this organelle in situ?

Question 44

Write an example of a single nucleotide polymorphism. To be considered a SNP, how frequent must the polymorphism be in the population?

Question 45

How could DNA microarrays be used in conducting a genome-wide association study to identify SNPs associated with,

Question 46

Variable number tandem repeats in the promoter region of the monoamine oxidase A gene have been linked to aggressive, impulsive, and violent behavior. A child has been classified as having the 3-repeat, low activity allele. Are they likely to show antisocial behavior as adults? Does this example support the statement "DNA is destiny?"

Question 47

A cigarette butt found at the scene of a violent crime is found to have a sufficient number of epithelial cells stuck to the paper for the DNA to be extracted and typed. Shown below are the results of typing for three probes (locus 1, locus 2, and locus 3) of the evidence (X) and 4 suspects (A through D). Which of the suspects can be excluded? Which cannot be excluded? Can you identify the criminal? Explain your reasoning.
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Question 48

Based on the DNA fingerprinting (minisatellite analysis with a multilocus probe) results shown in the figure below, is Mr. X or Mr. Y the child's father? Explain your answer.

Question 49

You separate a mixture of proteins by 2D-PAGE. From one protein spot, you obtain the following peptide sequence by mass spectrometry:
EQAGGDATENFEDVGHSTDAR
Use the BLAST tool to identify the unknown protein.

Question 50

After sequencing the entire genome of a novel organism by the whole-genome shotgun approach, you use a computer program to search for start/stop signals for translation and homology searches based on similarity to cDNAs in the database. You predict approximately 20,000 genes. Is this an accurate representation of the total number of genes in the organism? Why or why not?

Question 51

After SNP analysis of a region of the Apolipoprotein E gene, you determine that a patient carries the apoE4 allele. This allele is linked with Alzheimer's disease. Counsel the patient regarding their prognosis.

Question 52

cDNA derived from normal cell mRNA was labeled with a green fluorescent tag (represented as black). cDNA derived from diseased cell mRNA was labeled with a red fluorescent tag (represented as white; the presence of both green and red tags is represented by stripes). The labeled cDNAs were mixed and hybridized to a prepared DNA microarray. Results from a small section of the microarray grid are shown below. Which genes would you select for further analysis? Explain your answer.
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Question 53

In a study that involved 100 Caucasian males, you find a polymorphism in a gene for a neurotransmitter receptor. The "long allele" is linked with reckless behavior. What conclusions, if any, can you draw about the results of this study? Should you hold a press conference to announce the discovery of the "reckless" gene?