Molecular Biology Block 3

You are analyzing samples from various individuals, and you desire to find out which genes are being expressed on chromosome 5 at the time of sample extractions. You also wish to see the contents of their proteomes at the same time of the extraction. Which combination of techniques will give you the results you want? A. Using an Allele-Specific Oligonucleotide (ASO) Probe and Protein Microarray B. Carrying out FISH analysis followed by Western Blot C. Conducting RFLP analysis and Southern Blot D. Creating a Tiling array and Mass Spectrometry

ASO: a DNA marker resulting from a base pair difference at one particular site in a genome FISH: Detecting Microdeletions by FISH. ▪This technique allows the localization of large DNA fragments on metaphase chromosomes or interphase chromatin strands. ▪A DNA fragment is labeled (typically radioactive or fluorescent) and hybridized to metaphase chromosomes RFLP analysis and Southern Blot: Identification of specific DNA sequences within a genome Mass Spectrometry (MS): Detect ions and identify proteins via database

All of the following are disadvantages of GM (genetically modified) foods EXCEPT: A.Genes from transgenics can be transferred to wild-type population B.Food will be more nutritionally valuable than in their normal state C.There is a potential risk for human health endangerment D.GM plants and animals can create ecological imbalances

B

In conventional gene knockout technology: A. A gene is inserted by non-homologous recombination B. A mutant gene is replaced by a functional copy C. A functional gene is replaced by a mutant copy D. A functional gene is inserted in addition to a mutant copy

C

Reporter genes are useful for monitoring gene expression in transgenics. Which of the following reporter genes was isolated from fireflies? A. Green fluorescent gene B. β-galactosidase C. Luciferase D. X-Gal

C

A map that allows for comparison between normal chromosomes and those who have pieces missing during the metaphase stage of analysis is called: A. Physical clone map B. Chromosome map C. Mutational map D. Cytogenetic map

D

Adding a normal copy of the defective gene to the genome of a person with a genetic disease is: A. Xenotransplantation B. Biopharmaceuticals C. Bioreactions D. Human gene therapy

D

GM (genetically modified) food concerns have potential impact on the environment including all BUT: A.Unintended transfer of transgenes through cross-pollination B.Competition of transgenic plants with natural populations C.Loss of flora or fauna biodiversity D.Increase in antibiotic sensitivity

D

When studying functional genomics it is correct to say: A. The proteome is context independent B. The genome is context dependent C. The transcriptome is context independent D. None of these

D

Which of the following best describes a probe? A. A contig with a free 3' -OH group B. An antibody C. A fluorescently labeled cDNA D. A piece of single-stranded nucleic acid used to detect the presence of complementary sequences by hybridization

D

Which of the following is supplemented with vitamin A in order to improve its nutritional quality? A. Cotton B. Potato C. Tomato D. Rice

D

Which of the following methods compares the expression of genes between two different samples? A. Single channel DNA microarray B. Reporter genes C. Sanger Sequencing D. Two-channel microarray

D Sanger Sequencing: To determine the exact order of nucleotides in a given DNA or RNA sequence & to see smaller changes in whole genomes. Reporter genes: allows for detailed spatial and kinetic analyses of transcript accumulation Two-channel microarray: Similar microarray technology is being used to identify potential gene targets for therapies to treat human disease.

Which of these methods is NOT normally used for single gene expression analysis? A.Northern Blott B.Reporter gene based techniques C.PCR D.SAGE

D Sequencing-Based Methods To Detect Multiple Changes (SAGE and MPSS)

The use of the yeast two-hybrid system and phage display is associated with which application of proteomics? A. Structural Proteomics B. Post-translational Proteomics C. Protein - Transcription Factor Interaction D. Protein - Protein Interaction

D Yeast Two-Hybrid System: Screening for protein-protein interactions. •Proteins called activators control gene expression in eukaryotes. •An activator has to bind to DNA sequence upstream of a gene to stimulate RNA polymerase to copy the gene into RNA Acquisition of Protein Structure Information - Edman sequencing: Microsequencing to obtain N-terminal amino acid sequences. - Mass spectrometry: Sample preparation - Sample ionization - Mass analysis

Choose the most correct: A. Southern blot: molecular weight of restriction fragments (or a particular gene within the genome). B. Northern blot: locating a particular sequence of DNA C. Western blot: identifies DNA within the genome D. PCR: making larger amounts of DNA into smaller amounts

A

The conditional knockout system or Cre-loxP system allows for: A. Specific targeting and removal of genes in an organ/area without alteration of adjacent organs/ areas B. The removal or flip of a gene to maintain its function C. Knockout of genes using a targeting construct D. All of the above

A

Where in the genome are LoxP sites located in the Cre/Lox model? A. On either side of the gene that is to be knocked out B. Adjacent to the Cre recombinase gene C. Random sites throughout the genome D. In the liver

A

Which of the following components of a targeting construct allows recombination between the construct and the target genome? A. Region of homology B. Neomycin resistance gene C. Thymidine Kinase D. Blank region or region with the mutated gene

A

The yeast two-hybrid system technique uses which of the following: A. Transcription Factors B. Isotopes C. Microarrays D. Bacteriophages

A Yeast Two-Hybrid System • Screening for protein-protein interactions. Proteins called activators control gene expression in eukaryotes. An activator has to bind to DNA sequence upstream of a gene to stimulate RNA polymerase to copy the gene into RNA Activator is a transcription factor

If a mouse embryo in the blastocyst stage is infected with a retrovirus that contains DNA that causes the production of green cells, which of the following outcomes are you likely to observe when the mouse is grown if it is normally supposed to be white? A. A mouse that has green fur all over its body B. A spotted mouse that has green fur in only some places C. A mouse that is completely white D. None of the above

B

Karyotype analysis is normally used to detect: A. Microdeletions B. Chromosomal deletions C. Gene expression changes D. Single base mutations

B B: Karyotype A: FISH C: d: Single Nucleotide Polymorphism (SNP) CHIPS

Which of the following proteomic techniques used to analyze protein function allows proteins to interact with nucleic acids, antibodies and lipids? A. Yeast two-hybrid system B. Protein microarray C. Edman sequencing D. Phage display approach

B Protein Function Microarrays Used to screen for various types of protein interactions including ➢protein-protein, ➢protein-lipid, ➢protein-DNA, ➢protein-drug, and ➢protein-peptide interactions,

The Cre-LoxP system utilizes which of the following enzymes? A. P1 Bacteriophage B. Lox-P C. Cre-Recombinase D. Restriction Endonuclease

C

When making a "knockout" mouse, all of the following are present in the gene targeting construct EXCEPT: A.Antibiotic resistance gene B.Regions of Homology C.Ganciclovir D.Thymidine kinase selectable marker

C

Which of the following proteomic techniques would lead to the identification of a single protein? A. 1D Gel Electrophoresis B. 2D Gel Electrophoresis C. Western Blot D. Phage display approach

C

The broccoflower is a combination of broccoli and cauliflower using protoplast fusion. What is a protoplast? A. A plant cell wall B. A Ti plasmid C. A plant cell without the cell wall D. A plant cell without a nucleus

C Protoplast Fusion Injured cells produce a mass of cells called callus over the site of wound. protoplast is A plant cell without the cell wall

Which of the following statements about Agrobacterium tumefaciens is FALSE? A.It has a plasmid that contains T-DNA which causes a tumor in plants B.It is only able to infect dicotyledonous plants such as tomatoes and soybeans C.It contains a region that can be attenuated and used as a natural vector D.It is generally non-pathogenic and infects a wide variety of plants

D

Which of the following techniques involve blasting foreign DNA into plants using metal beads? A. Antisense technology B. Protoplast fusion C. Leaf fragment technique D. Particle bombardment

D

You are carrying out a test using the ASO (Allele-specific oligonucleotide) method. You are given a probe that can detect the mutated allele. You apply the probe to a sample that you previously selected, and you notice a light spot has appeared. What is your conclusion about the genotype of the individual? A. They are homozygous normal B. They do not carry the allele for the trait C. They are homozygous wildtype D. They are a carrier of the trait

D

A collection of microscopic DNA spots attached to solid surface are called: A. FISH B. Macroarray C. Cytogenetic map D. Microarray

D D: Genomics/transcriptomics: A microarray is a collection or a grid of microscopic spots of biological capture molecules (like DNA or proteins) Macroarray: transcriptomics - PCR-based: Detect Multiple Gene Transcriptional Changes The Cytogenetic Map: Genomics. The characteristic banding pattern. The nuclear DNA is densely packaged into chromosomes.

golden rice

beta-carotene, which is converted to vitamin A

Which of the following is NOT true about the techniques used in Sanger Sequencing? A.Dideoxynucleotides are used for termination of strand synthesis B.DNA fragments to be sequenced are created by partial digestion C.Radioactive labels are used to identify separated fragments of DNA D.The reactions for each ddNTP are run in separate tubes

B Sanger sequencing traditionally use radioactive probes.

Which of these techniques can identify transcriptionally active regions of DNA that have not previously been identified? A. Tiling Array B. Northern Blot C. Microarray D. Macroarray

A

Mass Spectrometry involves all of the following processes EXCEPT: A.Sequencing proteins by removing amino acids from the N-terminal B.Sample ionization and drying C.Database searching of sequenced fragments D.Peptide sequencing using mass analyzers

A Acquisition of Protein Structure Information - Edman sequencing: Microsequencing to obtain N-terminal amino acid sequences. •Mixed-peptide sequencing: - complex protein mixture separated by SDS-PAGE (1DE or 2DE) - proteins transferred to an inert membrane by electroblotting - proteins of interest visualized on the membrane surface, excised, and - fragmented chemically at methionine (by cyanogen bromide - CNBr) or tryptophan (by skatole) to give 3-5 peptide fragments, consistent with the frequency of occurrence of methionine and tryptophan in most proteins. Mass Spectrometry (MS) - Stages • Introduce sample (e.g from HPLC machine) to the instrument (Mass spectrometer). • Generate ions in the gas phase • Separate ions on the basis of differences in mass to charge (m/z) with a mass analyzer • Detect ions and identify proteins via database

Two parents have recently found out that they are carrying the gene for sickle cell. They have a 2-month-old daughter and do not know if she carries the disease. What test would be most appropriate for finding out the genotype of the child? A. ASO analysis B. FISH analysis C. RFLP analysis D. Microarray analysis

A B: FISH for microdeletion C: RFLP: Identification of specific DNA sequences within a genome. genomic DNA is isolated and digested with a restriction enzyme

ll of the following techniques require the use of probes EXCEPT: A.Reporter gene based techniques B.Northern Blot C.FISH D.Tissue Microarray

A Northern Blotting Hybridization-based. radioactive probes are used to identify a target mRNA species within an immobilized RNA sample Flouresence in situ hybridization (FISH): A DNA fragment is labeled (typically radioactive or fluorescent) and hybridized to metaphase chromosomes DNA microarrays (DNA chips or biochips): each spot contains predefined short (25- to 70-nucleotide) single-stranded DNA oligonucleotides or larger (200- to 800-basepair) double-stranded DNA, called probes.

Which of the following is FALSE regarding chloroplast engineering? A.The inserted genes are passed on to the offspring B.The genes inserted into the plant using this method will not be present in its pollen C.The chloroplast can accept many more new genes than the nucleus D.This method decreases the chance of transferring the transgene to non-target plants via cross-pollination

A • Chloroplast DNA can accept several new genes at once, unlike DNA in a cell's nucleus • A high percentage of genes inserted into the chloroplast will remain active when the plant matures. • DNA in chloroplast in separate from the DNA released in plant's pollen.

Isotope-Coded Affinity Tags (ICAT) is used for: A. Separation of peptides in a sample by size B. Identification of peptides in a sample by labeling with isotopes C. Separating proteins by liquid chromatography D. Creation of peptides by proteolysis using trypsin

B

The linked tags used in SAGE are called a: A. Contig B. Concatemer C. Fragment D. Antitag

B

The technique that is used to sequence and identify cDNA samples from mRNA using millions of copies that are hybridized to a bead is known as: A. SAGE B. MPSS C. cDNA expression array D. Tiling Array

B

Which of the following methods of producing transgenic animals will NOT result in offspring that are mosaic/chimera A.Embryonic stem cell method B.Pronucleus method C.Retrovirus mediated gene transfer method D.Micro-injection into the blastocyst method

B

Which option below describes a dideoxynucleotide? A. Lacks the 5' triphosphate group B. Contains a ribose sugar that lacks the 3' hydroxyl group C. Stops DNA transcription D. None of the above

B

You take two samples from the same individual and compare them to see what they contain. One sample is from pancreatic cells and another is from liver cells. What would you expect to find? A. DNA is different between the two types of cells B. DNA is the same in both types of cells C. RNA is the same in both types of cells D. Metabolites are different but proteins are the same

B

Name the reporter gene that acts on the synthetic polysaccharide X-Gluc. A. Luciferase gene B. GUS gene C. LAC gene D. GFP

B - The luciferase gene (isolated from fireflies) - bacterial GUS (b-glucuronidase) gene, which turns the compound X-Gluc blue - bacterial lac (b-galactosidase) gene, which turns X-Gal blue. - - jellyfish green fluorescent gene, which causes cells that express the GFP to glow green under blue light

What is the name of the enzyme which was silenced to delay the ripening process? A. Glyphosate B. Polygalacturonase C. Pectin D. Avidin

B Antisense Technology: Polyglacturonase (PG) - an enzyme that digests pectin on the wall of the plant to induce normal decay. Herbicide Resistant Plants: Traditional weed killers can also kill desirable plants. • Glyphosate blocks an enzyme (EPSPS) necessary for photosynthesis. the plant will resist the spray of glyphosate pectin: a protein that protects the fruit. PG destroy pectin so the fruit is decayed

Which of the following cell types would be negatively selected for upon the addition of ganciclovir to a cell culture? A. Cells with no insertion of the targeting construct B. Cells with random insertion of the targeting construct without recombination C. Cells containing the targeting construct by homologous recombination D. None of the above

B NO INTEGRATION (most probable) - negatively selected by neomycin RANDON INTEGRATION (next probable) - negatively selected by gancyclovir INTEGRATION BY HOMOLOGOUS RECOMBINATION (least probable) - positively selected by both neomycin and gancyclovir.

What is the most challenging issue facing genome sequencing? A. The inability to develop fast and accurate sequencing techniques B. The ethics of using information from genomes at the individual level C. The availability and stability of DNA D. All of the above

B Personalized Genomics: Challenges ❖Ethical, Legal and Social Implications (ELSI) ❖Privacy ❖Confidentiality ❖Discrimination (GINA in 2008 - USA) ❖Psychological Impact

Which of the following statements about western blot is FALSE? A.Proteins are identified using a secondary antibody conjugated to an enzyme B.Western blot is performed on the gel on which proteins are separated C.A chemiluminescent substrate is used to identify the protein of interest D.A coat of non-specific protein is usually applied to the blot

B Protein detection on Western Blot: 1) Blocking: blot is incubated with 5% skim milk to coat blot in non-specific protein.-attaches to the membrane in all places where the target proteins have not attached 2) Blot is incubated with primary antibody. 3) Blot is incubated with a secondary antibody that cross reacts with the primary antibody. An enzyme is conjugated to the secondary antibody. 4) Visualization usually involves reaction of the enzyme with a chemiluminescent substrate. The negative electrode is the cathode the positive electrode is the anode. Western blot allows you to identify a single specific protein.

Which of the following methods of creating transgenics is usually high efficiency, but also carries an inherent risk of danger to the host? A. Microinjection B. Electroporation C. Viral mediated gene transfer D. Protoplast fusion

C

A Single Nucleotide Polymorphism (SNP) is: A. A DNA sequence which can be recognized by a restriction enzyme B. A DNA sequence containing multiple mutations C. A DNA sequence which has a single base pair change D. A DNA sequence that is missing regulatory sequences

C A: RFLP

Which of the following techniques uses probe pairs that anneal to a region of RNA to detect genes? A. Illumina MiSeq RNA-Seq B. qRT-PCR C. Nanostring nCounter D. MPSS

C Illumina MiSeq RNA-Seq bridge amplifies nucleic acid samples to create clusters, which are then interpreted by the MiSeq system qRT-PCR amplifies a gene of interest and uses fluorescent probes or dyes to depict the gene expression NanoString nCounter uses probe pairs to anneal to a region of RNA and detect genes MPSS: cDNA fragments are cloned onto micro-beads using the Lynx Megaclone technology.

Which of the following is NOT a characteristic of the proteome? A.It is dynamic and changes often B.It cannot be amplified C.All molecules are homogeneous D.The quantity of proteins can vary drastically

C Proteome: dynamic No amplification possible Heterogenous molecules Large variability of the amount Genome: static Amplification possible Homogenous molecules No variability of the amount

Which of the following techniques do NOT require knowledge of the mRNA sequence? A.Tiling Array and Northern Blot B.SAGE and Northern Blot C.Serial Analysis of Gene Expression and Massively Parallel Signature Sequencing D.Two-channel and one-channel microarray

C SAGE generates sequences from cDNA fragments for the discovery of new genes and the quantification of their expression levels in a certain tissue. Link these small pieces of sequences together to form a long chain (or concatemer). Tiling Array: SNP chip and Microarray expression profiling applications use probes biased toward known and predicted gene structures. • Tiling arrays are made up of high density probes; • Used in identifying novel transcripts, exons which may not have been previously predicted. identify regions of chromosomes that are transcriptionally active. Massively Parallel Signature Sequencing (MPSS) • cDNA fragments are cloned onto micro-beads

Partial digestion of DNA by a restriction enzyme in the direct shotgun approach will result in: A. A series of non-overlapping DNA fragment that can be used in the sequencing of a large piece of DNA B. A series of overlapping DNA fragment that can be used as a diagnostic tool when a southern blot analysis is performed C. A series of overlapping DNA fragments that can be used in the sequencing of large pieces of DNA through a contig map D. A series a non-overlapping DNA fragment used as a diagnostic tool when a southern blot analysis is performed

C shotgun is overlapping A contig: --from the word "contiguous"--is a series of overlapping DNA sequences used to make a physical map