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Biology 2581B Study Guide - Midterm Guide: Centromere, Mendelian Inheritance, Null Allele

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5 Oct 2015
School
Western University
Department
Biology
Course
Biology 2581B
Professor
Jim Karagiannis

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Document Summary

Which of the following restriction enzymes is the most frequent cutter and leaves. / indicates the cut site only one of the two dna strands is shown but the cut sites are for double stranded dna. 5" gc/ggccgc 3": taqi, rsai, hindii, kpni, noti, 1, 2, 3, 4, 6, 3, 4, 6, 9, 10, a linear double stranded dna molecule has two target sites for restriction enzyme ecoi. 1: you are given a sample of a linear double stranded dna fragment. You are to determine the number and order of restriction cut sites in that dna. In your first experiment you digest one aliquot of the dna sample with ecorv (rv) and after gel electrophoresis you observed three bands indicating fragments 25kb 17kb and 15kb in size. You then digest the second aliquot with ecori (ri) and after gel electrophoresis you observe three bands indicating fragments that are 25kb, 20kb and 12kb in size.

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Related Questions

Which of the following did Erwin Chargaff observe?

A)

Base composition changes as the organism ages.

B)

Base composition of DNA does not vary from one species toanother.

C)

In all species the number of adenines equals the number ofguanines.

D)

In all species A + T = G + C.

E)

DNAs isolated from different tissues of the same species havethe same base composition.

The melting temperature (Tm) of a DNA duplex is:

A)

the temperature at which double-stranded nucleic acids degradeinto free nucleotides.

B)

the temperature at which double-stranded DNA is toosingle-stranded to ever renature back to double strands.

C)

the temperature at which double-stranded DNA is completelymelted.

D)

the temperature at which double-stranded DNA has become 50%single-stranded.

E)

the temperature at which double-stranded DNA begins to melt.

Given your knowledge and the descriptions of each of thesemethods, which of the following does NOT rely on the ability ofnucleic acids to hybridize with each other?

A)

Southern blotting for the detection of specific DNA fragmentsthat have been separated by gel electrophoresis.

B)

Colony blot hybridization to identify a specific sequence from acollection of sequences that have been inserted into bacteria.

C)

Northern blotting for the detection of specific RNA fragmentsthat have been separated by gel electrophoresis.

D)

A DNA oligonucleotide microarray incubated with probes made fromcDNA.

E)

Western blotting for the detection of specific proteins thathave been separated by gel electrophoresis.

Which of the following is a possible reason why DNA uses thymineinstead of uracil?

A)

Cytidine is deaminated to uracil so it would be difficult forany repair mechanism to differentiate between uracil that belongsin the sequence and uracil that resulted from deamination.

B)

Adenine is deaminated to uracil so it would be difficult for anyrepair mechanism to differentiate between uracil that belongs inthe sequence and uracil that resulted from deamination.

C)

When uracil is bound to a deoxyribose it will become morereactive, forming covalent bonds with other bases.

D)

None of the above.

Which of the following is an enzyme used in cloning to breakcovalent bonds?

A)

DNA ligase

B)

Restriction endonuclease

C)

Reverse transcriptase

D)

DNA polymerase I

E)

Alkaline phosphatase

Which of the following could you use to remove the 5' phosphatesafter cleavage of a plasmid with a single type of restrictionenzyme to ensure that the plasmid would not simply fuse backtogether upon addition of ligase?

A)

Reverse transcriptase

B)

Alkaline phosphatase

C)

DNA ligase

D)

DNA polymerase I

E)

Restriction endonuclease

Which of the following would you use to create a cDNA librarythat you would not use for a genomic library?

A)

Alkaline phosphatase

B)

Reverse transcriptase

C)

Restriction endonuclease

D)

DNA ligase

E)

DNA polymerase I

A plasmid vector typically has which of the followingfeatures?

A)

An origin of replication

B)

A selectable marker to ensure that the only bacteria growingcontain the intact or recombinant vector.

C)

Unique restriction sites for insertion of DNA.

D)

Small size to facilitate entry into the cell and biochemicalmanipulation of the DNA.

E)

All of the above are features of plasmid vectors.

Which of the following is FALSE of genomic or cDNAlibraries?

A)

Genes represented in cDNA libraries include control sequencesthat direct transcription.

B)

cDNA libraries contain cDNAs made from mRNA.

C)

Genomic libraries contain fragments of genomic DNA that aregenerated by partial digests with restriction enzymes.

D)

Genomic libraries usually contain large fragments and are likelyto be constructed in YAC or BAC vectors.

E)

cDNA libraries contain sequences from expressed genes only.

Which of the following is NOT a typical component of apolymerase chain reaction (PCR)?

A)

dNTPs

B)

DNA containing the sequences to be amplified

C)

DNA ligase to connect the fragments together

D)

Primers complementary to each end of the sequence to beamplified

E)

Heat stable Taq polymerase

How can a fusion protein be formed?

A)

Site-directed mutagenesis where a fragment is replaced with asynthetic sequence containing the altered DNA sequence.

B)

Two proteins can recombine in the bacterial cell to form a newhybrid protein.

C)

Portions of two different genes are ligated together to create anew hybrid gene. When expressed the gene product is a fusion of thetwo gene products.

D)

Using oligonucleotide-directed mutagenesis to introduce specificmutations that cause the expressed protein to fuse to otherproteins.

E)

A portion of the gene can be removed to form a shorter gene andtherefore a shorter protein.

Why is green fluorescent protein (GFP) so useful in visualizingfusion proteins in eukaryotes?

A)

The GFP protein recognizes and binds to fusion proteins allowingthe location of the fusion protein to be determined.

B)

The reaction is only dependent on the presence of GFP and oneother cofactor.

C)

It is easily cloned and expressed in bacterial cells.

D)

The presence of just a few molecules of GFP fusion proteins canbe sufficient for observing the proteins microscopically allowingthe study of its location and movements in the cell.

E)

It is derived from fire flies, which are easy to cultivate inthe lab.

You wish to determine the cellular location of a protein butunfortunately it is not particularly antigenic (can t develop astrong antibody response). How could you solve this problem?

A)

Create a fusion protein with an epitope tag that can bevisualized by incubation with fluorescently tagged antibody to theepitope.

B)

Create a fusion with green fluorescent protein (GFP).

C)

Express the protein as a fusion with biotin. The addition of GFPwill cause fluorescence.

D)

A and B might work.

E)

A, B, and C might work.

F)

None of the above will work.

A positive result for the yeast two-hybrid analysis means thefollowing:

A)

The proteins that you are studying can be made into fusionproteins, but do NOT interact with each other within the nucleus ofyeast.

B)

A fusion protein containing the Gal4p activation domain, hasbound to RNA polymerase resulting increase transcription ofnumerous genes, including the reporter gene, and formation ofcolonies.

C)

Two fusion proteins, one containing the Gal4p binding sitedomain and one containing the Gal4p activation domain, haveinteracted through their Gal4p domains resulting in transcriptionof the reporter gene.

D)

Two fusion proteins interact with each other and because of theGal4p binding site domain and the Gal4p activation domain containedin each fusion protein, the reporter genes are activated and thecells die resulting in no colonies.

E)

The colonies growing are expressing the two fusion proteins, butthe two proteins have not interacted with each other.

Which of the following is the approximate size of the humangenome?

A)

3 Gm

B)

300 Kb

C)

3 Mb

D)

3 Gb

E)

3 Mm

Which of the following is correct about the structure orlocation of genes?

Question 22 options:

A)

Prokaryotic genes typically possess their own regulatorysequences that only control expression of a single gene.

B)

Eukaryotic genes often encode introns that are spliced outbefore translation.

C)

Eukaryotic genes are mostly located at the telomeres and thecentromeres of chromosomes.

D)

Eukaryotic genes are typically arranged in operons.

E)

Prokaryotic genes often encode exons that are spliced out beforetranslation

ANSWER THE FOLLOWING QUESTIONS(COULD BE MORE THAN ONEANSWER)

19) Describe the roles of M13 genes and their proteins:

a) Genes 1, 4 and 11 produces proteins required for assemblingthe the phage.

b)Genes 3.6,7,8 and 9 produces capsid proteins.

c)Gene 2 nicks the circular phage ssDNA to make it doublestranded by DNA polymerase

d)Gene 5 produces single strand binding proteins and gene 10protein makes M13 SSDNA circular.

e)Protein five bound single stranded circular M13 moved to theE. coli membranne and is released out coated will proteins 3, 6, 7,8 and 9 .

2) What is a phagemid and how does it work?

a)it is a recombinant DNA with a filamentous phage genome and aplasmid genome.

b)it carries two origins of replication: eg., oir f1 and oriColE1

c)May carry a gene for selection: e.g. Ampr gene.

d)May carry a marker gene; e.g, lacZ gene with promoter andregulator

e)May contain MCS, as is pUC18.

3)For storing functional gene for future applications you willneed the following:

a)A vector DNA

b) A cloning site in the vector matching with the ends of a geneto be cloned

c)A host organism capable to hold the recombined vector.

d)A marker gene present in the recombinant vector

e)A functional gene of interest.

24)identify which of the following is true for thebacteriophage lambda?

a)It has two major body parts, the head and the tail.

b)The genome is approximately 49 thousand bases long.

c) It has a linear dsDNA with single stranded 12 bases long costerminals at both

d) The single stranded lambda DNA cos terminals appear to be asfollows: (a) GGGCGGCGACCT and (b)CCCGCCGCTGGA

e)it can accept 7-10 kb long foreign DNA replacing itsnon-essential b2 region.

29) For developing a recombinant lambda DNA with a gene ofinterest and expressing the gene in a host you have to take thefollowing steps:

a)Remove the b2 region from lambda DNA using a restrictionenzyme

b)digest the gene of interest, outside its stop and startcodons, with the same restriction enzyme.

c)Recombine the lambda DNA digest with the digested gene ofinterest carrying complementary overhangs with ligase.

d)Form lambda particles by adding head proteins, tail proteinsand packaging enzynes to the recombined lambda DNA.

e)Add the packaged lambda particles to Agrobacetrium tumefaciensand incubate them in culture.

f)Add the packaged lambda particles to laboratory strains ofEscherichia coli and incubate them in culture.

32)The amino acids coded by our genes differ by thefollowing:

a)Polarity

b) Acidity

c)Basicity

d)Aroma

e)Hydrophobicity

38)What is an M13 phage and what are its specialty?

a)They are rod shaped Escherichia coli bacteriophage.

b)ts genome is made of a single stranded circular DNA.

c)Its DNA is 6400 nucloetides long coding for elevenproteins.

d)After infecting a bacterial cell it starts replicating in 10minutes producing 1,000 phages in an hour

e) soon its kills the host Escherichia coli and gets out to theenvironment.

40)You have a gene with BamH cut sites out side its start andthe stop codons. You can use the following procedures to prepare aclone of the gene in pBR322 and select the transformed E.Coli cellscarrying pBR322, except:

a) Digest both the gene and the plasmid pR322 with BamH1

b) Ligate the fragments using T4 DNA ligase.

c)Transform E coli with the reconstructed plasmid

d)Select the cells transformed cells grow in Lb-agar-ampicilinplates

e)Select the cells transformed cells grow inLB-agar-tetracycline plates

Recombinant DNA Technology

The questions all relate to the same topic and somewhat interrelate

1. Plasmids used in vitro to clone foreign DNA fragments are called ___

A. Transgenic.

B. Clones.

C. Vectors.

D. Conjugants.

2. VNTR alleles are hypervariable regions of human DNA that differ from each other in:

A. Location of internal sites recognized by restriction enzymes.

B. Variable number of point mutations.

C. Number of copies of an internally repeated DNA sequence.

D. Variable location on different chromosomes.

3. Probability calculations are used in forensic applications of DNA fingerprinting to determine if:

A. DNA from two different sources has matching alleles.

B. DNA samples were degraded before analysis.

C. A match between alleles of different DNA samples might have occurred by chance.

D. An unknown DNA sample is from a male or a female.

4. Plasmid vectors used in cloning often contain a gene for the N-terminal 146 amino acids of the enzyme β-galactosidase. What is the purpose of including this gene in the vector?

A. It allows selection of E. coli host cells that contain the plasmid.

B. It allows selection of E. coli host cells that contain plasmid in which the insert has been ligated.

C. It cleaves the insert to allow it to be ligated into the vector.

D. It enables the plasmid vector to replicate in E. coli host cells.

5.The first gene therapy clinical trial took place in 1990, on patients with SCID (severe combined immunodeficiency syndrome). Is this true or false?

A. True

B. False