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INTER-LS 101 Lecture Notes - Lecture 3: Methyl Group, Uracil, Thymine

36 views2 pages
orchidraven432
14 Sep 2016
School
UW-Madison
Department
Interdisciplinary Courses
Course
INTER-LS 101
Professor
Bikash Pattnaik

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Document Summary

Central dogma - process where genomic information is used to make necessary proteins for biological systems. Message in chromosomes (the dna) that gets transferred to the rna to create and dictate the use of a protein. Gene - a specific sequence within dna that dictates the setup of a protein. Transcription - information from dna rna. Translation - information for rna that turns it into a protein. Enzyme transcriptase comes to dna to unzip so rna can transcript. Rna has protein uracil (u); dna has thymine (t) U and t have the same structure but thymine has a methyl group; uracel does not have. Methyl group in t gives stability to dna by not allowing enzymes to break dna down. Enzymes can dissolve rna because uracil is part of rna. From 1 gene within dna, multiple rna"s can be made. Exon - information that can exit the nucleus; used by rna for protein synthesis.

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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

If one is testing a goodness of fit to a 9:3:3:1 ratio, how many degrees of freedom would be associated with the Chi-square?

1

2

3

4

not enough information to determine

Which of the following choices does not describe a type of posttranslational modification of proteins?

The amino terminal methionine may be removed.
Glycoproteins are produced by the attachment of phosphates to newly synthesized proteins.
Precursor proteins are cleaved and trimmed by protease enzymes to produce a functional protein.
Molecular chaperones help proteins fold correctly.
Amino acids in the amino terminal of the protein can be acetylated.

A eukaryotic DNA sequence that affects transcription at distant promoters is called a(n)

long distance promotor
regulator
operon
enhancer

DNA methylation may be a significant mode of genetic regulation in eukaryotes. Meythylation refers to

altering RNA polymerase activity by adding methyl-groups
changes in DNA-DNA hydrogen bonding
altering translation activity via methylated tRNAs
adding methyl groups to certain cytosines in DNA

If a nucleotide lacks a 3’-OH group, what will happen?

it’s transformed into RNA
another nucleotide can bond at the 3’ site during replication
replication will halt
no effect

Which of the following describe posttranscriptional modifications commonly seen in mRNA of eukaryotes?

5’ capping, 3’-poly-A tail addition, splicing
3’ capping, 5’ poly-A tail addition, splicing
heteroduplex formation
5’ capping, 3’polyA tail addition, removal of exons

In birds, females are the heterogametic sex. This means that

females have chromosomes in pairs.
emales produce eggs.
females determine the gender of their offspring.

males have two identical sex chromosomes (ZZ)

An anticodon on a tRNA has the sequence 5'–GCA–3'. What would be the effect on translation if the G in the anticodon were mutated to a U?

The anticodon could pair to the serine codon 5'–UCA–3', and a cysteine would be incorporated at all points where a serine should have been incorporated.
The anticodon could pair to the threonine codon 5'–ACU–3', and a threonine would be incorporated at all points where a cysteine should have been incorporated.
The anticodon could pair to the serine codon 5'–AGU–3', and a serine would be incorporated at all points where a cysteine should have been incorporated.
The anticodon could pair to the stop codon 5'–UGA–3', and instead of stopping translation, a cysteine would be incorporated and translation could continue.