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Biochemistry 2280A Chapter Notes - Chapter 7: Small Nuclear Rna, Regulatory Sequence, Noncoding Dna

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greenporpoise254
23 Dec 2016
School
Western University
Department
Biochemistry
Course
Biochemistry 2280A
Professor
Dr.Mc Lachlin

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Document Summary

Chapter 7: from dna to protein: how cells read the genome. The segment of dna that is transcribed into an rna is called a gene. Central dogma: flow of information from dna to rna to proteins. Rna splicing: a process in eukaryotic cells n which segments of an rna transcript are removed and the remaining segments are stitched back together. Amplification of rna enables cells to rapidly synthesize large amounts of protein and also easily regulate the amount of protein produced. Transcription of a gene produces an rna complementary to one strand of dna. The nontemplate strand of the gene is called the coding strand since its sequence is equivalent to the rna product. By convention, an rna molecules is always depicted with its 5" end to the left: the 5" end is the first part that is synthesized. Transcription begins with the opening and unwinding of a small portion of the.

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Related Questions

5. Alpha amanitin is a drug that binds RNA polymerase andprevents it from functioning in the cell (this is the compound thatis found in poison mushrooms). The reason people die when theyconsume alpha amanitin is:

a) Alpha amanitin prevents gene expression from occurring in thecell

b) DNA replication is directly inhibited by alpha amantin

c) Alpha amanitin binds tightly to the messenger RNAs that aremade in the cell, preventing translation

d) Alpha amanitin binds to nuclear pores preventing thetransport of messenger RNA into the cytoplasm

6. In order for transcriptional initiation to begin in E. colithe following elements are needed:

a) an origin and RNA polymerase

b) initiator protein and a promoter

c) the sigma subunit of RNA polymerase and an RNA template

d) RNA polymerase and a promoter

e) helicase and primase

Questions 7 and 8. You are studying two species of closelyrelated snakes, one species lives in sandy desert area and has paletan skin and the species lives in a volcanic rock area and has darkbrown skin. You a sequence the DNA from each type of snake anddiscover a gene encoding a protein that transports pigment into theskin cells. The pigment transporter protein is responsible for skincolor. When you analyze the DNA coding sequence of the pigmenttransporter from each snake you find these two DNA sequences (hashmarks have been added to indicate the reading frame):

pale tan snake: GCG/TTG/GAC/TGC/ACC (DNA template strand)CGC/AAC/CTG/ACG/TGG (complementary strand) dark brown snake:ACG/TTG/GAC/TGC/ACC (DNA template strand) TGC/AAC/CTG/ACG/TGG(complementary strand)

7. From these sequences you conclude:

a) that the amino acid sequence of the pigment transporters forthe two proteins are almost identical

b) that the amino acid sequence of the pigment transporters forthe two proteins are very dissimilar

c) that the amino acid sequence of the pigment transporters forthe two proteins are identical

8. Since the skin color is different in each snake, you concludefrom the sequence data above that:

a) the genetic code in the skin cells in each of these snakes isdifferent

b) the DNA sequence encoding the entire gene for pigmenttransporters in these two snakes is different

c) that one of the codons in the gene for the pigmenttransporter in these two snakes is different

9. You are analyzing eukaryotic cells that have been exposed tothe radioactive uracil. In most cells the radioactive uracil isinitially localized in the nucleus and then moves from the nucleusto the cytoplasm. However, you observe that in some cells theradioactive molecules stay in the nucleus and never arrive in thecytoplasm. This is most likely a defect in:

a) the transcription of the DNA

b) the processing of the mRNA

c) the translation of the RNA

d) the labeling of the RNA

e) the replication of the DNA

10. Which of the following is true of both eukaryotic andbacterial transcription? (select all that are true)
a) Transcription factors must bind the promoter before RNApolymerase initiates transcription

b) Messenger RNAs must be spliced before translation begins inorder to produce the appropriate gene product

c) During transcription only one DNA strand is used as atemplate to make the messenger RNA

d) Termination of transcription occurs when the RNA polymerasetranscribes a hairpin structure in the RNA followed by a string ofU

Multiple answers to each question might be possible!

You decide to identify the CFTR mutation by analyzing the genomic DNA of your patients compared to healthy individuals. You specifically are looking to see whether a specific 3' gene truncation has occurred in the patients. You will determine this using hybridization techniques with samples from healthy and CF patients. Which of the following will allow you to accomplish this?

Using an RNA probe complementary to the region not removed by the truncation.

Using an RNA probe complementary to the region removed by the truncation.

Using an DNA probe complementary to the region not removed by the truncation.

Using an DNA probe complementary to the region removed by the truncation.

To conduct the hybridization experiment, you are trying to decide between using a DNA or RNA probe. Which would be ideal to use and why?

As both are composed of nucleic acids, using either would result in identical results.

An RNA probe because RNA has uracil bases.

An RNA probe because it could also be used in a translation experiment.

A DNA probe because it is more stable than RNA.

A DNA probe because RNA cannot bind to DNA.

One step of the Hershey/Chase experiment involved blending the virus/cell mixture before centrifugation and probing the pellet for radioactivity. Why was the blending step necessary?

To collect the bacteria at the bottom of the tube.

To break open the bacteria to release the genome.

To separate the bacteria from the bacteriophages.

To be able to detect the radioactivity.

Imagine Hershey/Chase had used an RNA virus (genome composed of RNA) instead of a DNA virus in their experiment. Would radioactivity still have been found in the pellet?

No, because only DNA can be labeled with radioactivity.

No, because the RNA genome would not enter the bacteria upon infection.

No, because while DNA and RNA nucleotides are similar, they are not identical.

Yes, because DNA and RNA nucleotides are similar.

Yes, because genome in any form (DNA, RNA, protein) would be labeled similarly.

The human genome consists mostly of non-coding DNA. Which of the following are benefits of this?

Random DNA mutations generally won't affect RNA and protein function.

It is faster to duplicate the genome when these are present.

The existence of introns can lead to multiple variations of proteins encoded by a single gene.

It is unlikely transposons would exist in the genome if there was too much protein coding DNA.

Explain the 5’ to 3’ directionality of a DNA stand.

It is due to the fact that the free 5’ carbon is on one end and the free 3’ carbon is on the other

It is due to the fact that new nucleotide are added to the 5’ carbon of the previous nucleotide

It is due to the fact that there are 3 phosphate groups attached to the 5’ carbon

It is due to the fact the complementary strand is 3’ to 5’

More than one of the above explain the 5’ to 3’ directionality

You accidentally add a mutant dNTP (which has an H instead of an OH connected to the 3’ carbon) to a reaction where DNA is being replicated. Which of the following is true of this mutant dNTP?

It can be incorporated into DNA strand but cannot form a phosphodiester bond with an incoming wild type dNTP

It can be incorporated into a DNA strand but cannot base pair with a complementary nucleotide

It can be incorporated into a DNA strand and can form a phosphodiester bond with an incoming dNTP, but only if it is another mutant dNTP

It cannot be incorporated into a DNA strand.

Why does DNA polymerase utilize an RNA primer?

DNA polymerase is unable to initiate strand synthesis but RNA polymerase can

DNA polymerase can only add a dNTP to an rNTP

DNA synthesis proceeds in the 3’ to 5’ when initiating strand synthesis

Chromosomal DNA contains interspersed RNA fragments

The RNA primer increases stability of the newly synthesized strand

DNA Structure and Function LabReport

  1. DNA Structure
  2. Which two scientists are credited with discovering DNA?
  1. Name the nitrogen bases that are purines.
  1. Which nitrogen base pairs with thymine?
  1. List the three components of a nucleotide.
  1. DNA Replication
  2. What is the purpose of DNA replication?
  1. How many times does replication occur in the life of acell?
  1. In the Lab, Exercise 2, the original strand on the left had thebases shown below. Input the new bases that correctly pair with theoriginal strand.

Original

New

C

A

G

T
  1. RNA Structure
  1. Describe the structure and function of RNA.
  1. Refer to Exercise 3 and record the bases of the RNA strandproduced from the replicated DNA strand.

DNA

RNA

C

A

G

T

  1. Record the differences between DNA and RNA in the tablebelow.

DNA

RNA

Sugars

Bases

Strands

  1. RNA Synthesis

  1. The process of assembling RNA is called _________.
  1. How is replication different from transcription?
  1. Refer to Exercise 4. Write the letters for the base sequence ofmRNA in the spaces below DNA. Note that the order is reversed;start with the 3’ end of the DNA strand and the 5’ end of the mRNAstrand. Transcription is DNA to mRNA. Note RNA contains Uracilinstead of Thymine; There is no thymine in RNA.

DNA

3’

C

G

T

C

G

T

C

C

A

A

T

T

5’

mRNA

5’

3’

  1. Protein Synthesis

  1. What type of RNA provides amino acids to build polypeptidechains?

  1. If a mRNA strand has the bases 5’ CUC 3’, what amino acid willbe translated? Refer to the printable chart in Exercise 5.

  1. Where in the cell does translation occur?
  1. Genes

  1. What could be the problem if there is a change in the basesequence of a gene as it is passed down to the offspring?
  1. Give an example of a disorder that results from changes in theamino acid sequence.
  1. What causes sickle cell anemia?
  1. Gene Cloning
  1. What is the function of a plasmid?
  1. Print the document from Lab, Exercise 6. Complete the activityalong with the video demonstration. Sign, date, and take an imageof your final product and include with this lab report.