BIOC 3400 Lecture Notes - Lecture 20: Transcription Bubble, Dna Footprinting, Extension Method

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coffeeoyster95

6 Nov 2015

School

Dalhousie University

Department

Biochem & Molecular Biology

Course

BIOC 3400

Professor

Liu Paul

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Document Summary

Both extend the nucleic acid chains in 5"-3" direction. Only one dna strand is transcribed (template strand); newly transcribed mrna is identical to non-template strand. Only a fraction of the genome is transcribed, while in dna replication, all of the dna is replicated. Different enzyme with different properties: transcription -- rna polymerase; dna replication -- dna polymerase ( much faster, more accurate). Slightly different base: u instead of t, ntps instead of dntps. Direct rna polymerase holoenzymes to the transcription start sites: similarities btw transcription. & dna replication: what is the function of subunit in prokaryotic. Rna polymerase: sigma factor ( subunit) a bacterial transcription initiation factor that enables specific binding of rna polymerase to gene promoters. The specific sigma factor used to initiate transcription of a given gene will vary, depending on the gene and on the environmental signals needed to initiate transcription of that gene. (different factors do difference things. )

Related Questions

89) During fasting, glucose is synthesized from gluconeogenesis.Where is glucose used?

During fasting glucose is directed to the brain.

90) Why does DNA polymerase need a RNA primer for replication ofchromosomes?

DNA polymerase cannot start synthesis, only extends on anexisting polynucleotide. RNA polymerase can synthesize without anexisting primer.

91) During replication of chromosomes, synthesis of one strandis continuously extending. Another strand extend discontinuously.Why?

92) Histone proteins are core of nucleosomes. DNA wraps aroundthem. Both DNA and histones are involved in regulation of geneexpression. Transcription factors and enhancers are other elementsof regulation. What would be like if a gene has a promoter but doesnot have tissue specific regulatory protein binding sites?

93) Some of cancer causing genes are involved in DNA repair suchBRCA1 and BRCA2. Why do defects in DNA repair increase chance ofgetting cancer?

copperwhale251

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 5â to 3â directionality of a DNA stand.

	It is due to the fact that the free 5â carbon is on one end and the free 3â carbon is on the other
	It is due to the fact that new nucleotide are added to the 5â carbon of the previous nucleotide
	It is due to the fact that there are 3 phosphate groups attached to the 5â carbon
	It is due to the fact the complementary strand is 3â to 5â
	More than one of the above explain the 5â to 3â directionality

You accidentally add a mutant dNTP (which has an H instead of an OH connected to the 3â 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 3â to 5â when initiating strand synthesis
	Chromosomal DNA contains interspersed RNA fragments
	The RNA primer increases stability of the newly synthesized strand

rosehippopotamus950

1. Two couples in which both partners have albinism each have three children. All three of the first coupleâs children have albinism, while all of the second coupleâs children have normal pigmentation. How can you explain these findings given that the development of pigmentation is a multi-step biochemical pathway?

2. All of the genome is replicated during the DNA synthesis phase of the cell cycle, but only part of the genome is transcribed each time transcription is initiated. How is it determined which base pairs of thegenome are transcribed into RNA?

3. To encode all 20 amino acids using a genetic code that is unambiguous, what would be the minimum codon size if there were ________ different bases (rather than four)?

a) two

b) five

c) Suppose that only the first two nucleotides of a three nucleotide codon are base-specific, and position three is dependent on whether it is occupied by a purine or pyrimidine, how many triplets of different meaning would there be?

4. A segment of a polypeptide chain is Arg-Gly-Ser-Phe-Val-Asp-Arg. If it is encoded by the followingsegment of DNA, which DNA strand acts as the template for transcription? Appropriately label the ends ofeach DNA strand with 5â and 3â.
- G G C T A G C T G C T T C C T T G G G G A â- C C G A T C G A C G A A G G A A C C C C T -

BIOC 3400 Lecture Notes - Lecture 20: Transcription Bubble, Dna Footprinting, Extension Method

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