Biology 1001A Lecture Notes - Dna Mismatch Repair, Retrotransposon, Dna Ligase

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sangriafly958

19 Nov 2012

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In bacteria, proofreading has reduced error from 1 mistake for every 1,000 to 10,000 nucleotides assembled to 1 mistake for every 1 million nucleotides assembled. Insertion sequences (is): simpler; inverted repeat, central sequence, inverted repeat: transposons: is element, central sequence (possibly including host genes), is element. Dna copy is then inserted into dna at a new location (original is left in place) Implications of insertion of mobile elements into dna. Tes inserted into chromosomes become permanent and are passed on during cell division, along with the rest of the dna. Tes inserted into dna of reproductive cells may be inherited, becoming part of the genetic material of a species. Mutations can accumulate in a te, altering it into a non-mobile, residual sequence in dna (causes eukaryotes to contain large amounts of non-functional te sequence) Transposons do not exist free of the dna in which they are integrated. Hence the term jumping genes is inaccurate.

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Please help to check if the following DNA repair description is correct. if not, please help to correct. thanks!!

1. Base Excision Repair

DNA plycosylase comes in and removes deaminated C Uracil. AP endonuclease recognizes the missing tooth created by DNA glysosylase and it removes the sugar while phosphodiesterase removes phosphate group leaving DNA helix with single nucleotide gap. DNA polymerase add new nucleotide and DNA ligase seals the nick

2. Nucleotide Excision Repair

NER uses to remove large mutation. Excision nuclease comes in and cut the pyrimidine primers in a big chunk. DNA helicase removes the big chunk. DNA polymeraze synthesize nucleotides and DNA ligase seals the nick.

3. Nonhomologous end joining

The overhangs ends is recognized by Ku heterodimers and they attach to the broken chromosomes end. Additional proteins attach and join covalently. Overhangs are then digested and ligase seals the nicks

4. The repair involves sister chromatids. One of the sister chromatids has double strand breaks. Exonuclease activity degrades the 5â end. The strand invasion begins by crossing over. The single strand interacts with healthy strand on sister chromatid DNA molecule. DNA polymerase synthesize missing nucleotides and ligase seals the nicks

silverreindeer987

1.When a protein binds to DNA at a site defined by a particular nucleotide sequence, with which parts of the DNA does the protein primarily interact?

A. the phosphate and deoxyribose groups in the DNA backbone

B. the phosphate and deoxyribose groups in the DNA backbone, and hydrophobic interactions with the nucleotide bases

C. nucleotide bases within the major grooves of the DNA

D. nucleotide bases within the major and minor grooves of the DNA

E. none of the above

2. Which of the following proteins binds to DNA with sequence specificity?

A. POI Ill holoenzyme

B. DnaA

C. DnaB

D. Dam methylase

E. Both B and D

3. Which of the following is NOT a functional parallel among all known cellular systems of DNA replication?

A. Replication is initiated at specific sites

B. Replication is continuous on the leading strand and discontinuous on the lagging strand

C. DNA replication is semiconservative

D. Replication forks move away from the origin in one direction

E. Nucleases, polymerases and ligases replace RNA primers with DNA and seal the remaining nick

4. A DNA polymerase cannot synthesize a DNA strand de novo (from the beginning) from a mixture of dNTPs. Which of the following explains the role of the primer in the reaction promoted by this enzyme?

A. The primer is an initiation protein with attached nucleotides that binds to the template and to which new nucleotides are added to the 3 ' end.

B. The primer is an initiation protein with attached nucleotides that binds to the template and to which new nucleotides are added to the 5' end.

C. The primer is a preexisting strand of RNA or DNA to which new nucleotides are added to the 3' end.

D. The primer is a preexisting strand of RNA or DNA to which new nucleotides are added to the 5' end.

E. The primer is a preexisting strand of DNA synthesized by DNA pol I, prior to replicative DNA synthesis by DNA pol Ill.

5. Universal features of DNA polymerases include:

A. 5'-3' exonuclease function.

B. Formation of an 'closed' conformation of the polymerase when the template-nucleotide base pair is correct.

C. Use of a single magnesium ion to orient reacting molecules and assist in dissipation of the negative charge that develops during nucleotidyl transfer.

D. Alignment of conserved residues in the active site for attack of the DNA primer by the 3 'OH on the incoming nucleotide.

E. Continuous unbinding and rebinding of the polymerase to the DNA template as each nucleotide is added.

byzantiumscorpion425

Please answer all

Why does a template-dependent DNA polymerase require a primer to initiate DNA synthesis?

	DNA polymerase require 5' phosphate to add a new nucleotide
	DNA polymerase require 3' hydroxyl group to add a new nucleotide

DNA polymerase require energy by hydrolizing the primers

Which of the following enzymes is template independent?

	Reverse transcriptase
	Klenow fragment

	DNA polymerase
	Terminal deoxynucleotidyl transferase

RNA polymerase

The natural function of a DNA ligase enzyme is:

	Joining together DNA sequences with compatible cohesive ends from two different organisms to yield a recombinant DNA molecule
	Sealing single stranded nicks in double stranded DNA molecules

	Joining together two blunt ended fragments of DNA within a cell
	Joining together two single stranded DNA molecules

The natural function of 3' -> 5' exonuclease activity of a DNA polymerase is to:

	Remove the 5' end of the DNA strand that is being copied
	Remove damaged nucleotide from the template strand

	Remove nucleotides from the end of DNA to generate blunt ends
	Remove incorrect nucleotides from the newly synthesized DNA

Which technique is used to resolve the different sizes of DNA fragments?

	Gene cloning
	PCR

	DNA sequencing
	Gel electrophoresis

Which of the following vectors does not contain bacterial origin of replication (oriC)?

	plasmid
	cosmid

	bacterial artificial chromosome
	lambda vector

Which process of bacteriophage is not used for gene cloning?

	Concatemer formation
	Lytic cycle

	Lysogenic cycle
	viral packaging

What vector would be best suited for creating a contig of bovine (cattle) chromosome 10?

	lambda vector
	Cosmid vector

	P1 vector
	Plasmid

E. coli takes up plasmid DNA by which of the following methods?

	Transduction
	Transformation

	Conjugation
	Transfection

The following times and temperatures are an example of the steps for PCR. You can use the Figure to help you answer the following questions.

Why is the first step is carried out at 94Â°C?

	To degrade the template
	To denature the template

	To activate the polymerase
	To facilitate the primer binding

What happens in the reaction when the temperature shifts to 55Â°C during cycling?

	the DNA polymerase will carry out DNA synthesis by extending the annealed primers
	the DNA polymerase will finish DNA synthesis

	the primers anneal to the single-stranded regions of the DNA
	the primers anneal to the double-stranded regions of the DNA

During cycling, what occurs when the temperature is at 72Â°C?

	the primers anneal to the double-stranded regions of the DNA
	the DNA polymerase will carry out DNA synthesis by extending the annealed primers

	the primers anneal to the single-stranded regions of the DNA
	the DNA polymerase will finish DNA synthesis

You designed a set of primers to amplify 1 kb DNA with polymerase chain reaction. By which cycle of polymerase chain reaction, we would expect to see the first double stranded DNA with expected size?

	The end of cycle 1
	The end of cycle 2

	The end of cycle3
	The end of cycle 4

Biology 1001A Lecture Notes - Dna Mismatch Repair, Retrotransposon, Dna Ligase

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