BIOCH200 Lecture Notes - Lecture 6: Nitrogenous Base, Nucleic Acid Thermodynamics, Deamination

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turquoisewalrus441

5 May 2018

School

University of Alberta

Department

Biochemistry

Course

BIOCH200

Professor

Jonathan Parrish

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Nucleic Acids

❏Polymers of nucleotides linked by 3’-5’ phosphodiester bonds.

❏Nucleotides are written from 5’ to 3’ by convention.

❏5’ end has a free phosphate group → not involved in a phosphodiester bond

❏3’ end has a free OH group not involved in phosphodiester bond.

❏Net Charge → Negative due to phosphates

❏RNA is more polar because of OH group (3 more H-bonds)

❏DNA backbone → Sugar and Phosphate → Polar

Representation of Primary Structures of Nucleic Acids

1. 5’-ATG-3’ → DNA due to presence of T.

2. 5’-ACG-3’ → likely RNA because DNA would be dAdCdG

3. 5-UCG-3’ → RNA due to presence of U

4. ACGC → By convention A is 5’ and C is 3’ → RNA because DNA would be dAdCdGdC

5. ACGCT → pApCpGpCpT → phosphodiester linkage, 5’ is A, 3’ is T, DNA due to presence of T.

Polynucleotides

❏Mononucleotide → one nitrogen base, sugar and phosphate

❏Dinucleotide → 2 bases, 2 sugars and 2 phosphates.

❏Oligonucleotide → 20-50

❏Polynucleotides → Large number of nucleic acids.

Hydrolysis of Phosphodiester bonds

❏Could occur on either side

❏You may also undergo alkaline hydrolysis of phosphodiester bonds where pH is typically greater

than 9 and the compound has an OH group.

❏RNa is more susceptible to alkaline hydrolysis due to OH group. DNA is more stable due

to lack of OH group.

Cytosine Deamination

❏Less serious in RNA → short life span

❏More serious in DNA → Larger life span.

Properties of the Bases (purines/pyrimidines)

❏Heterocyclic and Aromatic (electron delocalization)

❏Allow for Abs UV light → Max. ~260nm.

❏Planar, slight pucker in purine bases

❏Poorly soluble, and largely hydrophobic with some polar groups

❏Able to form H-bonds.

❏Sugar phosphate backbone is polar.

Electron delocalization allows bases to absorb UV light

❏Ratio of A260/A280 tells us the purity of DNA. At approx 1.8-1.9 it is Pure DNA.

❏If the Ratio is lower than 1.8-1.9 there is probably protein in the sample because it has a max

absorbance at ~280nm.

❏Determine amount DNA by graphing [DNA] in relation to A260nm. As [DNA] increases A260

should increase.

❏ssDNA absorbs higher than dsDNA

❏DNA and RNA are very similar that you can’t determine the two based on ratio.

DNA Structure

❏Erwin Chargaff → A=T, C=G in dsDNA

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Document Summary

Polymers of nucleotides linked by 3"-5" phosphodiester bonds. Nucleotides are written from 5" to 3" by convention. 5" end has a free phosphate group not involved in a phosphodiester bond. 3" end has a free oh group not involved in phosphodiester bond. Net charge negative due to phosphates. Rna is more polar because of oh group (3 more h-bonds) Dna backbone sugar and phosphate polar. Mononucleotide one nitrogen base, sugar and phosphate. Dinucleotide 2 bases, 2 sugars and 2 phosphates. Polynucleotides large number of nucleic acids. You may also undergo alkaline hydrolysis of phosphodiester bonds where ph is typically greater than 9 and the compound has an oh group. Rna is more susceptible to alkaline hydrolysis due to oh group. Dna is more stable due to lack of oh group. Less serious in rna short life span. More serious in dna larger life span. Allow for abs uv light max. Poorly soluble, and largely hydrophobic with some polar groups.

Related Questions

1. Unlike DNA, RNA contains

deoxyribose

a double strand

phosphates

uracil

Nucleic acid structure

2. In transcription, uracil will bond with:

thymine

cytosine

adenine

guanine

Transcription

3. The first team of scientist to document the structure of DNA was:

Franklin and Wilkins

Watson and Crick

Pauling and Chargoff

None of the above

DNA structure

4. Organelles that synthesize protein are:

lysosomes

ribosomes

endoplasmic reticulum

golgi bodies

5. Most of the time in a cell's life, it's DNA is in the form of:

Chromatin

Chromatids

Replicated chromosomes

Spindle fibers

6. Uracil is a nitrogen base that pairs with adenine. Using this information, one could conclude that uracil is a:

Purine

Pyrimidine

Neither a purine or pyrimidine

Not enough information

7. a nucleotide does not consist of a:

polymerase

5-carbon sugar

phosphate group

nitrogen base

8. The genetic code in DNA of an individual depends on the sequence (order) of:

nucleotides

purines only

phosphates

sugars

9. Before a cell divides, it must duplicate its DNA in a process known as:

translation

transformation

transcription

replication

10. The basic unit (building block) of a protein is a (an):

carbohydrate

amino acid

lipid

hydrogen bond

11. Unlike DNA, RNA contains:

deoxyribose

a double strand

phosphates

uracil

12. The structure of DNA was first documented in:

1945

1953

1956

1962

13. In DNA replication, the new molecules produced are:

of unequal length

both assembled in the same direction

built with purines as the backbone

assembled in opposite directions

DNA replication

14. The "backbone" of DNA is composed of:

ribose and phosphates

deoxyribose and phosphates

ribose and uracil

deoxyribose and thymine

DNA structure

15. RNA differs from DNA in which of the following ways?

RNA is single-stranded

RNA contains ribose

RNA does not contain thymine

All of the above

DNA structure

16. Which of the following is NOT required for the transcription process itself?

RNA polymerase

DNA

uracil-containing nucleotides

ribosomes

skyhamster121

Thinking about macromolecules and how their monomers come together to form the polymer match the following. A. glycosidic bonds B. phosphodiester C. ester bonds D. peptide bonds E. monosaccharaides F. amino acids G. nucleotides

1. Monomeric units of protein

2. Monomeric units of DNA

3. Monomeric units of carbohydrates

4. Monomeric units of a lipid

5. Proteins are held together by

6. The bond type that joins adjacent monomers in DNA and RNA

7. Carbohydrates like glycogen are formed by the bonding glucose molecules together via

8. The glycerol backbone of a lipid is bonded to the fatty acid tails by

9. These monomers have a amino group on one end and a carboxylic acid on the other.

10. Î±1-4 and Î²1-4 are two different types of this bond.

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

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BIOCH200 Lecture Notes - Lecture 6: Nitrogenous Base, Nucleic Acid Thermodynamics, Deamination

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