Nucleotides and Nucleic Acids Flashcards
What does DNA do
Stores information
What were the results of Avery-MacLoed-McCarty’s experiment
Rough strain (nonvirulent); mouse lives
Smooth strain (virulent); mouse dies
Heat-killed smooth strain; mouse lives
Rough strain and heat-killed smooth strain; mouse dies
There is some sort of transformative element
What is the basic virus structure
Protein coat relatively high in sulfur. DNA high is phosphorous
What happened to Sulfur-labeled protein after the Hershey-Chase experiments
After centrifugation, no sulphur was in the cells; nonradioactive viral progeny
What happened to Phosphorous labeled DNA after the Hershey-Chase experiments
After centrifugation, phosphorous was in the cells; radioactive viral progeny
What are the steps of the Hershey-Chase experiment
- Infection
- Blending
- Centrifugation
What are some roles of mono- and dinucleotides
Oxidation-reduction reactions. Energy transfer. Intercellular signalling and biosynthetic reaction
What are some roles of polynucleotides
Storage and decoding genetic information. As enzymes
What are nucleotides in a very basic sense
They are incorporated into nucleic acids and high-energy molecules
What composes a nucleotide
Sugar, Nitrogen-containing aromatic base and Phosphate
What are the common bases of nucleotides
Adenine, Cytosine, Guanine, Thymine and Uracil
What are the common sugars in nucleotides
Deoxyribose and ribose
What are the pyrimidine nucleotide bases
Uracil, Thymine and Cytosine
What are the purine nucleotide bases
Adenine and Guanine
Describe a pyrimidine
A 6-carbon ring with a nitrogen on the first and third carbon
Describe a purine
A 9-carbon ring (looks like hexagon attached to a pentagon). The nitrogen being attached to the first, third, seventh and ninth carbons
Describe the appearance of uracil
A pyrimidine, it has two nitrogens on the first and third positions on the carbon ring. There are two carbonyl groups attached at the 2 and 4 positions of the carbon ring
Describe the hydrogen bonds present in uracil
There is a possibility to form 6 hydrogen bonds, 2 as donors and 4 as acceptors. The 2 donors are the nitrogens. The 4 acceptors are from the lone pairs present from the carbonyl groups (2 lone pairs per oxygen)
Describe the appearance of thymine
A pyrimidine, it has two nitrogens at the first and third position on the carbon ring. There are two carbonyl groups at the 2 and 4 positions. There is also a methyl group on the fifth position of the carbon ring
Describe the hydrogen bonds present in thymine
There is a possibility to for 6 hydrogen bonds, 2 as donors and 4 as acceptors. The 2 donors the nitrogens. The 4 acceptors are from the carbonyl groups (2 lone pairs per oxygen).
What is the difference between uracil and thymine
Thymine has methyl group on the fifth carbon in the carbon ring that uracil does not have
Describe the appearance of cytosine
Cytosine is a pyrimidine. There is a nitrogen in the positions 1 and 3 on the carbon ring, a carbonyl group in position 2 and an NH2 in position 4.
Describe the hydrogen bonds that can be formed in cytosine
6 hydrogen bonds, 3 as donors and 3 as acceptors. The nitrogen in position 1 is a donor because it lacks hydrogen, the hydrogens in the NH2 in position 4 both also act as donors. The nitrogen in position 3 is an acceptor, the lone pairs from the oxygens also act as acceptors.
Describe the appearance of adenine
It is a purine, it has a nitrogen in the positions 1, 3, 7 and 9 in the carbon-ring. There is an NH2 group attached to carbon 6 in the carbon-ring
Describe the possible hydrogen bonds in adenine
There is possibility of forming 6 hydrogen bonds, 3 as donors and 3 as acceptors. The nitrogen in 1, 3, and 7 positions act as acceptors. The nitrogen in position 9, as well as the hydrogens a part of the NH2 group will act as donors
Describe the appearance of guanine
It is a purine. It has a nitrogen in positions 1, 3, 7 and 9. There is an NH2 in position 2 and a carbonyl group in position 6.
Describe the possible hydrogen bonds in guanine
It is capable of 8 hydrogen bonds, 4 as acceptors and 4 as donors. The nitrogen in positions 1 and 9 and the hydrogens from the NH2 group from position 2 will act as donors. The nitrogen in positions 3 and 7 and the lone pairs from the carbonyl group from position 6 will act as acceptors.
What is the basic information of RNA
Polymer of G, A, C, or U. Sugar portion of ribose. Hydroxyl group present on 2’ carbon
What is the basic information of DNA
Polymer of G, A, C or T. Sugar portion of deoxyribose. Hydrogen present on 2’ carbon.
What is a nucleoside
A nitrogen base and a sugar
Where do the nitrogen bases and sugar join to form nucleosides
The point of attachment between the sugar and bases is carbon 1 in pyrimidine and carbon 9 in purines. They both attach to carbon 1’ of the sugar molecule
How are the carbons numbered in the sugar ring (pentose)
They are numbered from 1’ to 5’.
What happens to the hydrogen bonds when pyrimidine is attached to a sugar
There are no hydrogen bond capabilities for a pyrimidine in the first position of it’s six carbon-ring. Everything else remains the same
What happens to the hydrogen bonds when purine is attached to a sugar
There are no hydrogen bond capabilities for a purine in the ninth position of it’s nine carbon-ring. Everything else remains the same
How do you name a purine nucleoside
-ine in purine becomes osine
Example: Adenine = adenosine
Guanine = guanosine
How do you name a pyrimidine nucleoside
Pyrimidine now ends in -idine
Example: Cytosine - cytidine
Thymine = Thymidine
Uracil = Uridine
What does a nucleotide comprise of
Nucleosides (nitrogen base and sugar) + phosphate
What is a phosphoester
They are phosphate esters they link carbon to phosphate groups
What is a phosphodiester
They link two different carbons to one phosphate group
What is a phosphoanyhydrides
They link two phosphates to each other
What is the net charge of nucleic acids
It is a net negative charge from the phosphate groups. Roughly consistent negative charge
Is the backbone of nucleic acids polar or non-polar
The backbone is sugar-phosphate-sugar-phosphate etc. It should be polar
Is the backbone in RNA or backbone in DNA more polar
Backbone in RNA is more polar than DNA because it contains the 2’ OH group, which has hydrogen bonding potential
If you are given the nucleic acid sequence
5’-ATGCAATG-3’ what can you conclude
It is likely DNA, because of the presence of Thymine
If you are given the nucleic acid sequence
5’-ACGCAAGG-3’ what can you conclude
Could be either RNA or DNA, there is no thymine or uracil so it’s inconclusive
If you are given the nucleic acid sequence
5’-UCGUUCA-3’ what can you conclude
It is likely RNA, because of the presence of Uracil
What are the nomenclature rules for naming nucleotides prefixes
1 - Mono
2 - Di
3 - Tri
4 - Tetra… etc.
How do we name nucleotides when they pass nine nucleotides
They are referred to as 10-mer and that number increases as the number of nucleotides increases
What is an oligonucleotides
Usually around but somewhat less than 50 nucleotides
What are Polynucleotides
It is a large number of nucleotides (over 50)
What is created in the hydrolysis of phosphodiester bonds
The phosphodiester bond separates and the products are 3’ hydroxyl and a 5’ phosphoester
Where does spontaneous hydrolysis of phosphodiester bonds occur
It is occurs in RNA when the pH is greater than 10
Why doesn’t spontaneous hydrolysis of phosphodiester bonds occur in DNA
In DNA, the absence of a 2’ OH prevents this reaction. This makes DNA more stable than RNA under alkaline conditions
What are the two nitrogen bases that can be spontaneously converted
Cytosine can have a spontaneous (uncatalyzed) reaction that converts it to Uracil
Why is the deamination of cytosine to uracil a problem
Uncorrected in DNA can cause a mutation. One role for thymine versus uracil isn’t present in DNA. DNA repair mechanisms will recognize uracil and remove it.
What is a dideoxynucleotide
It can only be incorporated at the end of the nucleic acid. There is Hydrogen on the 3’ part of the pentose.
Why must a dideoxynucleotide be at the end of the nucleic acid chain
There are no phosphodiester capabilities which forces it be at the end of the chain.
What are the properties of the nitrogen bases
Heterocyclic. Aromatic, electron delocalization. Basically planar, with a slight pucker in purine base. Poorly soluble in water.
Why are nitrogen bases poorly soluble in water
Relatively hydrophobic, there are hydrogen bond capabilities on the outer area of the ring, but the inner ring makes it poorly soluble
When does DNA absorb ultraviolet light
It absorbs at around 260 nm
When does protein absorb ultraviolet light
It absorbs at around 280 nm
Why do we use ultraviolet light to look at DNA
It can see if there is any protein contaminations. Lower values have typically reflected in protein contamination
What is the ideal ratio for DNA in an absorbance of A260 nm / A280 nm
Approximately 1.95 for pure DNA
What is Beer-Lambert Law
A=(ϵl)c A = Absorbance ϵ = extinction coefficient l = path length c = concentration
How do absorbance and concentration relate in the Beer-Lambert Law
Absorbance varies directly with concentration
What is the primary structure of DNA
Primary structure is the sequence of nucleotide residues
What do higher order structures of DNA formed by
Higher order structures are formed by chains of nucleotides
What form does DNA take
DNA forms a double helix. Each chain is connected to the other through hydrogen bonds between the bases (non-covalent)
In DNA structure what are the bases that go next to each other or Chargaff’s Rules
Purine = Pyrimidine pairing A = T/U G = C (A + G = C + T) Chargaff's rules are only obeyed in the duplex structure
How did Chargaff help Watson and Crick
Helped Watson and Crick deduce the double helical structure of DNA
For H-bonds to form between or within biochemical macromolecules they must be shield from water?
In nucleic acids, hydrogen bonds are isolated from the aqueous environment to prevent it from becoming destabilized.
What is DNA (B-form)
The strands are anti-parallel, with an overall right-handed twist. Stabilized by base stacking interactions and hydrogen bonds. Base stacking is the primary stabilizing force.
What is Base stacking
Primarily Van der Waals. Also, hydrophobic forces
What is the major groove in DNA good for
Good place for proteins to bond/interact
What is the minor groove in DNA good for
It is a place for proteins to bond/interact with but it is less integral than the major groove
What are the general features of B-form DNA
Hydrophobic core / polar exterior. Bases largely excluded from H2O (surrounding aqueous environment). Stabilize H-bonds. Ribose / deoxyribose and phosphates are exposed to H2O. H-bonds in pairing interactions (base pairs). ~10 base pairs per turn (one complete right-handed turn)
What does the axial view of DNA looks like
The polar sugar / phosphate backbone is found on the outside with the more hydrophobic bases stack in the core of the structure.
What is an example of complementary sequences
5’ - A T G C G G - 3’
3’ - T A C G C C - 5’
The strands are anti-parallel
The two polynucleotide strands are non-identical
What must we assume if we are not told otherwise about the directions of DNA strands
If we are not told otherwise, we must assume that we are looking at a 5’ to 3’ strand
