nucleic acids

Question 1

functions of nucleotides and nucleic acids

Answer 1

nucleotides:
Energy for metabolism (ATP)
Enzyme cofactors
signal transduction

nucleic acid:
storage of genetic information (DNA)
transmission of genetic info (mRNA)
processing of genetic info (ribosomes)
protein synthesis (tRNA and rRNA)

Question 2

what is the sugar in nucleotides? both DNA and RNA

Answer 2

Beta-D-ribofuranose in RNA

Beta-2’-deoxy-D-ribofuranose in DNA (one less OH)

Question 3

Nucleobases absorb light in what range?

Answer 3

absorb UV light around 250-270 nm due to π-π electronic transitions

Question 4

Purines vs Pyrimidines structure and numbering

Answer 4

Purines: two ringed (9 ring members). Starts at left most N (1) then moves down and counterclockwise on that ring (2,3,4,5,6) then jumps to top N of other ring and moves down for 7,8,9
Pyrimidines: one ring (6 members). Starts at bottom N (1) and moves left and clockwise to C=O (2) and so forth till 6

Question 5

How is the Nucleobases attached to the pentose ring?

Answer 5

N-glycosidic bond to anomeric carbon of the sugar in Beta configuration. Bond is on N1 in pyrimidines and N9 in purines

Question 6

What is the torsion angle about the N-glycosidic bond defined by? What are the angles for syn and anti?

Answer 6

torsion angle is denoted by c and atoms that define the angle are O4’-C1’-N9-C4 in purines and O4’-C1’-N1-C2 in pyrimidines. (Draw it out)
syn: 0 degrees
anti: 180 degrees
Anti is normal conformation in B-DNA

Question 7

What’s the deal with the phosphate group?

Answer 7

negatively charged at neutral pH
usually attached to the 5’ position, other attachments are possible at 3’ and 2’
nucleic acids are built using triphosphate (ATP, GTP, TTP, CTP) but nucleic acids will only contain one phosphate moiety per nucleotide.

Question 8

what are some minor nucleotides in DNA?

Answer 8

5-methylcytidine and N6-methyladenosine. modifications are done after synthesis (epigenetic markers)

Question 9

what are some minor nucleotides in RNA?

Answer 9

Inosine and Pseudouridine. inosine is in the wobble position of the anticodon (made from de-aminating adenosine). Pseudouridine stabilizes tRNA structure and helps folding rRNA (made from uridine by isomerization)

Question 10

How are polynucleotides formed?

Answer 10

covalent bonds via phosphodiester linkages of 5’ to 3’. This mades it negatively charged and makes DNA a stable backbone but RNA an unstable backbone

Question 11

how is RNA degraded?

Answer 11

Base catalyzed RNA hydrolysis where the hydroxide ion causes a 2’,3’ cyclic monophosphate derivative to form and releases the shortened RNA

Question 12

How does hydrogen bonding occur between nucleotides?

Answer 12

for monomers any pairing is possible. in polynucleotides only a few possibilities exist. A pairs T and C pairs G.
A and T have two H bonds (Draw them)
C and G have three H bonds (Draw them)

Question 13

what are the three forms of DNA?

Answer 13

B-DNA: standard form. right handed, 20 A diameter. 3.4 A per bp, 36 A per turn
A-DNA: compressed form. right handed. 26 A diameter. 2.6 A per bp. 28 A per turn
Z-DNA: wacky form. left handed. 18 A diameter. 3.7 A per bp. has both anti and syn conformations of glycosyl bond

Question 14

How can one mRNA code for more than one protein?

Answer 14

prokaryotes have polycistronic mRNA that contains multiple genes. All the genes in the strand can be expressed in to proteins. Eukaryotes have monocistronic mRNA with just one gene

Question 15

What creates hairpin structures in RNA?

Answer 15

palindromic repeats that are complimentary and so will pair and form a hairpin loop

Question 16

what does DNA denaturation do to the strand?

Answer 16

covalent bonds remain in tact (so genetic code is intact) but hydrogen bonds are broken so the two strands separate. Base stacking (π-π) is lost so UV absorbance increases (260 nm)
can be induced by heat or high pH
denaturation is reversible (annealing) with low temp

Question 17

what factors affect DNA denaturation melting point (Tm)?

Answer 17

base composition: more CG increases Tm (more H bonds)
DNA length: longer DNA increases Tm (more H bonds)
pH and ionic strength: high salt increases Tm (stabilizes phosphate backbone by reducing charge repulsion between the two strands)

Question 18

2 mechanisms of spontaneous mutagenesis

Answer 18

Deamination: changes cytosine to uracil. about 100 events per day in mammalian cell
Depurination: N-glycosidic bond is hydrolyzed. results in 10,000 purines lost per day in mammalian cell

Question 19

mechanisms of oxidative and chemical mutagenesis

Answer 19

oxidative damage: hydroxylation of guanine (mitochondria most susceptible)
chemical alkylation: methylation of guanine

Question 20

mechanisms of radiation induced mutagenesis

Answer 20

UV light induces dimerization of pyrimidines (Thymine dimers) which kinks the DNA
X-rays and gamma rays cause ring openings and strand breaking