chapter 8 - Nucleic acids

Question 1

describe the numbering scheme for the carbons of the pentose sugar in a nucleic acid

Answer 1

• 1’ is C attached to nitrogenous base
• goes around to 5’ C attached to phosphate

Question 2

what are the three components of a nucleotide

Answer 2

• nitrogenous base, pentose sugar, phosphate group

Question 3

which carbons on the sugar connect to phosphate groups in the sugar-pentose backbone?

Answer 3

5’ and 3’

Question 4

which carbon on the pentose sugar connects to the nitrogenous base

Answer 4

1’

Question 5

how many carbon bonds do each type of base pair form

Answer 5

• CG forms 3
• AT forms 2

Question 6

how would you recognize the 5’ vs 3’ end of a DNA strand

Answer 6

• 5’ has the phosphate group
• 3’ has the hydroxyl group

Question 7

what causes major and minor grooves in DNA

Answer 7

• offset pairing of strands

Question 8

which type of groove has unambiguous sequence information and which is not completely unambiguous

Answer 8

• major groove has unambiguous sequence
• minor groove is not completely unambiguous

Question 9

what are the three major types of RNA

Answer 9

tRNA
rRNA
mRNA

Question 10

what does mRNA do

Answer 10

• intermediate between gene and protein
• codes for proteins
• not in the genome itself

Question 11

what does tRNA do

Answer 11

• carries amino acids to the ribosome for protein synthesis

Question 12

what does rRNA do

Answer 12

• makes up ribosomes

Question 13

what are the 3 major differences between DNA and RNA

Answer 13

• DNA is double stranded and RNA is single stranded (RNA can fold over to form some base pairing)
• sugar phosphate backbone has ribose instead of 2’deoxyribose
• RNA has uracil instead of thymine

Question 14

what non-standard base pairings can happen between tRNA and mRNA

Answer 14

• G can pair with C or U
• tRNA has inosine nucleosides that can pair with C, U, and A
• some anticodons of tRNA can bind more than 1 codon - more mRNA codons than tRNA
  
  • between 3’ on mRNA and 5’ of tRNA

Question 15

what are factors that allow RNA to take on a variety of shapes

Answer 15

• single stranded gives more rotational freedom
• when G bonds with U instead of C, it has less H-bonds
• weak interactions (base stacking and H-bonds) stabilize these structures

Question 16

why is RNA less stable than DNA

Answer 16

the 2’ OH group makes it susceptible to RNAse catalyzed breakdown

Question 17

what are three ways to denature double-stranded DNA in lab

Answer 17

• heat
• formamide and urea (destabilize H bonds)
• salt (more salt = more stable)

Question 18

what does Tm mean for nucleic acids

Answer 18

• temperature where half the DNA present is singe stranded

Question 19

Why does denaturation of a DNA sequence under high salt conditions require more heat than for the same DNA sequence in low salt conditions?

Answer 19

• negative charge of DNA causes the strands to repel each other
• salts provide cations that help shield the negative charge

Question 20

what are 3 general roles for nucleoside-containing molecules that are not part of a nucleic acid polymer

Answer 20

• they can have 1-3 phosphates attached which can provide energy for cellular reactions why hydrolyzed
• can act as cofactors for enzymes
• can act as signaling and regulatory molecules (ex: cAMP)