Nucleic Acids

Question 1

What is the difference beween a nucleoside and a nucleotide

Answer 1

A nucleoside is a nitrogenous base + a pentose sugar, with no phosphate group. A nucleotide has a phosphate group

Question 2

Purines have a ____-ring struncture, and pyrimidines have a ____- ring structrue

Answer 2

Purines have a two-ring struncture, and pyrimidines have a one- ring structrue

Question 3

Name the mmnenonic for purines and pyrimidines

Answer 3

pure as gold (purines = adenine and guanine)
CUT the PIE (cytosine, uracil, thymine for CUT and PIE reminds you of the first two letters in pyrimidines)

Question 4

Uracil is the demethylated version of what nitrogenous base?

Answer 4

Thymine

Question 5

adenine and guanine differ by adenine’s ____ group and guanine’s ____ group

Answer 5

adenine and guanine differ by adenine’s amine group and guanine’s carbonyl group

Question 6

cytosine is the only pyrmidine with one ____ group

Answer 6

primary amine

Question 7

the phosphodiester bond is the linkage between the 3’ carbon atom of one sugar molecule and the 5’ carbon atom of another, deoxyribose in DNA and ribose in RNA

Answer 7

phosphodiester bond

Strong covalent bonds form between the phosphate group and two 5-carbon ring carbohydrates (pentoses) over two ester bonds

Question 8

We read DNA strands from the 5’ end to the 3’ end. The 5’ end is by the ____ group, and the 3’ end is by the ____ group

Answer 8

The 5’ end is by the phosphate group, and the 3’ end is by the OH group

Question 9

Name this molecule

Answer 9

ATP!

Note, the nitrogenous base has one adenine

Question 10

Name this molcule

Answer 10

GTP!

Note, the nitrogenous base is a guanine

Question 11

Name this molecule

Answer 11

Cyclic adenosine monophosphate cAMP

crucial intracellular signaling molecule

in nucleotide monophosphates, a single phosphate group can attach to both 3’ and 5’ carbons, such as in cAMP

Question 12

True or false

In shorthand form, nitrogenous bases are always written in the 5’ to 3’ direction, but nitrogenous bases are connected by 3’ to 5’ phosphodiester bonds

Answer 12

True

Question 13

FAD, FMN, NAD, NADP+ and CoA are all ____

Answer 13

nucleotides that are cofactors

Question 14

How many hydrogen bonds form between A and T?

Answer 14

2

Question 15

How many hydrogen bonds are between C and G?

Answer 15

3

stands with more C-G pairs require higher temperatures for the strands to denature because there are more bonds

Question 16

True or False

Purines pair with each other, and so do pyrimidines

Answer 16

False

purines pair with pyrimidines and vice versa

Question 17

Name this term

In DNA there is always equality in quantity between the bases A and T and between the bases G and C

Answer 17

Chargaff’s rule

%A=%T. %C = %G

Question 18

There are three types of DNA, A, B, and Z. The most commonly known one in which Watson and Crick applied their principles is B-DNA. Compare and contrast these 3 types of DNA

Answer 18

• B-DNA is the typical right-handed double stranded helix, 10.5 bp per turn
• A-DNA is deyhydrated & tighter than B-DNA, 11 bp per turn
• Z-DNA is found in methylated DNA, is left-handed and looser, and has 12 bp per turn

Question 19

the over- or under-winding of a DNA strand, and is an expression of the strain on that strand

Answer 19

supercoiling

Question 20

a DNA segment that is overwound is ____ supercoiled, and one that is underwound is ____ supercoiled

Answer 20

a DNA segment that is overwound is positively supercoiled, and one that is underwound is negatively supercoiled

Question 21

a typical DNA strand is ____ supercoiled, making unwinding of the double helix for transcription more energetically favorable

Answer 21

negatively

negatively supercoiled = underwound

Question 22

the process in which complementary base pairs combine

Answer 22

Hybridization

the driving force of this is formation of hydrogen bonds between pairs

Question 23

the melting of annealed (joined) strands via heat application; can cause the reversible dissociation of the base-paired complex

in DNA, not in proteins

Answer 23

thermal denaturation

the heat causes the double stranded helix to unwind as the hydrophobic interactions between bases become insufficient to maintain a base-paired complex

Question 24

the temperature at which half of the DNA strands in a sample are in their single stranded (ssDNA) state

Answer 24

melting temperature (T_m)

depends on nucelotide length and sequence

C-G requires more heat to denature than A-T

Question 25

what is the significance of denaturation and hybridization in PCR?

Answer 25

Denaturation is used to seperate strands and subsequent hybridization is used right before the amplification process to anneal the strands