MMT: purines and pyrimidines

Question 1

which base is this? name and classification (purine vs pyrimidine)

Answer 1

uracil; pyrimidine

Question 2

which base is this? name and classification (purine vs pyrimidine)

Answer 2

cystosine; pyrimidine

Question 3

which base is this? name and classification (purine vs pyrimidine)

Answer 3

guanine; purine

Question 4

which base is this? name and classification (purine vs pyrimidine)

Answer 4

adenine; purine

Question 5

which base is this? name and classification (purine vs pyrimidine)

Answer 5

thymine; pyrimidine

Question 6

Describe the molecular properties of purines and pyrimidines.

Answer 6

in general, they are both heterocyclic, flat molecules. they’re weak bases and hydrophobic at neutral pH, absorb UV light, and participate in hydrogen bonding and pi stacking between base pairs.

Question 7

differentiate between ribose and deoxyribose

Answer 7

A ribose has a hydroxyl group on carbon 2, where deoxyribose has a hydrogen at carbon 2. They otherwise have the same base structure.

Question 8

name the two main components of a nucleoside

Answer 8

a base and a sugar

Question 9

Differentiate between a nucleoside and nucleotide.

Answer 9

Nucleoside: a base + a sugar connected by the glycosidic bond (purine or pyrimidine + ribose or deoxyribose)

Nucleotide: a nucleoside + phosphate ester via phosphodiester bond connected to the carbon opposite of the glycosidic bond. More phosphate esters can add to each other via phosphoanhydride bonds and form molecules such as ADP (adenosine diphosphate) and ATP

Question 10

Identify the glycosidic bond, phosphoester bond and phosphoanhydride bond(s) of a nucleotide.

Answer 10

Question 11

Differentiate between syn and anti conformations of the glycosidic bond.

Answer 11

Syn: glycosidic bond is rotated with the purine/pyrimidine facing inward

Anti: glycosidic bond is rotated with the purine/pyrimidine facing inward

Question 12

Distinguish between the a-, b- and g-phosphates in a nucleoside triphosphate molecule

Answer 12

alpha is closest to the sugar residue, beta is in the middle, and gamma is farthest from the sugar residue

Question 13

Describe how nucleotides function as building blocks for nucleic acids

Answer 13

The bases get linked in a chain by phosphoester bonds to create nucleic acids.

Question 14

Describe how nucleotides function as chemical energy carriers

Answer 14

Hydrolysis of phosphoanhydryde bonds and phosphoester bonds can provide energy for cellular reactions. ATP is a big ex.

Question 15

Describe how nucleotides function as intermediates in biosynthesis.

Answer 15

• in RNA and DNA the bases get linked in a chain by phosphoester bonds.
• Hydrolysis of phosphoanhydryde bonds and phosphoester bonds can provide energy for cellular reactions. ATP is a big ex.
• Many coenzymes contain adenosine
• Nucleotides can be used as second messengers in signal transduction. Ex is adenylyl cyclase turning ATP to cAMP by removing a PPi and allowing the remaining phosphate ty cyclize and connect to a hydroxyl group on the sugar. cAMP activates protein kinase.

Question 16

Describe how nucleotides function as secondary messengers in cell signaling.

Answer 16

Nucleotides can be used as second messengers in signal transduction. Ex is adenylyl cyclase turning ATP to cAMP by removing a PPi and allowing the remaining phosphate ty cyclize and connect to a hydroxyl group on the sugar. cAMP activates protein kinase.

Question 17

Describe how nucleotides relate to coenzymes

Answer 17

Many coenzymes contain adenosine (adenine + sugar), and serve as a backbone for the coenzyme. The coenzyme binds to a nucleotide binding domain or fold in a target enzyme

Question 18

Describe how the activity of G-proteins is regulated by GTP

Answer 18

G proteins are in an active conformation when linked to GTP. This form promotes interacting with effectors. When GTP is hydrolyzed to GDP-Pi by a GTPase, the conformation changes to an inactive state and the protein will no longer interact with effectors. GEFs stimulate dissociated of GDP-Pi and loading of GTP to activate the protein.

Question 19

what is the configuration of ribose and deoxyribose in the body?

Answer 19

Beta and anti-conformation (purine or pyrimidine facing outward from the sugar)

Question 20

describe the glycosidic bonds seen in purines and pyrimidines

Answer 20

purine: N-glycosidic from N9 of purine and C1 of sugar

pyrimidine: N-glycosidic from N1 of pyrimidine and C1 of sugar

Question 21

what is this structure?

Answer 21

inosine; it is a nucleoside made from hypoxanthine and ribose. it is often found in anticodons of tRNA

Question 22

what is this structure?

Answer 22

hypoxanthine; made from deamination of adenine