Lecture 5 - Nucleotides and Nucleic Acids

Question 1

What are the functions of nucleotides? (7)

Answer 1

1. energy metabolism (ATP)
2. enzyme cofactors (NAD+)
3. signal transduction (AMP)
4. storage of genetic information (DNA)
5. Transmission of genetic information (mRNA)
6. catalysis (ribozymes)
7. protein synthesis (tRNA and rRNA)

Question 2

What is a nucleotide?

Answer 2

a nitrogenous base with a pentose and phosphate moiety attached to it

Question 3

What is a nucleoside?

Answer 3

a nitrogenous base with a pentose attached (no phosphate)

Question 4

What is a base?

Answer 4

a nitrogenous base attached

Question 5

What does a prime(‘) indicate?

Answer 5

it indicates that they are associated with the sugar referring to the carbons on that sugar molecule

Question 6

When is a molecule ribose?

Answer 6

when there is a hydroxyl group associated on the two prime (OH)

Question 7

When is a molecule deoxyribose?

Answer 7

when the 2’ prime OH group is not there, instead there is a hydrogen atom

Question 8

A 5’ hydroxyl occurs on a?

Answer 8

nucleoside

Question 9

A 5’ phosphate occurs on a ?

Answer 9

nucleotide

Question 10

What is the charge of a phosphate group at neutral pH?

Answer 10

negative

Question 11

Nucleic acids are built using what?

Answer 11

5’-triphosphates

Question 12

how many phosphate moieties does nucleic acids contain per nucleotide?

Answer 12

one

Question 13

If the OH goes to the right, what is its configuration?

Answer 13

D

Question 14

What are the two forms that pentose exist in solution?

Answer 14

1. linear

2. cyclic

Question 15

What are the characteristics of Nucleobases? (4)

Answer 15

1. derive from pyrimidine or purine
2. nitrogen containing heteroaromatic molecules
3. planar or almost planar structures
4. absorb UV light around 250- 270 nm

Question 16

In pyrimidine bases, cytosine is found only in?

Answer 16

both RNA and DNA

Question 17

In pyrimidine bases, thymine is found only in?

Answer 17

DNA

Question 18

In pyrimidine bases, uracil is found only in?

Answer 18

RNA

Question 19

In purine bases, adenine and guanine are found in?

Answer 19

both rna and dna

Question 20

What other name is the first carbon prime referred to as?

Answer 20

anomeric

Question 21

In nucleosides and nucleotides, the pentose ring is attached to the base via an?

Answer 21

N-glycosidic bond

Question 22

The bond in a B-N-Glycosidic molecule is fomed to: (2)

Answer 22

1. to position N1 in pyrimidines

2. to position N9 in purines

Question 23

anti conformation is found in?

Answer 23

normal B-DNA

Question 24

5-methyldeoxycytidylate is common in ___ and found in ___

Answer 24

eukaryotes; bacteria

Question 25

How does a epigenetic marker work in prokaryotes?

Answer 25

it is a way to mark your own DNA so that cells can degrade foreign DNA

Question 26

What is epigenetic marker: negative regulation in eukaryotes?

Answer 26

ways to mark which genes should be active

Question 27

Pseudouridine is found widely in?

Answer 27

tRNA and rRNA

Question 28

In polynucleotides, covalent bonds are formed via?

Answer 28

phosphodiester linkages with a negatively charged backbone

Question 29

DNA backbone is ___ while rna backbone is ____

Answer 29

stable; unstable (mrna will degrade in a few hours)

Question 30

Why is RNA less stable than DNA?

Answer 30

the presence of the 2' hydroxyl group is the difference between the two

Question 31

What is RNase?

Answer 31

an enzyme that will catalyze the hydrolysis, do if it's hydrolyzing then RNase can activate the water molecule and nail the nucleophile

Question 32

characteristics of the Watson Crick Model of B-DNA

Answer 32

1. double stranded dna structure 2. right handed helix 3. 10.5 base pairs per turn 4. minor groove = 3.4 A 5. major groove = 36 A

Question 33

How does your protein read the nucleotide sequence of your DNA?

Answer 33

by slipping into the major groove; the protein will hydrogen bond to the sequence that it is suppose to read; the kd will dictate how well it binds, the greater the affinity the more it's going to bind

Question 34

Complementarity of DNA strands: (3)

Answer 34

1. two chains differ in sequence 2. two chains are complementary 3. two chains run anti-parallel

Question 35

what is polycistronic?

Answer 35

coding for one or more protein

Question 36

what is messenger RNA?

Answer 36

it is a code carrier for the sequence of proteins

Question 37

mRNA is synthesized during?

Answer 37

DNA template

Question 38

mRNA contains: (3)

Answer 38

1. ribose instead of deoxyribose 2. uracil instead of thymine 3. single strand

Question 39

what is tRNA?

Answer 39

matching amino acids with the mRNA code