Intro to Nucleic Acids

Question 1

What is the full name for the nucleoside’s deoxyadenosine nucleotide?

Answer 1

Deoxyadenylate 5’-monophosphate

Question 2

What are abbreviations for the nucleotide deoxyadenylate 5’-monophosphate?

Answer 2

A, dA, dAMP

Question 3

What is the full nucleotide name for the nucleoside deoxyguanosine?

Answer 3

Deoxyguanylate 5’-monophosphate

Question 4

What is the nucleoside name for the nucleotide deoxythymidylate 5’-monophosphate

Answer 4

deoxythymidine

Question 5

Name the purines

Answer 5

Adenosine

Guanosine

Question 6

What is the nucleotide name for the ribonucleoside adenosine?

Answer 6

adenylate 5’-monophosphate

Question 7

Which ribonucleotide contains a base that deoxynucleotides do not?

Answer 7

Uridylate 5’-monophosphate

Question 8

What are the components of a nucleoside?

Answer 8

Base and pentose

Question 9

What are the components of a nucleotide?

Answer 9

Nucleoside (base + pentose) and phosphate

Question 10

Name the pyrimidines

Answer 10

Cytosine
Thymine
Uracil

Question 11

Which carbon in DNA is deoxygenated? Which one has a hydroxyl?

Answer 11

2’ carbon is H

3’ carbon is OH

Question 12

What is the structure of adenine?

Answer 12

Two rings, 2 nitrogens in each ring and one NH2 projecting off the 6’ carbon

The 1’ carbon is next to the 6’ carbon with NH2

Question 13

Describe the structure of thymine

Answer 13

A 6 member ring, with two Nitrogens in the ring and 2 ketones and 1 methyl group

Question 14

How is it possible for a ribonucleotide to form different conformations? Give examples

Answer 14

The phosphate can bond with the 2’ and 3’ hydroxyls to make a cyclic bond. Also, it doesn’t have to bond to the 5’ methyl group on the pentose, it can bind to the 2’ or 3’ hydroxyls as well, or the 5’ methyl and 3’ hydroxyl.

Question 15

What is the name for a nucleoside bonded with 1 phosphate? Give example with adenosine

Answer 15

nucleoside monophosphate (AMP)

Question 16

What is the name for a nucleoside bonded with 2 phosphates? Give example with adenosine

Answer 16

nucleoside diphosphate (ADP)

Question 17

What is the name for a nucleoside bonded with 3 phosphates? Give example with adenosine

Answer 17

Nucleoside triphosphate (ATP)

Question 18

What are nucleoside analogues commonly used for? How do they work?

Answer 18

Antiviral drugs and chemotherapy agents to treat cancer. They are similar enough to nucleosides to be incorporated into growing DNA strands, they act as chain terminators to stop viral DNA polymerase or reverse transcriptase

Question 19

What is the pKa of the primary and secondary phosphoryl groups?

Answer 19

primary: 1
secondary: 6

Question 20

Which is the most acidic nuclear base?

Answer 20

thymine

Question 21

Which is the most basic nuclear base?

Answer 21

Adenosine

Question 22

What pH = pKa, what does this mean for a nucleic acid?

Answer 22

That 50% has been deprotonated

Question 23

What pH > pKa, what does this mean for a nucleic acid?

Answer 23

That approximately all has been deprotonated

Question 24

When pH < pKa, what does this mean for a nucleic acid?

Answer 24

That approximately all has been protonated

Question 25

What is the charge of an protonated acid group?

Answer 25

0

Question 26

What is the charge of a deprotonated acid group?

Answer 26

-1

Question 27

What is the charge of a protonated basic group?

Answer 27

+1

Question 28

What is the charge of a deprotonated basic group?

Answer 28

0

Question 29

What is the charge of an deoxyadenosine 3'-monophosphate at pH 7?

Answer 29

- 2 | - 1 for the primary phosphate and -1 for the secondary phosphate

Question 30

What is the charge of a deoxytidine 5'-triphosphate at pH 7?

Answer 30

-4 - 3 for primary phosphates - 1 for the secondary phosphate

Question 31

How many secondary phosphates does a chain of 3 phosphates have?

Answer 31

Just 1, at the end of the chain

Question 32

Adenosine is to _____s as adenylate is to ______ Nucleotide/nucleoside

Answer 32

Adenosine - Nucleoside | Adenylate - Nucleotide

Question 33

What are the three symbols indicating phosphates on a chain?

Answer 33

alpha beta gamma

Question 34

What is a nucleoside with a 3' oxygen removed?

Answer 34

di-deoxynucleoside 5'-monophosphate

Question 35

What are ddNTDs important for?

Answer 35

Gene sequencing, they stop DNA replication because DNA Pol has no 3' OH to attach phosphate to

Question 36

dCTP, AKA deoxycytidine 5'-triphosphate is what?

Answer 36

A radioactively labeled nucleotide. [α 32P]dCTP is a way to denote that the alpha phosphate is radioactively labeled

Question 37

What happens if a nucleoside analog is incorporated into DNA?

Answer 37

It will terminate activity of DNA polymerase

Question 38

What is the pKa of a secondary phosphoryl group?

Answer 38

pKa 6

Question 39

What is the pKa of a primary phosphoryl group?

Answer 39

pKa 1

Question 40

How many angstroms are between adenine and thymine base pairs?

Answer 40

11.1

Question 41

How many angstroms are between cytosine and guanine?

Answer 41

10.8

Question 42

Do you know the numbering of purines and pyrimidines?

Answer 42

9 members in purines 6 members in pyrimidines If you can't loosely draw them, then give this question a red and PRACTICE

Question 43

What type of bond is between the base and pentose ring of nucleosides?

Answer 43

Glycosidic bond

Question 44

Can you recognize nitrogenous bases???

Answer 44

If yes, then good for you. If no... PRACTICE

Question 45

Easy way to recognize nucleotides. Which pyrimidine has a sticky uppy amine group?

Answer 45

Cytosine

Question 46

Easy way to recognize nucleotides. Which purine has a sticky uppy amine group?

Answer 46

Adenine

Question 47

Easy way to recognize nucleotides. Which pyrimidine has a sticky uppy ketone group?

Answer 47

Thymine

Question 48

Easy way to recognize nucleotides. Which purine has a sticky uppy ketone group?

Answer 48

Guanine

Question 49

What are the four Deoxyribonucleotide names?

Answer 49

- Deoxyadenosine - Deoxyguanosine - Deoxythymidine - Deoxycytidine

Question 50

What are the four ribonucleotide names?

Answer 50

- Adenosine - Guanosine - Cytidine - Uridine

Question 51

Is the backbone of DNA hydrophilic or hydrophobic?

Answer 51

Hydrophilic

Question 52

Why is DNA backbone so much more stabler than RNA's?

Answer 52

Because it doesn't have a hydroxyl on its 2' pentose carbon. This hydroxyl in RNA is directly involved in the hydrolysis of RNA in alkali solutions.

Question 53

Pyrimidines and purines are planar or non-planar?

Answer 53

Pyrimidines are planar purines have a slight pucker

Question 54

What are sequences of DNA where two complementary strands can be read in the 5' to 3' direction or 3' to 5' direction with the same sequences?

Answer 54

Palindromic sequences Palindromes