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Nucleic Acid Biochem I > Intro to Nucleic Acids > Flashcards

Intro to Nucleic Acids Flashcards

Readings 175 - 195

1
Q

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

A

Deoxyadenylate 5’-monophosphate

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2
Q

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

A

A, dA, dAMP

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3
Q

What is the full nucleotide name for the nucleoside deoxyguanosine?

A

Deoxyguanylate 5’-monophosphate

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4
Q

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

A

deoxythymidine

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5
Q

Name the purines

A

Adenosine

Guanosine

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6
Q

What is the nucleotide name for the ribonucleoside adenosine?

A

adenylate 5’-monophosphate

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7
Q

Which ribonucleotide contains a base that deoxynucleotides do not?

A

Uridylate 5’-monophosphate

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8
Q

What are the components of a nucleoside?

A

Base and pentose

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9
Q

What are the components of a nucleotide?

A

Nucleoside (base + pentose) and phosphate

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10
Q

Name the pyrimidines

A

Cytosine
Thymine
Uracil

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11
Q

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

A

2’ carbon is H

3’ carbon is OH

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12
Q

What is the structure of adenine?

A

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

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13
Q

Describe the structure of thymine

A

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

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14
Q

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

A

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.

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15
Q

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

A

nucleoside monophosphate (AMP)

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16
Q

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

A

nucleoside diphosphate (ADP)

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17
Q

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

A

Nucleoside triphosphate (ATP)

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18
Q

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

A

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

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19
Q

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

A

primary: 1
secondary: 6

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20
Q

Which is the most acidic nuclear base?

A

thymine

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21
Q

Which is the most basic nuclear base?

A

Adenosine

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22
Q

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

A

That 50% has been deprotonated

23
Q

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

A

That approximately all has been deprotonated

24
Q

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

A

That approximately all has been protonated

25
Q

What is the charge of an protonated acid group?

A

0

26
Q

What is the charge of a deprotonated acid group?

A

-1

27
Q

What is the charge of a protonated basic group?

A

+1

28
Q

What is the charge of a deprotonated basic group?

A

0

29
Q

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

A
  • 2

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

30
Q

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

A

-4

  • 3 for primary phosphates
  • 1 for the secondary phosphate
31
Q

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

A

Just 1, at the end of the chain

32
Q

Adenosine is to _____s as adenylate is to ______

Nucleotide/nucleoside

A

Adenosine - Nucleoside

Adenylate - Nucleotide

33
Q

What are the three symbols indicating phosphates on a chain?

A

alpha
beta
gamma

34
Q

What is a nucleoside with a 3’ oxygen removed?

A

di-deoxynucleoside 5’-monophosphate

35
Q

What are ddNTDs important for?

A

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

36
Q

dCTP, AKA deoxycytidine 5’-triphosphate is what?

A

A radioactively labeled nucleotide.

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

37
Q

What happens if a nucleoside analog is incorporated into DNA?

A

It will terminate activity of DNA polymerase

38
Q

What is the pKa of a secondary phosphoryl group?

A

pKa 6

39
Q

What is the pKa of a primary phosphoryl group?

A

pKa 1

40
Q

How many angstroms are between adenine and thymine base pairs?

A

11.1

41
Q

How many angstroms are between cytosine and guanine?

A

10.8

42
Q

Do you know the numbering of purines and pyrimidines?

A

9 members in purines
6 members in pyrimidines

If you can’t loosely draw them, then give this question a red and PRACTICE

43
Q

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

A

Glycosidic bond

44
Q

Can you recognize nitrogenous bases???

A

If yes, then good for you. If no…

PRACTICE

45
Q

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

A

Cytosine

46
Q

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

A

Adenine

47
Q

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

A

Thymine

48
Q

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

A

Guanine

49
Q

What are the four Deoxyribonucleotide names?

A
  • Deoxyadenosine
  • Deoxyguanosine
  • Deoxythymidine
  • Deoxycytidine
50
Q

What are the four ribonucleotide names?

A
  • Adenosine
  • Guanosine
  • Cytidine
  • Uridine
51
Q

Is the backbone of DNA hydrophilic or hydrophobic?

A

Hydrophilic

52
Q

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

A

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.

53
Q

Pyrimidines and purines are planar or non-planar?

A

Pyrimidines are planar

purines have a slight pucker

54
Q

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?

A

Palindromic sequences

Palindromes

Nucleic Acid Biochem I (5 decks)

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