Intro to Nucleic Acids Flashcards
Readings 175 - 195
What is the full name for the nucleoside’s deoxyadenosine nucleotide?
Deoxyadenylate 5’-monophosphate
What are abbreviations for the nucleotide deoxyadenylate 5’-monophosphate?
A, dA, dAMP
What is the full nucleotide name for the nucleoside deoxyguanosine?
Deoxyguanylate 5’-monophosphate
What is the nucleoside name for the nucleotide deoxythymidylate 5’-monophosphate
deoxythymidine
Name the purines
Adenosine
Guanosine
What is the nucleotide name for the ribonucleoside adenosine?
adenylate 5’-monophosphate
Which ribonucleotide contains a base that deoxynucleotides do not?
Uridylate 5’-monophosphate
What are the components of a nucleoside?
Base and pentose
What are the components of a nucleotide?
Nucleoside (base + pentose) and phosphate
Name the pyrimidines
Cytosine
Thymine
Uracil
Which carbon in DNA is deoxygenated? Which one has a hydroxyl?
2’ carbon is H
3’ carbon is OH
What is the structure of adenine?
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
Describe the structure of thymine
A 6 member ring, with two Nitrogens in the ring and 2 ketones and 1 methyl group
How is it possible for a ribonucleotide to form different conformations? Give examples
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.
What is the name for a nucleoside bonded with 1 phosphate? Give example with adenosine
nucleoside monophosphate (AMP)
What is the name for a nucleoside bonded with 2 phosphates? Give example with adenosine
nucleoside diphosphate (ADP)
What is the name for a nucleoside bonded with 3 phosphates? Give example with adenosine
Nucleoside triphosphate (ATP)
What are nucleoside analogues commonly used for? How do they work?
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
What is the pKa of the primary and secondary phosphoryl groups?
primary: 1
secondary: 6
Which is the most acidic nuclear base?
thymine
Which is the most basic nuclear base?
Adenosine
What pH = pKa, what does this mean for a nucleic acid?
That 50% has been deprotonated
What pH > pKa, what does this mean for a nucleic acid?
That approximately all has been deprotonated
When pH < pKa, what does this mean for a nucleic acid?
That approximately all has been protonated
What is the charge of an protonated acid group?
0
What is the charge of a deprotonated acid group?
-1
What is the charge of a protonated basic group?
+1
What is the charge of a deprotonated basic group?
0
What is the charge of an deoxyadenosine 3’-monophosphate at pH 7?
- 2
- 1 for the primary phosphate and -1 for the secondary phosphate
What is the charge of a deoxytidine 5’-triphosphate at pH 7?
-4
- 3 for primary phosphates
- 1 for the secondary phosphate
How many secondary phosphates does a chain of 3 phosphates have?
Just 1, at the end of the chain
Adenosine is to _____s as adenylate is to ______
Nucleotide/nucleoside
Adenosine - Nucleoside
Adenylate - Nucleotide
What are the three symbols indicating phosphates on a chain?
alpha
beta
gamma
What is a nucleoside with a 3’ oxygen removed?
di-deoxynucleoside 5’-monophosphate
What are ddNTDs important for?
Gene sequencing, they stop DNA replication because DNA Pol has no 3’ OH to attach phosphate to
dCTP, AKA deoxycytidine 5’-triphosphate is what?
A radioactively labeled nucleotide.
[α 32P]dCTP is a way to denote that the alpha phosphate is radioactively labeled
What happens if a nucleoside analog is incorporated into DNA?
It will terminate activity of DNA polymerase
What is the pKa of a secondary phosphoryl group?
pKa 6
What is the pKa of a primary phosphoryl group?
pKa 1
How many angstroms are between adenine and thymine base pairs?
11.1
How many angstroms are between cytosine and guanine?
10.8
Do you know the numbering of purines and pyrimidines?
9 members in purines
6 members in pyrimidines
If you can’t loosely draw them, then give this question a red and PRACTICE
What type of bond is between the base and pentose ring of nucleosides?
Glycosidic bond
Can you recognize nitrogenous bases???
If yes, then good for you. If no…
PRACTICE
Easy way to recognize nucleotides. Which pyrimidine has a sticky uppy amine group?
Cytosine
Easy way to recognize nucleotides. Which purine has a sticky uppy amine group?
Adenine
Easy way to recognize nucleotides. Which pyrimidine has a sticky uppy ketone group?
Thymine
Easy way to recognize nucleotides. Which purine has a sticky uppy ketone group?
Guanine
What are the four Deoxyribonucleotide names?
- Deoxyadenosine
- Deoxyguanosine
- Deoxythymidine
- Deoxycytidine
What are the four ribonucleotide names?
- Adenosine
- Guanosine
- Cytidine
- Uridine
Is the backbone of DNA hydrophilic or hydrophobic?
Hydrophilic
Why is DNA backbone so much more stabler than RNA’s?
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.
Pyrimidines and purines are planar or non-planar?
Pyrimidines are planar
purines have a slight pucker
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?
Palindromic sequences
Palindromes
