Lecture 3 - Nucleic Acid Structure and Function Flashcards
What are the parts of a nucleic acid?
L3 S3,5,&14
- phosphate
- sugar
- nitrogenous base
Differentiate between a nucleotide and nucleoside.
L3 S4
Nucleotide:
- has a phosphate group
- lower pH due to deprotonated oxygens on phosphate (pH ~0-2)
Nucleoside:
-lacks a phosphate group
What are the important features about each carbon in the sugar of DNA?
L3 S12
1’: carbonyl involved in glycosidic bond
2’: either -OH or -H determining RNA or DNA respectively
3’: hydroxyl involved in phosphodiester bond
4’: hydroxyl involved in pentose ring
5’: hydroxyl involved in attachment of phosphate group
What is different between purines and pyrimidines? Which nitrogenous bases fall in each category?
L3 S16
Purine:
- two membered ring
- adenine
- guanine
Pyrimidine:
- single membered ring
- cytosine
- thymine
- uracil
What is the rule of base-pairing? How many hydrogen bonds are involved in each possible pairing?
L3 S19
Purines always base pair with pyrimidines and vice-versa.
Adenine and thymine (uracil) only base-pair with each other and form 2 hydrogen bonds.
Guanine and cytosine only base-pair with each other and form 3 hydrogen bonds
The direction of DNA synthesis is __________ in situ.
The direction of oligonucleotide synthesis in vitro is __________.
5’->3’
3’->5’
What different helix structures exist?
Which of these structures are physiologically relevant form and the form that the major and minor groove named based off of?
A form, B form, C form, and Z form
B form is the physiologically relevant and where the major groove is wide and deep while the minor groove is narrow and shallow.
The other three forms are only found artificially.
What are the three models that were proposed for DNA replication?
Which model actually occurs?
Whose experiment determined this?
L3 S25
Conservative:
-one molecule contains all new DNA, the other contains all parent DNA
Semi-conservative (actual method):
-both molecules contain one new strand and one new strand
Dispersive:
-all strand contain a mix of new and parent DNA
The Meselson/Stahl experiment determined the true mechanism based off use of different molecular weight nitrogen
What non-traditional DNA structures exist and under what conditions are they found?
L3 S33
Hairpins/cruciforms:
- require palindromic (inverted repeats)
- created by superhelical strain
Triplexes
- requires homopurine and homopyrimidine duplex
- uses Hoogsteenn hydrogen bonds
Quadruplexes:
- requires guanine only strands
- occurs at telomeres and some promoters
How is the temperature for which DNA is denatured determined?
L3 S35
It’s the temperature at which half the sample of DNA is denatured.
What sorts of sequences denature due to temperature most easily and why?
L3 S36
A-T rich sequences denature first due to having less hydrogen bonds to break than G-C rich sequences.
