18 - Nucleic Acids I Flashcards
What are some biological roles of nucleic acids?
Virus infection, nucleic processes (replication, transcription), and translation
How did Watson and Crick propose the DNA structure?
- Franklin’s X-rays predicted a double helix
- Chargaff’s rules (A=T, C=G)
- Chemical structure of each nucleotide
What were the contributions of Watson and Crick to the DNA model?
Crick developed theory for X-ray diffraction of helices, while Watson built models
What was the “average DNA” model proposed in 1953?
Anti-parallel, right handed, double helix with H bonds base pairs on inside and sugar-phosphate backbone on outside
What were the implications of the Watson and Crick model?
Complementary strands suggested mechanisms of replication, heredity, and recognition (3’ to 5’ polarity)
What was Rosalind Franklin’s contribution to the 1953 model?
X-ray diffraction, showed helix with symmetry (10 bp/repeat, 3.4 A between base pairs) (photo 51)
What is A DNA?
Dehydrated DNA
What is B DNA?
“Standard” DNA
What is Z DNA?
A special DNA with high GC and high ionic salt concentrations
What is the difference between A DNA and B DNA?
A DNA has a greater tilt, and the center of the helix is free, and it is shorter and wider
What is the difference between Z DNA and B DNA?
Z DNA is a left handed helix, and is more stretched out
What is the significance of the Dickerson dodecamer?
It proved the Watson and Crick model in 1981
What is the sequence of the Dickerson dodecamer?
CGCGAATTCGCG
What were the results of the Dickerson dodecamer?
B-DNA, not a straight rod, had sequence dependent characteristics, water bound on outside
How come the Dickerson dodecamer was good for crystallization?
It was self complementary (had same conformation for good crystallization), and has GCs at the end to help prevent fraying (3 H-bonds)
What is a nucleoside?
A nitrogenous base plus a sugar
What are the names of the nitrogenous bases?
Adenine, cytosine, thymine, guanine, and uracil
What is a pyrimidine?
1 ring
Which nitrogenous bases are pyrimidines?
Cytosine, thymine, and uracil
What is a purine?
2 rings
Which nitrogenous bases are purines?
Adenine and guanine
What links the nitrogenous base to the sugar?
A glycosidic bond
What are the nucleosides in DNA?
Deoxyadenosine, deoxyguanosine, deoxycytidine, and thymidine
What are the nucleosides in RNA?
Adenosine, guanosine, cytidine, and uridine
Where is the glycosidic bond in a purine?
1’C to 9N
Where is the glycosidic bond in a pyrimidine?
1’C to 1N
What is a nucleotide?
A nucleoside + phosphate
What bond connects the phosphate to a nucleoside?
A phosphoester bond
What are some examples of nucleotides?
AMP, dADP, ATP, cAMP, NAD+, etc.
What bond connects two nucleotides together?
A phosphodiester bond
How is the length of a DNA polymer named?
As an “n-mer”, where n is the number of nucleotides
What are the properties of the phosphate backbone in DNA?
Phosphate pKa < 1, acid sensitive, base stable
What is an exocyclic amine?
An amine not in the ring
How is the numbering distinguished in a nucleotide?
Regular numbering on the base, prime numbering on the ribose sugar
What can be at the termini of a DNA strand?
A hydroxyl, a phosphate, or something else (solid surface, sugar, etc.)
What is a lot of nucleic acid chemistry based on?
Hydrogen bonds
What are the requirements for an H-bond?
- Hydrogen with partial positive charge
2. Source of electron density (lone pair, usually carbonyl or amine)
What is a sugar pucker?
Point glycosidic bond/base in a different direction
What is the normal sugar pucker in DNA?
51.5 degrees
What sugar pucker occurs in A DNA?
C3’ endo N pucker
What sugar pucker occurs in B DNA?
C2’ endo S pucker
What is an anti glycosidic bond angle?
Oxygens in pyrimidine is anti
What is a syn glycosidic bond angle?
Group is pointed in a different direction
What is the significance of a syn/anti glycosidic bond?
Different orientation relative to ribose structure, so different functionalities for H-bonding and major/minor groove
What happens when G is Br-ated?
It goes from anti to syn
What are most glycosidic bonds in DNA?
Anti (a sin to be syn)
What state are the nitrogenous bases at pH = 7?
Deprotonated
What higher order structures are seen in DNA?
DNA supercoils
What is a supercoil?
A wrapping of a coil
When does DNA supercoil?
When locally unwinding DNA (gene expression), and packaging at nucleosomes
What is the packing of DNA?
DNA –> beads on a string –> chromatin fiber –> condensed scaffold –> chromosome
What is the significance of DNA supercoiling?
It was a significant problem to overcome for crystal structure of nucleosomes (get ordered crystal)
What secondary structures are present in mRNA?
Stem and loop (local helical structure with single strand connections)
What is the stability of RNA?
Phosphate pKa < 1, acid sensitive, base sensitive
What does tRNA do?
It recognized both the code (mRNA) and protein (amino acid)
Where is the active site of a ribozyme found?
In the hammerhead
What are the parts of a tRNA molecule?
Amino acid attachment site, T-phi-C loop, variable arm, anticodon loop, DHU loop, and phosphorylated 5’ terminus
Where do most of the catalytic activity in ribosomes come from?
The nucleic acids
Is DNA acidic or basic and why?
Acidic (hydrophilic) due to the phosphate groups
How does DNA and RNA look like?
DNA is a white fiber, RNA is a white power
How can DNA be precipitated?
By ethanol (insoluble in organic solvent)
How come DNA has UV absorption?
Due to aromatic groups
What absorbances are used for nucleic acids and proteins?
Nucleic acids: A260; Proteins: A280
Is DNA hypochromic or hyperchromic?
Hypochromic (dsDNA breaks into ssDNA when heated)
What is the hyperchromic shift?
When dsDNA –> ssDNA, A260 (extinction coefficient) changes
What is the significance of a hyperchromic shift?
It can quantity stability of DNA helix and disruption
What is Tm?
Melting temperature: temperature at which 1/2 of FNA is separated into single strands
What forces (4) stabilize dsDNA?
- Hydrophobic effect (purines and pyrimidines buried in interior)
- Stacking (VDW, pi stacking of aromatic rings)
- H-bonds (between base pairs)
- Electrostatics (negatively charged phosphates and cations like Mg2+)
