Lecture 2: Structure Of Nucleic Acids Flashcards
Structural feature of DNA facilitates what?
Replication and Transcription
Key structural difference of RNA to DNA and its function
• Smaller and less stable than DNA
• Acts as a template for protein synthesis
What are nucleic acids?
Unbranched polymers (polynucleotides) made up of nucleotide monomers
Three characteristic (structural) components of nucleotides
• A nitrogenous base
• One or more phosphates
• A pentose sugar
Phosphate Group is responsible for the acidic property of nucleic acids:
True or False
O
||
O- — P — O
|
O-
True
[ Because of Phosphoric Acid ]
O
||
HO — P — OH
|
OH
What is the difference between DNA’s pentose (5 Carbons, read from the right) sugar and RNA’s?
What does that say about RNA?
2-Deoxyribose (No oxygen) (DNA) has an H, while Ribose (RNA) has an OH group.
RNA is more reactive and unstable because of the OH group.
What are Purines and Pyrimidines? What are their differences?
Purines (Adenine & Guanine) have a double ring,
Pyrimidines (Thymine, Uracil, & Cytosine) have a single ring
Difference between Nucleoside and Nucleotide
Nucleoside: Base + Sugar (joined by an N-glycosidic bond)
Nucleotide: Nucleoside + Phosphate (joined by a phosphoester bond)
Structural features of the DNA structure
• Two strands running anti-parallel
• Sugar-phosphate backbone linked between the 3’ of one nucleotide to the 5’ carbon of the next via a phosphodiester bond
• Each strand has a 5’ end (phosphate) and a 3’ end (hydroxyl)
• 5’ end of one strand is paired with the 3’ end of the other strand
• Strands held together by H bonds between bases
• Bases are planar with respect to the sugar phosphate backbone (Bases are flat)
Features of B-DNA’s structure (most common form in solution)
• Right-handed double helix (width 2nm)
• Hydrophobic core
• Hydrophilic backbone
• Major & Minor Grooves
• Helical structure brings bases-pairs closer together (spacing of 0.34 nm)
Factors contributing to the stability and structure of the DNA double helix
• Backbones need to be separated as far as possible to avoid electrostatic repulsion and allow exposure to solvent
• Bases form mutually stabilising hydrogen bonds
• Bases stack to maximise interactions between aromatic rings
• Bases attracted to each other
How many H-bond acceptors & donors are between Thymine (or Uracil) and Adenine?
1 donor (O)
1 acceptor (N-H) -> T or U
1 donor (H-N)
1 acceptor (N) -> A
Thymine (or U) and Adenine share 2 bonds
How many H-bond acceptors and donors do Cytosine and Guanine have?
1 donor
2 acceptors -> Cytosine
2 donors
1 acceptors -> Guanine
Cytosine and Guanine share 3 bonds, so they are stronger than T (or U) and A paired together
What do non-standard pairings do to DNA? (G&T, G&A, C&T)
They distort the geometry of the double helix. The distance between bases remains to be no longer 1.1 nm.
Characteristics and functional features of the base stacking interactions
• Hydrophobic interactions drive the bases to the inside of the helix
• Aromatic rings of the bases are attracted to each other
How do proteins bind to DNA?
Via the major and minor grooves
What links bases and sugars together?
Glycosidic bonds
Characteristics of glycosidic bonds between bases and sugars
• Approximately in the same place in all base-pairs
• Angled with respect to one another
How do sequence-specific DNA binding proteins “read” the DNA code without unwinding the helix
They access chemical information in the grooves (chemical information rich – especially the M.G.)
Major Groove: Wider and more accessible
Minor Groove: Narrower but still accessible
Define and describe the structure of the RNA
• Unbranched polymer of ribonucleotides (primary structure)
• Predominantly single-stranded but can form complex secondary and tertiary structure
• Moves in 5’ to 3’ direction
Difference between DNA and RNA
DNA has Thymine while RNA has Uracil
Why does DNA have thymine and not uracil?
More stable than Uracil, less chance of mutations forming
(-NH3 -> +H2O)
Uracil in DNA can be recognised & removed by DNA repair processes because it isn’t normally present in DNA
Why does RNA have Uracil and not Thymine?
Thymine is methylated-Uracil (has CH3).
• It’s more energetically costly to produce.
• There is no biosynthetic pathway in cells to produce the thymidine ribonucleotide.
Explain why RNA is intrinsically less stable than DNA
2’ Hydroxyl acts as an internal nucleophile in an internal displacement reaction.
That breaks the phosphodiester backbone.
2’-3’ -cyclic monophosphate is produced.
Definition of glycosidic bond and where it occurs
The bond that is created after a condensation reaction between a deoxyribose sugar and a base (O is shared).
