Nucleic Acids, DNA Replication & Repair Flashcards
What is a tautomer?
Structural isomers that can interconvert between different forms quickly
What are nitrogenous bases?
- Aromatic, hydrophobic, Carbon based ring systems
- Purine or pyramidine
A* (Tautomer of Adenine)
H moves from amino group (imino form); binds with C
C* (Tautomer of Cytosine)
H moves from amino group (imino); binds with A
T* (Tautomer of Thymine)
H moves creating alcohol group (enol); binds with G
G* (Tautomer of Guanine)
H moves create alcohol group (enol); binds with T
Common Pyramidine bases
- Cytosine (2-oxy-4-amino pyrimidine)
- Uracil (2-oxy-4-oxy pyrimidine)
- Thymine (2-oxy-4-oxy-5-methyl pyrimidine)
Common Purine Bases
- Adenine (6-amino purine)
- Guanine (2-amino-6-oxy purine)
What is the acid dissociation constant?
o Quantitative measure of the strength of an acid in solution
o Larger pKa = smaller extent of dissociation
What is tautomerism?
Conformational change of Nitrogenous base between its 2 conformational states.
UV Absorption of Nucleotide bases
- Rings of bases made up of alternating single and double bonds.
o Such systems absorb in the UV spectrum - Each of 4 nucleotide bases has a slightly different absorption spectrum
o Spectrum of DNA is the average of them - A pure DNA solution appears transparent to the eye
o Absorption doesn’t become measurable until 320nm
o Peak at about 260nm followed by a dip between 220 and 230
o Then solution becomes opaque in the far UV range. - When DNA helix is denatured to become single stranded – absorbance is increased about 30%.
o Called HYPERCHROMIC EFFECT
o Reflects interaction between electronic dipoles in stacked bases of native helix.
What is a nucleoside?
Comounds formed when a nitrogenous base is linked to a pentose sugar
What is the structure of nucleosides?
- Base linked to sugar via glycosidic bond (N9 in purines; N1 of pyrimidines)
- Carbon of the glycosidic bond is anomeric.
- All beta formations
- Named by adding -idine to root name of pyrimidine (cytidine), and -osine to root name of purine (adenosine).
- Conformation can be syn or anti
o Rotation around the glycosidic bond is sterically hindered; syn goes left over sugar molecule; anti goes right (forms ‘S’)
o Pyrimidines usually anti and not syn as the 2’-O atoms sterically hinders the ring position above the ribose.
Nucleoside triphosphates
- More than 1 P group attached
• Hydrolysis of phosphoanhydride bonds releases energy (Like in ATP)
- Cyclic nucleotides are signal mols and regulators of cellular metabolism and reproduction.
What is a nucleotide?
Nucleoside bonded to phosphate group C5 of pentose sugar
What are 4 common ribonucleotides?
- AMP – adenosine 5’-monophsophate
- GMP – Guanosine 5’-monophosphate
- CMP – Cytidine 5’-monophosphate
- UMP – Uridine 5’-monophosphate
What are the functions of nucleotides?
- Nucleoside 5’-triphosphates are carriers of energy
o ATP is central to energy metabolism
o GTP drives protein synthesis
o CTP drives lipid synthesis
o UTP drives carbohydrate metabolism - Cyclic nucleotides are signal mols and regulators of cellular metabolism and reproduction
- Bases serve as recognition units.
DNA vs RNA
- Backbone is the same, nitrogenous bases change
- DNA is more stable than RNA
o Presence of 2’-OH makes RNA susceptible to alkaline hydrolysis
o Gives RNA a short half-life – allows cell to regulate gene expression (protein synthesis) at a pre-translational level - Presence of Uracil in RNA
Why does DNA have Thymine & not Uracil?
o Cytosine spontaneously deaminates to form uracil at a finite rate in vivo.
o i.e. loses anime group.
o C in DNA strand pairs with G in other strands, whereas U would pair with A.
o Conversion of a C to a U could potentially result in a heritable change of C:G pair to a U:A pair.
o Such a change in nucleotide sequence would constitute a mutation in the DNA
o Repair enzymes recognize these ‘mutations’ and replace these U’s with C’s.
- Thymine is methylated, so anything that doesn’t resemble that is replaced with thymine -5-methyl.
Secondary structure of ribosomal RNA
- High intrastrand sequence complementarity leads to extensive base-pairing
- Secondary structure features seem to be conserved, whereas sequence is not
o There must be common designs and functions that need to be conserved
Secondary and tertiary structure of tRNA
o Extensive H-bonding creates four double helical domains, three capped by loops, one by a stem
o Only one tRNA structure is known
o Phenylalanine tRNA is ‘L-shaped’.
o Many non-canonical base pairs found in tRNA.
What is Chargaff’s rule?
The total number of purines in a DNA molecule must = the total number of pyrimidines
Structure of Nucleic acids
- Very stable because of:
o H-bonds between complementary bases and sugar phosphate backbone and H20
o Electrostatic interactions: neg charged phosphate groups repel one another and interact with Mg2+
o Van der Waals and Hydrophobic interactions: stacking of base pairs - Helix is anti-parallel
- Helix dimensions conserved. Each turn is about 10bp (base pairs)
- Major and minor grooves:
o ‘tops’ of bases (as we draw them) line the ‘floor’ of major groove
o Major groove is large enough to accommodate an alpha helix of a protein
o Regulatory proteins (transcription factors) can recognize the pattern of bases and H bonding possibilities in the major groove.
What are the canonical base pairs?
The base Paris that occur most frequently
i.e. A:T & G:C
(A:T - 2 H Bonds
G:C - 3 H Bonds)
