nucleic acids & DNA

what is DNA packing?

• human genome (n) is 23 chromosomes comprised of 3 × 10^9 base pairs

• diploid cells (2n) have 6 × 10^9 base pairs of DNA spread over 23 chromosomes

• if B-DNA has a length of 0.34nm/base pair, then a human cell would need to be ~2m long to fit all the DNA

• average eukaryotic nucleus diameter is 6 micrometers

how is DNA packed?

• chromatin

  • packing ratio - the length of the DNA is divided by the length into which it is packaged

• chromatin creates scaffolds during metaphase

what are the nucleic acids?

• RNA & DNA

• both are composed of nucleotides = cyclic nitrogenous bases, pentose sugars, phosphate groups

what are the bases of nucleic acids?

pyrimidines = uracil, thymine, cytosine

purines = adenine, guanine

• GUArdian Angels are PURe and TWO wINGED (Guanine and Adenine are Purines and Two Ringed)

what are polymers and monomers?

polymer = a molecular structure formed from a large number of similar units (monomers) linked together. (nucleic acid)

• polymerisation = the chemical process by which two or more monomers are linked together to form a polymer

monomer = nucleotide, specifically G, A, T, U & C

what are pentose sugars?

• ribose, deoxyribose

• positions on the ribose ring are described with a prime (‘) to distinguish them from positions on the base ring

what are nucleosides?

• adenosine, guanosine, cytidine, uridine

• deoxyadenosine, deocyguanosine, deoxycytidine, deoxythymidine (thymidine)

what are polynucleotides?

• successive deoxyribose residues of a polynucleotide chain are joined by a phosphate group between the 3’ position of one sugar and the 5’ position of the next sugar.

• one end of the chain (usually the left) has a free 5’ end and the other end has a free 3’ end.

• 3’-5’ phosphodiester linkage

how is DNA structured?

• double stranded antiparallel helix

• hydrogen bonds (hydrogen bond donor & acceptors)

• -ve charged molecule, conferred by phosphate groups, facilitate interactions w water

• hydrogen bonds between nucleotides hold bases together

• base stacking & non covalent interactions like van der waals forces & electrostatic attractions contribute to the stability of the helix

what is chargaff’s rule?

• A=T

• C=G

  • Purines = Pyrimidines

what are the features of DNA?

• can be denatured by heat or chemicals

• reannealing to

• reaanealing to DNA or RNA

• susceptible to enzymes

• carries an overall negative charge

describe the process of reannealing

• the two strands that make double stranded DNA come apart when heated

• when cooked, the two strands will pair back and denature the duplex → reannealing

• the ability of single strands of DNA or RNA to pair with its exact complementary strand is the most important property of nucleic acids.

• complementary pairing is crucial for the physiological role of DNA and lies at the heart of several important molecular bio techniques

what enzymes is DNA susceptible to?

• nucleases

• DNases & RNases

• endo- and exonucleases

• specific dsDNA or ssDNA

• restriction endonucleases - cleave both strands of dsDNA at specific sequences

  • restriction endonucleases (type II) - recognition sites are palindromic

what is the function of sticky ends?

• compatible sticky ends - join different DNA strands using two compatible enzymes

what is gel electrophoresis?

exploitation of DNA charge

• fractionation of nucleic acids by gel electrophoresis