Genetics (Midterm)

• DNA or deoxyribonucleic acid is a macromolecule composed of a chain of nucleotides.
• Each nucleotide is composed of a pentose sugar called deoxyribose, which has a phosphate group attached to its 4th carbon, and a nitrogenous base attached to its 1st carbon
• Nucleotide is composed:

  • pentose sugar (deoxyribose)
  • phosphate group at 4th carbon
  • nitrogenous base at 1st carbon
• Adjacent nucleotides are joined by phosphodiester bond, which forms through condensation accompanied by the release of water.
• Phosphodiester bond formation occurs by the removal of a water molecule when 2 hydroxyl groups from 2 different sugars bond with a phosphate group, thus it is known as a condensation reaction.
• Adjacent nucleotides are linked together by phosphodiester bond which what happens during the polymerization process in the assembly of nucleotides into nucleic acids, DNA is formed
• In the assembly of nucleotides, polymerization is the process by which nucleotides are linked together to form a nucleic acid polymer, such as DNA or RNA. This process involves the formation of phosphodiester bonds between the sugar-phosphate backbone of adjacent nucleotides
• Nitrogenous bases includes:

  1. Purines - Adenine & Guanine
  2. Pyrimidines - Thymine, Uracil, Cytosine
• Sugars associated with DNA and RNA are:

  • D-Deoxyribose (in DNA)
  • D-Ribose (in RNA)
• Components of nucleotide

  • Nitrogenous bases
  • Sugars
  • Phosphate Group
• Deoxyribose has H (hydrogen atom) attached in 2nd carbon while ribose has OH (hydroxyl group) attached in 2nd carbon
• The formation of phosphodiester bond between adjacent nucleotides causes condensation reaction
• Two DNA strands are antiparallel:

  • Upper end left strand - 5
  • Upper end right strand - 3
  • Lower end left strand - 3
  • Lower end right strand 5
• sugar and phosphate form the backbone of the DNA molecule.
• Purines have double ring structures while pyrimidines have single ring structures.
• Complementary base-pairing involves hydrogen bond formation between a purine and a pyrimidine. The pairing is specific between adenine (A) and thymine (T) and between guanine (G) and cytosine (C).
• Base-pairing involving hydrogen formation between purine and pyrimidine:

  • Adenine & Thymine
  • Guanine & Cytosine
• If base-pairing only involves 2 purines, both being of double ring structures, it could be so crowded in the middle of the helix
• If base-pairing involves 2 pyrimidines, it will leave too much space between them.
• Base-pairing pattern:

  • Purine & Pyrimidine - equal
  • Two purines - too crowded
  • Two pyrimidines - too much space
• Base pairing involves large purine and small pyrimidine that satisfies the spatial requirements of the base pairs
• H bonds are weak bonds but if it has many numbers of them can give the DNA molecule a stable structure
• Chargaff's rule - DNA should have a 1:1 ratio of pyrimidine and purine in base-pairing
• Chargaff rule - the same number of adenine and thymine and same number of guanine and cytosine
• Erwin Chargaff - contributed the Chargaff's rule which was a big help to Watson and Crick when they were developing their base pair model for the double helix structure of DNA
• Prokaryotic cells usually have a single chromosome and one or a few plasmids, which are extrachromosomal DNA molecules with their own replicons that carry non-essential genes such as those that increase adaptation of their host cells to specific environments or those that aid growth in specific conditions or encode antibiotic resistance.
• Prokaryotic chromosomes are almost always circular. They are either completely devoid of centromeres or carry the so-called “plasmid centromeres” which are not essential
• In terms of condensation and packing, prokaryotic DNA appears naked in that the isolated nucleoids look like a collection of wire loops, loosely held together by a proteinaceous core
• Prokaryotic nucleoids are always known to segregate continuously, as they replicate, and without additional condensation.
• Supercoiling, which is one way that prokaryotes compress their DNA into smaller spaces, is made possible with the help of unique topoisomerases
• Supercoils are either:

  • negative or right-handed
  • positive or left-handed supercoils
• Mesophilic prokaryotes use DNA gyrase to create negative supercoils while thermophilic prokaryotes use reverse gyrase to create positive supercoils
• Mesophilic prokaryotes use DNA gyrase to create negative supercoils
• thermophilic prokaryotes use reverse gyrase to create positive supercoils
• Genomes can be negatively supercoiled, meaning that the DNA is twisted in the opposite direction of the double helix, or positively supercoiled, meaning that the DNA is twisted in the same direction as the double helix.
• Genomes can be:

  • negatively supercoiled - DNA is twisted in opposite direction of double helix
  • positively supercoiled - DNA is twisted in same directio of double helix
• Bacterial genomes are negatively supercoiled during normal growth
• Once the genome has been condensed:

  • DNA topoisomerase I
  • DNA gyrase
  • other proteins

  helps maintain the supercoils
• Prokaryotic genomes are:

  • small but terrible
  • packed with genes with noncoding sequence
  • dominated by horizontal gene transfer
  • can move into any environment compatible with general metabolism
  • have few active mobile elements, which are always tightly controlled
  • always reduces adaptation and is often lethal
• Prokaryotic genomes strongly prefer to delete rather than insert DNA