week 4

• Genetics


  The study of inheritance
• Genome


  The sum of ALL genetic material in a cell or virus - the entire sequence of DNA
• Prokaryotic and eukaryotic cells use DNA as their genetic material
• Viruses use either DNA or RNA as their genetic material
• DNA structure


  A polymer of deoxyribonucleotides: a phosphate group, a sugar (deoxyribose) and a nitrogen-containing base
• Purines


  Adenine (A), guanine (G)
• Pyrimidines


  Cytosine (C), thymine (T)
• DNA consists of 2 nucleotide chains held together by hydrogen bonds
• The 2 chains are antiparallel
• The chains form a double helix
• Eukaryotic genomes


  • Larger
  • More regulatory sequences
  • Much noncoding DNA
  • Multiple chromosomes
  • Translation and transcription physically separated allowing many points of regulation before translation begins
• Eukaryotic DNA


  Organised into linear chromosomes of DNA associated with proteins, located in the nucleus, wound around histones into nucleosomes that further compact to form chromatin fibres
• Prokaryotic genome


  Consists of a single circular chromosome of DNA, localised in the cytoplasmic nucleoid, may have extrachromosomal DNA - plasmids
• Bacterial chromosome is ~400 times longer than a bacterial cell, so it must be compacted and stabilized by proteins into loop domains
• Plasmids


  Small, double stranded, circular DNA molecules, fraction of the size of the bacterial chromosome, replicate independently of the chromosome, encode genes for self replication, conjugation, and accessory genes
• Binary fission


  Rapid bacterial reproduction, daughter cells identical to mother cell except for mutations, plasmids may not be evenly distributed
• DNA replication


  Double helix unwound, new DNA synthesis occurs in 5'-3' direction, new nucleotides added to 3' end, sequence determined by complementary base pairing
• Replication fork


  Where DNA replication occurs, with leading and lagging strands
• Okazaki fragments


  Discontinuous DNA fragments produced on the lagging strand during replication
• Proteins involved in DNA replication

  • DNA polymerase III, primase, helicase, topoisomerase, DNA gyrase, DNA binding proteins, DNA ligase
• Rolling circle replication


  Plasmid replication independent of chromosomal replication
• Plasmids


  • Naturally occurring plasmid of E. coli pS88
• Plasmids are single stranded circular molecules of DNA
• Genotype


  Genetic composition - the DNA sequence
• Phenotype


  Observable trait - physical appearance, biochemical, behavioural
• Not all genes are expressed all of the time
• Central dogma of molecular biology

  DNA(DNA replication) <--> RNA (transcription) -> Protein (translation)
• Gene

  DNA sequence that codes for a protein, polypeptide, tRNA or rRNA, containing a promoter, coding region, and terminator, may also include a leader and trailer
• Transcription


  DNA to RNA, has 3 stages: initiation, elongation, termination
• Initiation of transcription


  Requires a promoter sequence recognized by RNA polymerase, binding to the promoter which determines template strand, start site, and direction
• Elongation of transcription


  RNA polymerase unwinds DNA and synthesizes RNA using A, G, U and C
• Termination of transcription


  A special DNA sequence signals RNA polymerase to stop transcribing
• Genetic code


  Specifies which amino acids will be used to build a protein, with codons of 3 bases each
• Start codons


  AUG, GUG, UUG, AUU - initiation signal for translation
• Stop codons


  UAA, UAG, UGA - stop translation and release polypeptide
• Reading frame


  The DNA "template" strand goes 3' to 5', mRNA is complementary and goes 5' to 3'
• Ribosome


  Translates mRNA into protein, has 30S and 50S subunits in prokaryotes
• Initiation of translation


  Amino acids attached to tRNA bind to A site, peptide bond formed, ribosome moves to next codon
• Elongation of translation


  Amino acids added one by one to growing polypeptide chain
• Termination of translation


  Ribosome reaches stop codon, release factors aid ribosome dissociation from mRNA