Genetics and Metabolism

• Genetics and Metabolism


  The study of genetic information and metabolic processes in living organisms
• Biosynthesis


  A series of reactions that make complex compounds from simple compounds using enzymes
• Anabolic reactions


  Take up energy as complex compounds are being built up
• Catabolic reactions


  Break down larger material often with the production of energy to produce more ATP
• Anabolism


  Synthesis of complex molecules in living organisms from simpler ones together with the storage of energy

  
• Biosynthesis of Amino Acids and Nucleotides

  1. Proteins are synthesised from the monomer amino acids

  2. Nucleic acids are made from the monomer nucleotides
• Amino acids


  • Carbon skeletons come almost exclusively from intermediates of glycolysis or the citric acid cycle
  • Amino group usually derived from an inorganic nitrogen source, such as ammonia
  • Organisms that can't obtain some or all of their amino acids from the environment must synthesise them from glucose or other carbon sources
• Incorporation of ammonia into amino acids

  1. Ammonia is most often incorporated during biosynthesis of the amino acids glutamate or glutamine

  2. When ammonia is present at high levels, glutamate dehydrogenase or other amino acid dehydrogenases are used

  3. When ammonia is at low levels, glutamine synthetase with its energy-consuming reaction mechanism and correspondingly high affinity for its substrate is employed
• Biosynthesis of Nucleotides


  1. Purines are constructed from the key compound, inosinic acid

  2. Pyrimidines are constructed from the key compound, uridylate

  3. Purines are constructed literally atom by atom from several carbon and nitrogen sources, including carbon dioxide

  4. Pyrimidines are also constructed from several sources, with the pyrimidine nucleotide skeleton uridylate as the predecessor
• Biosynthesis of Sugars and Polysaccharides

  1. Polysaccharides are synthesised from activated forms of glucose, either uridine diphosphoglucose UDPG or adenosine diphosphoglucose ADPG

  2. UDPG forms several glucose derivatives used in the biosynthesis of important structural polysaccharides

  3. Polysaccharides are formed by adding activated glucose to a pre-existing polymer fragment

  
• Gluconeogenesis


  Process by which glucose is biosynthesised from other carbon compounds, using phosphoenolpyruvate as a starting material and travelling backwards through the glycolytic pathway
• Biosynthesis of Fatty Acids and Lipids

  1. Fatty acids are biosynthesised two carbon atoms at a time using acyl carrier protein ACP

  2. Malonate is a key compound in the synthesis of lipids and fatty acids, attaching to ACP and then cleaving off one carbon as CO2 to leave a 2 carbon compound

  3. Lipids are then grown in length by the addition of 2 carbon compounds derived from malonate

  
• Fatty acids


  • Biosynthesis of short-chain and unsaturated fatty acids is promoted at low temperatures, while longer-chain and more saturated fatty acids are produced at higher temperatures
  • Unsaturated fatty acids contain one or more double bonds, often species or group-specific, formed by desaturation of saturated bonds
  • Branched chain and odd-carbon-number fatty acids are biosynthesised using different initiating molecules

  
• Lipid formulation


  1. Simple triglycerides (fats) are formed when all three glycerol carbons are esterified with fatty acids

  2. Complex lipids are formed when one of the glycerol carbons is embellished with a polar molecule like phosphate, ethanolamine or carbohydrate
• Respiration


  Aerobic or anaerobic catabolism in which an organic or inorganic electron donor is oxidised with oxygen (aerobic) or another compound (anaerobic) as the electron acceptor
• Glycolysis


  1. Common pathway found in all bacterial cells, in which glucose is oxidised to pyruvate

  2. Consists of preparatory reactions, redox reactions that conserve energy, and redox balancing reactions that form fermentation products

  
• Fermentation


  Anaerobic catabolism in which organic compounds both donate and accept electrons, achieving redox balance without external electron acceptors
• Krebs Cycle


  Series of biochemical reactions in bacteria that release large amounts of potential chemical energy, producing various products
• Metabolism of Fatty Acids

  Bacteria can break down fatty acids into acetic acid and produce energy, using a modified Krebs cycle (glyoxylate cycle) that doesn't involve loss of carbon dioxide
• Genetic Information


  Genetic material is DNA, which is expressed through synthesis of specific RNAs and proteins

  
• Bacterial chromosome replication


  During binary fission, the process is called semi-conservative replication, where each strand of the DNA double helix provides a template for a new strand
• Bacteria breaking down fatty acids


  1. Break down into acetic acid

  2. Produce energy from this process
• Glyoxylate cycle


  Modified Krebs cycle used by bacteria when fatty acids are the sole source of carbon, where there is often no loss of carbon dioxide and is only found in bacterial cells
• Genetic material


  DNA, expressed by synthesis of specific RNAs and proteins (via transcription and translation)

  
• Bacterial chromosomes


  • Often singular, covalently closed, circular molecules of double-stranded DNA, but can be linear and can be found free in the cytosol or attached to the cell membrane
• Semi-conservative replication


  Process where each strand of the DNA double strand provides a template for replication
• Induction


  Process where the presence of a substrate in the environment switches on certain genes to break it down
• Repression


  Process where a by-product switches off certain genes
• Operons


  Groups of contiguous genes that are transcribed as a single unit and translated to produce the corresponding gene products, can be induced or repressed
• Regulon


  Alters the expression of a group of genes or operons, e.g. binary fission
• Inducible genes


  Genes whose expression is turned on by the presence of a substance, e.g. lactose inducing the lac genes

  
• Catabolite repression


  Inducible operons are controlled by inducers, regulatory genes, and the level of glucose in the environment, as glucose is preferentially digested
• Lac operon genes


  • Lac i (regulatory gene)
  • Lac o (operator)
  • Lac p (promoter)
  • Lac z (β-Galactosidase enzyme)
  • Lac y (permease protein)
  • Lac a (transacetylase)

  
• Repressible genes


  Genes whose expression is turned off by the presence of a substance, e.g. tryptophan repressing the trp genes
• Attenuation


  Premature termination of transcription in repressible operons if the bacteria has enough of the product
• Plasmids


  Extra-chromosomal DNA that replicate separately from the chromosome, can code for traits not essential for bacterial viability
• Types of plasmids


  • Stringent (replicate only when chromosome replicates)
  • Relaxed (replicate on their own)
• Bacteriophages


  • Viruses that infect bacteria, obligate intracellular parasites, contain genetic information (DNA or RNA) in a capsid, have a contractile tail sheath to inject nucleic acid into bacterial cell

  
• Transformation


  Genetic information transfer where a bacterial cell dies, releases genetic information, and recipient cells take it up
• Transduction


  Genetic information transfer via bacteriophages (viruses) as vectors