Week 3

Week 3

1. Genes to Proteins

   • DNA to RNA to Protein
     • DNA to RNA
       • transcription - 3' to 5'
       • RNA polymerase
       • nucleus
     • RNA to Protein
       • translation - 5' to 3'
       • ribosome and cytoplasm
   • Proteins
     • Processes
       • enzyme catalysis
       • transport
       • signal transduction
       • immune protection
       • coordinated motion
       • mechanical support
       • storage
     • structure
       • amino acid chain
       • starts at the N terminus
       • finishes at the C terminus
       • primary
         • amino acid sequence - 2D
       • secondary
         • alpha helix
           • each aa forms a hydrogen bond with an aa 4 above and below
           • clockwise helix
           • 3.6 aa per turn
         • beta sheet
           • beta strands
           • parallel or anti-parallel
         • chain held together in conformational shape with hydrogen bonds
         • hydrophobic forces bind alpha helices and beta sheets together
       • tertiary
         • folded into globular structure
       • quaternary
         • 3D
         • multi-part protein complex
     • globular proteins
       • interior - hydrophobic
       • exterior - hydrophilic
       • composed of secondary structure proteins
       • amino acid chain change direction
       • the turns often require conformational properties of Gly and Pro amino acids
       • domains
         • individual globules on a globular protein
         • self contained units
   • Amino Acids
     • 20 naturally occuring
     • all L isomers
     • peptide bonds link the individual acids
       • bonds don't rotate
       • fixed in trans formation
     • Disulphide Bonds
       • attachement between 2 side chains
       • doesn't occur in the cytoplasm
   • DNA & RNA Structure
     • phosphodiester bonds link the 3rd carbon of one sugar to the 5th carbon of another
     • DNA
       • helix has a major and minor groove
       • LAC processor binds to major groove and blocks RNA polymerase
       • bases form hydrophobic stacking interactions with bases above and below
       • when lactose is present LAC processor can't bind and replication can occur
       • LAC processor stops energy being wasted on enzyme production for a substance that isn't present
       • DNA forms a complex with proteins to form chromatin
       • proteins in chromatin are histones
       • nucleosome is made up of 8 histones and 200 base pairs
     • RNA
       • forms fuctional structures - stem & loop, hairpin and pseudo-knot
       • riboswitch - segment of RNA that regulates mRNA's activities
       • ribozyme - RNA molecule that acts in a simliar way to enzymes
       • tRNA
         • single chain of 73-93 ribonucleotides
         • contains unusual bases
         • amino acid attaches to the adenosine at the 3' end
   • DNA Replication
     • helicases unwind the DNA
     • ss binding proteins bind to the strands to stop them reforming
     • happens at the replication fork
     • transcription bubble
       • RNA polymerase is 17 base pairs long
       • NTPs are added to the 3 end
       • promotor region where the bubble attaches
     • translation
       • differences within an individual amino acid arise from the redundancy of codons
       • a common difference between codons that code for the same aa is the 3rd base
       • 3rd base is the wobble base
       • Met aa is the start codon so is always the first codon present
   • Protein Synthesis
     • a small subunit recognises the ribosome binding site and binds to the mRNA
       • this area is about 15 bases to the 3' end of the start codon
     • a large subunit binds to the small subunit
     • the large subunit is divided into A and P sites
     • tRNA binds at the A site
     • tRNA is then moved into the P site and a new tRNA binds in the A site
     • the 2 amino acids form a peptide bond
     • the tRNA in the P site is released and the ribosome translocates by 1 codon

2. Bioenergetics

   • Definitions
     • metabolism - all reactions in the body
     • catabolism - breakdown of nutrients to make energy and raw materials
     • anabolism - synthesis of complex molecules from simple building blocks
   • Nutritional Requirements of Organisms are Reflected in their Sources of Metabolic Energy
     • autotrophs
       • produces complex complounds from simple mollecules in its surroundings
       • phototrophs use light energy
       • chemolithotrophs use energy from the oxidation of inorganic compounds
     • heterotrophs
       • obtain energy from oxidation of organic compounds
       • depend on autotrophs for these substances
       • require a balanced intake of proteins, carbs and lipids
       • cannot synthesise vitamins
       • minerals are required for biomolecules and tissues
   • Respiration
     • glycolysis
       • T.I.M. enzyme catalyses the interconversion of P-GAP and DHAP-P
       • producing pyruvate from simple sugars
     • link reaction
     • krebs cycle
     • ETC
       • 10 protons pumped per NADH
       • Quino carries electrons down the ETC
     • 28 ATP net yield
     • anaerobic
       • lactate - homolactic fermentation in animals, 31% efficient
       • CO2 & ethanol - alcoholic fermentation in plants, 26% efficient
       • produces 2 ATP
   • Glycogen
     • each granule is about 120,000 monomers
     • blood glucose should be about 5mM
   • Gluconeogenesis
     • synthesis of glucose from non-carb precursors
     • all precursors are converted to oxaloacetate
     • leucine and lysine aa's can't be converted
     • fatty acid breakdown provides most of the ATP needed
     • generation of oxaloxacetate only occurs in the mitochondria
     • the enzymes that convert phosphenolpyruvate are cytosolic
     • location of PEPCK can either be in the cytosol or mitochondrion
     • to continue generation of glucose oxalocetate or PEP must leave the mitochondria
     • PEP is transported by transport systems but oxaloacetate is more complex
     • oxaloacetate transportation
       • must be converted to either malate or aspartate
       • specific transporters for malate and aspartate
       • difference between routes lies in the reducing equivalent transfer
       • conversion to malate and malate transfer results in transfer of reducing equivalents into the cytosol
       • conversion of aspartate doesn't transport reducing equivalents
       • gluconeogenisis requires NADH so the malate route is the most common route
   • Phosphofructokinase
     • catalyses the major rate determining step of glycolysis
     • other regulatory points of glycolysis are hexokinase and pyruvate kinase but both can be over rided
     • tetramer
     • 2 conformational states in equilibrium - R and T
     • ATP is an inhibitor of PFK
     • ADP, AMP and Fructose-2,6-bisphosphate are activators
     • each subunit has 2 ATP binding sites so there is a total of 8 sites
     • the active site binds ATP in both states
     • the inhibitor site binds ATP in the inactive state
     • F6P binds only in the active state
     • T state - inactive
     • R state - active
     • high ATP concentrations shift the TR equilibrium towards T, which decreases PFKs affinity for F6P
     • activators bind to the R state
     • low metabolic demand
       • [ATP] high
       • PFK inhibited
       • flux through glycolysis is low
     • high metabolic demand
       • [ATP] low
       • PFK active
       • flux through glycolysis is high
     • [ATP] varies by 10%
     • glycolysis flux varies by more than x100
     • inhibition
       • inhibited by ATP
       • relieved by ADP and AMP
       • [ATP] only drops 10% when exercising as it is buffered by creatine and adenylate kinase
       • adenylate kinase catalyses 2ADP -> ATP + AMP
       • adenylate kinase equilibrates the ADP generated
       • a 10% change in [ATP] can result in more than 400% increase in [AMP]
       • a metabolic signal, decrease in [ATP], too small to activate PFK is amplified by adenylate kinase to a strong signal, [AMP], that can activate PFK
   • Glycogen Phosphorylase
     • dimer
     • large n-terminal domain
     • small c-terminal domain
     • phosphorylated form is phophorylase A and the dephosph form is phophorylase B
     • A is sensitive to ATP, G6P and AMP
     • B is sensitive to glucose
     • T and R states
       • phosphorylation of Ser14 promotes conversion of T to R
       • negative regulators preferentially bind the T state of the dephospho enzyme
       • AMP preferentially binds to the R state of the dephospho enzyme
       • only glucose binds the phosphorylates T state acting as an inactivator
   • Transport and Storage of Lipids
     • lipids - collective term for natural molecules that don't dissolve in water
     • Triacylglycerols can't cross the cell membrane but can be broken down into fatty acids by lipoprotein lipase - lipolysis
     • lipids are transported by lipoproteins with a TAC in the core
     • there are several classes of lipoproteins depending on the amount of TAC and cholesterol they contain
       • chylomicron
       • very low density
       • intermediate density
       • low density
       • high density