Week 3

Week 3

Genes to Proteins
1. DNA to RNA to Protein
  1. DNA to RNA
    1. transcription - 3' to 5'
    2. RNA polymerase
    3. nucleus
  2. RNA to Protein
    1. translation - 5' to 3'
    2. ribosome and cytoplasm
2. Proteins
  1. Processes
    1. enzyme catalysis
    2. transport
    3. signal transduction
    4. immune protection
    5. coordinated motion
    6. mechanical support
    7. storage
  2. structure
    1. amino acid chain
    2. starts at the N terminus
    3. finishes at the C terminus
    4. primary
      1. amino acid sequence - 2D
    5. secondary
      1. alpha helix
        each aa forms a hydrogen bond with an aa 4 above and below
        clockwise helix
        3.6 aa per turn
      2. beta sheet
        beta strands
        parallel or anti-parallel
      3. chain held together in conformational shape with hydrogen bonds
      4. hydrophobic forces bind alpha helices and beta sheets together
    6. tertiary
      1. folded into globular structure
    7. quaternary
      1. 3D
      2. multi-part protein complex
  3. globular proteins
    1. interior - hydrophobic
    2. exterior - hydrophilic
    3. composed of secondary structure proteins
    4. amino acid chain change direction
    5. the turns often require conformational properties of Gly and Pro amino acids
    6. domains
      1. individual globules on a globular protein
      2. self contained units
3. Amino Acids
  1. 20 naturally occuring
  2. all L isomers
  3. peptide bonds link the individual acids
    1. bonds don't rotate
    2. fixed in trans formation
  4. Disulphide Bonds
    1. attachement between 2 side chains
    2. doesn't occur in the cytoplasm
4. DNA & RNA Structure
  1. phosphodiester bonds link the 3rd carbon of one sugar to the 5th carbon of another
  2. DNA
    1. helix has a major and minor groove
    2. LAC processor binds to major groove and blocks RNA polymerase
    3. bases form hydrophobic stacking interactions with bases above and below
    4. when lactose is present LAC processor can't bind and replication can occur
    5. LAC processor stops energy being wasted on enzyme production for a substance that isn't present
    6. DNA forms a complex with proteins to form chromatin
    7. proteins in chromatin are histones
    8. nucleosome is made up of 8 histones and 200 base pairs
  3. RNA
    1. forms fuctional structures - stem & loop, hairpin and pseudo-knot
    2. riboswitch - segment of RNA that regulates mRNA's activities
    3. ribozyme - RNA molecule that acts in a simliar way to enzymes
    4. tRNA
      1. single chain of 73-93 ribonucleotides
      2. contains unusual bases
      3. amino acid attaches to the adenosine at the 3' end
5. DNA Replication
  1. helicases unwind the DNA
  2. ss binding proteins bind to the strands to stop them reforming
  3. happens at the replication fork
  4. transcription bubble
    1. RNA polymerase is 17 base pairs long
    2. NTPs are added to the 3 end
    3. promotor region where the bubble attaches
  5. translation
    1. differences within an individual amino acid arise from the redundancy of codons
    2. a common difference between codons that code for the same aa is the 3rd base
    3. 3rd base is the wobble base
    4. Met aa is the start codon so is always the first codon present
6. Protein Synthesis
  1. a small subunit recognises the ribosome binding site and binds to the mRNA
    1. this area is about 15 bases to the 3' end of the start codon
  2. a large subunit binds to the small subunit
  3. the large subunit is divided into A and P sites
  4. tRNA binds at the A site
  5. tRNA is then moved into the P site and a new tRNA binds in the A site
  6. the 2 amino acids form a peptide bond
  7. the tRNA in the P site is released and the ribosome translocates by 1 codon
Bioenergetics
1. Definitions
  1. metabolism - all reactions in the body
  2. catabolism - breakdown of nutrients to make energy and raw materials
  3. anabolism - synthesis of complex molecules from simple building blocks
2. Nutritional Requirements of Organisms are Reflected in their Sources of Metabolic Energy
  1. autotrophs
    1. produces complex complounds from simple mollecules in its surroundings
    2. phototrophs use light energy
    3. chemolithotrophs use energy from the oxidation of inorganic compounds
  2. heterotrophs
    1. obtain energy from oxidation of organic compounds
    2. depend on autotrophs for these substances
    3. require a balanced intake of proteins, carbs and lipids
    4. cannot synthesise vitamins
    5. minerals are required for biomolecules and tissues
3. Respiration
  1. glycolysis
    1. T.I.M. enzyme catalyses the interconversion of P-GAP and DHAP-P
    2. producing pyruvate from simple sugars
  2. link reaction
  3. krebs cycle
  4. ETC
    1. 10 protons pumped per NADH
    2. Quino carries electrons down the ETC
  5. 28 ATP net yield
  6. anaerobic
    1. lactate - homolactic fermentation in animals, 31% efficient
    2. CO2 & ethanol - alcoholic fermentation in plants, 26% efficient
    3. produces 2 ATP
4. Glycogen
  1. each granule is about 120,000 monomers
  2. blood glucose should be about 5mM
5. Gluconeogenesis
  1. synthesis of glucose from non-carb precursors
  2. all precursors are converted to oxaloacetate
  3. leucine and lysine aa's can't be converted
  4. fatty acid breakdown provides most of the ATP needed
  5. generation of oxaloxacetate only occurs in the mitochondria
  6. the enzymes that convert phosphenolpyruvate are cytosolic
  7. location of PEPCK can either be in the cytosol or mitochondrion
  8. to continue generation of glucose oxalocetate or PEP must leave the mitochondria
  9. PEP is transported by transport systems but oxaloacetate is more complex
  10. oxaloacetate transportation
    1. must be converted to either malate or aspartate
    2. specific transporters for malate and aspartate
    3. difference between routes lies in the reducing equivalent transfer
    4. conversion to malate and malate transfer results in transfer of reducing equivalents into the cytosol
    5. conversion of aspartate doesn't transport reducing equivalents
    6. gluconeogenisis requires NADH so the malate route is the most common route
6. Phosphofructokinase
  1. catalyses the major rate determining step of glycolysis
  2. other regulatory points of glycolysis are hexokinase and pyruvate kinase but both can be over rided
  3. tetramer
  4. 2 conformational states in equilibrium - R and T
  5. ATP is an inhibitor of PFK
  6. ADP, AMP and Fructose-2,6-bisphosphate are activators
  7. each subunit has 2 ATP binding sites so there is a total of 8 sites
  8. the active site binds ATP in both states
  9. the inhibitor site binds ATP in the inactive state
  10. F6P binds only in the active state
  11. T state - inactive
  12. R state - active
  13. high ATP concentrations shift the TR equilibrium towards T, which decreases PFKs affinity for F6P
  14. activators bind to the R state
  15. low metabolic demand
    1. [ATP] high
    2. PFK inhibited
    3. flux through glycolysis is low
  16. high metabolic demand
    1. [ATP] low
    2. PFK active
    3. flux through glycolysis is high
  17. [ATP] varies by 10%
  18. glycolysis flux varies by more than x100
  19. inhibition
    1. inhibited by ATP
    2. relieved by ADP and AMP
    3. [ATP] only drops 10% when exercising as it is buffered by creatine and adenylate kinase
    4. adenylate kinase catalyses 2ADP -> ATP + AMP
    5. adenylate kinase equilibrates the ADP generated
    6. a 10% change in [ATP] can result in more than 400% increase in [AMP]
    7. 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
7. Glycogen Phosphorylase
  1. dimer
  2. large n-terminal domain
  3. small c-terminal domain
  4. phosphorylated form is phophorylase A and the dephosph form is phophorylase B
  5. A is sensitive to ATP, G6P and AMP
  6. B is sensitive to glucose
  7. T and R states
    1. phosphorylation of Ser14 promotes conversion of T to R
    2. negative regulators preferentially bind the T state of the dephospho enzyme
    3. AMP preferentially binds to the R state of the dephospho enzyme
    4. only glucose binds the phosphorylates T state acting as an inactivator
8. Transport and Storage of Lipids
  1. lipids - collective term for natural molecules that don't dissolve in water
  2. Triacylglycerols can't cross the cell membrane but can be broken down into fatty acids by lipoprotein lipase - lipolysis
  3. lipids are transported by lipoproteins with a TAC in the core
  4. there are several classes of lipoproteins depending on the amount of TAC and cholesterol they contain
    1. chylomicron
    2. very low density
    3. intermediate density
    4. low density
    5. high density

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