BIOCHEMISTRY

    Cards (28)

    • what do nucleic acids contain?
      what's the chemical name of DNA?
      • a phospahte group
      • a five carbon sugar (pentose which is a ribose in DNA)
      • a nitrogen containing base
      • DNA= beta -D-2 DeoxyriboNucleicAcid
    • what are linear hydrogen bonds and what do they do
      • hydrogen bonds in a straight line, help with the formation of the double helix structure of DNA
      • they connect guanine to cytosine and adenine to thymine
    • what are the main differences between the structure of DNA and RNA molecules ?
      • RNA - has a ribose sugar instead of a deoxyribose
      • chemical name is RiboNucleicAcid
      • RNA has a hydroxyl group (OH) at position 2
      • RNA uses Uracil instead of Thymine
    • from DNA to RNA to Proteins
      1. A transcription protein binds at the beginning of a DNA segment coding for a gene ( process includes RNA polymerase )
      2. RNA polymerase does the transcription, making RNA from DNA
      3. mRNA leaves the nucleus and it is bond by ribosomes
      4. (translator molecule is needed)
    • why is a translator molecule needed when turning RNA into Protein from DNA?
      • DNA to RNA info transfer is easy due to 1-1 complementary base pairs so DNA acts as a template while amino acids do not align to nucleic acids so mRNA cannot be a direct template
      • translator molecule must be able to recognise both nucleic acids and amino acids ( recognises 3 RNA nucleic acids and 1 out of 20 amino acids )
      • in summary it's needed to bring the correct amino acids to the ribosome , recognize codons on m RNA and ensure accurate protein synthesis
    • enzyme kinetics:
      what is a steady state ?
      initial velocity at low and high substrate concentration
      • initial velocity- rate calculated at the very beginning of the reaction
      • at low substrate conc, initial velocity us proportional to S so reaction follows the mass of action law= reaction rate is directly proportional to the concentration of the reactants (1st order)
      • at high substrate conc, initial velocity becomes independent of S (0 order)
      • steady state- when the formation rate of a species is the same as its consumption rate so its concentration doesn't change during the steady state interval
    • main steps during enzyme catalysis:
      • binding step= enzyme substrate complex formation
      • chemical step= substate conversion into product
      • product release step: enzyme is free for the next turnover
    • what does Vmax and Km stand for?

      • Vmax- maximal velocity; the limiting velocity of an enzyme- catalysed reaction as the substrate conc tends to infinity
      • Km- the michaelis constant; numerically it's equal to the substrate conc at which the velocity of the enzyme catalysed reaction is half maximal while conceptually it's a measure of the affinity between enzyme and substrate
      • the smaller the Km the more tightly the enzyme binds the substrate
    • what is the eyring-polanyi equations?
      • it relates the amount of activation energy required to bring the substrate to the transition state conformation with the rate constant of the entire reaction
      • for reactions with a single transition state , the rate constant k from the equation corresponds to k2 from the michaelis-menten model (elementary reaction mechanism)
      • activation energy barriers are bund to exist regardless of whether the overall reaction is reversible or irreversible
    • the steady state and initial velocity (V0)
      • 1.The Michaelis-Menten equation was derived from an important assumption:  the concentration of substrate must be much greater than the enzyme concentration: [S] >>> [E].
      2.Under this condition [S] >>> [E], the changes in the concentration of the intermediate ES  over time is  zero [D(ES)/Dt = 0 ]. 
      3.By definition, steady-state conditions hold at the initial stages of an enzymatic reaction and decay quickly (usually after 1 minute).
      • in the MM model- this refers to enzyme substrate complex
    • what is a hydrogen bond ?
      how does it bond with other atoms ?
      • it occurs when two electronegative atoms compete for the same hydrogen atom
      • it is bonded one of the atoms (donor) while interacting with the second negative atom at the same time (acceptor)
    • catalytic strategies: proximity
      enzyme binds to two substrate molecules and orients them precisely to encourage a reaction to occur between them
      • proximity- enzymes can bring two molecules together in solution; probability of two molecules coming close together is very low in free solution
      • if these two molecules can bind separately and tightly to the enzyme's active site, the two components can react with each other more efficiently
    • catalytic strategies: orientation/ electrostatic effects
      • orientation- even when two molecules collide with enough energy to cause a reaction, they don't necessarily form products.
      • they have to be oriented so that the energy of the colliding molecules is transferred to the reactive bond.
      • enzymes bind substrates so that the reactive groups are steered to the direction that can lead to a reaction
      • binding of substrate to enzyme rearranges electrons in the substrate, creating partial negative and positive charges that favor a reaction
    • catalytic strategies :
      electrostatic effects
      • increasing electrostatic interactions by providing a water free environment
      • the binding site of most enzymes is located in a hydrophobic pocket
      • water's high dielectric constant causes the weakening of any electrostatic interaction between a substrate and a protein
      • this is avoided by the binding site being water free ( hydrophobic)
      • enzyme strains the bound substrate molecule, forcing it toward a transition state to favor a reaction
    • catalytic strategies: induced fit/ substrate straining
      • induced fit- after an enzyme binds to its substrate , it changes conformation forcing the substrate to be strained or distorted into a shape that resembles the transition state
      • ADP- P= ADPP= ATP enzyme-- ATP synthetase
    • citric acid cycle (krebs cycle )
      • occurs in the mitochondrial matrix
      • acetyl-coa oxidised to CO2
      • most energy from oxidation transferred to; FADH2-NADH, electron transportes allow the generation of H* gradient, final acceptor of electrons is O2 (H2O), H* gradient is dissipated and activates the synthesis of ATP
      • one molecule of GTP produced per turn (substrate level phosphorylation)
      • intermediates of the cycle are generated
      • cycle is amphibolic- serves catabolism and anabolism
    • citric acid cycle overview
      picture
    • the formation of acetyl-CoA
      • pyruvate enters the mitochondrial matrix in 2 steps;
      • diffusion through point in the outer membrane
      • translocation through the inner membrane by pyruvate translocase (a symporter with H*)
      • beta oxidation of fatty acids will also produce acetyl CoA
      • many amino acid degradation also generate Acetyl CoA
    • what is pyruvate dehydrogenase complex and what are its advantages ?
      • multi enzyme complex crucial in conversion of pyruvate into acetyl- CoA - allows continuation of energy production through the krebs cycle leading to the generation of ATP
      • fast and efficient
      • reduces side reactions
      • activity of complex can be controlled as a unit
    • overview
      1. citrate formation
      2. citrate to isocitrate (enzyme= aconitase)
      3. isocitrate to alpha- ketoglutarate (enzyme= isocitrate dehydrogenase), loss of CO2 and oxidation, removal of two protons and electrons transferred to NAD*
      4. alpha-ketoglutarate to succinyl-CoA (oxidative decarboxylation again)
      5. succinyl coA to succinate
      6. succinate to fumarate ( succcinate dehydrogenase)
      7. fumarate to malate (fumarase )
      8. Malate to oxaloacetate (malate dehydrogenase)
    • what are three irreversible reactions in the cycle ?
      • citrate synthase
      • isocitrate dehydrogenase
      • alpha- ketoglutarate dehydrogenase
      • inhibited when ATP is high (and when NADH accumulates)
    • what is a amphibolic process ?
      • amphi =both (catabolic and anabolic) so involved in both the breakdown of molecules to release energy and the synthesis of larger molecules from smaller units
      • the cycle is also a source of precursors for the synthesis:
    • what is a polar molecule?
      are they hydrophilic or hydrophobic?
      what type of bonds do they contain?
      • the uneven distribution of electrons in molecules could lead to partial electrical fields across the molecule called dipoles
      • molecule that has net dipole moment due to presence of polar bonds
      • one atoms attracts the shared electrons more strongly (higher electronegativity) than the other
      • they're hydrophilic
    • what is a non polar molecule?
      what are they soluble in?
      what are the examples
      • no significant difference in electronegativity, even distribution of electron density
      • electrons and protons tend to cancel out each other so there's not poles
      • soluble in non polar solvents
      • examples of non polar amino side chains: alanine , glycine, valine, proline
    • what is the hydrophobic effect?
      • results from the lack of hydrogen bonding between non polar side chains in water , so they aggregate in aqueous solutions and exclude water (repulsion of water)
      • non polar amino acids do not interact with each other as they lack any dipoles
      • as non polar amino acids are confined within the inner core their degree of freedom decreases so the entropy of the system decreases
    • hydrophobic vs hydrophilic surfaces 

      • hydrophobic residues provide the structural core
      • hydrophilic residues confer solubility
      • protein solubility is a result of fine balance between non polar and polar interactions
    • what is the salting out effect?
      • occurs when the solubility of a substance in a solution decreases due to the presence of salts
      • at high concentration some salts can steal the solvating water away from the proteins resulting in reduced hydrophilicity that is reduced solubility
      • those salts then make hydrogen bonds with water
      • compete with molecules in water solutions
      • upon losing its solvating shell a protein becomes insoluble and precipitate out of a solution (pellet)
    • salting out vs salting in
      • Protein 'salting out' results from interfacial effects of strongly hydrated anions near  the protein surface so removing water molecules from protein solvation and dehydrating the surface. The greatest effect is due to the most strongly  hydrated anions.
      • Protein 'salting in' (solubility increase on the addition of low levels of salt) results from protein-counter ion binding and the consequent higher net protein charge and solvation . In this case the greatest effect is due to the most weakly hydrated anions
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