AP Bio Unit 3

Work

  • Three main Types

    • Chemical

      • Endergonic reactions that would not occur spontaneously

        • Endergonic=absorbing energy

    • Transport

      • Movement of substances up their concentration gradient

    • Mechanical

      • Typically cellular movement

  • Energy Coupling

    • Using the energy from exergonic reactions to fuel this Work

      • Exergonic=releasing energy

ATP & ADP

  • ATP

    • Adenosine triphosphate

    • Responsible for mediating most energy coupling reaction in cells

    • Structure

      • A sugar (ribose)

      • A nitrogenous base (adenine)

      • Three phosphate groups

        • Negatively Charged

  • Catabolism of ATP

    • Catabolism= the breakdown of complex molecules into numerous simple ones.

    • Catabolism of ATP into ADP is an exergonic reaction

    • Equation

      • ATP+H2O→ADP+Pi+ free energy

      • ∆G=-7.3 kcal/mol (-30.5 kj/mol)

        • ∆G=Free energy

    • Phosphate groups during catabolism

      • The 3 negatively charged phosphate groups are bound closely together. So, when one of those bonds is broken during catabolism, the repulsion of the charges act like a spring and shoot out the phosphate group. This how ATP donates phosphate groups to other molecules (like proteins).

  • ATP Coupled Reactions

    • When ΔG of an endergonic reaction is less than the amount of energy released by the hydrolysis of ATP, the two reactions can be coupled to form an overall exergonic reaction

      • Hydrolosis= the chemical breakdown of a compound due to reaction with water. (AKA its a different name for ATP catabolism)

    • Phosphorylated intermediate

      • The result of ATP Phosphorylating a molecule (usually a reactant).

  • Mechanical Reactions

    • Movement of proteins are usually caused by the phosphorylation of ATP

  • Regeneration of ATP

    • Adding a phosphate group to ADP 

    • ADP+Pi→ATP+H2O

    • ∆G=+7.3 kcal/mol (+30.5 kj/mol)

    • Process that forms ATP is cellular respiration

Enzymes

  • Biological Catalysts

  • Catalysts function by lowering activation energy required for a reaction to occur.

  • Does not effect ∆G because catalysts only affects the activation energy and not the initial or final states of the reactants and products

  • Substrate specific

    • Substrate – the reactant of an enzyme catalyzed reaction

  • Enzyme-substrate complex

    • Intermediate step created by enzymes binding to substrates

    • Enzyme + Substrate(s) ↔ Enzyme-Substrate Complex ↔ Enzyme + Product(s)

  • Active Site

    • The region in which an enzyme binds

  • Shape of an Enzyme

    • The specificity of an enzyme is a result of its shape (which is a consequence of the amino acid sequence)

    • Enzymes are “fluid” in the body (not a stiff structure), no strict shape

    • Enzymes change between different conformations

    • The shape that binds the enzyme isn’t necessarily the shape with the lowest free energy (most stable), the enzyme sometimes briefly changes to a more ideal shape to more quickly bind the substrate

    • As the substrate binds to a part of the active site, the protein will slightly change shape conforming to the substrate


  • Induced Fit

    • Process of the protein changing shape based upon the binding of the substrate

    • The chemical bonds formed between the substrate and enzyme bring the active site into a position that is conducive to catalyzing a reaction

  • Enzyme Mechanisms

  1. In multiple reactant reactions, the active site provides a template on which substrates can come together in the proper orientation

  2. Puts stress on the chemical bonds that must be broken in order for the reaction to occur

    1. Activation energy is normally based upon the amount of energy required to break the bonds

  3. Provide a microenvironment that is conducive to a particular type of reaction

    1. Active site might be a pocket of low pH in a otherwise neutral cell to facilitate proton transfer to change the substrate

  4. Direct participation of the active site in the chemical reaction

    1. Involves brief covalent bonding between the substrate and the side chain of the amino acid in the active site

      1. Covalent Bond= the interatomic linkage that results from the sharing of an electron pair between two atoms

    2. Reactions after the reaction restore active site to original state

Effects of conditions on Enzymes

  • Temperature

    • To a certain point, increasing temperature will increase enzyme activity

      • At a higher temperature, molecules move rapidly increasing the amount of collisions between molecules and the enzyme

      • Every enzyme has an optimal temperature, where the reaction rate is at maximum without denaturing the protein

        • Most optimal temperature for human enzymes is 35-40 degrees Celsius (human body temperature) while optimal temperature of thermophilic bacteria is around 70 degrees Celsius.

  • pH

    • Each enzyme has an ideal pH level

      • Most enzymes in the human body work optimally in neutral pH ranges (6-8) while other enzymes work well in highly acidic environments (2)

        • Depends on where the enzymes work

  • Cofactors/Coenzymes

    • They’re the nonprotein helpers that many enzymes require

    • Cofactors = Inorganic

    • Coenzymes = Organic

    • They can bind tightly to the enzyme or bind with the substrate loosely to the enzyme

    • Ex; Metal ions (Zinc, iron and copper (in ionic form))

  • Inhibition

    • Bind to the enzyme covalently and are typically irreversible

    • Competitive

      • Mimic the structure of substrate molecules and bind to the active site

      • Since binding is temporary, the substrate is unable to bind to the enzyme while the inhibitor is there. However, once it unbinds the active site is available again.

    • Non-competitive

      • Change the shape of the active site so that it is no longer conductive to bind to substrate

      • Many forms of toxins and poisons are irreversible enzyme inhibitors

Regulation of Enzymes

  • If a cell has all metabolic process occurring at all time the cell would fall into chaos

  • Allosteric Regulation

    • Regulators that bind to the enzyme at a site other than the active site

    • Most allosterically regulated enzymes are composed of subunits

    • This process maintains ideal levels of operation in the cell

  • Two main ways in which regulators can affect an enzyme

    • Binding to a regulatory site (or allosteric site)

      • Regulator binds to the adjoining area of the subunits “freezing” the enzyme in its active or inactive form

    • Cooperation

    • fixes the form of the things it’s attached to