Biochemistry
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Biochemistry. Enzymes. Enzymes. Enzymes are protein molecules that control the rates of cellular reactions The substrate is the reactant that an enzyme acts on when it catalyzes a chemical reaction (there may be more than one)

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Biochemistry

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Biochemistry

Biochemistry

Enzymes


Enzymes

Enzymes

  • Enzymes are protein molecules that control the rates of cellular reactions

  • The substrate is the reactant that an enzyme acts on when it catalyzes a chemical reaction (there may be more than one)

  • The active site is a groove or crevice where a substrate matches in shape and size and can bind

  • Reactions can be anabolic (more than one substrate) or catabolic (one substrate) reactions


Enzymes1

Enzymes

  • Recall collision theory: molecules must collide with enough energy and in the right orientation for a successful collision

  • Enzymes increase the likelihood of a successful collision, and so lower the activation energy (EA)

    catabolic reactionanabolic reaction


Enzymes2

Enzymes

  • Like catalysts, enzymes are not used up in the reaction; they can be used over and over

  • Enzymes are usually much larger than their substrates

  • They are synthesized in the same way as other proteins – encoded in the DNA


Lock and key model

Lock-and-Key Model

  • Enzymes are very specific and this is because both the enzyme and the substrate have complementary geometric shapes that fit exactly into one another

  • This idea is called the Lock-and-Key model, and while it explains enzyme specificity, it fails to explain the stabilization of the transition state that enzymes achieve

  • While it is still a useful tool for understanding enzymes, this model has proven inaccurate over time


Induced fit model

Induced-Fit Model

  • Like the Lock-and-Key model, in the induced-fit model the active site of the enzyme is specially shaped to fit the appropriate substrate(s)

  • When the substrate enters the active site, new intermolecular forces are created – this influences the interaction of the protein’s R-groups and causes a conformational change (shape change)

  • The activated state is reached when this shape change creates tighter fit for the enzyme-substrate complex

  • Once the substrate fits; the reaction can proceed to the transition state


Induced fit model1

Induced-Fit Model


Enzymes are sensitive to ph and t

Enzymes are sensitive to pH and ΔT

  • As temperature increases, reaction rates decrease because the heat energy disrupts the weak bonds that hold the enzyme in its 3-D shape, thereby altering the active site so that the substrates can no longer bind to it

  • Enzymes work best at a specific pH; when pH values are higher or lower the enzyme structure and therefore function is disrupted

  • Examples:

    • salivary amylase works best in the pH of the mouth, and loses its function in the stomach, where the pH is between 0-1

    • an enzyme that controls DNA replication in the archaebacteriumThermusaquaticus operates best between 90°C - 110°C


Denaturation coagulation

Denaturation & Coagulation

  • When the pH goes beyond the optimum pH for an enzyme, it begins to lose it’s shape – we say it is denatured

  • As long as the pH or temperature goes back to normal, the enzyme can return to it’s functional state

  • If the pH or temperature changes for too long, the enzyme can coagulate

  • Coagulation is a permanent change


Cofactors and coenzymes

Cofactors and Coenzymes

  • Cofactors: non-protein components (can be inorganic or organic) that are needed by some enzymes in order to function

  • Coenzymes: are specifically organic non-protein cofactors (mostly from vitamins)

  • Many coenzymes shuttle molecules from one enzyme to another

  • e.g.: NAD+ and FAD pick up H+atoms given off during glucose breakdown and carry them to other reaction sites (along with a pair of e- attracted to the positive charge), thereby becoming NADH and FADH2


Control of enzyme activity

Control of Enzyme Activity

  • If enzymes were allowed to continue working unchecked, they would produce too much of their product

  • This would waste a cell’s energy, and it could build up the products to toxic levels

  • Several methods are used to control the activity of enzymes

    • Competitive inhibition

    • Non-competitive inhibition

    • Feedback inhibition

    • Allosteric regulation


Competitive inhibition

Competitive inhibition

  • Molecules that match the shape of the active site (or at least a part of the active site)

  • These bind to the enzymes, blocking the substrate from reaching the active site


Noncompetitive inhibition

Noncompetitive inhibition

  • Molecules can attach to some part of an enzyme other than the active site

  • The intermolecular forces in the enzyme are influenced by this new molecule, causing a conformational change

  • This changes the shape of the active site, preventing attachment of the substrate


Feedback inhibition

Feedback inhibition

  • Many products in cells are created in a biochemical pathway or cascade, where each step is controlled by a separate enzyme

  • Sometimes the final product will interact with one of the enzymes in the cascade

As the concentration of final product increases, many of them bind to the molecules of enzyme A.


Feedback inhibition1

Feedback Inhibition


Allosteric regulation

Allosteric Regulation

  • Some enzymes are controlled by special molecules which either inhibit or activate

  • These enzymes usually have 4° structure and posses receptor sites, called allosteric sites that are separate from the active site

  • If an allosteric activator binds to an allosteric site, it stabilizes the protein structure and keeps all active sites available to substrates

  • If an allosteric inhibitor binds to an allosteric site, it will stabilize the inactive form of the enzyme


Allosteric regulation1

Allosteric regulation


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