Lecture 10

Introduction to Metabolism II

LIF1019-2-2014Sunday Dr. Jonaki Sen

ATP-The Cell’s Energy CurrencyIn cells, ATP couples energy release from exergonic reactions with energy-requiring ones.

Many enzymes can cleave the covalent bond between the two outermost phosphate groups of ATP and then attach it to another substance. This transfer of a phosphate group to a molecule is called phosphorylation.

The energy transferred during such events is sufficient to activate many different molecules and drive many diverse cellular activities.

ATP: Adenosine Tri Phosphate

ATP

ADP + Pi

Energy input

Energy output for diverse cellular reactions

Example of cellular activities driven by phosphate transfer from ATP

1. Contraction of muscle cells.

2. Pumping of substances across the cell membrane.

3. Synthesis and breakdown of organic compounds.

Phosphate group transfers from ATP are a renewable, rapid and almost universal mechanism for coupling energy-releasing and energy requiring events.

Electron transfersCells release energy from a substance by a series of small steps, each involving transfer of electrons.

Oxidation-reduction reactions mean the same as electron transfer.

A molecule that gives up electrons is oxidized

A molecule that accepts electrons is reduced

Glucose + fire = CO2 + H2O + heat Cells release energy from glucose more efficiently by transferring electrons from glucose through electron transport systems. The energy that is released at each of this electron transfer steps drives the synthesis of ATP.

Comparing uncontrolled and controlled energy release

Metabolic PathwaysEnergy inputs drive thousands of reactions inside the cell. These reactions occur in an orderly manner, are enzyme-mediated and are called metabolic pathways.

Biosynthetic pathways: small molecules are assembled into molecules of higher bond energies e.g. complex carbohydrates, proteins and lipids.Degradative pathways : Large molecules are broken down into products of lower bond energies.

The participants of metabolic pathways:Substrates: Substances that enter the reaction

Intermediates: Any substance that forms between the start and end of the pathway

End products: Substances remaining at the end of the pathway.

Enzymes: Molecules that speed up specific reactions.

Energy carriers: ATP and other molecules that can activate substances by delivering energy.

Cofactors: molecules that assist enzymes by picking up electrons, atoms or functional groups at one reaction and carry them over to another reaction.

Transport proteins: That span a cell membrane and let substances cross in a controlled way.

Enzyme structure and functionCells control their internal concentrations of substances with respect to the surroundings, and eukaryotic cells also control the concentrations across membranes of organelles.

Molecules or ions are in constant motion which makes them collide with each other. The higher the concentration the higher the frequency of collision. Energy associated with collision might be enough to cause a metabolic reaction-that is to make a molecule combine with something else, split into smaller parts or change its shape.

Nearly all metabolic reactions are reversible

Substrates ProductsForward reaction

Reverse reaction

Any reversible reactions tends to run spontaneously towards chemical equilibrium

Four features of enzymesEnzymes are catalytic molecules ; they speed the rate at which reactions approach equilibrium

All enzymes have the following features:

1) Enzymes do not make anything happen that could not happen on its own, but they make it happen hundreds to million times faster.

2) Reactions do not permanently alter or use up enzyme molecules.

3) The same type of enzyme usually works for both the forward and reverse directions of a reaction.

4) Each enzyme is very specific about it substrates that it can chemically recognize, bind and modify in certain ways.

Enzyme-substrate interactionsA metabolic reaction occurs when participating molecules collide with some minimum amount of energy (activation energy). Collisions can be spontaneous or enzymes can promote it. Activation energy is like a hill, an energy barrier that must be crossed before a reaction can proceed.

Enzymes can make the energy barrier smaller.

How does the enzyme make the energy barrier smaller?

The enzyme has one or more active sites. At these surface crevices an enzyme interacts with its substrate and catalyzes a reaction. Model shows how a molecule of glucose binds to the active site of the enzyme hexokinase. When the glucose molecule makes contact with the active site parts of the active site close around it and prod the molecule to enter into the reaction.

An example of an active site

This one is an hexokinase, an enzyme that phosphorylates glucose and other six-carbon sugars.

Daniel Koshland’s induced-fit model

The surface region of each substrate has chemical groups that are almost but not exactly complimentary to chemical groups in the enzyme active site.

When substrates first interact with the active site the contact strains certain bonds.

Strained bonds are easier to break, so they promote the formation of new bonds in the product.

When substrates fit most precisely into the active site of the enzyme they are in an activated transition stateand will now react spontaneously. Thus the reaction must proceed.

What induces the transition state?

The mechanisms involved are as follows:

1. Helping substrates get together. The probability of collision among substrate molecules is increased locally by binding at the active site.

2. Orienting substrates in positions favoring reaction. On their own substrates collide in random directions. Binding to the active site orients them such that the chemical groups can collide in a precise manner.

3. Promoting acid-base reactions. In many active sites the side chains of amino acids of the enzyme are such that they can accept or donate hydrogen atoms to the substrates. This addition or loss of hydrogen may destabilize the covalent bonds in the substrate and make it easier to break.

4. Shutting out water. Some active sites bind substrates so tightly that some or all water is shut out of the site. A non-polar environment lowers the activation energy of certain reactions.

Factors influencing enzyme activity

Temperature

Salt

Increased molecular motion beyond a certain point disrupts weak bonds holding the enzyme in shape and the enzyme falls apart.

Increase in salt concentrations disrupt the interactions that hold the three dimensional shape of the protein together.

pH Increase of decrease of pH beyond 6-8 disrupts the enzyme structure

How is enzyme action controlled?

1. By changing the availability of the enzyme by regulating its synthesis and degradation rates as well as by regulating the availability of the active form of the enzyme.

2. By regulating the availability of the substrate.

Allosteric regulation of enzyme activity

Feedback inhibition of enzyme activity

Substrate

Enzyme 1

Enzyme 2

Five kinds of enzymes are working in sequence to convert a substrate to a product (tryptophan).

When the end product accumulates, some excess molecules bind to the first enzyme blocking the entire pathway.

Reactants, products and cell membranesThe cell membrane maintains the concentration of reactants and products on either side of it by selectively allowing some substances to pass through and not others at certain times and in certain ways.

Means by which substances can cross the plasma membraneSmall nonpolar molecules and gases can go through the lipid bilayer. Water molecules can sometimes squeeze through gaps when the hydrocarbon chains of lipids flex.

Polar molecules or ions have to go through channels or transporters.

Bulk exportation and importation occurs through exocytosis and endocytosis

Working with and against concentration gradientsConcentration gradient: Difference in the number of molecules and ions of a substance in two adjoining regions.

Diffusion : The net movement of like molecules or ions down the concentration gradient

The rate of diffusion depends on the following five factors:

Size : It takes more energy to move a larger molecule than a smaller molecule therefore smaller molecules diffuse faster.

Temperature : Molecules move faster at higher temperature and therefore collide more and thus the rate of diffusion is higher at a higher temperature.

Steepness of the concentration gradient: Molecules collide more often in the regions of higher concentration hence the rate of diffusion is higher with steeper gradients.

Charge : Charge can affect the rate and direction of diffusion between two regions because each ion or charges particle in a fluid contributes to the overall charge of the fluid. A difference in the charge between two regions can affect the rate and direction of diffusion between the two.

Pressure: Pressure squeezes molecules together hence they collide more often and thus diffusion occurs faster at higher pressure.

Passive transport

Flow of solutes through the interior of transport proteins down their concentration gradient.

Active transportEnergy driven mechanisms where “membrane pumps” make solutes cross against their concentration gradients.