Intro to Metabolism

METABOLISM

Metabolism all of an organism’s chemical reactions

CATABOLIC PATHWAY

Catabolic Rxn 

• Releases energy/ “down”

• breaks down complex  molecules to simpler molecules.

• Released energy becomes available to do the work of the cell.

ANABOLIC PATHWAY

Anabolic Rxn 

• Net input of energy/ “uphill”

• Builds more complex molecules from simpler ones.

• Energy released from catabolic pathways can be stored for later use

Pathways Quiz
Release energy? catabolic

1. Store energy? anabolic

2. Build larger molecules? anabolic

3. Break down molecules? catabolic

4. Downhill? catabolic

5. Uphill? anabolic

6. What type of rxn is cellular respiration? catabolic

7. What type of rxn is photosynthesis? anabolic

8. Require enzymes? anabolic and catabolic

ENERGY -- THE CAPACITY TO CAUSE CHANGE

Kinetic Energy

• Energy of Motion 

  • Heat -- associated with the random movement of atoms or molecules

  • Light -- can be harnessed to perform work

Potential Energy 

•  Due to location, position or structure

  • chemical energy -- stored in chemical bonds because of the arrangement of atoms

  • Standing on top of a hill possesses P_E because of its altitude above sea level
    

THERMODYNAMICS

• 1st Law: the energy of the universe is constant; it can be transferred and transformed, but it cannot be created nor destroyed.

• 2nd Law: every energy transfer or transformation increases the entropy of the universe (some energy is lost as heat)

  • Entropy is the measure of disorder or randomness of matter. 

Spontaneous Process -- process is energetically favorable (can be quick or slow)

FREE ENERGY

• Free energy: energy that can perform work

  • Represent this with a ∆G.  

  • Free energy change: ∆G = G_final - G_initial 

EXERGONIC REACTIONS

Exergonic Rxns

• Net release of free energy

• Spontaneous

• G_reactants > G_products

• -∆G

ENDERGONIC REACTIONS

Endergonic Rxns

• net input of free energy

• Never spontaneous

• G_reactants < G_products

• + ∆G

3 MAIN TYPES OF WORK

1. Chemical Work -- the pushing of endergonic reactions that would not occur spontaneously  (ex: dehydration synthesis)

2. Transport Work -- pumping of substances across membranes/requires input of energy (ex: active transport of hydrogen ions in electron transport chains)

3. Mechanical Work -- physical movement (ex: movement of chromosomes during mitosis)

ATP: STRUCTURE 

ATP CYCLE

ENZYMES

Enzymes 

• Act as a  catalyst -- a chemical agent that speeds up a reaction 

Enzymes speed up reactions by lowering the activation energy

• activation energy (E_A) -- the initial investment of energy for starting a reaction 

  • the energy required to contort the reactant molecules so the bonds can break.

  • transition state = when the molecules have absorbed enough energy for the bonds to break 

ENZYMES LOWER E_A 

ENZYME-SUBSTRATE

• Substrate - the reactant an enzyme acts on 

  • the catalytic action of the enzyme converts the substrate to the product

• Reaction catalyzed by each enzyme is very specific = results from its shape -- shape of the active site and substrate is a compatible fit.

• Active site - typically a pocket or groove on the surface of the enzyme where catalysis occurs

INDUCED FIT

• As the substrate enters the active site, the enzyme slightly changes shape

• This shape change makes the active site fit more snugly around the substrate  

• This enhances their ability to catalyze chemical reactions= induced fit

4 MECHANISMS TO LOWER E_A

These 4 mechanisms reduce the amount of energy that must be absorbed to reach the transition state(E_A is proportional to difficulty breaking the bonds). 

1. Proper Orientation for a rxn to occur between the substrates

2. Bond Contortion: the enzymes may stretch, stress, distort, and bend the critical bonds bringing them to their transition state 

3. Microenvironment: Active site provides a microenvironment that is more conducive to a particular type of rxn

4. Direct Participation: Active site may participate directly in the rxn.

CONVERSION RATE

Conversion rate 

• more substrate available = more frequently they access the active sites

• At saturation

  • all enzyme molecules have their active sites engaged

  • as soon as product exits, another substrate enters

  • rate is determined by how fast the active site converts substrate to product

  • can only increase speed by adding more enzyme

OPTIMAL CONDITIONS

• Temperature -- faster molecular motion allows for more frequent collisions between substrates and active sites.

  • lower temperature means fewer collisions

  • too high? disrupts weak interactions in protein structure = denature

  • Each enzyme has its own optimal temperature (usually around body temperature)

• pH -- most fall in the 6-8 range

  • denature when out of the optimal pH

COFACTORS

• Cofactors -- Nonprotein helpers for catalytic activity

  • can be inorganic (zinc, iron, and copper)

  • coenzymes = organic cofactor (vitamins)

COMPETITIVE INHIBITOR

Competitive Inhibition

• Inhibitor binds to the active site

• Blocks the substrate from entering the active site

• active site becomes less effective 

NONCOMPETITIVE INHIBITOR

Noncompetitive Inhibition 

• Inhibitor does not bind to active site (“non- competitive” for active site)

• The binding of the inhibitor changes the shape of the protein

• active site becomes less effective 

ALLOSTERIC REGULATION

Allosteric regulation 

• Changes between 2 different shapes: active and inactive

• Can be inhibition or activation 

• It is a non-competitive interaction

ALLOSTERIC INHIBITION

• An inhibitor binds to the regulatory site and stabilizes the inactive form of the enzyme

• Binding of one inhibitor will affect the active sites of all subunits.

ALLOSTERIC ACTIVATION

• An activator binds to the regulatory site and stabilizes the active form of the enzyme

• Binding of one activator will affect the active sites of all subunits.

FEEDBACK INHIBITION

• Metabolic pathway is switched off by the binding of its end product to an enzyme that acts early in the pathway.

• End product acts as the inhibitor

• Prevents the cell from wasting chemical resources by making more than is necessary