Koster text: Life5th Edition - Purves..: Read Chapter 6  for this lecture

General Biology2 Spring 2000

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ENERGY, ENZYMES, AND METABOLISM
 

I. Energy of Reactions

A. Thermodynamics = study of energy of reactions
 -- life depends on controlled flow of energy.

 1. Energy exists in different forms:
  a. kinetic = due to motion [car rolling down hill]
  b. potential = due to position [car parked at top of hill]
  c. chemical = due to composition (potential in molecular structure)
   [sugar vs. CO2]
  d. thermal = due to temperature (molecular motion)

 2. Organisms transform energy from one form to another, according to the Laws of Thermodynamics.

B. Laws of Thermodynamics

 1. First = "Conservation of Energy" = Total amount of energy in the universe is constant.
 Energy can be transferred and transformed, but it can be neither created nor destroyed.

 2. Second = "Law of Entropy" =  Every energy transfer or transformation in universe increases the entropy or disorder of the universe.
 Entropy = measure of disorder or randomness, often seen as heat, which is random thermal energy.
 Example: running car's engine
  25% of energy expended produces motion
  75% of energy produces heat

 So, for all energy transformations from chemical or potential energy, only part of the energy can actually be used to do work (usually kinetic energy).  The rest of the energy will be lost as an increase in entropy (usually heat).  The part of the total energy that can actually be used to do work is called free energy.

 3. Free energy = portion of system's energy that can perform work.  Symbolized by "G". (for Gibbs Free Energy)

C. Spontaneous reactions depend on change in free energy.

 Intuition can tell us whether many reactions will occur:
e.g., toss lit match into balloon full of H2 (Hindenburg), and a reaction occurs explosively. (Explosion = increased disorder or entropy!)
 reactants --> products
 2H2 + O2 (+ match)--> 2H2O + heat

But you don't expect to see water suddenly suck up heat from surroundings and produce H2 and O2.

Similarly, if we hold a lit match to wood, it will burn, releasing CO2, H2O, ashes, and heat.  However, you don't expect to see CO2, H2O, and ashes ever spontaneously aggregate to form a chunk of wood!

Many reactions are not obvious, though, so we need to develop rules to predict whether or not reactions can occur.

1. In any spontaneous process, the free energy of the system decreases.
 Reactants lose free energy to form products.   (Fig. 6.5)
  a.  G = change in free energy during reaction =
   Gproducts - Greactants
  b.  G is negative for spontaneous reactions or processes.
    G < 0

 2. Loss of free energy often, but not always, occurs as a liberation of heat.
   a. Spontaneous reactions are called exergonic because energy is lost.  Exergonic = energy outward.
  b. If free energy is lost as heat, reaction is also called exothermic (heat outward).

 3. Spontaneous reactions can sometimes be reversed by putting free energy into the system.
  a. endergonic (energy inward).
  b. If the energy input is in the form of heat, the reactions are also called endothermic (heat inward).
 

D. Equilibrium

 1. Chemical reactions are reversible.      (Fig. 6.6)
Reactants <--> Products
At some point during the process, the rate at which reactants are being converted
to products equals the rate at which products are being converted back into reactants.
This point is called the equilibrium point of the reaction.

 2. At Equilibrium point, there is no further net change in the system, so  DG = 0.

 3. Depends on the initial DG of the reaction.
The more negative D G is, the farther the net reaction will proceed towards the products.  In other words, if the free energy if the products is very much less than the free energy of the reactants, thermodynamics dictates that most of the reactants will be converted to products.  In these cases, the equilibrium point lies far to the right, towards the products.
  Can visualize reaction as proceeding from an initial state where there is a high free energy in reactants towards a final state where there is a low free energy, with a mix of products and reactants.  The ratio of products to reactants at end depends on their relative free energies.

 4. Equilibrium equals Death
Remember that at equilibrium point,   DG = 0.  Because DG is measure of ability to do work, when a reaction reaches equilibrium, no more work can be done by the system.  This happens in a test tube, but would not be good in a cell.  Living cells constantly use strategies to keep the system away from equilibrium.

  a. Metabolic pathways link multiple reactions together in series within cell so that the products of one reaction are used as reactants in the next.  Thus, the products of the first reaction never accumulate, and first reaction never comes to equilibrium.  The same tactic uses products of second reaction as reactants of third reaction, keeping second reactions from reaching equilibrium.
This can occur with many reactions linked together, none of which come to equilibrium within the living system.

   i) Metabolism = totality of an organism's chemical processes.

   ii)Catabolic pathways = reactions that break down complex molecules to simpler molecules.  These pathways usually result in the net release of energy

   iii) Anabolic pathways = reactions that consume energy to build complex molecules out of simple ones.

E. Energy Flow in Living Systems
     Bioenergetics = study of energy flow in living systems
1.  Why is energy needed for life?  Because the reactions that characterize living systems often do not have  DG < 0.  Without inputs of energy, living organisms could not:
  a. synthesize complex molecules
  b. do mechanical work (muscle contraction, flagella beating, etc.)
  c. transport molecules across membranes against diffusion
  d. perform other types of work

2.  Energy in living systems is often carried within the structure of a molecule called ATP, adenosine triphosphate.
 (chemical or potential energy)
  a. Structure: adenosine (nucleotide) + 3 phosphates stuck together on one end. (Fig. 6.7)
  It takes energy to force the negatively charged phosphates together (like compressing a spring), so energy is released when a phosphate is broken off (releasing spring).
   i) ATP hydrolysis:
  ATP + H2O --> ADP + Pi ,  where ADP = adenosine diphosphate, Pi = inorganic phosphate
   DG = -7.3 kcal/mol (standard state; in cell it's more like -12 kcal/mol)
 (calorie = energy needed to raise temp of 1 g of water by 1 C;
 kcal = 1000 cal = dietary Calorie)

 3. ATP can be used to fuel endergonic reactions in living systems through process called energy coupling.   (Fig. 6.10, 6.16)
 Energy coupling = endergonic reactions ( DG > 0) can be fueled by the release of energy from exergonic reactions (D G < 0).
 Thus, a non-spontaneous reaction can be made to occur in a living system by providing energy from another reaction that is coupled to it.
 e.g. glucose + fructose --> sucrose + H2O   DG = 5.5 kcal/mol
  ATP + H2O --> ADP + Pi      DG = -7.3 kcal/mol
         net  DG = -1.8 kcal/mol
 The net  DG of the coupled reactions is < 0, so they are spontaneous.
 By itself, sucrose synthesis could not occur, but coupled to ATP hydrolysis, it can.

 4. ATP contains a useful amount of energy for most biological work. [money-wise, it's like a $1 bill.]
 work to get it -- energy input to make ATP
 carry it around -- moves around cell
 trade it for other things -- use it to provide energy for biological work
  a. short-term energy storage
  living systems use other molecules for long-term energy storage:
   carbohydrates, lipids [$100 bills]
  b. cells need to convert carbohydrates and lipids into ATP to provide useful energy currency.
  c. coupling reactions is like buying something and getting no change, so want to use smallest possible currency to cover cost.  Just as you wouldn't want to use a $100 bill to buy a can of Coke, you wouldn't want to use something like glucose to fuel a single endergonic reaction.
 

II. Kinetics of Reactions

A.  Free energy of a reaction (DG) tells us if that reaction
    will occur, but tells us nothing about the rate of the reaction.
 1. Activation energy = Ea = barrier that must be overcome before a reaction can occur, even for a spontaneous reaction.    (Fig. 6.11)
  May represent:
  a. energy needed to start reaction
  b. physical separation of reactants
  c. unfavorable chemical environment for reaction
  (e.g., pH, ionic strength)
  d. other factors that hinder progress of reaction

2. Heat can overcome activation energy (like lit match starts wood burning), but too much heat is not good for cellular structures.  High temperatures denature (disrupt) cellular structures by destroying the hydrogen bonds that hold them in their shapes.
 3. Catalysts lower activation energy of reactions, so allow favorable reactions to proceed without large inputs of heat.   (Fig. 6.14)
  may work by:
  a. bringing reactants together
  b. altering chemical environment around reactants
  c. doing other things to remove obstacles to reaction progress.
 
 4. Catalyst = something that speeds up a reaction but is unchanged when the reaction is over.
  a. speeds up rate of spontaneous reactions (where D G< 0)
  b. does not affect  DG.  Cannot force a reaction to occur if  DG > 0.
  c. does not affect equilibrium point.  Just allows reaction to reach equilibrium point faster.
  d. does not add energy to reactions; lowers the Ea.

B. Enzymes = proteins that act as biological catalysts.
    Most prevalent catalysts in biological systems.     (Fig. 6.13)

C. Ribozymes = RNA molecules that act as biological catalysts.
    Recently discovered.  Believed to be primitive, possibly first
    type of biological catalyst.  Catalyze few reactions involving
    RNA in cells.

III. Enzymes

A. Generalized formula for enzyme-catalyzed reaction:
         E + S --> E-S complex --> E + P
where E = enzyme, S = substrate (reactant), P = product

Enzyme physically binds to substrate during catalysis.  When reaction is complete, enzyme releases product and starts over with new substrate.

B. Catalysis = process by which enzymes speed up
    metabolic reactions by lowering Ea.
1. Rate of enzyme-catalyzed reaction may be 1 million to 1 trillion times faster than same reaction without enzyme.
 2. Turnover number = # of reactions catalyzed per second by a single enzyme.  Ranges from 100/sec to 10 million/sec.
 3. Activity = general term for how fast an enzyme functions.
  Depends on many factors, including:
  a. turnover number
  b. number of enzyme molecules
  c. regulation by cell (we'll discuss more later)

C. Enzymes are substrate-specific
1. Each type of enzyme only catalyzes one type of reaction for a substrate, or sometimes, for closely related substrates.
 e.g., Amylose and cellulose are both polymers of glucose, but they differ in the shape of the bond that links the glucose units together.
Amylose = starch; Cellulose = plant cell walls: paper, cotton, etc.
Humans have an enzyme (amylase) that can break the bonds in amylose to release energy for our cells' needs.  This enzyme is highly specific and does not recognize the bonds in cellulose, so it passes through without being broken down.

D. Active site = site on enzyme that binds substrate(s)
    and catalyzes reaction.
1. Tertiary structure of protein forms surfaces with clefts lined by the amino acids that form the enzyme.  Active site is usually located in cleft or crevice on surface of enzyme.
 2. These active sites have distinct shapes and chemical properties because of the amino acids that form them.  Therefore, only certain substrate molecules can fit into these active sites and be worked on.  This is the physical reason for the specificity of an enzyme.
 3. Enzymes recognize substrate(s) based on their molecular shape, charge, polarity, and other chemical properties.
 4. Amino acids that line active site are often involved in catalysis by binding to substrates and pulling or pushing them into shape needed for the reaction.
 5. Induced fit = in many cases, enzyme changes shape as substrate is bound.  This helps the substrate fit better and also makes the E-S complex more reactive to lower the Ea.   (Fig. 6.18)

E. Cofactors = non-protein molecules that are needed for the activity of a particular enzyme.
 1. May be simple, like inorganic metal atoms or ions,
  e.g., Zn, Fe, Cu, Mg
 2. May be complex organic molecule = coenzyme. (Fig. 6.19)
  a. most vitamins are coenzymes or their precursors.
 3. Cofactors may always be bound to the enzyme, or they may only bind at the same time as the substrate(s).
 
F. Enzymes can couple endergonic and exergonic reactions.
 1. Physically link two reactions so that exergonic reaction fuels endergonic one.
 2. Both reactions can proceed if net DG < 0.

IV. Control of Enzyme Activity

A. Enzymes control metabolism in biological systems.

1. Metabolism = chemical reactions in organism that are catalyzed by enzymes.
  a. anabolic and catabolic reactions
  b. rates are regulated by enzyme activity
  c. most enzyme-catalyzed reactions are reversible (with the same enzyme); extent of reaction depends on  DG (as usual)
  d. enzymes physically link coupled reactions

 2. Enzymes are proteins and, thus, are products of gene action.
  a. Genes on DNA that code for enzymes can be transcribed and translated to make more enzyme molecules.

B. Enzyme activity is affected by inorganic factors.
 1. Temperature:   (Fig. 6.26)
  a. Each enzyme has an optimal temperature; its activity is less at temperatures greater than or less than the optimal temp.
  b. for mammalian enzymes, the optimal temp. is usually around 40 C (body temp.)
  c. enzymes from other organisms may have other optimal temps. e.g., thermophilic bacteria from hot springs have enzymes with optimal temperatures near 80 C.
 
 2. pH:     (Fig. 6.25)
  a. each enzyme has an optimal pH; activity is less at other pH value.
  b. most pH optima range between pH 6 and pH 8, but some are more extreme, depending on the environment in which the enzyme normally functions.
  e.g., pepsin digests protein in stomach: pH optimum is ~2
  trypsin digests protein in intestine: pH optimum is ~8
 
 3. Denaturation = physical and/or chemical effects that alter the shape of the enzyme such that its activity is hindered.
e.g., heat, pH changes
 

C. Enzyme Regulation
1. Enzyme concentration:
  a. Number of enzyme molecules usually is not great (because enzymes are reusable) but can be increased by gene action.
 2. Substrate concentration:
  a. Activity increases with concentration until enzyme becomes saturated.  Additional substrate cannot increase overall activity once all enzyme molecules are working as fast as they can.
 3. Enzyme inhibitors = molecules that bind to enzymes and decrease their activity.
  a. Competitive inhibitors = molecules that bind to the active site of the enzyme and prevent substrate molecules from binding.
   i) reversible = adding more substrate can boost activity by outcompeting the inhibitor.  (Fig. 6.21)
   ii) irreversible = the inhibitor binds irreversibly to the enzyme and is toxic. e.g., cyanide binds to active sites for O2 and cause those enzymes to be non-functional.   (Fig. 6.20)
  b. Non-competitive inhibitors = molecules that bind to enzyme away from the active site and change shape of the enzyme so that it can no longer bind the substrate and/or catalyze the reaction well.   (Fig. 6.21)
 4. Allosteric regulation = regulation of enzymes by cellular molecules as part of normal metabolism.   (Fig. 6.23)
  a. Regulators bind to the enzymes at a site called the allosteric site, which is a site away from the active site.
  b. Allosteric activators alter enzyme to increase its activity.
  c. Allosteric inhibitors alter enzyme to decrease its activity.
 

D. Metabolic pathways  (Fig. 6.24)
 1. Usually involve several steps, each catalyzed and regulated by its own enzyme.
 2. Slowest step in pathway is called rate-limiting reaction.
  a. often early in the pathway
  b. often regulated by cell to control the rate of the entire pathway.
 3. Feedback-inhibition = product of pathway acts as allosteric inhibitor of an enzyme early in the pathway (usually rate-limiting reaction).  Acts to slow the pathway when enough of the product is present.
 4. Structural order also helps regulate metabolic pathways.
  a. often have multienzyme complexes = several enzymes that bind together and perform several steps of a metabolic pathway.
  b. compartmentation within organelles also facilitates the efficient performance of metabolic pathways.
  e.g., aerobic respiration confined to mitochondria,
  -- photosynthesis within chloroplast
  -- lipid synthesis within membranes
 

CELLULAR RESPIRATION

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