Bioenergetics

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• Bioenergetics
• - The flow of energy in the cell.
• Energy is needed for four important changes
• in a living organism
• Biosynthesis
• 2. Mechanical work
• 3. Concentration work and ion pumps
• 4. Heat

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• Biosynthesis
• All biological materials go through constant
• turn over of degradation and synthesis
• For small molecules to combine and form
• macromolecules, new chemical bonds are
• formed.
• Bond formation is energy consuming.

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2. Mechanical work physical change of
position and orientation Muscle
contraction, movement of flagella Cellular
transportaion (endocytosis/ exocytosis)
Movement of chromosome during cell division
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3. Concentration work and ion pumps Membrane
pumps moves ions and other molecules across
membranes against their concentration
gradient. E.g. Glucose absorption, Ca storage
and membrane potential.
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4. Heat 2/3 of energy is produced in the form of
heat. To maintain the body temperature at 37 C.
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Most organisms obtain energy from sunlight or
food materials. Depending on the different
energy source, there are two categories of
organisms Phototrophs Energy from
light Chemotrophs Energy from organic compoun
ds
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There is constant flow of energy in
nature. Light energy from the Sun can be
absorbed by phototrophs, which allows
biosynthesis and growth in plants. Organic
compounds in plants can be ingested by
chemotrophs, become oxidized. Energy is produced
in the forms of ATP and heat Heat and CO2 are
released into nature. CO2 is used by phototrophs
for photosynthesis
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Law of thermodynamics The total amount of
energy in the universe remains constant,
although the form of the energy may change. In
a single organism, energy transformation occurs
along with the metabolism and energy flows
between one molecule to another.
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Standard Free Energy Change ?G free energy
change ?Go free energy change under standard
condition (1 atmosphere at 25oC, solute
concentration 1M). ?Go' Standard free energy
change when pH 7 It defines the difference
b/w the energy content of products and the
energy content of reactants under standard
condition.
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?Go can be calculated In a reaction A B C
D
?Go - 2.303RT logKeq R, the gas constant
8.315 J/mol T, the absolute temperature 298K
(corresponding to 25oC) Keq, the
equilibrium constant under standard
condition. Keq C D A B
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By knowing the sign and value of ?Go, one can
predict whether a biochemical reaction is
thermodynamically favorable or not and how much
energy is released or required.
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• ?Go 0 System at equilibrium, no release or
  requirement of energy.
• ?Go lt 0 Reactants have higher energy level.
• Reaction releases energy as it approaches
  equilibrium (exergonic).
• ?Go gt 0 Reactants have lower energy level.
• Energy needs to be added in, in order for
  the products form (endergonic).

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If a reaction is favorable under standard
condition (releasing energy) the ?Go' value will
be negative. If a reaction is
thermodynamically unfavorable, the ?Go' value
will be positive.   For exp., a reaction with
?Go' of 100 kJ/mol is more favorable than the
one with ?Go' of 10 kJ/mol.
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• Introduction to Enzyme
• Permit reactions to go at conditions that the
  body can tolerate.
• Enzymes are typically very large proteins.
• Can process millions of molecules every second.
• Very specific only react with one or a few
  types of molecules.

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• How does an enzyme work?
• It accelerate a reaction by lowering activation
  energy.
• All chemical reactions require a minimum
• energy input (activation energy) to get
  initiated.

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activation energy
Energy
reactants
2 H2O2
products
?H
2 H2O O2
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• Properties of Enzymes
• Enzymes speed up reaction by lowering
• activation energy
• They do not change the position of the reaction
• equilibrium the amount of the products is not
• increased, but the rate for reaching the
• equilibrium is increased.

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 2. Enzymes are highly specific Each enzyme
usually catalyzes a single reaction.   Before
reaction substrate has to bind to the enzyme at
a specific site active site.   Enzyme
substrate ? ES ? enzyme product The active
site (where substrate binds) has to match with
the substrate in shape lock and key
relationship.
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3. Enzymes can be saturated Usually each enzyme
has only one or a few active sites, one on each
subunit. The concentration of substrate
molecules is usually higher than that of enzyme
active sites. Therefore, enzymes can be
saturated. A reaction can only reach certain
rate (Vmax) due to the limited enzyme active
sites
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4. Enzymes are not changed by the biochemical
reactions. Enzyme substrate ? ES ? enzyme
product They can be reused after the reaction.

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• Some enzymes require a second species to be
• present in order to do their work.
• Cofactor - usually a metal ion that holds
  protein in the proper shape.
• Coenzymes - are usually small organic molecules
• associated with vitamins.
•  
• Apoenzyme Coenzyme ? Holoenzyme
• (Inactive form) (or Cofactor) (active
  form)

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Coenzyme Vitamin NAD Niacin FAD
Riboflavin Biotin Biotin Coenzyme
A Pentothenic acid Other vitamins related
with cozymes vitamin C, vitamin B family.
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Factors that affect enzyme activities a.
Substrate concentration   b. Enzyme
concentration     
The higher E, the higher the reaction rate,
as long as there are enough substrate.
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c. pH optimal pH for most enzymes range from
6-8. Wrong pH ? protein denature.
However, there are some exceptions.
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d. Temperature optimal temperature for most
enzymes range from 25 40oC.
When is T lt 37oC, the reaction rate will
increase proportionally with the increase of
temperature, until reaching certain point.
temperature

• T gt 53 C, most enzymes are denatured, but there
  are
• exceptions

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• Classification of enzymes based on type of
  reaction
• Oxidoreductase catalyze a reduction-oxidation
  reaction
• Transferase transfer a functional group
• Hydrolase cause hydrolysis reactions
• Lyase cause formation of double bonds
• Isomerases rearrange functional groups
• Ligase join two molecules by forming
• C-C, C-O, C-S, C-N
  bonds

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• Characteristics of Enzyme Active Sites
• Active site or catalytic site or binding site
• iss where substrate binds with the enzyme
• And where the reaction actually occurs.
• There are two theories to interpret enzyme-
• substrate binding.

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Fig. 6-6
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Cellular Regulation of Enzymes
1). Allosteric interaction Most allosteric
enzymes are oligomeric proteins with two binding
sites catalytic site and regulatory site.
  The binding of an effecter to the regulatory
site causes conformational change of the protein
and influences the activity of the catalytic
site.  
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• Effectors or modulators
• Small molecules that binds to the enzyme
• and alters the conformation of the active site.

• Positive effectors - stimulate an enzyme
• Negative effectors - inhibit an enzyme

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• A positive modulator or effector is similar to a
  coenzyme.

Example of positive allosterism.
Allosteric enzymes transmit messages via
conformational changes between regulatory site
and catalytic site.
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• Reactions in a metabolic pathway are often
• grouped in sequences.
• The first enzyme is usually a regulatory enzyme
• that controls the rate for the entire sequence.
• E1 can be stimulated by the starting material
  A.
• It may also be inhibited by the final product
  P.

A B C D
F P
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• Negative feed back control - end product
  inhibition
• Enzyme - substrate reaction is in an equilibrium
• If product builds up, the reaction slows.
• E S ES ES EP
  E P

Equilibrium shifts to left if product starts to
build up
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• 2). Regulation by addition and removal of
• chemical groups
• Phosphorylation of an enzyme can either activate
  or inhibit it.
• For example, glycogen phosphorylase, an enzyme
• that catalyses the hydrolysis of glycogen can be
• Activated by the attachment of a phosphate group
• (phosphorylation) and inactivated by the removal
  of it
• dephosphorylation)

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  3). Proteolytic Activation Some enzymes are
synthesized in an inactive form, which is later
activated at an appropriate situation.    
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• Activation by proteolytic cleavage
• Proteolytic cleavage - breakage of peptide bonds
• by peptidases or proteases.
• Some enzymes are initially produced in an
  inactive form zymogen, and are activated by the
  removal of one or more short pieces of peptide
  sequences

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Many digestive enzymes are regulated this way.
For. Example, chymotrypsinogen ?
?-Chymotrypsin ? ?-chymotrypsin   The activation
process is completed by same type of enzymes or
even the active form of the same enzyme.
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Activation of Chymotrypsin
chymotrypsinogen (inactive)
trypsin
?-chymotrypsin (active)
chymotrypsin
Ser - Arg and Thr - Asn 14 15
147 148
?-chymotrypsin (active)
The three pieces are held together by inter chain
disulfide bonds.
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RNA molecules as enzymes - ribozymes
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