Transcript Energy, Catalysis, and Biosynthesis

Energy, Catalysis, and
Biosynthesis
The Chemistry & Physics of Life
Laws of Thermodynamics

1st Law

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The total amount of energy in any process
stays constant OR energy in the universe
stays constant
2nd Law

Although the total energy in the universe
doesn’t change, less and less is available for
work
What is Work?
Moving an object against a force
 4 types

Mechanical – moving against a force
 Chemical – creating chemical bonds
 Concentration – changing concentration from
one area to another
 Electrical – changing the separation of
charges

1st Law of
Thermodynamics

Energy can be
converted from
one form to
another but cannot
be created or
destroyed
Universal Tendency – More Disorder

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2nd Law of Thermodynamics – degree of disorder increases
Movement towards disorder is a spontaneous process
Measure of disorder is entropy,
greater disorder = greater entropy
Energy can be transformed
from one form to another
FREE ENERGY
(available for work)
vs.
HEAT
(not available for work)
Thermodynamics of Cells

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Part of the energy that cells use is converted to heat
and is released into the area around the cell
While inside the cell becomes more ordered, the heat
put into the area around the cell causes more
disorder – disorder is greater outside the cell than the
order inside the cell
CHEMICAL REACTIONS AND ENERGY TRANSFERS
ARE CONTROLLED IN LIVING SYSTEMS
Enzymes - mediate chemical reactions
Energy transfers are done in steps

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Example: There are two ways to get from the top of a very tall
building to the bottom floor. Keep in mind that a person on the top
floor of a building has a lot of potential energy relative to the
ground level.
 Jump out the window!
 Take the stairs and expend the potential energy a little at a time
until you get to the bottom floor.
Both methods get you to the bottom floor but one method is
destructive, while the other is not. These two situations are
analogous to uncontrolled vs. controlled energy transfers.
Potential energy transferred gradually so more work is done than
heat.
Hydrogen gas + oxygen + activation energy  water and explosion
of heat, light and sound! (see
http://www.youtube.com/watch?v=iwBYhJ2jHWw)
Hydrogen is broken; electrons and protons released; electron
transport system extracts some free energy from electrons in a
stepwise manner (redox reactions) + heat; low energy electron
combines with oxygen and hydrogen to produce water  process
is non-destructive to life & some energy used to do work!
Regulation of energy-releasing (cellular
respiration) and energy-acquiring chemical
reactions in biological systems
•Chemically-mediated by enzymes and co-factors
•Occur in a step-wise manner
2H2 + O2  2H2O + energy

+

+
2H-H + O=O  2H2O + energy
Modes of Energy Transformation: Rapid &
Uncontrolled
2H2 + O2  2H2O + energy
 Release of energy can be uncontrolled
and liberated mostly as heat!

On May 6th, 1937 in Lakehurst,
New Jersey. The German
passenger Zeppelin Airship called
the Hindenburg, was attempting a
mooring when it exploded.
Modes of Energy Transformation: Released
in controlled steps or stages

2H2 + O2  2H2O + energy

Released in steps to salvage free energy and minimize
heat production
The electrons from the
hydrogen bond go through a
series of oxidation & reduction
reactions. During each step
some energy is harvested, while
the remainder is released as
heat.
Chemical Reactions
 Occur
in the cell under the control of
specialized proteins called enzymes
 Each one accelerates or catalyzes
just one of the many reactions of the
cells
Enzymes
Metabolic pathways
• series of enzyme-controlled reactions leading to formation of a
product
• each new substrate is the product of the previous reaction
Enzyme names commonly
• reflect the substrate
• have the suffix – ase
• sucrase, lactase, protease, lipase
Tyrosinase and Melanin
Grey
Squirrels:
Melanic and
Albino Forms
tyrosinase - A copper-containing
enzyme of plant and animal
tissues that catalyzes the
production of melanin and other
pigments from tyrosine by
oxidation, as in the blackening of a
peeled or sliced potato exposed to
air.
Factors that influence enzymatic activity
Cofactors
• make some
enzymes active
• ions or coenzymes
Factors that alter enzymes
• temperature and heat
• radiation
• electricity
• chemicals
• changes in pH
Coenzymes
• organic molecules
that act as cofactors
• vitamins
Factors that influence enzymatic activity
Competitive inhibitor - a substance that
binds to the active site of the enzyme and
compete with the substrate for this place.
Non-competitive or allosteric inhibitor - a
substance that binds to another part of the
enzyme and cause an allosteric change in
the overall shape of the enzyme; this
changes the form of the active site so the
substrate can't bind to it.
Allosteric Activators - essentially this is the
reverse of an allosteric inhibitor.
Temperature Sensitive Tyrosinase –
Siamese Cats & Himalayan Rabbits
Cells Chemical
Pathways All
Interconnect
PHOTOSYNTHESIS & CHEMOSYNTHESIS

Almost all plants are photosynthetic autotrophs, as
are some bacteria and protists
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Autotrophs generate their own organic matter through
photosynthesis or chemosynthesis
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Sunlight energy is transformed into the energy stored in the form of
chemical bonds
Chemical energy is transformed into the energy stored in the form of
chemical bonds
(c) Euglena
(b) Kelp
(a) Mosses, ferns, and
flowering plants
(d) Cyanobacteria
Bacteria in Thermal Vents on the Sea Floor
Tubeworms and
other animals
living around
thermal vents in
the ocean
depend on
chemosynthetic
bacteria for
food.
THE SUN: MAIN SOURCE OF
ENERGY FOR LIFE ON EARTH
Light Energy Harvested by Plants &
Other Photosynthetic Autotrophs
6 CO2 + 6 H2O + light energy → C6H12O6 + 6
O2
Sunlight – Ultimate Energy Source
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All organisms live on the organic molecules that are
made by photosynthetic organisms
Photosynthesis traps the energy of the sun in the
chemical bonds of sugars which can be turned into
nucleotides, amino acids and fatty acids
2 steps
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Energy stored in ATP and NADPH, release O2
ATP and NADPH drive carbon fixation  H2O and CO2 from
air and make sugars
Food Chain
THE FOOD WEB
Metabolism
2
opposing pathways
make up metabolism
– process of
obtaining energy and
building blocks from
‘food’ molecules
 Anabolism – process of
using energy and
building blocks to create
the macromolecules
that make up the cell
 Catabolism
Energy Releasing Metabolic Reactions
Energy
• ability to do work or change something
• heat, light, sound, electricity, mechanical energy, chemical
energy
• changed from one form to another
• involved in all metabolic reactions
Release of chemical energy
• most metabolic processes depend on chemical energy
• oxidation of glucose generates chemical energy
• cellular respiration releases chemical energy from molecules
and makes it available for cellular use
Oxidation of Organic Molecules
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Oxidation can be the process of adding O atoms
Cells can obtain energy from sugars by allowing the C and
H to combine with O2 to produce H2O and CO2 in a
process called respiration
Photosynthesis and respiration work together
Oxidation and Reduction

Oxidation can also be the process of electron
transfer from one atom to another
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Oxidation is the removal of electrons
Reduction is the addition of the electrons
Oxidation and reduction always occur
simultaneously
These reactions also occur in molecules with a
partial shift of electrons as in polar bonds
Also with the addition of a H+ (hydrogenation
reaction) or the removal of a H+ (dehydrogenation
reaction)
Reducing and Oxidizing Agents
Reducing agent
(electron donor)
Oxidizing agent
(electron acceptor)
A
e-
B
e-
A is oxidized –
loses electron
B is reduced –
gains electron
e-
e-
A
B
Oxidized
Reduced
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Free Energy
Free Energy (G)
Energy that can be harvested to do
work or drive a chemical reaction
(remember the 4 types of work)
 Exergonic reactions – go from higher to
lower energy level and are spontaneous
 Endergonic reactions – go from lower to
higher energy levels and require an
input of energy
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Reactions
Barriers to Chemical Reactions
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Chemical reactions
only proceed in the
direction of the loss
of free energy
Molecules in stable
states need to have
an input of energy to
cause them to go to
a lower energy state
– activation energy,
always positive
Activation Energy
Activation Energy
In chemistry, molecules that decrease
activation energy are catalyst such as
platinum and zinc
 In cells the activation energy is reduced
by a special protein - enzyme
 Enzymes link 1 or 2 molecules called
substrates and hold them in a way that
greatly decreases the activation energy
– transition state

Transition States
Energy Graph
Enzymes as Catalysts
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Speed up reaction rates (x ~1014)
Selective – usually 1 enzyme for 1 reaction
Have a unique shape that contains the active site
and only a particular substrate can fit
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site where reaction takes place
Remain unchanged and can be used over and over
Reactions
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For reactions to occur, the enzyme and the
substrate(s) need to be in contact with one
another
Heat from other reactions keep the substrate
moving through the cell by diffusion, can cover
great distances
Enzyme is large and relatively motionless
This arrangement allows for the substrate to
finally collide with the active site, held there by
multiple weak interactions until they dissociate
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If too strong, then would not dissociate
If wrong substrate gets into the active site, no
interactions will hold it there and it will leave quickly
Enzymatic Reactions are Coupled
Even though enzymes are good catalysts,
they are unable to perform reactions that
are thermodynamically unfavorable
 Enzyme reactions are coupled to harvest
the energy and heat from a favorable
reaction to drive an unfavorable reaction
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Coupled Reactions
G – Change
in Free Energy
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Value of G is only important
when the system undergoes a
change
G is the measure of the
amount of disorder when a
reaction takes place
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-G occur spontaneously
+G are unfavorable
Need to link a -G reaction with
a +G so that the overall G is
negative
Coupled Reactions
Concentration of Reactants
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The amount of reactants in the reaction mix is
important for the G
In a reversible reaction, i.e., can go from A to B
and from B to A, when there is more A present,
the tendency will be to go from A to B rather
than B to A
G° or standard free-energy change –
depends on intrinsic characters of the reacting
molecules
Equilibrium – forward and reverse reactions
proceed at exactly equals rates so that no net
chemical change occurs
Equilibrium

Equilibrium
constant (K) –
number that
characterizes the
equilibrium state
for a reversible
chemical reaction;
given by the ratio
of the forward and
reverse rate
constants of the
reaction
Enzymes and K
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Enzymes will lower the activation energy in
the A to B direction to the same degree as in
the B to A direction
The equilibrium constant and G° remain
unchanged
Sequential Reactions

Most of the G°
values are
known for the
reactions of the
cells and so we
can determine
overall G for a
pathway – add
up the G for
each step
Activated Carriers
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Energy released by
catabolism is stored in
the chemical bonds of
carrier molecules
The energy can be
moved around the cell
to where it is needed
Carrier molecules in
the cell are ATP, NADH
and NADPH
Activated Carriers in Metabolism
Activated Carrier
Group Carried in
High-Energy
Linkage
ATP
phosphate
NADH, NADPH, FADH2
electrons and hydrogens
Acetyl CoA
acetyl group
Carboxylated biotin
carboxyl group
S-Adenosylmethionine
methyl group
Uridine diphosphate glucose
glucose
Coupled Reactions
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Enzyme catalyzed reactions capture the
energy released from the oxidation of glucose
in a chemically useful form rather than as
heat
ATP
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ATP – adenosine
triphosphate – is the
most important and
abundant activated
carrier in the cell
Synthesized by adding
a phosphate group to
ADP (adenosine
diphosphate) in an
energy unfavorable
reaction
ATP can release the
energy when it is
needed by hydrolysis
Phosphate Transfer
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Process of transferring
a phosphate group to
another molecule is
the phosphorylation
reaction
Enzyme that performs
this reaction is a
kinase
ATP Functions in
Condensation Reactions
Transfer of a Carboxyl Group
Synthesis of Polymers
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Condensation reactions are unfavorable, require
energy input
Hydrolysis reactions are favorable, can occur
spontaneously
Polysaccharides
Proteins
Nucleic
Acids
Nucleic Acid Synthesis
NADH and NADPH
NADH and NADPH are activated carriers
that carry energy and H+
 NAD+ - nicotinamide adenine dinucleotide
 NADP+ - nicotinamide adenine
dinucleotide phophate
 Both can pick up a H+ and become
reduced, carries 2 e- and H+
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NADPH
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The phosphate
group at the end of
the molecule causes
the molecule to
have a different
shape and therefore
can interact with
different enzymes
than NADH
Purpose of NADPH and NADH
NADPH operates with enzymes that
catalyze anabolic reactions – synthesis
reactions
 NADH usually works in catabolic reactions
that generate ATP through the breakdown
of food particles
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