Transcript Ch 5 The Working Cell

The Working Cell
Chapter 5
Overview
• Energy
• Metabolism
• Enzymes
• Metabolic
Pathways
Energy
The capacity to do work
In living organisms, chemical bonds are
made & broken so that energy can be
exchanged or transformed
Kinetic Energy
Energy of motion
Work needed to accelerate
an object from rest to its
current velocity
Includes light, sound,
electricity, & heat energy
Potential Energy
The stored energy of position
The work done by a certain force (e.g. gravity)
on an object relative to its position
Includes chemical & battery energy
Kinetic and Potential Energy as a
Pair
Potential energy is converted into kinetic
energy & vice versa
Imagine a rubber band:
When you stretch a rubber band, you give
it potential energy
When you release it, it has kinetic energy
Thermodynamics
The study of the effects of work, heat, &
energy on a closed system
Energy can be exchanged between
physical systems as heat or work
1st Law of Thermodynamics
“Energy can not be created or destroyed”
A finite amount exists in various forms,
which can be converted to other forms of
energy
e.g. from work to heat, from heat to light, from
chemical to heat, etc.
e.g. The chemical energy released from burning a substance
is converted into light & heat energy
In the conversion of energy from one form
to another, some energy is lost as heat
(i.e. not 100% efficient)
Therefore, energy is unavailable to do
work
Heat is a disordered form of energy
Release of heat makes universe more
random & disorganized
 energy conversions ↓ order & ↑ entropy
2nd law of thermodynamics
“Energy tends to flow from concentrated to
less concentrated forms”
Goes from being localized to being spread
out
(why hot things cool down when removed from
heat, why air in a tire will escape from a small
hole, etc.)
Entropy
The magnitude that concentrated energy has
been dispersed after an energy change
= how much energy is spread out or how widely it
spreads out
Unavailable energy
(in a closed system, entropy can not decrease)
Measure of disorder of a system
(nature tends to go from order to disorder in closed
systems)
Time’s Arrow
All energy spontaneously spreads out from
a localized area to a more dispersed
pattern
(opposite does not occur spontaneously)
In a closed system, everything will become
more simple (i.e. will degenerate) over
time
Evolution’s basis is that simple organisms
diversified into highly complex organisms
So why don’t highly ordered living organisms
violate the 2nd law of thermodynamics?
Thermodynamics = closed system
Earth = open system
(earth exchanges heat, light, matter with its
surroundings, including the sun)
Organisms have low entropy and use
energy to fight entropy
If stop using energy → die
Energy Flow Through The
Biosphere
Solar radiation is the ultimate source of energy in all
food webs
(captured by photoautotrophs)
Glucose produced by each level is used up by
level above
At all levels, respiration occurs
(releasing CO2, H2O, and energy from glucose)
Energy is lost as heat between each level
= 1-way flow where energy is used and dispersed
90% of
energy lost
between
each level
Metabolism and Energy
Chemical reactions convert reactants to
products by making or breaking bonds
that hold atoms together
Requires net inputs of energy to combine
small molecules into larger ones that are
more concentrated forms of energy
Larger molecules can spontaneously
degrade into smaller molecules, which
ends with a release of energy
Components of a Metabolic
Reaction
Reactant: Starting substance
Intermediates: Formed before reaction ends
Product: Substance remaining at end of
reaction
Some rxns are linear:
Products formed directly from reactants
Some rxns are cyclic:
Final rxn regenerates the reactant
molecule from the 1st step of the rxn;
rxn then runs again
Some rxns are branched:
Intermediates or reactants are directed
into 2 or more different series of rxns
Most are reversible:
Run spontaneously towards chemical
equilibrium
Rxn rate is about equal in both directions
Allows cell to change activities via control
of enzymes that enable steps of
reversible metabolic pathways
e.g. when cells need energy, glucose is split
into 2 pyruvates via glycolysis (a 9-step
pathway)
When cells need glucose, they reverse the
pathway & make glucose from pyruvate and
other molecules
If reversible pathway did not exist, cells would
not be able to compensate for starvation
episodes when glucose is low
= cell death
Endergonic Reactions
Require energy
Do not occur spontaneously
(activation energy barrier is relatively high)
Usually anabolic: A + B → AB
(products have higher potential energy than
reactants)
Most reactions in cells are endergonic so cells
have to store energy until it is needed
e.g. biosynthesis of proteins
Exergonic Reactions
Generate energy (end with release of energy)
Usually occur spontaneously
(activation energy barrier is very low)
Usually catabolic: AB → A + B
(products have lower potential energy than
reactants)
e.g. hydrolysis, cellular respiration
Coupled Reactions
Reactions that require energy are paired with
reactions that release energy
e.g. sun releases energy that is needed to
drive photosynthesis
More energy is released from exergonic
reactions than is used in endergonic reactions
(extra energy is lost as heat)
Coupled reactions often occur in different
regions of the cell
Living organisms require a mechanism for
transporting energy released by exergonic
reaction to site of endergonic reaction
Energy-Carrier Molecules
Are rechargeable
Used only for short-term energy storage
(unstable)
Used only within a cell
(not between cells)
Most common energy-carrying molecule is ATP
ATP
Stores & releases chemical energy for all
life processes
Energy released during breakdown of
nutrients (glucose, etc.) is captured as
ATP
ATP is coupling agent/energy carrier for
most metabolic reactions
When ATP gives up P, ADP forms
Exergonic reaction = releases energy
Energy can be used in endergonic
reactions
ATP reforms when ADP binds to inorganic
phosphate or phosphate group from
different molecule
Endergonic reaction = requires energy
Uses energy from other exergonic reactions
ATP/ADP CYCLE
ADENOSINE
P
P
P
ENDERGONIC
EXERGONIC
Energy via glucose
P
ADENOSINE
P
P
+
So essentially:
ATP
ADP
+
P
+
energy
energy
Some of energy at each step is lost as
heat
This heat warms living bodies
Heat also provides activation energy for
chemical reactions
Electron Carriers
Also transport energy within cells
Play important role in metabolism
During glucose breakdown & photosynthesis,
some of energy is transferred to e-s
E- carriers transport these high-energy e-s to other
parts of cell
Include NAD+ & FAD
FAD
NADH
Electron Transfer Chains
Membrane-bound groups of enzymes /
molecules
Accept & give up e-s in sequence
E-s enter chain at higher energy level than when
they leave it
Lose energy at each descending step of chain
Oxidation-Reduction (Redox Rxns)
Stepwise electron transfers
One molecule gives up e-s = oxidized
One molecule gains e-s = reduced
H+ atoms released simultaneously
(are attracted to negative charge of e-s)
Coenzymes pick up e-s & H+ from
substrates and deliver to e- transfer
chains
If glucose was broken down all at once,
all of the released energy would be lost
as heat
= Inefficient! Can’t be used to do work!
Redox reactions allow efficient energy
release
Energy can be used to do cellular work
e.g. ATP formation
Metabolism
All of the chemical reactions that occur within living
cells
Allow growth, reproduction, responsiveness, etc.
Necessary for maintenance of life
Metabolic pathways are series of linked
reactions
Photosynthesis
Light energy converted into glucose
12H2O + 6CO2  6O2 + C6H12O6 + 6H2O
Glycolysis
Glucose converted into ATP
Glucose → 2 pyruvate + 2 NADH + 2 ATP
Cellular respiration (aerobic)
Glucose converted into ATP in presence of O2
Glucose + 6O2 → 6CO2 + 6H2O + 36 ATP
Fermentation
Glucose converted into ATP in absence of O2
Glucose → 2 pyruvate + 2 NADH + 2 ATP
Many interrelated chemical reactions &
pathways
= cells need mechanisms to control, coordinate,
& connect these reactions
1. Enzymes act to ↑ rxn rate
2. Cells couple exergonic & endergonic rxns
3. Cells make energy-carrier molecules for
short-term storage & transport of energy
from exergonic rxns to endergonic rxns
Reactions occur slowly
Activation energy required for reactions to occur
Rxn rate generally ↑ with ↑ heat
Body temperature not enough to meet activation
energy needs of most chemical rxns
Cells use enzymes to ↓ activation energy needed
= allows rxns to occur at body temperature
Activation Energy
= Minimum amount of energy required for a
reaction to run
Molecules have to collide with enough
energy and in the correct orientation in order
for molecules to react
Overcomes repulsion between e- clouds of
molecules so that bonds can be rearranged
Cells can control when & how fast reactions
occur by controlling energy inputs into
reactions
Catalysts
Speed up rxn rates
(lower the activation energy required to
run a rxn)
Are not used up
Are not permanently altered
Can be re-used
Enzymes
= biological catalysts
Bind to molecules in ways that make it more
likely that bonds will break & reactants will
interact in the right way
Usually proteins
Structurally stable
Substrate-specific (based on structure)
Can be regulated
Structure of an Enzyme
Active site:
Where substrate (reactant) enters enzyme
Has right shape, size, & charge environment for
substrate
Allows for specificity
Substrate
The molecule upon which an enzyme acts
Substrates have some structure that is
complementary to an enzyme’s active site
= allows for substrate recognition
Substrate binds with active site
Forms enzyme-substrate complex
Both change shape due to binding
Interactions between substrate & enzyme cause
bonds to break and / or be formed
Products produced do not fit in active site so are
released from active site
Enzyme returns to original shape & can be reused
Induced-Fit Model
Substrate is not exactly complementary to
active site
Enzyme molds substrate into specific shape
that moves substrate to transition state
= point at which colliding reactant molecules
will always go on to form products
Activation Energy
Energy required to line up reactive chemical
groups, destabilize electric charges, &
break bonds
Substrate reaches a transition state where
bonds break & the reaction runs
How Enzymes Work to Lower Activation
Energy
Enzyme binds weakly to substrate & energy is
released
Transition state is stabilized:
Enzymes & substrate are kept together so
reaction can run
Other Helpful Enzymatic Things
Help substrates get together
Localize concentrations so that molecules can
react
Position substrates so reaction is favoured
Bonds at active site put reactive groups close
together so more directed collisions can occur
Shut out water molecules
Active sites have non-polar (hydrophobic) amino
acids that repel water so that unwanted Hbonding doesn’t occur
Controls over Enzymes
Chemical reactions must be controlled
Regulation of enzymes is 1° mechanism for
controlling rxn rate
Can be regulated via:
• Adjusting speed of enzyme synthesis
• Maintaining, increasing, or decreasing
substance concentrations
• Activating / inhibiting enzymes
• Feedback inhibition
• Allosteric regulation
• Competitive inhibition
Effects of Concentration
Increased substrate concentration
increases enzymatic activity
Note:
There is a point of
saturation where all
active sites are bound
to substrate &
reaction rate levels off
Activation of Enzymes
e.g. pepsin
Can digest any protein
Produced in non-active form
Activated only in gastric fluid (pH 1 - 2)
If activated pepsin leaked out of the
stomach, would digest proteins in
tissues
Feedback Inhibition
Maintains homeostasis in a cell by slowing
metabolic pathways when products begin to
accumulate
Product produced as result of enzyme activity acts to
reduce function of enzyme
(if you already have enough of the product, why waste
energy making more?)
Inhibitors
Decrease enzyme activity
Irreversible:
Changes enzyme chemically so can’t be used anymore
Usually involves formation of covalent bonds
Reversible:
Non-covalent bonds that do not change enzyme
Differential effects depending on what part of enzyme or
enzyme-substrate complex is bound
Allosteric Regulation
A molecule binds at site other than active site
= allosteric site
Shape of enzyme is changed
Active site is hidden (inhibited) or exposed
(activated)
Competitive Inhibition
Inhibitor has similar structure as substrate so has
affinity for active site of enzyme
Competes with substrate for access to active site
Increased concentration of substrate helps it outcompete inhibitor
Many toxins / poisons act as competitive inhibitors
Environmental Controls of
Enzymes
Enzymatic rates depend on environmental
conditions
Conditions that denature proteins will
decrease or stop enzymatic activity
Enzymes are affected by:
– Temperature
– pH
– Salinity
– Coenzymes
Temperature
As temperature , reaction rate 
(increased probability of collisions between
molecules)
Increase in substrate’s internal energy pushes
reaction closer to activation energy
At extreme temperatures, weak bonds are
broken
= alters enzyme shape (denaturation)
Substrate can’t bind to active site, so reaction rate
decreases / stops
pH
Most enzymes work best at pH 6 - 8
If not at optimal pH, rxn rate may decrease /
stop
Extreme pH values can cause denaturation
of enzymes
Coenzymes
Organic compounds that may or
may not have vitamin group
Bind to enzymes
Are necessary for enzyme function
but are not part of the enzyme
itself
Are modified during the reaction but
are regenerated elsewhere
NADH
Concept Check
Enzymes catalyze the many reactions in a cell.
There are hundreds of different enzymes in a
cell—each with a unique three-dimensional
shape. Why do cells have so many different
enzymes?
a.
Each enzyme molecule can only be used
once.
b.
The shape of an enzyme’s active site generally
fits a specific substrate.
c.
The substrate molecules react with enzymes to
create new enzymes.
d.
Enzymes are randomly produced. With
thousands of different shapes, one is likely to
work.
Concept Check
In order to start an exergonic
reaction, a certain amount of
energy must be absorbed by
the reactants. This is called
the energy of activation.
Which of the following is the
normal energy of activation?
–
A
–
B
–
C
Concept Check
Which of the following
represents the energy of
activation that is modified by
an enzyme?
–
A
–
B
–
C