Download Chapter 6 2015 - Franklin College

Figure 8-01
This new material we begin
today will be on exam #2
Material for exam #1 (March 4) will include
these textbook chapters:
Chapter 3-water
Chapter 4-Carbon and the Molecular
Diversity of Life (especially functional
groups)
Chapter 6-Cell Structure and Function
Chapter 7-Cell Membranes
An Introduction to Metabolism
I. Metabolism, Energy and Life
•
The chemistry of life is organized into metabolic pathways
•
Organisms transform energy
•
The energy transformations of life are subject to two laws of
thermodynamics
•
Organisms live at the expense of free energy
•
ATP powers cellular work by coupling exergonic to endergonic
reactions
II. Enzymes
•
Enzymes speed up metabolic reactions by lowering energy barriers
•
Enzymes are substrate-specific
•
The active site is an enzyme’s catalytic center
III. The Control of Metabolism
•
Metabolic control often demands allosteric regulation
•
The location of enzymes within a cell helps to order metabolism
Cell Energetics
• Energy definition-capacity to do work.
In terms of cell, what are some types of
work that have to be done to stay alive?
Figure 6.2x1 Kinetic and potential energy: dam
Important forms of kinetic and potential
energy for living organisms
• Kinetic-sunlight; heat
• Potential-chemical bond energy (glucose,
ATP, etc.)
Cell Energetics are Governed by
the Laws of Thermodynamics
• First Law of Thermodynamics
(law of Conservation of Energy)
• Energy cannot be created or destroyed but
it can be changed in form.
• Energy transformation is permissible (life
depends on this happening)sunlightchemical
LE 8-2
On the platform,
the diver has
more potential
energy.
Diving converts
potential
energy to
kinetic energy.
Climbing up converts
kinetic energy of
muscle movement to
potential energy.
In the water, the
diver has less
potential energy.
Second Law of Thermodynamics
• All matter tends to spontaneously move to the
greatest possible state of stability (bonding)
• All matter tends to spontaneously move from
areas of higher concentration to lower
concentration (diffusion)
• All matter tends to spontaneously move from
states of higher free energy (less stable, more
concentrated) to states of lower free energy
(more stable, less concentrated)
Entropy-Another way to look at the 2nd law of
Thermodynamics
• We’ve defined the 2nd law previously in
terms of stability and free energy.
• Another way is to understand the 2nd Law
is to use the concept of entropy.
• Entropy is the measure of the
disorganization of a system
• All systems spontaneously assume the
state of greatest entropy.
Cells, entropy, and the 2nd Law of
Thermodynamics
• Cells are very organized (low entropy)
• How can a cell exist in the face of the 2nd Law (maintain
organization)? Expend energy.
• It’s work to stay alive!
• The key is that the cell decreases its entropy at the
expense of increasing the entropy of its surroundings.
• Cells take ordered (high energy molecules from the
environment and return unordered waste products).
• The cell is an open system (can exchange energy with
its environment).
• Can a closed system maintain a state of low entropy?
LE 8-3
Heat
Chemical
energy
First law of thermodynamics
CO2
H2O
Second law of thermodynamics
What does the 2nd Law of Thermodynamics say
about Life?
• Life is improbable.
• Life cannot violate the principle that entropy increases.
• Living things live at the expense of their environment
(living things are able to maintain a state of decreased
entropy because the entropy of the entire universe
(system + surroundings) is increasing
• Life can only exist if energy is constantly being
expended.
What form of energy does the cell use to
maintain its organization?
• ATP
• ATP cycle
LE 8-8
Adenine
Phosphate groups
Ribose
LE 8-9
P
P
P
Adenosine triphosphate (ATP)
H2O
Pi
+
Inorganic phosphate
P
P
Adenosine diphosphate (ADP)
+
Energy
ATP hydrolysis “releases” energy
so that cellular work can be done
• bond breaking versus bond formation
Why does ATP hydrolysis “release”
energy?
ATP and cellular work
• How does ATP hydrolysis power cellular
work?
• Phosphorylation and dephosphorylation of
proteins
LE 8-11
Pi
P
Motor protein
Protein moved
Mechanical work: ATP phosphorylates motor proteins
Membrane
protein
ADP
+
Pi
ATP
Pi
P
Solute transported
Solute
Transport work: ATP phosphorylates transport proteins
P
NH2
Glu
+
NH3
+
Pi
Glu
Reactants: Glutamic acid
and ammonia
Product (glutamine)
made
Chemical work: ATP phosphorylates key reactants
How is ATP produced?
• Cellular respiration (cash versus check
analogy)
• Difference in autotrophs and
heterotrophs
LE 8-UN141
Enzyme 1
A
B
Reaction 1
Starting
molecule
Enzyme 2
Enzyme 3
D
C
Reaction 2
Reaction 3
Product
Metabolism and Spontaneous
reactions
• Previously stated that catabolic reactions
were spontaneous and anabolic were not
spontaneous.
Metabolism
• Cell respiration is one example of a
metabolic pathway. The chemistry of life is
organized into metabolic pathways (complex
and regulated by enzymes). (street analogy).
• 2 types of metabolic pathways
• a. catabolic-degradative, energy releasing
(downhill), oxidative, spontaneous
• b. anabolic-synthetic, energy requiring (up hill),
reduction, not spontaneous
Figure 6.1 The complexity of metabolism
Spontaneous reactions
• What are they?
• They happen on their own without an input
of energy
• They are a result of the 2nd law of
Thermodynamics
LE 8-5
Gravitational motion
Diffusion
Chemical reaction
What determines spontaneity of a chemical
reaction?
• A +B  C+D (substrate products)
• Spontaneous-decrease in free energy (downhill), not
spontaneous-increase free energy (uphill)
• What is free energy? Energy available to do work.
G=H-TS
• Maximum amount of free energy that can be harvested
from a reaction is the free energy change of the reaction
(D G).
 DG=DH-T D S
 D G-energy available to do work (keep cells alive)
 D H-total energy
 DS-energy unavailable to do work
How is D G determined for a reaction?
FE of products –FE of reactants.
• a. If D G is negative (the free energy of the
reactants is > fe of products), the reaction
is spontaneous (downhill).
• b. If D G is positive (the fe of the reactants
is < fe of products), the reaction is not
spontaneous (uphill).
• c. If D G is 0-no free energy difference.
The reaction is at equilibrium. No work
can be done from that reaction.
Figure 6.5 The relationship of free energy to stability, work capacity, and
spontaneous change
LE 8-6a
Free energy
Reactants
Amount of
energy
released
(DG < 0)
Energy
Products
Progress of the reaction
Exergonic reaction: energy released
LE 8-6b
Free energy
Products
Energy
Reactants
Progress of the reaction
Endergonic reaction: energy required
Amount of
energy
required
(DG > 0)
Exergonic and Endergonic
reactions
• Reactions can also be classified based
on free energy changes. Endergonic
and exergonic reactions.
Differences in Exergonic and
Endergonic Reactions
Metabolic reactions and equilibrium
• What would be the problem for a cell if its
metabolic reactions (especially catabolic ones)
were allowed to reach equilibrium?
• Cellular metabolism is normally not allowed to
reach equilibrium.
• Metabolism generally involves multi-step
pathways where the product of one reaction
becomes the substrate of the next reaction.
• This strategy only works because cells are open
systems
LE 8-7a
DG < 0
A closed hydroelectric system
DG = 0
LE 8-7b
DG < 0
An open hydroelectric system
LE 8-7c
DG < 0
DG < 0
DG < 0
A multistep open hydroelectric system
Relationship between catabolic and
anabolic reactions
• Coupling endergonic and exergonic
reactions
• example.
LE 8-12
ATP
Energy for cellular work
(endergonic, energyconsuming processes)
Energy from catabolism
(exergonic, energyyielding processes)
ADP +
P
i
LE 8-10
Endergonic reaction: DG is positive, reaction
is not spontaneous
NH2
Glu
+
NH3
Ammonia
Glutamic
acid
DG = +3.4 kcal/mol
Glu
Glutamine
Exergonic reaction: DG is negative, reaction
is spontaneous
ATP
+
H2O
ADP
Coupled reactions: Overall DG is negative;
together, reactions are spontaneous
+
Pi
DG = –7.3 kcal/mol
DG = –3.9 kcal/mol
LE 8-13
Sucrose
C12H22O11
Glucose
C6H12O6
Fructose
C6H12O6
Enzymes
• Characteristics
LE 8-17
Substrates enter active site; enzyme
changes shape so its active site
embraces the substrates (induced fit).
Substrates held in
active site by weak
interactions, such as
hydrogen bonds and
ionic bonds.
Substrates
Enzyme-substrate
complex
Active
site is
available
for two new
substrate
molecules.
Enzyme
Products are
released.
Substrates are
converted into
products.
Products
Active site (and R groups of
its amino acids) can lower EA
and speed up a reaction by
• acting as a template for
substrate orientation,
• stressing the substrates
and stabilizing the
transition state,
• providing a favorable
microenvironment,
• participating directly in the
catalytic reaction.
LE 8-16
Substrate
Active site
Enzyme
Enzyme-substrate
complex
Catalysis
• Properties of a catalyst
• How do enzymes increase the rate of a
chemical reaction
• Why don’t enzymes alter the D of a
reaction?
LE 8-14
A
B
C
D
Free energy
Transition state
A
B
C
D
EA
Reactants
A
B
DG < O
C
D
Products
Progress of the reaction
LE 8-15
Free energy
Course of
reaction
without
enzyme
EA
without
enzyme
EA with
enzyme
is lower
Reactants
Course of
reaction
with enzyme
DG is unaffected
by enzyme
Products
Progress of the reaction
Factors influencing enzyme activity
Factors influencing enzyme activity
• Temperature
• pH
LE 8-18a
Optimal temperature for
typical human enzyme
0
20
40
60
Temperature (°C)
Optimal temperature for two enzymes
Optimal temperature for
enzyme of thermophilic
(heat-tolerant
bacteria
80
100
LE 8-18b
Optimal pH for pepsin
(stomach enzyme)
0
1
2
3
4
Optimal pH
for trypsin
(intestinal
enzyme)
5
pH
Optimal pH for two enzymes
6
7
8
9
10
Factors influencing enzyme activity
Inhibitors:
A. nonreversible
B. Reversible
1. Competitive inhibition
2. Noncompetitive inhibition
LE 8-19a
Substrate
A substrate can
bind normally to the
active site of an
enzyme.
Active site
Enzyme
Normal binding
LE 8-19b
A competitive
inhibitor mimics the
substrate, competing
for the active site.
Competitive
inhibitor
Competitive inhibition
LE 8-19c
A noncompetitive
inhibitor binds to the
enzyme away from the
active site, altering the
conformation of the
enzyme so that its
active site no longer
functions.
Noncompetitive inhibitor
Noncompetitive inhibition
A practical application of
noncompetitive inhibition
• Feedback Inhibition
• Purpose of feedback inhibition
LE 8-UN159
–
–
L
M
N
Q
P
O
R
–
S
LE 8-21
Initial substrate
(threonine)
Active site
available
Isoleucine
used up by
cell
Threonine
in active site
Enzyme 1
(threonine
deaminase)
Intermediate A
Feedback
inhibition
Enzyme 2
Active site of
enzyme 1 can’t
bind
Intermediate B
theonine
pathway off
Enzyme 3
Isoleucine
binds to
allosteric
site
Intermediate C
Enzyme 4
Intermediate D
Enzyme 5
End product
(isoleucine)