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BSC 2010 - Exam I Lectures and Text Pages
• I. Intro to Biology (2-29)
• II. Chemistry of Life
–
Chemistry review (30-46)
–
Water (47-57)
–
Carbon (58-67)
–
Macromolecules (68-91)
• III. Cells and Membranes
–
Cell structure (92-123)
–
Membranes (124-140)
• IV. Introductory Biochemistry
–
Energy and Metabolism (141-159)
–
Cellular Respiration (160-180)
–
Photosynthesis (181-200)
ATP: powers cellular work by coupling exergonic to endergonic reactions.
ATP (adenosine triphosphate) = energy currency
of the cell
•
a. Type of nucleotide with
an adenine, a ribose, and 3
phosphate groups (fig 8.8)
P
•
b. Phosphate groups are
pulled off (hydrolysis) to
release energy
–
P
P
Adenosine triphosphate (ATP)
fig 8.9: ATP + H2O  ADP
+ Pi (∆G = -7.3 kcal/mol)
P
i
H2O
+
Figure 8.9 Inorganic phosphate
P
P
Adenosine diphosphate (ADP)
Energy
How ATP Performs Work
Key to coupling exergonic w/ endergonic rxns is
making a phosphorylated intermediate
• a. Phosphorylation = transfer of a phosphate
group to another molecule
• b. Powered by hydrolysis of ATP (fig 8.11)
ATP is Renewable
• ATP is renewable  shuttle Pi + energy (fig 8.12)
ATP hydrolysis to
ADP + P i yields energy
ATP synthesis from
ADP + P i requires energy
ATP
Energy from catabolism
(exergonic, energy yielding
processes)
Figure 8.12
Energy for cellular work
(endergonic, energyconsuming processes)
ADP + P
i
• Respiration & photosynthesis provide energy
to drive the endergonic process of ATP
formation (∆G = +7.3 kcal/mol)
ENZYMES:
Speed up Metabolic Pathways by Lowering Energy Barriers
1. Enzymes = catalytic proteins that speed up chemical rxns (don’t make
rxns happen that would not happen on their own)
2. Converting a molecule into another involves contorting the original
molecule into an unstable state
•
a. This takes energy = activation energy. (EA) = amt of energy you
put into a rxn to get it over the hill so the downhill part of the rxn can
start
•
b. Ex (fig 8.14): AB + CD  AC + BD
3. EA often supplied by adding heat (absorbed by reactant molecules) usually too high a heat for rxns to happen at room temperature
Why is it inappropriate to add a lot of heat to biological systems?
Enzymes speed up metabolic reactions by lowering energy barriers
• Enzymes are catalysts.
• A catalyst
– Is a chemical agent that speeds up a reaction
without being consumed by the reaction
The Activation Barrier
• Every chemical reaction between molecules
involves both bond breaking and bond forming
• Hydrolysis is an example of a chemical
reaction
CH2OH
CH2OH
O
O
H H
H
H
OH
H HO
O
+
CH2OH
H
OH H
OH
Sucrase
H2O
CH2OH
O H
H
H
OH H
OH
HO
H
OH
CH2OH
O
HO
H HO
H
CH2OH
OH H
Sucrose
Glucose
Fructose
C12H22O11
C6H12O6
C6H12O6
Figure 8.13
The activation energy, EA
• The activation energy, EA
–
Is the initial amount of energy needed to start a chemical reaction
–
Is often supplied in the form of heat from the surroundings in a
system
A
B
C
D
Free energy
Transition state
A
B
C
D
EA
Reactants
A
B
C
D
∆G < O
Products
Progress of the reaction
Figure 8.14
Effect of enzymes on reaction rate
• An enzyme catalyzes (speeds up) reactions by
lowering the EA barrier
Course of
reaction
without
enzyme
EA
without
enzyme
Free energy
EA with
enzyme
is lower
Reactants
∆G is unaffected
by enzyme
Course of
reaction
with enzyme
Products
Progress of the reaction
Figure 8.15
How an enzyme works:
• 1. Substrate = reactant that enzymes acts on  forms an
enzyme-substrate complex
• 2. The 3-D structure of an enzyme gives it specificity
• 3. Active site = specific site where an enzyme and
substrate bind (typically a groove/pocket on the protein’s
surface)
• 4. Changes shape as substrate binds to it, so that it fits
even more snugly around reactant (= induced fit, fig 8.16)
• 5. Brings chemical groups of active site into position to
enhance catalyzing the rxn
• 6. Enzymes return to their original conformation after
releasing converted substrate  they can be re-used
Substrate Specificity of Enzymes
• The substrate
– Is the reactant an enzyme acts on
• The enzyme
– Binds to its substrate, forming an enzymesubstrate complex
The Active Site
• Is the region on the enzyme where the
substrate binds, and where catalysis occurs.
Substate
Active site
Enzyme
Figure 8.16
(a)
Induced fit of a substrate
• Induced fit of a substrate
– Brings chemical groups of the active site into
positions that enhance their ability to catalyze
the chemical reaction
Enzyme- substrate
complex
Figure 8.16
(b)
The catalytic cycle of an enzyme
1 Substrates enter active site; enzyme
changes shape so its active site
embraces the substrates (induced fit).
Substrates
Enzyme-substrate
complex
6 Active site
Is available for
two new substrate
Mole.
Enzyme
5 Products are
Released.
Figure 8.17
Products
2 Substrates held in
active site by weak
interactions, such as
hydrogen bonds and
ionic bonds.
3 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.
4 Substrates are
Converted into
Products.
Ways the active site can lower an EA barrier
• The active site can lower an EA barrier by
– Orienting substrates correctly
– Straining substrate bonds and forcing
transition states
– Providing a favorable microenvironment (such
as specific pH)
– Covalently bonding (temporarily) to the
substrate (direct participation)
Enzyme activity is affected by the environment:
• 1. Temperature and pH can increase enzyme activity, but
can also denature enzymes (fig 8.18)
• 2. Cofactors and coenzymes are small molecules that
bind to enzymes and are necessary for catalytic function.
–
Cofactors = non-protein helpers
–
Coenzymes = organic cofactors
• 3. Enzyme inhibitors bind to an enzyme to make it
inactive (fig 8.19)
–
a. Noncompetitive inhibitors change the 3-D structure of
active site by binding elsewhere on the enzyme
–
b. Competitive inhibitors directly block substrate from
active site
Effects of Temperature
• Each enzyme has an optimal temperature at
which it can function best
Optimal temperature for
typical human enzyme
Optimal temperature for
enzyme of thermophilic
Rate of reaction
(heat-tolerant)
bacteria
0
20
40
Temperature (Cº)
(a) Optimal temperature for two enzymes
Figure 8.18
80
100
Effects of pH
• Each enzyme has an optimal pH at which it can
function best
Optimal pH for pepsin
(stomach enzyme)
Rate of reaction
Optimal pH
for trypsin
(intestinal
enzyme)
3
4
0
2
1
(b) Optimal pH for two enzymes
Figure 8.18
5
6
7
8
9
Cofactors small molecules that bind to enzymes and are necessary for catalytic function.
• Cofactors
– Are nonprotein enzyme helpers
• Coenzymes
– Are organic cofactors
Enzyme Inhibitors
• Competitive inhibitors bind to the active site of an
enzyme, competing with the substrate
A substrate can
bind normally to the
active site of an
enzyme.
Substrate
Active site
Enzyme
(a) Normal binding
A competitive
inhibitor mimics the
substrate, competing
for the active site.
Figure 8.19
(b) Competitive inhibition
Competitive
inhibitor
Enzyme Inhibitors
• Noncompetitive inhibitors bind to another part
of an enzyme, changing the function
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
Figure 8.19
(c) Noncompetitive inhibition
Cells have to regulate enzyme activity (control metabolism):
•
They can either switch genes on/off
•
Or they can regulate the proteins once they’re made
Regulating Proteins ---
•
•
A. Allosteric regulation = affecting an enzyme’s activity by attaching
a regulatory molecule that changes its 3-D structure
–
1. Feedback inhibition = when a metabolic pathway is switched off
by inhibitory binding of its end product to an enzyme that acts early in
the pathway (fig 8.21)
–
2. Cooperativity These enzymes are usually composed of more
than one polypeptide chain (fig 8.20). Inhibition/activation at one site
affects all other active sites on the same molecule
B. Where are enzymes in the cell? This facilitates metabolic
order.
–
1. Embedded in phospholipid bilayers (membranes)
–
2. In solution within an organelle (lysosomes)
Allosteric Regulation of Enzymes
• Allosteric regulation
– Is the term used to describe any case in which
a protein’s function at one site is affected by
binding of a regulatory molecule at another site
– Function may be activated or inhibited.
Many enzymes are allosterically regulated
– They change shape when regulatory molecules bind
to specific sites, affecting function
Allosteric enyzme
with four subunits
Regulatory
site (one
of four)
Active site
(one of four)
Activator
Active form
Stabilized active form
Oscillation
Allosteric inhibitor
stabilizes inactive form
NonInactive form Inhibitor
functional
active
site
Figure 8.20
Allosteric activator
stabilizes active from
Stabilized inactive
form
(a) Allosteric activators and inhibitors. In the cell, activators and inhibitors
dissociate when at low concentrations. The enzyme can then oscillate again.
Cooperativity
– Is a form of allosteric regulation that can
amplify enzyme activity
Binding of one substrate molecule to
active site of one subunit locks
all subunits in active conformation.
Substrate
Inactive form
Figure 8.20
Stabilized active form
(b) Cooperativity: another type of allosteric activation. Note that the
inactive form shown on the left oscillates back and forth with the active
form when the active form is not stabilized by substrate.
Feedback inhibition
• In feedback
inhibition, the end
product of a
metabolic pathway
shuts down the
pathway
Active site
available
Initial substrate
(threonine)
Threonine
in active site
Enzyme 1
(threonine
deaminase)
Isoleucine
used up by
cell
Intermediate A
Feedback
inhibition
Active site of
enzyme 1 no
longer binds
threonine;
pathway is
switched off
Enzyme 2
Intermediate B
Enzyme 3
Intermediate C
Isoleucine
binds to
allosteric
site
Enzyme 4
Intermediate D
Enzyme 5
Figure 8.21
End product
(isoleucine)
Enzyme Location in the Cell
• 1. Grouped into complexes and embedded in phospholipid
bilayers (membranes)
• 2. In solution within an organelle (lysosomes)
• This facilitates metabolic order.
Mitochondria, sites of cellular respiration
Figure 8.22
1 µm