Download Metabolism & Enzymes - San Juan Unified School District

Metabolism & Enzymes
AP Biology
Day 1 - Flow of energy through life
 Life is built on chemical reactions

transforming energy from one form to
organic molecules  ATP
another
& organic molecules
sun
solar energy 
AP
Biology
ATP
& organic molecules
organic molecules 
ATP & organic molecules
Reactions in a closed system

Eventually reach equilibrium
∆G < 0
Figure 8.7 A
AP Biology
∆G = 0
(a) A closed hydroelectric system. Water flowing downhill turns a turbine
that drives a generator providing electricity to a light bulb, but only until
the system reaches equilibrium.
Reactions in an open system
 Cells in our body

Experience a constant flow of
materials in and out, preventing
metabolic pathways from reaching
equilibrium
∆G < 0
∆G < 0
∆G < 0
Figure 8.7
AP Biology
(c) A multi-step open hydroelectric system. Cellular respiration is
analogous to this system: Glucose is broken down in a series
of exergonic reactions that power the work of the cell. The product
of each reaction becomes the reactant for the next, so no reaction
reaches equilibrium.
Metabolism
A cell is a miniature factory where thousands
of reactions occur

Metabolism is the totality of an organism’s
chemical reactions
 Arises from interactions between molecules
 Transforms matter and energy, subject to the laws
of thermodynamics
AP Biology
1st Law of Thermodynamics
Chemical
energy
(a)
AP Biology
Figure 8.3
First law of thermodynamics: Energy
can be transferred or transformed but
Neither created nor destroyed. For
example, the chemical (potential) energy
in food will be converted to the kinetic
energy of the cheetah’s movement in (b).
2nd Law of Thermodynamics
Heat
co2
+
H2O
(b)
Figure 8.3
AP Biology
Second law of thermodynamics: Every energy transfer or transformation increases
the disorder (entropy) of the universe. For example, disorder is added to the cheetah’s
surroundings in the form of heat and the small molecules that are the by-products
of metabolism.
Living systems
Increase the
entropy of the
universe
 Use energy to
maintain order

AP Biology
Metabolism
 Chemical reactions of life

forming bonds between molecules
 dehydration synthesis
 synthesis
 anabolic reactions

breaking bonds between molecules
 hydrolysis
 digestion
 catabolic reactions
AP Biology
AP Biology
Examples
 dehydration synthesis (synthesis)-anabolic
enzyme
 hydrolysis (digestion) - catabolic
enzyme
AP Biology
∆G is Gibbs Free Energy
Calculation to tell us if a reaction will proceed
to the left or to the right…..
 The sign of ∆ G tells us in what direction the
reaction has to shift to reach equilibrium.

Reactions go towards a NEGATIVE ∆ G
 The magnitude of ∆ G tells us how far the
reaction is from equilibrium at that moment.
AP Biology
At maximum stability-The system is at
equilibrium
• More free energy (higher G)
• Less stable
• Greater work capacity
In a spontaneously change
• The free energy of the system
decreases (∆G <0)
• The system becomes more stable
• The released free energy can
be harnessed to do work
.
• Less free energy (lower G)
• More stable
• Less work capacity
(a)
Figure 8.5
AP Biology
Gravitational motion. Objects
move spontaneously from a
higher altitude to a lower one.
(b)
Diffusion. Molecules(c)
in a drop of dye diffuse
until they are randomly
dispersed.
Chemical reaction. In a
cell, a sugar molecule is
broken down into simpler
molecules.
Endergonic vs. exergonic reactions
exergonic
endergonic
- energy released
- digestion
- energy invested
- synthesis
+G
-G
AP Biology
G = change in free energy = ability to do work
Energy & life
 Organisms require energy to live

where does that energy come from?
 coupling exergonic reactions (releasing energy)
with endergonic reactions (needing energy)
+
digestion
synthesis
+
AP Biology
+
energy
+
energy
ATP – Adenosine Tri-phosphate
 ATP powers cellular work by coupling
exergonic reactions to endergonic
reactions
 A cell does three main kinds of work
Mechanical
 Transport
 Chemical

AP Biology
The Structure and Hydrolysis of
ATP

Provides energy for cellular functions
Adenine
N
O
O
-O
O
-
O
-
Phosphate groups
Figure 8.8
AP Biology
O
O
C
C
N
HC
O
O
O
NH2
N
CH2
-
O
H
N
H
H
H
OH
CH
C
OH
Ribose
Energy is released from ATP
When the terminal phosphate bond is broken
and the negative charge on the PO4 groups
repel
P
P
P
Adenosine triphosphate (ATP)
H2O
P
i
+
Figure 8.9 Inorganic phosphate
AP Biology
P
P
Adenosine diphosphate (ADP)
Energy
ATP hydrolysis
can be coupled to other reactions
Endergonic reaction: ∆G is positive, reaction
is not spontaneous
NH2
Glu
+
Glutamic
acid
ATP
hydrolysis
AP Biology
Glu
Ammonia
Glutamine
∆G = +3.4 kcal/mol
Exergonic reaction: ∆ G is negative, reaction
is spontaneous
ATP
Figure 8.10
NH3
+
H2O
ADP +
P
Coupled reactions: Overall ∆G is negative;
together, reactions are spontaneous
∆G = - 7.3 kcal/mol
∆G = –3.9 kcal/mol
ATP drives endergonic reactions
By phosphorylation, transferring
a phosphate
to other
molecules
P
i
P
Motor protein
Protein moved
(a) Mechanical work: ATP phosphorylates motor proteins
Three types of
cellular work are
powered by the
hydrolysis of
ATP
Membrane
protein
ADP
ATP
+
P
P
AP Biology
i
Solute
Solute transported
(b) Transport work: ATP phosphorylates transport proteins
P
Glu + NH3
Reactants: Glutamic acid
and ammonia
Figure 8.11
P
NH2
Glu
+
P
i
Product (glutamine)
made
(c) Chemical work: ATP phosphorylates key reactants
i
The Regeneration of ATP
 Catabolic pathways

Drive the regeneration of ATP from ADP and
phosphate
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
AP Biology
Energy for cellular work
(endergonic, energyconsuming processes)
ADP + P
i
∆ G = +7.3
kcal/mol
∆ G = -7.3
kcal/mol
AP Biology
Day 2
Enzymes and Activation Energy
AP Biology
What drives reactions?
 If reactions are “downhill”, why don’t
polymers spontaneously digest into their
monomers

because covalent bonds are stable bonds
starch
AP Biology
Activation energy
 Breaking down large molecules
requires an initial input of energy
activation energy
 large biomolecules are stable
 must absorb energy to break bonds

AP Biology
cellulose
energy
CO2 + H2O + heat
Too much activation energy for life
 Activation energy
amount of energy needed to destabilize
the bonds of a molecule
 moves the reaction over an “energy hill”

glucose
AP Biology
Not a match!
That’s too much
energy to expose
living cells to!
Catalysts
 So what’s a cell got to do to reduce
activation energy?

get help! … chemical help… ENZYMES
G
AP Biology
Reducing Activation energy
 Enzymes are Biological Catalysts

reduce the amount of energy to
start a reaction
uncatalyzed reaction
catalyzed reaction
NEW activation energy
reactant
product
AP Biology
Enzymes
 are proteins (& RNA)

facilitate chemical reactions
 increase rate of reaction without being consumed
 reduce activation energy
 don’t change free energy (G) released or required


required for most biological reactions
highly specific
 thousands of different enzymes in cells

AP Biology
control reactions
of life
Naming conventions
 Enzymes named for reaction they catalyze




sucrase breaks down sucrose
proteases break down proteins
lipases break
down lipids
DNA polymerase builds DNA
 adds nucleotides
to DNA strand

pepsin breaks down
proteins (polypeptides)
AP Biology
Enzymes vocabulary
substrate
 reactant which binds to enzyme
 enzyme-substrate complex: temporary association
product
 end result of reaction
active site
 enzyme’s catalytic site; substrate fits into active site
active site
substrate
enzyme
AP Biology
products
The active site can lower an EA
barrier by:

Orienting substrates correctly
 Synthesis: brings substrate closer
together so they can bond to one another

Straining substrate bonds
 Digestion: active site binds substrate and
puts stress on bonds that must be broken,
making it easier to separate molecules
Providing a favorable microenvironment
 Covalently bonding to the substrate

AP Biology
Properties of enzymes
 Reaction specific

each enzyme works with a specific substrate
 chemical fit between active site & substrate
 H bonds & ionic bonds
 Not consumed in reaction

single enzyme molecule can catalyze
thousands or more reactions per second
 enzymes unaffected by the reaction
 Affected by cellular conditions

any condition that affects protein structure
 temperature, pH, salinity
AP Biology
Lock and Key model
 Simplistic model of
enzyme action

substrate fits into 3-D
structure of enzyme’
active site
 H bonds between
substrate & enzyme

AP Biology
like “key fits into lock”
In biology…
Size
doesn’t matter…
Shape matters!
Induced fit model
 More accurate model of enzyme action
3-D structure of enzyme fits substrate
 substrate binding cause enzyme to
change shape leading to a tighter fit

 “conformational change”
 bring chemical groups in position to catalyze
reaction
AP Biology
Factors that Affect Enzymes
AP Biology
2007-2008
Factors Affecting Enzyme Function
 Enzyme concentration
 Substrate concentration
 Temperature
 pH
 Salinity
 Activators
 Inhibitors
AP Biology
catalase
Factors affecting enzyme function
 Enzyme concentration

as  enzyme =  reaction rate
 more enzymes = more frequently collide with
substrate

reaction rate levels off
reaction rate
 substrate becomes limiting factor
 not all enzyme molecules can find substrate
AP Biology
enzyme concentration
Factors affecting enzyme function
 Substrate concentration

as  substrate =  reaction rate
 more substrate = more frequently collide with
enzyme

reaction rate levels off
reaction rate
 all enzymes have active site engaged
 enzyme is saturated
 maximum rate of reaction
AP Biology
substrate concentration
Factors affecting enzyme function
 Temperature

Optimum T°
 greatest number of molecular collisions
 human enzymes = 35°- 40°C
 body temp = 37°C

Heat: increase beyond optimum T°
 increased energy level of molecules disrupts
bonds in enzyme & between enzyme & substrate
 H, ionic = weak bonds
 denaturation = lose 3D shape (3° structure)

Cold: decrease T°
 molecules move slower
 decrease collisions between enzyme & substrate
AP Biology
Factors affecting enzyme function
 pH

changes in pH
 adds or remove H+
 disrupts bonds, disrupts 3D shape
 disrupts attractions between charged amino acids
 affect 2° & 3° structure
 denatures protein

optimal pH?
 most human enzymes = pH 6-8
 depends on localized conditions
 pepsin (stomach) = pH 2-3
 trypsin (small intestines) = pH 8
AP Biology
0 1 2 3 4 5 6 7 8 9 10 11
Factors affecting enzyme function
 Salt concentration

changes in salinity
 adds or removes cations (+) & anions (–)
 disrupts bonds, disrupts 3D shape
 disrupts attractions between charged amino acids
 affect 2° & 3° structure
 denatures protein

enzymes intolerant of extreme salinity
 Dead Sea is called dead for a reason!
AP Biology
Compounds which help enzymes
Fe in
 Activators
hemoglobin

cofactors
 non-protein, small inorganic
compounds & ions
 Mg, K, Ca, Zn, Fe, Cu
 bound within enzyme molecule

coenzymes
 non-protein, organic molecules
 bind temporarily or permanently to
enzyme near active site
AP Biology
 many vitamins
 NAD (niacin; B3)
 FAD (riboflavin; B2)
 Coenzyme A
Mg in
chlorophyll
Compounds which regulate enzymes
 Inhibitors
molecules that reduce enzyme activity
 competitive inhibition
 noncompetitive inhibition
 irreversible inhibition
 feedback inhibition

AP Biology
Competitive Inhibitor
 Inhibitor & substrate “compete” for active site


penicillin
blocks enzyme bacteria use to build cell walls
disulfiram (Antabuse)
treats chronic alcoholism
 blocks enzyme that
breaks down alcohol
 severe hangover & vomiting
5-10 minutes after drinking
 Overcome by increasing substrate
concentration

AP Biology
saturate solution with substrate
so it out-competes inhibitor
for active site on enzyme
Non-Competitive Inhibitor
 Inhibitor binds to site other than active site


allosteric inhibitor binds to allosteric site
causes enzyme to change shape
 conformational change
 active site is no longer functional binding site
 keeps enzyme inactive

some anti-cancer drugs
inhibit enzymes involved in DNA synthesis
 stop DNA production
 stop division of more cancer cells

cyanide poisoning
irreversible inhibitor of Cytochrome C,
an enzyme in cellular respiration
 stops production of ATP
AP Biology
Irreversible inhibition
 Inhibitor permanently binds to enzyme

competitor
 permanently binds to active site

allosteric
 permanently binds to allosteric site
 permanently changes shape of enzyme
 nerve gas, sarin, many insecticides
(malathion, parathion…)
 cholinesterase inhibitors

AP Biology
doesn’t breakdown the neurotransmitter,
acetylcholine
Allosteric regulation
 Conformational changes by regulatory
molecules

inhibitors
 keeps enzyme in inactive form

activators
 keeps enzyme in active form
AP Biology Conformational
changes
Allosteric regulation
Metabolic pathways

3


2



ABCDEFG
4
5
6
enzyme enzyme enzyme enzyme enzyme enzyme
1
 Chemical reactions of life
are organized in pathways

AP Biology
divide chemical reaction
into many small steps
 artifact of evolution
  efficiency
 intermediate branching points
  control = regulation
Efficiency
 Organized groups of enzymes

enzymes are embedded in membrane
and arranged sequentially
 Link endergonic & exergonic reactions
AP Biology
Feedback Inhibition
 Regulation & coordination of production


product is used by next step in pathway
final product is inhibitor of earlier step
 allosteric inhibitor of earlier enzyme
 feedback inhibition

no unnecessary accumulation of product






ABCDEFG
1
2
3
4
5
6
X
enzyme enzyme enzyme enzyme enzyme enzyme
AP Biology
allosteric inhibitor of enzyme 1
threonine
Feedback inhibition
 Example
synthesis of amino
acid, isoleucine from
amino acid, threonine
 isoleucine becomes
the allosteric
inhibitor of the first
step in the pathway

 as product
accumulates it
collides with enzyme
more often than
substrate does
AP Biology
isoleucin
e
Review Feedback Loops
 Learned about feedback loops at the
start of school (August)
Negative Feedback Loops
 Positive Feedback Loops

 The END!
AP Biology
pH
What’s
happening here?!
trypsin
reaction rate
pepsin
pepsin
trypsin
0
AP Biology
1
2
3
4
5
6
pH
7
8
9
10
11
12
13
14
Enzymes and temperature
 Different enzymes function in different
organisms in different environments
reaction rate
human enzyme
hot spring
bacteria enzyme
37°C
AP Biology
temperature
70°C
(158°F)