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AP Biology
From food webs to the life of a cell
energy
energy
energy
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AP Biology
Enzyme catalyze reactions
dehydration synthesis (synthesis)
hydrolysis (digestion)
+
H2O
+
H2O
enzyme
enzyme
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AP Biology
Examples
dehydration synthesis (synthesis)
hydrolysis (digestion)
enzyme
enzyme
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AP Biology
How does ATP transfer energy?
P
O– O–
O
–O P
O– O–
O
–O P
O– O–
O
–O 7.3
energy + P
O– O–
O
–O
ATP ADP
releases energy ∆G = -7.3 kcal/mole
Fuels other reactions
Phosphorylation
released Pi can transfer to other molecules destabilizing the other molecules
enzyme that phosphorylates = “kinase”
ATP Pi
ADP +
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AP Biology
ATP Hydrolysis
ATP + H2O → ADP + Pi
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AP Biology
An example of Phosphorylation… Building polymers from monomers
need to destabilize the monomers
phosphorylate!
C
H
OH
H
HO
C C
H
O
H
C + H2O + +4.2 kcal/mol
C
H
OH
C
H
P + ATP + ADP
H
HO
C + C
H
O
H
C C
H
P + Pi
“kinase”
enzyme
-7.3 kcal/mol
-3.1 kcal/mol
enzyme
H
OH C
H
HO C
synthesis
Explain.
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AP Biology
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AP Biology
METABOLISM
Chapter 8
An Introduction to Metabolism
Metabolism = total of
an organism’s
chemical reactions
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AP Biology
Lipid
Metabolism
Carbohydrate
Metabolism Amino Acid
Metabolism
Nucleotide
Metabolism
Glycan Metabolism
Cofactors
& Vitamins
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AP Biology
Metabolism
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AP Biology
Can’t store ATP good energy donor,
not good energy storage
too reactive
transfers Pi too easily
only short term energy
storage
carbohydrates & fats are
long term energy storage
ATP - ADP cycle
A working muscle recycles over
10 million ATPs per second
I need some glucose (and O2)!
ATP
ADP Pi +
7.3 kcal/mole
cellular respiration
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AP Biology
What drives reactions? If reactions are “downhill”, why don’t they
just happen spontaneously?
because covalent bonds are stable bonds
Why don’t stable polymers spontaneously
digest into their monomers?
starch
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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
energy cellulose CO2 + H2O + heat
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AP Biology
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”
Not a match! That’s too much energy to expose living cells to!
glucose
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AP Biology
Uphill is hard
How can it be made easier?
Lower the hill!
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AP Biology
Catalysts So what’s a cell got to do to reduce
activation energy?
get help! … chemical help… ENZYMES
G
Call in the ENZYMES!
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AP Biology
Reducing Activation energy
Catalysts
reducing the amount of energy to
start a reaction
That takes a lot
less energy!
reactant
product
uncatalyzed reaction
catalyzed reaction
NEW activation energy
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AP Biology
______gonic Reaction
Energy + Reactants Products
___G
Reaction progress
Fre
e E
nerg
y
Reactants
Products
Reactants
Products
Fre
e E
nerg
y
Reaction Progress
_______gonic
_________
__________
______gonic
Reactants Products + Energy
______gonic Reaction
Describe each type of reaction. Label the energy diagrams.
___G
_________
__________
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AP Biology
Endergonic Reaction
Energy + Reactants Products
+G
Reaction progress
Fre
e E
nerg
y
Reactants
Products Activation
Energy
Reactants
Products
-G F
ree
En
erg
y
Reaction Progress
Exergonic
Activation
Energy
Endergonic
Reactants Products + Energy
Exergonic Reaction
Know the difference. Be able to label.
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AP Biology
Effect of Catalyst on Reaction Rate
reactants
products
En
erg
y
___________________
Reaction Progress
___________________
Describe what a catalyst does..
Indicate the activation energy for the uncatalyzed reaction
and for the catalyzed reaction.
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AP Biology
Effect of Catalyst on Reaction Rate
reactants
products
En
erg
y
activation energy
for catalyzed reaction
Reaction Progress
No catalyst
Catalyst lowers the activation energy for the reaction.
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AP Biology
Enzymes Biological catalysts
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
control reactions of life
(Ribozymes –
RNA can have catalytic properties)
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AP Biology
Enzymes vocabulary
substrate
enzyme
products active site
http://highered.mcgraw-
hill.com/sites/0072495855/student_view0/chapter2/animation__how_en
zymes_work.html
enzyme-
substrate
complex
http://www.kscience.co.uk/animations/anim_2.htm
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
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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
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AP Biology
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)
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AP Biology
Lock and Key model In biology…
Shape matters!
http://highered.mcgraw-
hill.com/sites/0072495855/student_view0/chapter2/anim
ation__how_enzymes_work.html
Simplistic model of enzyme action
substrate fits into 3-D structure of enzyme active site H bonds, ionic bonds between
substrate & enzyme
like “key fits into lock”
specificity
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AP Biology
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
http://web.chem.ucsb.edu/~molvisual/ABLE/induced_fit/
http://www.indiana.edu/~oso/animations/hexokinase.html
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AP Biology
Models of enzyme activity
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AP Biology
Enzymes are proteins Enzymes interact with substrate
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AP Biology
terminal peptide bond of substrate also twisted & strained
once bond is strained, easy to break
proper substrate binding causes carboxypeptidase to "twist" a little
proper substrate binding causes carboxypeptidase to
"twist" a little
Carboxypeptidase: Fit, strain, cut
twisting enzyme brings 3 "R" groups closer to active site
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AP Biology
How does it work?
Variety of mechanisms to:
lower activation energy & speed up reaction
synthesis
active site orients substrates in correct position for
reaction
enzyme brings substrate closer together
digestion
active site binds substrate & puts stress on bonds that
must be broken, making it easier to separate molecules
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AP Biology
Factors Affecting Enzyme Function
Enzyme concentration
Substrate concentration
Temperature
pH
Salinity
Activators
Inhibitors catalase
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AP Biology
Enzyme concentration
enzyme concentration
rea
cti
on
ra
te
What’s happening here?!
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AP Biology
Factors affecting enzyme function
Enzyme concentration
as enzyme = reaction rate more enzymes = more frequently collide with
substrate
reaction rate levels off substrate becomes limiting factor
not all enzyme molecules can find substrate
enzyme concentration
reacti
on
rate
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AP Biology
Substrate concentration
substrate concentration
rea
cti
on
ra
te
What’s happening here?!
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AP Biology
Factors affecting enzyme function
substrate concentration
reacti
on
rate
Substrate concentration
as substrate = reaction rate more substrate = more frequently collide with
enzyme
reaction rate levels off all enzymes have active site engaged
enzyme is saturated
maximum rate of reaction
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AP Biology
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
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AP Biology
37°
Temperature
temperature
rea
cti
on
ra
te
What’s happening here?!
http://www.wiley.com/college/boyer/0470003790/animations/protein_folding/prote
in_folding.htm
![Page 39: ch 8 METABOLISM part 2 ENZYMES...2014/02/04 · Chapter 8 An Introduction to Metabolism Metabolism = total of an organism’s chemical reactions AP Biology Lipid Metabolism Carbohydrate](https://reader034.vdocuments.us/reader034/viewer/2022052314/5f12f43a8cc0284dba11b9af/html5/thumbnails/39.jpg)
AP Biology
Enzymes and temperature Different enzymes function in different
organisms in different environments
37°C
temperature
rea
cti
on
ra
te
70°C
human enzyme hot spring bacteria enzyme
(158°F)
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AP Biology
7
pH
pH
rea
cti
on
ra
te
2 0 1 3 4 5 6 8 9 10
pepsin trypsin
What’s happening here?!
11 12 13 14
pepsin
trypsin
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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
7 2 0 1 3 4 5 6 8 9 10 11
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AP Biology
Salinity
salt concentration
rea
cti
on
rate
What’s happening here?!
![Page 43: ch 8 METABOLISM part 2 ENZYMES...2014/02/04 · Chapter 8 An Introduction to Metabolism Metabolism = total of an organism’s chemical reactions AP Biology Lipid Metabolism Carbohydrate](https://reader034.vdocuments.us/reader034/viewer/2022052314/5f12f43a8cc0284dba11b9af/html5/thumbnails/43.jpg)
AP Biology
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!
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AP Biology
Compounds that help enzymes Activators
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
many vitamins NAD (niacin; B3)
FAD (riboflavin; B2)
Coenzyme A
Mg in chlorophyll
Fe in hemoglobin
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AP Biology
Compounds that regulate enzymes Inhibitors: molecules that reduce enzyme activity
competitive inhibition
noncompetitive inhibition
irreversible inhibition
feedback inhibition
Distinguish
between the
mechanism of
competitive and
noncompetitive
inhibitors.
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AP Biology
Competitive & Noncompetitive Inhibitors
Competitive Inhibition Noncompetitive Inhibition
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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
saturate solution with substrate so it out-competes inhibitor for active site on enzyme
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AP Biology
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 cancer cells
cyanide poisoning
irreversible inhibitor of Cytochrome C,
an enzyme in cellular respiration
stops production of ATP
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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
doesn’t breakdown the neurotransmitter,
acetylcholine
http://www.kscience.co.uk/animations/model.swf
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AP Biology
Allosteric regulation Conformational changes by regulatory
molecules
inhibitors keeps enzyme in inactive form
activators keeps enzyme in active form
Conformational changes Allosteric regulation
http://usmanscience.com/12bio/enzyme/en
zyme_animations.htm
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AP Biology
Metabolic pathways
A B C D E F G
enzyme
1
enzyme
2
enzyme
3
enzyme
4
enzyme
5
enzyme
6
Chemical reactions of life
are organized in pathways
divide chemical reaction
into many small steps Advantageous evolutionarily
efficiency
intermediate branching points
control = regulation
B C D E F G A
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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
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AP Biology
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
threonine
isoleucine
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AP Biology
Cooperativity Substrate acts as an activator
substrate causes conformational
change in enzyme
induced fit
favors binding of substrate at 2nd site
makes enzyme more active & effective
hemoglobin
Hemoglobin
4 polypeptide chains
can bind 4 O2;
1st O2 binds
now easier for other
3 O2 to bind
http://www.dnatube.com/video/274/Hemoglobin-
Oxygen-Binding
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AP Biology 2013-2014
Don’t be inhibited! Ask Questions!