General biology:
Metabolism
Jin Changjiang
Email: jincj@ustc.edu.cn
Enzymes
• Enzymes are large biological molecules responsible for
the thousands of metabolic processes that sustain life
• They are highly selective catalysts, greatly accelerating
both the rate and specificity of metabolic reactions, from
the digestion of food to the synthesis of DNA.
• Most enzymes are proteins, although some catalytic
RNA molecules have been identified.
• Enzymes adopt a specific three-dimensional structure,
and may employ organic (e.g. biotin) and inorganic (e.g.
magnesium ion) cofactors to assist in catalysis.
Thermodynamics
"Lock and key" model
Human glyoxalase I
Two zinc ions that are needed for the enzyme to catalyze its reaction are
shown as purple spheres, and an enzyme inhibitor called S-hexylglutathione
is shown as a space-filling model, filling the two active sites.
Factors that Affect
Enzymes
Factors Affecting Enzyme Function
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Enzyme concentration
Substrate concentration
Temperature
pH
Salinity
Activators
Inhibitors
catalase
• 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
enzyme concentration
• 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
• 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
Enzymes and temperature
• Different enzymes function in different
organisms in different environments
reaction rate
human enzyme
hot spring
bacteria enzyme
37°C
temperature
70°C
(158°F)
How do ectotherms do it?
• 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
pepsin
trypsin
0 1 2 3 4 5 6 7 8 9 10 11
• 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!
Compounds which help enzymes
• Activators
Fe in
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
• 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
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
Competitive inhibition
Non-Competitive Inhibitor
• Inhibitor binds to site other than active site
– allosteric site
– allosteric inhibitor
• regulation of enzyme function
– 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
– causes enzyme to change shape
• conformational change
• active site is no longer
a functional binding site
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
Allosteric regulation
• Conformational changes by regulatory
molecules
– inhibitors
• keeps enzyme in inactive form
– activators
• keeps enzyme in active form
Conformational changes
Allosteric regulation
The top-level classification of enzymes
• EC 1 Oxidoreductases: catalyze oxidation/reduction reactions
• EC 2 Transferases: transfer a functional group (e.g. a methyl or
phosphate group)
• EC 3 Hydrolases: catalyze the hydrolysis of various bonds
• EC 4 Lyases: cleave various bonds by means other than hydrolysis
and oxidation
• EC 5 Isomerases: catalyze isomerization changes within a single
molecule
• EC 6 Ligases: join two molecules with covalent bonds.
Metabolic pathways
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3
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2
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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
– divide chemical reaction into
many small steps
• efficiency
– intermediate branching points
• control = regulation
Efficiency
• Organized groups of enzymes
– if enzymes are embedded in membrane
they are arranged sequentially
• Link endergonic & exergonic reactions
Whoa!
All that going on
in those little
mitochondria!
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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ABCDEFG
enzyme
X enzyme enzyme enzyme enzyme enzyme
1
2
3
4
5
6
allosteric inhibitor of enzyme 1
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
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
Metabolic Regulation Is Achieved by
Controlling the Activity of Enzymes
Thousands of reactions mediated by an
equal number of enzymes are occurring at
any given instant within the cell.
Metabolism has many branch points,
cycles, and interconnections.
This metabolic regulation is achieved
through controls on enzyme activity so
that the rates of cellular reactions are
appropriate to cellular requirements.
Metabolism proceeds by discrete steps
• A metabolic pathway has many steps
– That begin with a specific molecule and end
with a product
– That are each catalyzed by a specific enzyme
Enzyme 1
A
Enzyme 3
D
C
B
Reaction 1
Starting
molecule
Enzyme 2
Reaction 2
Reaction 3
Product
Glycolytic enzymes and their functions in the metabolic pathway of glycolysis
己糖激酶
烯醇化酶
变位酶
醛缩酶
丙糖磷酸异构酶
• One reason for multiple steps is the
limitied reaction specificity of enzymes.
• Another reason for multiple steps in
metabolic pathways is to control energy
input and output.
• Finally, multiple steps provide
opportunities to establish control points.
metabolic pathways are regulated
• The flow of material through a metabolic
pathway, or flux, depends not only on the
supply of substrates and the removal of
products but also on the activities of the
enzymes that catalyze individual
reactions.
Properties of Metabolic Pathways
• Irreversible (overall): reversibility of
individual steps
• Separate Anabolic and Catabolic Pathways
• First Committed (Exergonic) Step: others
close to equilibrium
• Regulation (usually first committed step):
often rate-limiting
Features of Metabolic Pathways
A ——> B ——> C ——> D ——> E
(1) Sequences and Energetics
(2) Enzymes and Mechanisms
(3) Control Mechanisms (Regulation)
(4) Compartmentation
Compartmentation and interorgan metabolism
Vesicle trafficking systems
Steps of vesicle trafficking
http://t.cn/hoJcx
The 2013 Nobel Prize in Physiology or Medicine
The three scientists were awarded the prize "for their discoveries of
machinery regulating vesicle traffic, a major transport system in our
cells."
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James E. Rothman is the Fergus F. Wallace Professor of
Biomedical Sciences at Yale University and Chairman of the
Department of Cell Biology at Yale University Medical School.
Randy W. Schekman, professor of molecular and cell biology at
the University of California, Berkeley.
Thomas Südhof, MD, professor of molecular and cellular
physiology at the Stanford School of Medicine, Neuroscientist.
There is unity in diversity
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DNA and/RNA is/are genetic material.
The cell is the basic unit of life.
Living things acquire materials and energy
All living things came from ONE organism, so we are all
alike but different.
• Similarities exists when common ancestors are recent,
diversity occurs when genetics and environment interact
and natural selection occurs.
• Evolution is "descent with modification", according to
Darwin, accounting for Unity and Diversity.