Download Basic Principle in Plant Physiology

II. Enzymes
• Proteins
• Organic catalysts that speed up the rate of a
reaction, but are not used up
• Lower energy of activation
• Are specific in action, i.e., act on a specific
substrate
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II. Enzymes, cont.
• 1. Substrate (S) combines at active
(catalytic) site of enzyme (E).
• 2. Enzyme-substrate complex [ES] is
formed.
• 3. The substrate is transformed into a
product (P).
• 4. The products are released from enzyme.
• 5. The enzyme is recovered.
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E + S
[ES]
EP
[ES]
EP
E +
P
S = Substrate
P = Product
E = Enzyme
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II. Enzymes, cont.
• Naming of enzymes according to reaction:
– oxidoreductase Involved in oxidation and
reduction reactions.
– transferase Transfers functional groups.
– hydrolase Hydrolysis.
– lyase Removes atoms without hydrolysis.
– isomerase Rearranges atoms in a molecule.
– ligase Joins two molecules.
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II. Enzymes, cont.
• Location of enzymes:
– intracellular Endoenzymes. Act inside the cell.
– extracellular Exoenzymes. Act outside the cell.
• Enzyme components:
– apoprotein Protein portion.
– cofactor Nonprotein portion. May be a metal ion
or an organic molecule which is called a
coenzyme.
– holoprotein Apoprotein + cofactor.
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II. Enzymes, cont.
• Coenzymes
– Bind to an enzyme transiently
– Are “carrier” molecules. They carry atoms (or
electrons) to the substrate or take atoms (or
electrons) from the substrate.
– Examples
• NAD+ is an electron carrier.
• NADP is an electron carrier.
• ATP is a phosphate and energy carrier.
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II. Enzymes - Factors affecting activity
• 1.Temperature
– Enzyme activity
increases with
increasing
temperature.
– Activity drops
when heat
denatures
enzyme.
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II. Enzymes - Factors affecting activity
• 2. pH
– Enzymes have
an optimum pH.
– Hydrogen ions
alter protein
structure.
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II. Enzymes - Factors affecting activity
• 3. Substrate Conc.
– Rate of reaction
increases until all
active sites are
filled.
– At saturation,
maximum rate is
reached.
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II. Enzymes - Factors affecting activity
4. Inhibitors
– competitive react at the
substrate site.
– noncompetitive do not react at
the substrate
site.
• e.g., allosteric
inhibitors
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II. Enzymes, cont.
• Control of enzyme activity
– genetic regulation The control of enzyme
synthesis.
– metabolic regulation The control of enzyme
activity following enzyme synthesis.
• Allosteric activators increase enzyme activity.
• Allosteric inhibitors decrease enzyme activity, e.g., in
feedback inhibition, the end product of a pathway turns
off the first enzyme of the pathway.
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III. Energy production
• Carbohydrates, proteins, lipids are energy rich.
• Each is a reduced molecule, i.e., has many
hydrogen atoms (an electron, e- , & a proton, H+)
• Upon being oxidized, the molecule loses electrons.
• The energy associated with the electrons is
ultimately conserved in ATP.
• Are catabolic reactions
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LARGE MOLECULES
CATABOLISM
energy
ANABOLISM
energy
SMALL MOLECULES
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Enzymes
• Biological catalysts produced by cells
• Nearly all are proteins
• Enormous catalytic power
– Reactions occur at lower temperatures and at
higher rates
• Ordinarily highly specific
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Induced-Fit Model of Enzymes
• Explains how enzyme works
• Substrate: reacting substance
• Active site: where chemical
reaction takes place and
where substrate fits
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Cofactors
• Something other than polypeptide chain
required by enzyme
• May be metal
– Iron in hemoglobin
• May be organic cofactor
– Coenzyme
• Apoenzyme: does not have cofactor
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Inhibition of Enzymes
• Lets cell control when
an enzyme works
• Inhibitor binds to
allosteric site
• Prevents substrate
from binding
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Enzyme Classification I
Systematic Names
and Recommended
Names are based
on the reaction type
and the molecular
structure of the
substrates
(But: they do not
represent the holoenzyme)
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Enzyme Classification II
1. Oxidoreductases - catalyzing oxidation reduction
reactions.
2. Transferases - catalyzing transfer of functional
groups.
3. Hydrolases - catalyzing hydrolysis reactions.
4. Lyases - catalyzing group elimination reactions to
form double bonds.
5. Isomerases - catalyzing isomerizations (bond
rearrangements).
6. Ligases - catalyzing bond formation reactions
couples with ATP hydrolysis.
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1-Oxidoreductases
1.1 Acting on the CH-OH group of donors
1.1.1. With NAD or NADP as acceptor
1.1.2. With a cytochrome as acceptor
1.1.3.With oxygen as acceptor
1.1.4.With a disulfide as acceptor
1.1.5.With a quinone or similar compound as
acceptor
1.1.99. With other acceptors
1.2 Acting on the aldehyde or oxo group of donors
1.3 Acting on the CH-CH group of donors
1.4 Acting on the CH-NH2 group of donors
…
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2. Transferases
2.1 Transferring one-carbon groups
2.1.1. Methyltransferases
2.1.2. Hydroxymethyl-, Formyl- and Related
Transferases
2.1.3. Carboxyl- and Carbamoyltransferases
2.1.4. Amidinotransferases
2.2 Transferring aldehyde or ketonic groups
2.3 Acyltransferases
2.4 Glycosyltransferase
...
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3. Hydrolases
3.1 Acting on ester bonds
3.1.1 Carboxylic Ester Hydrolases
3.1.2 Thiolester Hydrolases
3.1.3 Phosphoric Monoester Hydrolases
3.1.4 Phosphoric Diester Hydrolases
3.1.5 Triphosphoric Monoester Hydrolases
...
3.2 Glycosylases
3.3 Acting on ether bonds
3.4 Acting on peptide bonds (peptidases)
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4. Lyasen
4.1 Carbon-carbon lyases
4.1.1 Carboxy-lyases
4.1.2 Aldehyde-lyases
4.1.3 Oxo-acid-lyases
4.1.99 Other Carbon-carbon lyases
4.2 Carbon-oxygen lyases
4.3 Carbon-nitrogen lyases
4.4 Carbon-sulfur lyases
4.5 Carbon-halide lyases
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5. Isomerases
5.1 Racemases and epimerases
5.1.1. Acting on Amino Acids and Derivatives
5.1.2. Acting on Hydroxy Acids and Derivatives
5.1.3. Acting on Carbohydrates and Derivatives
5.1.99. Acting on Other Compounds
5.2 cis-trans-Isomerases
5.3 Intramolecular isomerases
5.4 Intramolecular transferases (mutases)
5.5 Intramolecular lyases
5.99 Other isomerases
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6. Ligases
6.1 Forming carbon—oxygen bonds
6.1.1. Ligases Forming Aminoacyl-tRNA and
Related Compounds
6.2 Forming carbon—sulfur bonds
6.2.1. Ligases Forming Aminoacyl-tRNA and
Related Compounds
6.3 Forming carbon—nitrogen bonds
6.4 Forming carbon—carbon bonds
6.5 Forming phosphoric ester bonds
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