Download Enzymes

Cell Biology
Note: the following notes include material covered
9-11-01 and 9-13-01. Separate notes are available for the lecture on
metabolism.
Protein Classification
- globular proteins
o spherical, compact, and soluble
o most proteins
 enzymes, antibodies, hormones, intracellular signaling
proteins
- fibrous or structural proteins
o very stable; provides strength; insoluble
o often long filaments built from identical subunits
o  keratin
 hair, horn and nails; waterproofs our skin
o collagen
 most abundant protein in body
 3 polypeptide chains twisted together
 in bones, cartilage, and tendons; holds tissues together
o Spider silk (large amount of  sheets)
Protein Families
- proteins that have a similar amino acid sequence and structure (i.e.
sequence homology)
- suggests similar function and an evolutionary relationship
Protein Binding Function Depends on Conformation
- biological function depends on protein recognizing and binding
another molecule
o can bind ions, fats, sugars, nucleic acids, and other proteins
- binding is very specific
o ligand = what protein binds to
o binding site = point on protein where ligand fits
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o involves noncovalent interactions; fit must be perfect
- binding site often consists of relatively few amino acids brought
together from distance parts of molecule
Most Proteins are Allosteric
- can adopt 2 or more different conformations
- other molecules bind to allosteric site
- activates or inactivates protein
Protein Phosphorylation
- covalent addition of a phosphate group from ATP to protein
o phosphate group is negatively charged
o added to serine, threonine, or tyrosine R groups
- can cause a conformational change that activates or inactivates the
protein
- protein kinases; adds phosphate groups
- protein phosphatases
o remove phosphate group
o can activate or inactivate protein
o leaves inorganic phosphate (Pi), an ion
Enzymes
- Globular proteins
- accelerate or catalyze almost all cellular reactions
- Most names end in –ase
o Protease, nuclease, kinase, lipase, etc
- Biological catalyst
o Increases rate of reaction without being consumed by the
reaction
o cannot make an energetically unfavorable reaction occur
o only required in small amounts
- Specifically binds substrate(s) and “holds” it so a chemical reaction
occurs and a product is formed
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o Involves making and breaking covalent bonds
Predicating Chemical Reactions
- Free energy (G)
o Energy that can be extracted from a system to do work or
drive a chemical reaction when temperature is uniform (as in
a cell) (expressed as kcal/mole)
o measure of a systems instability or tendency to change to a
more stable state
o Complex organic molecules that have a high energy tend to
change spontaneously to a more stable state.
- G
o difference between the free energy content of the reactants
and products
o For the reaction A + B  C + D
G = free energy (C + D) – free energy (A + B)
o Says nothing about its rate
- Exergonic reactions
o Spontaneous or energetically favorable reactions that have a
negative G
 (Gproducts – Greactants) = < 0
o Release free energy
- Endergonic reactions
o Unfavorable reactions
o Require input of energy
o Have a postive G
Reaction Profile
- Plot of free energy vs. course of reaction
- Reactant(s), product(s), and G
- activation energy (EA)
o energy barrier separating reactants and products
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o prevents energy-rich molecules in cell from decomposing
spontaneously
- transition state
o reaction intermediate (bonds being broken/reformed)
o high free energy
Enzymes and EA
- enzymes cant make an unfavorable reaction occur (G > 0)
- enzymes speed up reactions by lowering the activation energy for
exergonic reactions (G < 0)
o hydrolysis of sucrose to glucose and fructose has a negative
G but would take years without an enzyme
- ways enzymes lower EA
o binds, orients, and concentrates substrate(s)
o changes ionic structure (makes/breaks bonds)
o forces/bends substrate toward its transition state
Enzyme are Substrate Specific
enzyme
substrate(s)

product(s)
sucrase
sucrose

glucose +fructose
Enzyme Active Site
- pocket or groove on enzyme that binds substrate
- formed by only a few amino acids
- induced-fit model
o activate site changes to better fit substrate transition state
 tightest binding but least stable
Factors that Affect Enzyme Function
- temperature
o to low – not enough thermal collisions with active site
o to high – denature enzyme
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o humans – 35-40C; bacteria in hot springs - > 70C
o more black on ears/paws of Siamese cats – enzyme that
regulates melanin is less active in warmer parts of body
- pH
o most require pH 6-8; pepsin in stomach is pH 2
- cofactors
o nonprotein molecules required for enzyme activity
(e.g. metals)
o coenzymes – organic cofactors – e.g. vitamins
- substrate concentration
o as [substrate] raised, rate of product formation reaches
maximum value termed Vmax
 active site saturated
o enzyme kinetics
 study of the rate of enzyme catalyzed reactions
 rate or velocity typically measure by amount of product
formed in a given time at a fixed [enzyme]
 rate varies between enzymes
- Enzyme Inhibitors
o Irreversible
 Attach by covalent bonds
 Penicillin inhibits bacterial enzyme used to make cell
walls
o competitive
o noncompetitive
Competitive
Noncompetitive
Attaches via noncovalent bonds
Attaches via noncovalent bonds
Resembles substrate
Does not resemble substrate
Binds to active site
Binds to allosteric site and
changes enzymes shape
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Reversible if add  substrate
Not reversible if add  substrate
Enzyme Regulation
- increase or decrease activity of gene (enzyme)
- confine to particular compartment (e.g. lysosome)
- feedback inhibition
o enzyme acting early in a reaction pathway is inhibited by a
late product of pathway (often allosterically)
- positive regulation
o enzyme is stimulate by a product of another pathway as ATP
 ADP, ADP binds and activates certain enzymes that break
down sugars
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