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BIOCH 200 studyGuide pt2.docx


Department
Biochemistry
Course Code
BIOCH200
Professor
Rachel Milner

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1
Enzymes
What are Enzymes?
Define the term “enzyme.”
Proteins, function varies with structure, extract energy from environment against
entropy, ex glucose. You turn glucose into CO2 and water (37 degrees and 1
atmosphere- body conditions); athletes burn hydrocarbon fuel better (fatty acids
to fuel contraction)
Help in chemical synthesis ex. Fixing nitrogen
Help in chemical breakdown ex. Digesting breakfast
Proteins that act as catalysts and speed up reaction without being changed
themselves
Highly specific, every reaction has its own enzyme; each reaction is highly
specific (enzyme always does the same thing)
Typical globular protein (same levels of structure, some with quaternary
structure, stabilized by same non-covalent forces especially the hydrophobic
effect
What are the 6 classes of Enzymes?
Oxidoreductase – oxidation/reduction reaction
Transferases - transfer of functional groups, 2 products and 2 substrates
Hydrolases - hydrolysis (break bond with water), release of water
Lyases - group elimination (left with double bond)
Isomerase - isomerization
Ligases - bond formation coupled with ATP hydrolysis
What’s the general way of naming enzymes?
- Based on enzyme substrate (S) or sometimes the product
- Ends in ‘ase’
Pyruvate
Carboxylase
belongs to
Ligase class

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2
Describe the structure of enzymes and state how it is stabilized.
- Same as proteins
- Stabilized by hydrophobic interactions
State what is meant when we describe enzymes as “specific.”
- “Lock n key” model
- 1 reaction = 1 enzyme
Define the term “substrate.”
-Molecule upon which an enzyme acts
- Enzymes catalyze chemical reactions involving the substrate(s)
- The substrate bonds with the enzyme active site, and an enzyme-substrate
complex is formed, substrate is transformed into one or more products, which are
then released from the active site, active site is now free to accept another
substrate molecule. In the case of more than one substrate, these may bind in a
particular order to the active site, before reacting together to produce products.
State why the regulation of enzymes is possible.
- Can be turned on/off
- Just like hemoglobin they are proteins that can change shape
Ex. when mammalian cells both catabolize and synthesize glucose.
-Remember that the Second Law of Thermodynamics states that entropy
increases in a favored reaction; entropy is wasted energy in that it can't be used
to carry out work.
-Sometimes an enzyme that uses ATP as a substrate to transfer phosphate to
another molecule can hydrolyze ATP to ADP and inorganic phosphate in the
absence of the other substrate. This kind of reaction would obviously consume
the cell's energy without doing useful work.
What is Allosteric Enzyme Regulation?
[Type text]
Phosphoenolpyruvate
carboxykinase belongs
to Lyase class

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3
Change in the kinetic properties of an enzyme caused by binding to another
molecule
The binding of a small molecule to the enzyme alters its conformation so that
it carries out catalysis more or less efficiently.
For example, the binding of one molecule of a substrate to an enzyme can
cause it to undergo a conformational change so that it binds the next
molecule of substrate more efficiently.
The first conformation is termed the T (tense) state; the second is called the R
(relaxed) state.
Higher concentrations of substrate favor the conversion of the T state to the
R state. This special case of regulation by substrate concentration is called
cooperativity. Another case of cooperativity is the cooperative binding of
oxygen to hemoglobin. Cooperativity only operates on enzymes with more
than one subunit.
Enzymes can be allosterically regulated by association with other molecules.
This concept is similar to the conformational changes that occur in
hemoglobin in response to changes in pH, fructose bisphosphate (FBP), and
other conditions.
How Do Enzymes Work?
Sketch a free energy diagram to compare thermodynamically favorable and non-
favorable reactions.
Free energy = G = gibbs
Diagram looks at relative energies
Can’t tell which is faster (determined by activation energy)
Shows reaction of Reactant/substrates  products
Free energy change MUST BE NEGATIVE to be
favorable/exergonic/spontaneous
Products are lower than reactants
[Change in G = free energy product – free energy of reactants]
ΔG is the actual change in free energy in the cell.
ΔG°' is the change in free energy measured under standard biochemical
conditions.
All reactants and products start at 1 M, and the reaction occurs at 25°C and 1
atmosphere of pressure.
The " ' " indicates the reaction is at pH 7, and not a [H+] of 1 M (pH 0), which
would be the case under standard chemical conditions, denoted by " ° ".
The effect an increased metabolite has on a pathway depends on which
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