1. Altering any molecule requires energy
Molecules are stable; must absorb energy to break bonds in a reaction
activation energy gets the rxn going
energy
Need a spark to start a fire
cellulose
CO2 + H2O + heat

2. Activation Energy
Energy for destabilizing covalent bonds of reactant(s)
Moves the reaction over an energy barrier/’hill’
Even if the reaction is exergonic and free energy is liberated
glucose
2nd Law of thermodynamics
Universe tends to disorder
so why don’t proteins, carbohydrates & other biomolecules breakdown?
at temperatures typical of the cell, molecules don’t make it over the hump of activation energy
but, a cell must be metabolically active
heat would speed reactions, but… would denature proteins & kill cells

3. Reducing Activation energy
Catalysts reduce the amount of activation energy needed
In cells, catalysts include enzymes (most common) and ribozymes (RNA design; first bio catalyst?)
uncatalyzed reaction
watch the vocab:
catabolic rxn
catalyst to initiate rxn
Catalase is an enzyme that
breaks down H2O2
catalyzed reaction
reactant
product

4. Virtually all cell processes require a catalyst
replication

5. Enzymes Vocabulary -ase • enzyme suffix • often reflects molecule name
Substrate • reactant which binds to enzyme
• enzyme-substrate complex: temporary association
Active site • enzyme’s catalytic site; substrate fits into active site
Product • end result of reaction
active site
products
substrate
enzyme

6. Properties of enzymes Reaction specific
specific enzyme-substrate pairing
physical/chemical fit between active site & substrate
Not consumed in reaction
single enzyme molecule can catalyze thousands or more reactions per second
Affected by cellular conditions
any condition that affects protein structure
A denatured enzyme will not perform function
i.e. temperature, pH, salinity

7. Enzyme models Catabolic: stressing bonds
Anabolic: arranging molecules in optimal position to form bonds

8. Enzyme models • ‘Lock and Key’ ‘Induced Fit’
Perfect 3-D at active site
‘Induced Fit’
Rough fit, substrate binds, enzyme changes shape
H bonding between substrate & enzyme

10. Regulating enzyme function: Cofactors
Cofactors activate/enhance enzyme activity
any substance required for the proper functioning of an enzyme, such as minerals, ions, vitamins (coenzymes)
ex: coenzyme A, NAD (niacin; B3), FAD (riboflavin; B2)
Hemoglobin is aided by Fe
Chlorophyll is aided by Mg
All sequenced genomes encode enzymes that employ coenzyme A in fatty acid & pyruvate metabolism

11. Regulating enzyme function: Inhibitors
Inhibitors prevent the formation of the enzyme-substrate complex, shutting done the pathway
a way to end a reaction when no longer needed
overcome inhibition by increasing substrate concentration: saturate the solution with substrate so it out-competes inhibitor for active site
Competitive inhibition
Methanol (wood alcohol) poisoning occurs because methanol is oxidized to formaldehyde and formic acid which attack the optic nerve causing blindness. Ethanol is given as an antidote for methanol poisoning because ethanol competitively inhibits the oxidation of methanol. Ethanol is oxidized in preference to methanol and consequently, the oxidation of methanol is slowed down so that the toxic by-products do not have a chance to accumulate.

12. examples EX: penicillin blocks active site of the
enzyme bacteria use to build cell walls
EX: Ethanol  acetaldehyde  acetic acid
w/ dehydrogenase w/ aldehyde oxidase
1. Disulfiram (Antabuse) inhibits aldehyde oxidase
2. Acetaldehyde accumulates
3. Side-effects of build up:
Methanol (wood alcohol) poisoning occurs because methanol is oxidized to formaldehyde and formic acid which attack the optic nerve causing blindness. Ethanol is given as an antidote for methanol poisoning because ethanol competitively inhibits the oxidation of methanol. Ethanol is oxidized in preference to methanol and consequently, the oxidation of methanol is slowed down so that the toxic by-products do not have a chance to accumulate.
Penicillin binds at the active site of the transpeptidase enzyme that cross-links the peptidoglycan strands. It does this by mimicking the D-alanyl-D-alanine residues that would normally bind to this site. Penicillin irreversibly inhibits the enzyme transpeptidase by reacting with a serine residue in the transpeptidase. This reaction is irreversible and so the growth of the bacterial cell wall is inhibited.

13. Allosteric Sites • Secondary binding sites on an enzyme
- an engaged molecule causes a change in shape of active site
- can activate or inhibit
- alters reaction rate
The sites form weak, noncovalent bonds with these molecules, causing a change in the conformation of the enzyme. This change in conformation translates to the active site, which
non-competitive inhibition

14. example • This case is negative feedback
poisoning
For example, the amino acid alanine noncompetitively inhibits the enzyme pyruvate kinase. Alanine is one product of a series of enzyme-catalyzed reactions, the first step of which is catalyzed by pyruvate kinase.
Basis of most chemotherapytreatments is enzyme inhibition. Many health disorders can be controlled, in principle, by inhibiting selected enzymes. Two examples include methotrexate and FdUMP, common anticancer drugs which inhibit enzymes involved in the synthesis of thymidine and hence DNA.
Since many enzymes contain sulfhydral (-SH), alcohol, or acid groups as part of their active sites, any chemical which can react with them acts as a noncompetitive inhibitor. Heavy metals such as silver (Ag+), mercury (Hg2+), lead ( Pb2+) have strong affinities for -SH groups.
Cyanide combines with the copper prosthetic groups of the enzyme cytochrome C oxidase, thus inhibiting respiration which causes an organism to run out of ATP (energy)
Oxalic and citric acid inhibit blood clotting by forming complexes with calcium ions necessary for the enzyme metal ion activator.
• This case is negative feedback
- product is the inhibitor, shuts down pathway

15. Metabolic Pathways Reactant to Product requires multiple steps
a principal chemical is modified by a series of chemical reactions
enzymes catalyze each reaction, often requiring cofactors in order to function properly
metabolic pathways can be elaborate!

16. A metabolic pathway begins with a specific reactant…
Enzyme 1
Enzyme 2
Enzyme 3 C D B
product
reactant A
…which is altered,
in stages, with the
help of enzymes… …producing a
final product

17. Example
glycolysis - glucose oxidation to ATP
urea cycle - disposal of NH4+ in less toxic forms
gluconeogenesis - glucose synthesis from smaller precursors, to be used by the brain.

19. Factors affecting enzyme function : Inhibitors
Ask: Why is the competitive inhibitor less effective?

20. Concentration: substrate or enzymeX
saturated
Ask: How is the rate limited? By # of enzymes
What if the number of enzymes was far lower than substrate – would concentration of substrate matter?

21. Temperature
-20C 4C
10C 30
30C
60C
% substrate remaining

22. Temperature reaction rate temperature Cold Molecules move more slowly
Collisions between
enzyme/substrate
decreased
Heat
Molecules energized
More frequent collisions
Too high = enzyme denatured
shape is changed, no longer
functions
However, increasing temperature also increases the Vibrational Energy that molecules have, specifically in this case enzyme molecules, which puts strain on the bonds that hold them together.
As temperature increases, more bonds, especially the weaker Hydrogen and Ionic bonds, will break as a result of this strain. Breaking bonds within the enzyme will cause the Active Site to change shape.
This change in shape means that the Active Site is less Complementary to the shape of the Substrate, so that it is less likely to catalyse the reaction. Eventually, the enzyme will become Denatured and will no longer function.
temperature

23. Temperature reaction rate temperature Homo sapiens
Thermus thermophilius
37°C
70°C
reaction rate
temperature
(158°F)

24. pH
Changing pH (H+) disrupts the proteins bonds, altering 3D shape

25. Salinity
In high salt, one disrupts the electrostatic interactions because the salt competes for the electrostatic interactions within the protein weakening them. Some salts also disrupt the structure of water which weakens the interactions pushing the protein into its shape.
In zero salt R chains will attract to one another, denaturing the protein (enzyme)
An intermediate salt concentration such as that of human blood (0.9% ) or cytoplasm ins the optimum for many enzymes.

26. pH
Not all enzymes have the same optimal pH