Class notes

Chapters 6-16 Intro to Biology

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Course
Bio 102

Institution
The City College Of New York

These notes go in depth on chapters 6-16 of the OpenStax 2e biology textbook, while also including some details from slides covered in class. These are the study guides used for the second and third exams of this class. They are very helpful if utilized and studied for memorization.

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CH. 6: Enzymes & Metabolism
Metabolism - totality of chemical pathways in a living cell, involving the biochemical
modification of organic molecules
Ex: photosynthesis & cellular respiration
Anabolic - smaller molecules assembling into larger ones; requires energy
Ex: dehydration synthesis of ATP (ADP + Pi = ATP)
Catabolic - larger molecules breaking down into smaller ones; releases energy
Ex: hydrolysis of ATP (ATP+ H2O ⇋ ADP + Pi + Energy)
1st Law of Thermodynamics - energy cannot be created or destroyed, only
transferred/transformed
2nd Law of Thermodynamics - all energy transfers involve losing energy in an unstable
transfer; transfer of energy is not completely efficient; sometimes lost to heat, which increases
universal entropy
● Total entropy of the universe is always increasing due to loss of usable energy
● Ex: cheetah runs, absorbs the energy provided from the food it eats to power its running;
releases heat, CO2, and H2O into the atmosphere, increasing entropy of surroundings
Free Energy (G) - energy available to do work
Kinetic - energy in motion
Ex: running
Potential - energy that is stored, it has the ‘potential’ to do work
Ex: chemical energy stored in bonds
- Electrochemical gradients are potential
Exergonic - when change in G is less than 0; substrates have
more free energy than products
- Occur spontaneously; don’t happen quickly
- Don’t require energy (catabolic)
Ex: Hydrolysis of sucrose
Endergonic - when change in G is greater than 0; products
have more free energy than reactants
- More bonds, more energy stored in them
- Anabolic, requires an input of energy, absorbs energy
Ex: Dehydration synthesis of ATP
Activation Energy (EA) - energy required for a reaction to proceed
- Causes chemical bonds of reactants to become
contorted, unstable; bonds can now be broken or
made
- Brings to unstable state, Transition State
Catalysts - decrease amount of energy needed to start
reaction
- Speed up reaction but aren’t affected by the
reaction
- Very specific proteins, catalyze specific reactions
then are used to catalyze different reactions

,ATP - adenosine backbone with three phosphate groups
and a ribose sugar; nucleotide; inherently unstable
because the p-groups are all negative, so they repel each
other
- Main energy currency of the cell
ATP hydrolysis - ATP+ H2O ⇋ ADP + Pi + Energy
- Catabolic, exergonic
- Releases -7.3kcal/mol
- If energy released from ATP hydrolysis is not used,
it’s lost as heat
- if coupled, energy is harnessed to drive endergonic rxn
Energy coupling - exergonic reaction drives an endergonic reaction
- Harness the energy released from exergonic to drive an endergonic
(product of exer is picked up by an ender)
Ex: synthesis of sucrose
Synthesis of Glutamine
1. Glutamate is first phosphorylated using ATP
Glutamate+ATP→γ-glutamyl phosphate+ADP (exergonic)
2. Ammonia reacts with y-glutamyl phosphate intermediate, forming
glutamine
γ-glutamyl phosphate+NH₃→Glutamine+Pi (endergonic)
Enzymes - catalytic proteins that speed up reactions by lowering activation energy; stabilize
transition sites; expose reactant molecules to altered charge environments, promote catalysis;
change substrate shape
● Bind with reactant, promotes bond-breaking or bond-formation
● Specific, as in only binds with one or a couple of substrates
● Reusable: after it binds and catalyzes, it’s released, unchanged, and can be used for
another reaction
What factors influence enzymes?
1. Temperature: raising temperature generally speeds up
reactions, while lower temperatures slow down rxns. Extremely
high temps. Cause the proteins in the enzyme to denature
(shape loss), and stop working.
- ex:cell wall degrading enzyme
- Reveals when adding a disulfide bridge to enzyme, will have
greatest activity at higher temp, and denature at higher temp

- ex: same enzyme at same
temp in marine animals denaturing at diff periods
- denaturing at diff time exposures could be due to mutations,
which would change enzyme stability OR prions, which are
misfolded proteins due to evolution, that would lead to diff
denaturing periods

, 2. pH: each enzyme has an optimum pH range. Changing the pH outside of the optimum
range slows down the enzyme activity. Extreme pH values cause the enzyme to
denature.
3. Enzyme Concentration: increasing enzyme concentration will speed up the reaction, as
long as there is substrate available to bind to. Once all of the substrate is bound, the
reaction will no longer speed because there is nothing else for it to bind to.
4. Substrate concentration: increases rate of reaction to a
certain point. Once all enzymes are bound, increasing
substrate concentration will have no effect on reaction
rate.
Substrate - reactant, determines specificity; interact with active
site
Induced Fit - as substrate binds to enzyme, enzyme changes in
conformation so substrate can bind better; contorts them so they
become unstable
● An enzymes shape is determined by its AA sequence
within the PP
○ This allows for binding with unique substrates
● Active site is changing-> the enzyme allows the rxn to
proceed with less energy; making the rxn occur faster
Cofactors - provide essential chemical groups that the enzyme is
lacking
● Cofactors are inorganic ions ex: Fe+, Mn+
● Coenzymes are organic molecules derived primarily from
diet ex: ATP, vitamins
Molybdenum Cofactor Deficiency:
- Mutations occur in MOCS1 gene (1st step)
- Prevents the cell from making cPMP
- Since cPMP is inhibited (step 2) you cannot
make MoCo (step 4) which is necessary for the brain
- This leads to a loss of sulfite, and build up of
sulfite and SSC
- This increases the likelihood seizures and
delayed development, ultimately leading to death
- Reveals the importance of
cofactors/coenzymes
- Nulibry is a cPMP replacement drug, that can
replace the product of the 1st enzymatic rxn,
allowing the pathway to proceed

Enzyme Kinetics
Vmax - plateau at which the enzyme is fully saturated by the substrate

, - Depends on enzyme concentration
Km - ½ Vmax
- Reveals how quickly the rxn rate increases
- Also measure of the enzymes affinity of binding
to the substrate
- Lower Km means higher binding affinity to the
substrate and vice versa
- Always the same for a particular enzyme
Enzyme Regulation
1. Modifications to temperature/pH
2. Production of molecules that inhibit/promote
enzyme function
3. Availability of coenzymes and cofactors
Competitive Inhibition - binds to the active site, prevents substrate from binding
● Dependant on the dosage of inhibition bc if the concentration of the substrate is greater,
it will bind over the competitive inhibition
○ Competes with substrate
○ Increases Km (further down on X axis)
○ decreases initial rxn rate
○ Leaves fewer enzyme molecules for the
substrate to bind to
Noncompetitive Inhibition - binds anywhere BUT the active
site, causes a protein shape change which alters the active
site, the substrate can no longer bind
● Dosage doesn’t
matter because the active
site is changing
● Increases Km; decreases Vmax
● Decreases initial rxn rate and rate of rxn
Allosteric Activators - binds to the allosteric site, changes
the shape of the enzyme active site and increases the
binding affinity
Allosteric Inhibitors - binds to allosteric site, changes the
shape of enzyme active site, reduces binding affinity
Feedback Inhibition - the way in which a metabolic pathway
regulates its own synthesis; utilizes the product of a later step to inhibit an earlier step
- This changes the shape of the enzyme, forcing the enzyme to want more of different,
competing pathways
Regulation of Chorismate Mutase
- Chorismate starts by making prephenate to Arogenate
which makes Phe and Tyr
- Once enough Phe and Tyr are made, they go back and
inhibit Chorismate mutase, letting the enzyme know that enough
is made and it can stop producing it

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