Qualitatively

Km[constant, rate of forward and reverse, concentration of substrate that will reach ½]
Apparent Km[in the presence of an inhibitor and how that will change Km]
Apparent Vmax[ affected by the presence of an inhibitor]

Competitive Inhibitor- SAME active site as the substrate itself. They bind reversibly.
Ki-Enzyme binding to inhibitor.Concentration where the I would bind 50% of the enzyme.
Basically Km, but an inhibitor version.If, Ki is ↑it has for ↓ affinity for enzymes.
Vmax- stay still
Km-changes, slope changes

UNCompetitive Inhibitor-CHANGE Vmax ( B [Y] and [X] value, slope remains same)
Ki’-when [I] bind, it locks away enzymes from participating in [E]total. If the inhibitor is bound, it
cannot reach Vmax, theoretically. However, less enzymes at play, can reach smaller Vmax
sooner. Less substrates are needed to reach ½ Vmax.
Ki’ increases, the value of alpha is lower, in a sense, means closer to 1 and Vmax would be
lower.

Mixed Inhibitor- km can change but not necessarily because new x-intercept, its - ɑ’/ɑKm
If these- ɑ’/ɑ cancel out, left with just -1/km. As such, x intercept is unchanged.

Ratios: 1) When the numerator increases and the denominator stays the same, the fraction as
a whole increases. When the numerator decreases and the denominator stays the same, the
fraction as a whole decreases. 2) When the denominator increases and the numerator stays the
same, the fraction as a whole decreases.

March 21st, 2023

[Base/Acid] [Product/Reactant]
Keq-broad umbrella where we look a Keq of [reactants] and [products] for a given reaction
Keq only exist for reversible reactions
At dynamic equilibrium, it may actually be constant [stagnant].
At a molecular level, products and reactants may osculate and may not be [stagnant].

Keq|Q relationship
Shifting in the direction to get to Keq depending on concentration of [products] and [reactants]
Keq>Q at equilibrium | greater concentration of [products] as such, shifts forward.

Le Chatelier's principle
Intents to mitigate the value of Q [reduce the value of Q] by reducing the concentration of
[products]. This can be done by:
Physical isolation by keeping concentration of [products] low
Another enzyme facilitating the reaction like an intermediate

[ ·
G ]
At standard pressure [1 atm], temperature [298k]. A constant.
A way to show relative favorability of a given reaction.

Keq|[ ·
G ] relationship.

As Keq increases, [ ·
G ] more negative.[Qualitatively] As Keq increases, we’re favoring the

formation of products as such, [ ·

G ] decreases, becoming more favorable.

Q|[ ·
G ] relationship.
Temperature [average kinetic energy] increases the impact of whatever its x by

As Q increase, ·
G also increases.
Q [disjointed from K]. Q [given experimental conditions]
Q>Keq then that doesn’t necessarily make the reaction more spontaneous. In fact, it makes it

less favorable because Q is greater than K. As As Q increase, ·

G approaches zero.

Pathways
Efficiency by coupling. Example breakdown of ATP.

Alpha [first] closest to alpha carbon. As a breakdown ATP, gamma goes first!
Repeatability of subunits makes it highly efficient.

Most oxidized carbon [bonded to 3 Os oxygen].

Oxidizing encompasses increasing the bonds to electron withdrawing groups.
Electron density-the more reduced something is, the more dense the electrons are around that
particular atom. The more oxidized something is, the less dense the electrons are around that
atom.
Why can’t we oxidize tertiary alcohol? It would disturb that octet.
A primary alcohol can be oxidized twice. A secondary ketone can be oxidized and reduced.
It all comes down to the flow and availability of energy.
Random: Phosphorylate is a replacement reaction between a hydroxyl and phosphate group.

Glycolysis Pathway and Gluconeogenesis pathway- a lot of recycling!

Glucose is versatile. Utilization differs from extraction.
Glucose-storage as glycogen which has more bioavailable than fats
Glycolysis- a breakdown mechanism. Generate energy-oxidizing glucose, removing electron
density from glucose and adding it to other molecules like NAD+ -> NADH] NADH short term.
Pentose phosphate pathway-generates NADPH. Drops electron density into fatty acids.
NADPH is more important for long-term energy storage. Also create other sugars like
deoxyribose. A constructive pathway for making things.
Anaerobic-lack of oxygen | Aerobic-lots of oxygen [O2-H20] reduced!
Oxygen is obtaining electron density when it becomes reduced.

NADH | ATP [Important carriers]

NADH electron carrier to get to ETC to drop off electrons for aerobic respiration.
Anaerobic-> build up of NADH and electrons.
Cancers love anaerobic (non-traditional environments).
Cancer is essentially the manifestation of irregular cell growth.
Glucose has a lot of energy and can be oxidized. However, sugar is more cyclic and so
restrains and hinders ability to stack. Protein works too but most efficiently is -fat!

Glycolysis ends with Pyruvate [super important!] A carbon skeleton used to create other
molecules. Also, it can be further oxidized.
Glycolysis creates ATP directly:
ETC by oxidative phosphorylation
Substrate level phosphorylation [moving the phosphate group] back to ADP molecule to create
ATP [not a very substantive pathway] However, it is a good way to make ATP if you have no
oxygen present [substandard conditions].

Ken’s Mnemonics
Krebs Cycle
Citrate Is Krebs Special Substrate For Making Oxaloacetate

Citrate- citrate
Is-Isocitrate
Krebs-Ketoglutarate
Special-Succinyl-CoA
Substrate-Succinate
For-Fumarate
Making-Malate
Oxaloacetate-Oxaloacetate

Glycolysis Intermediates
Girls Get Fine Food | Gentlemen Dine Girls | Boys Prefer (to) Pick (up) Pepperoni Pizza
Girls- Glu
Get-Glu-6-P
Fine-Fru-6-P
Food-Fru-1,6-6P
Gentlemen-G3P
Dine-DHAP
Girls-G3P
Boys- 2x 1,3-BPG
Prefer (to)- 2x 3-PG
Pick (up)- 2x 2-PG
Pepperoni- 2x PEP
Pizza- 2x Pyr

Disaccharides
Super Glowing Frogs Leave Gardens Glowing
Sucrose=glucose + fructose
Lactose=galactose + glucose

March 24th, 2023

Glucose-mainly a source of energy, but moreso, a source of carbons!
Glycolysis is just one of the many ways we can use glucose.Glucose contributes to the
backbone of other biomolecules and partakes in many other reactions-duh!
Pay attention to how the presence/absence of certain enzymes will alter pathways.
How Le Chatelier's principle/ environmental conditions will predict certain pathways, etc.

Glycolysis [A feeder into the optimal pathway, Krebs!]

Preparatory phase-all about making high energy metabolites. Involves breaking glucose in half
and making it more available for energy extraction-that is oxidation (extracting the electron).
Cells prefer aerobic conditions [however, they do still function under suboptimal conditions]
Without oxygen, we cannot oxidize NADH. Oxygen is the final acceptor of electrons on the ETC
chain. The electrons that proceed down the ETC is from NADH (NAD+ is a cofactor)
Stage 1: Let’s go!
6-C with OH attached, seeks to achieve symmetry. Eventually splits into DHAP + GAP
These two interconvert. DHAP-> GAP because:
1)Its sterically impossible to have split into the two exact same molecules
2)It would be more efficient to use one enzyme and interconvert

Pay off phase-the regeneration of expended ATP & generate new ATP :)
This phase uses free floating (inorganic) phosphates to make new ATP LOL
High energy [3 carbon intermediates] are able to form a bond with phosphate and subsequently,
the phosphate can be broken off and used to form ATP- this is essentially, substrate level
phosphorylation.
Notes: two types of phosphorylation:
Oxidative phosphorylation-where NADH is oxidized in a series of redox reactions
Substrate level phosphorylation-the formation of ATP from ADP and a phosphorylated
intermediate

Note: this reaction is happening twice at this point-so 2 x everything.

Pay attention to: favorability, reversibility and molecular regulation of this step such as such
would play a part in the negative feedback loop.

Preparatory phase
First step in glycolysis is NOT the step that commits glucose to the cell. As such, glucose-6-
phosphate can be used in other reactions and pathways. This step involves phosphorylation of
glucose into glucose-6-phosphate using hexokinase.
Hexokinase allows for the phosphorylation, specifically of the OH group attached to the 6 -C.
Mg++ shields the negative charges on the ATP molecule. This allows the negatively charged
ATP molecule and negatively polarized OH group to get close to one another.
Mg++ is notably divalent which makes it very efficient <3
Now, we’re left with glucose-6-phosphate and the is G-16.7KJ/mol. Moreover, since this is a
- G, this means its spontaneous and will favor product formation. Keq will be >1.

Combination reaction/ coupled reactions

glucose + P -> glucose-6-phosphate (+)
ATP -> ADP + P (-)
Highly thermodynamically favorable/irreversible but still not quite committed at this first step.
Step Two: Proceed to try and achieve symmetry and make it more reactive.
Shifting the position of oxygen in the ring. Moving it from 1-C to 2-C and now a 5 member ring.
We’re not reducing the no. of C, we’re reducing the no of C in the ring.