mega set

Equilibrium Constant ($K$)

The ratio of the concentration of products over the concentration of reactants ($[Products]/[Reactants]$).

Large Equilibrium Constant ($K$)

Indicates a reaction that produces a high concentration of products, essentially going toward completion.

Unfavorable Reaction Coupling

An unfavorable reaction can be driven forward by coupling it to a subsequent highly favorable reaction that depletes the product (Le Chatelier’s principle).

Anabolic vs Catabolic Pathways

Anabolic pathways synthesize molecules and require energy, while catabolic pathways degrade molecules and release energy.

Least Free Energy Liberation in Hydrolysis

Glucose-6-phosphate ($G6P$) liberates the least free energy when hydrolyzed compared to $ATP$, $PEP$, and $PP_{i}$.

Stability of $ATP$ Hydrolysis Products

$ATP$ hydrolysis products are more stable due to the relief of charge-charge repulsions and resonance stabilization of the products.

Polarity of Water

Water is considered a polar molecule due to its net dipole moment caused by electronegativity differences and bent shape.

Nonpolar $CO_{2}$ despite Polar Bonds

$CO_{2}$ is nonpolar because it is linear, causing individual bond dipoles to cancel each other out.

Hydrogen Bond Donor

The atom ($O$ or $N$) that is covalently bonded to the hydrogen atom in a hydrogen bond.

Hydrogen Bond Acceptor

The atom with a lone pair of electrons that interacts with the hydrogen atom in a hydrogen bond.

Hydrogen Bonds from a Water Molecule

A single water molecule can form $4$ hydrogen bonds.

Salt Bridge in Protein Structure

An electrostatic (ionic) interaction between oppositely charged groups.

Dielectric Constant Effect on Ionic Bonds

A lower dielectric constant increases the strength of ionic bonds compared to water.

Pi Stacking

A weak interaction between electron clouds of aromatic rings, important for $DNA$ stability.

Amphipathic Molecule

A molecule containing both polar (hydrophilic) and nonpolar (hydrophobic) regions.

Entropy Changes with Hydrophobic Aggregation

Entropy decreases (becomes more negative) when hydrophobic molecules aggregate in water.

Physiological $pH$ Range in Blood

The physiological $pH$ range for human blood is $7.35$ to $7.45$.

Bronsted-Lowry Acid Definition

A molecule that acts as a proton ($H^{+}$) donor.

Amphoteric Substance

A substance capable of acting as either an acid or a base, like water.

$pKa$ Value Significance

The $pKa$ value indicates acid strength; lower $pKa$ means a stronger acid.

Henderson-Hasselbalch Equation

$$pH = pKa + \log([A^{-}]/[HA])$$

Midpoint of a Titration Curve

At the midpoint, the $pH$ equals the $pKa$ when the concentration of the weak acid equals its conjugate base.

Effective Buffering Range for Weak Acid

The effective buffering range for a weak acid is $pKa \pm 1 \text{ pH unit}$.

Hyperventilation Effect on Blood $pH$

Hyperventilation decreases $CO_{2}$ levels, increasing $pH$ and causing alkalosis.

Hypoventilation Effect on Blood $pH$

Hypoventilation increases $CO_{2}$ levels, decreasing $pH$ and causing acidosis.

Predominant Buffer System in Blood

The bicarbonate system ($CO<em>{2}/H</em>{2}CO<em>{3}/HCO</em>{3}^{-}$).

Importance of Phosphate $pKa$

The $pKa$ of phosphate ($7.20$) is close to physiological $pH$ ($7.40$), allowing it to function as a buffer.

Charge on Phosphate at $pH$ $7.40$

Approximately $-1.61$.

Problems with High Phosphate Concentrations

High phosphate can form insoluble precipitates with ions like Calcium ($Ca^{2+}$).

Exothermic vs. Endothermic Reactions

An exothermic reaction ($\Delta H < 0$) releases heat, while an endothermic reaction ($\Delta H > 0$) absorbs heat.

Significance of Gibbs Free Energy ($\Delta G$) Sign

A negative $\Delta G$ means a reaction is exergonic (spontaneous); a positive $\Delta G$ means it is endergonic (non-spontaneous).

Thermodynamics vs. Kinetics

Thermodynamics determines if a reaction will happen (spontaneity), whereas kinetics determines how fast it occurs.

Fundamental Gibbs Free Energy Equation

$$\Delta G = \Delta H - T\Delta S$$

Second Law of Thermodynamics and Entropy

The second law states that the disorder (entropy, $\Delta S$) of the universe is constantly increasing.

Significance of the 'Prime' Symbol ($'$) in $\Delta G^{\circ '}$

It signifies standard conditions specifically at $pH$ $7.0$, the standard for biochemical reactions.

Gas Constant ($R$) in $\Delta G$ Calculations

The constant $R$ is $8.314 \text{ J/mol} \cdot \text{K}$.

Relationship between $\Delta G^{\circ '}$ and Equilibrium Constant ($K$)

If $\Delta G^{\circ '} < 0$, then $K > 1$, meaning the reaction favors product formation at equilibrium.

Reaction Quotient ($Q$) vs. Equilibrium Constant ($K$)

$Q$ is used for non-standard or non-equilibrium concentrations; $K$ is used only at equilibrium.

Spontaneity of the Hydrophobic Effect

The separation of oil and water is a spontaneous process where $\Delta G$ is negative.

Entropy Changes in the Hydrophobic Effect

The entropy ($\Delta S$) of water increases as water molecules are released from ordered cages around hydrophobic solutes.

Cellular Organization and the Second Law

A cell remains organized by releasing heat and increasing the entropy of its surroundings, thus increasing total universal disorder.

Types of Phosphate Bonds in $ATP$

$ATP$ contains two high-energy phosphoanhydride bonds and one phosphoester bond.

Standard Free Energy ($\Delta G^{\circ '}$) of $ATP$ Hydrolysis

The value for the hydrolysis of $ATP$ to $ADP$ and $P_{i}$ is $-30.5 \text{ kJ/mol}$.

Driving Endergonic Reactions

Endergonic reactions are driven forward by coupling them to highly favorable reactions, typically $ATP$ hydrolysis.

Kinetic Stability of $ATP$

$ATP$ is kinetically stable in water because the negative charges of the phosphate groups repel water nucleophiles, requiring enzymes for catalysis.

Reasons for High Energy Release in $ATP$ Hydrolysis

1. Relief of electrostatic charge repulsion; 2. Higher resonance stability of products; 3. Better solvation of products by water.

Hydrolysis of $ATP$ vs. Pyrophosphate ($PP_{i}$)

Hydrolysis of $PP<em>{i}$ to $2P</em>{i}$ releases more energy ($\Delta G^{\circ '} = -33.5 \text{ kJ/mol}$) than $ATP$ to $ADP$.

Net Charge of $ATP$ at Physiological $pH$

At physiological $pH$, $ATP$ has a net charge of approximately $-4$.

$\Delta G^{\circ '}$ for $ATP$ Hydrolysis to $AMP$ and $PP_{i}$

$-32.2 \text{ kJ/mol}$.

Specific Bond Broken in $ATP$ or $PP_{i}$ Hydrolysis

A phosphoanhydride bond.

$\Delta G^{\circ '}$ of Glucose-6-phosphate ($G6P$) Hydrolysis

It is significantly less negative than $ATP$, at $-13.8 \text{ kJ/mol}$.

$\Delta G^{\circ '}$ for Phosphoenolpyruvate ($PEP$) Hydrolysis

$-61.9 \text{ kJ/mol}$.

Biological Process Coupled to $PEP$ Hydrolysis

The synthesis of $ATP$ from $ADP$ during glycolysis.

Nucleophile in Phosphate Hydrolysis

Water ($H_{2}O$).

Electrophile in Phosphate Hydrolysis

The phosphorus atom ($P$) of the $P=O$ group.

Zwitterion

A molecule or ion with separate positively and negatively charged groups, resulting in a net neutral charge.

Core Amino Acid $pKa$ Values

The carboxylic acid $pKa$ is $\approx 2$, and the amino group $pKa$ is $\approx 9$.

Protonation Rule: pH > pKa

When pH > pKa, the molecule will lose a proton ($H^{+}$).

Protonation Rule: pH < pKa

When pH < pKa, the molecule will retain its proton ($H^{+}$).

Amphoteric Nature of Amino Acids

Amino acids can act as both acids (donating $H^{+}$) and bases (accepting $H^{+}$).

Acidity of Amino Acid Carboxyl Group vs. Acetic Acid

The amino acid carboxyl group is more acidic ($pKa \approx 2$) than acetic acid ($pKa = 4.76$).

Location of Nonpolar Amino Acids in Proteins

They are typically buried in the interior of the protein to avoid contact with the aqueous environment.

Aromatic Nonpolar Amino Acids

Phenylalanine ($Phe$) and Tryptophan ($Trp$).

Polar & Neutral R-Groups

Functional groups capable of forming hydrogen bonds without carrying a charge at physiological $pH$.

Amino Acids for Signaling Phosphorylation

Serine ($Ser$), Threonine ($Thr$), and Tyrosine ($Tyr$), due to their hydroxyl ($-OH$) groups.

Protonation of Asparagine ($Asn$) and Glutamine ($Gln$) Amides

The amide nitrogens are never protonated under physiological conditions.

The Nine Nonpolar Amino Acids

Glycine, Alanine, Valine, Leucine, Isoleucine, Methionine, Phenylalanine, Tryptophan, and Proline.