Comprehensive Chemistry: Equilibrium, Buffer Systems, and Protein Structure

Le Chatelier's Principle

A principle stating that if a dynamic equilibrium is disturbed by changing the conditions, the position of equilibrium shifts to counteract the change.

Buffer

A solution that resists changes in pH when small amounts of acid or base are added, typically composed of a weak acid and its conjugate base.

Equilibrium Shift

The change in the position of equilibrium in response to a change in concentration, pressure, or temperature.

Endothermic Reaction

A reaction that absorbs heat from the surroundings.

Exothermic Reaction

A reaction that releases heat to the surroundings.

pH

A measure of the acidity or basicity of a solution, calculated as pH = -log[H3O+].

Dihydrogen Sulfide

A chemical compound with the formula H2S, which can affect the direction of equilibrium in reactions.

Carbon Disulfide

A chemical compound with the formula CS2, which can affect the direction of equilibrium in reactions.

Methane

A chemical compound with the formula CH4, which can affect the direction of equilibrium in reactions.

Buffer Equilibrium

The state of balance in a buffer solution where the concentrations of the weak acid and its conjugate base remain relatively constant.

Strong Acid

An acid that completely dissociates in solution, resulting in a high concentration of H3O+ ions.

Weak Acid

An acid that partially dissociates in solution, resulting in a lower concentration of H3O+ ions.

Weak Base

A base that partially dissociates in solution, resulting in a lower concentration of OH- ions.

Ka

The acid dissociation constant, a measure of the strength of an acid in solution.

pKa

The negative logarithm of the acid dissociation constant (Ka), used to express the strength of an acid.

Zwitterion

A molecule that has both a positive and a negative charge but is overall neutral, commonly found in amino acids.

Physiological pH

The pH level of human blood, typically around 7.4.

Concentration

The amount of a substance in a given volume of solution, often expressed in molarity (M).

Pressure

The force exerted by the substance per unit area, which can influence the direction of equilibrium.

Volume

The amount of space that a substance occupies, which can influence the direction of equilibrium.

Sodium Propionate

A sodium salt of propionic acid, used in buffer solutions.

Propionic Acid

A carboxylic acid with the formula CH3CH2COOH, used in buffer solutions.

NaNO2

Sodium nitrite, a compound that can be used in buffer solutions.

HNO2

Nitrous acid, a weak acid that can be used in buffer solutions.

Aqueous reactions

Reactions taking place in water, using water to break bonds.

Base and Acid Hydrolysis reactions of Amide

Reactions involving the breakdown of amides in the presence of a base or acid.

(CH3)2CHNHCOCH2CH(CH3)2

N-isopropyl-3-methylbutanamide.

Reactants for N-methyl-2-methyl-propanamide

Methylamine and 2-methylpropanoic acid.

Reactants to make an amide

Carboxylic acid and amine.

Type of reaction with no products

No reaction.

Acid Base reaction products

Amine Salt and Carboxylate.

Reaction of butanoic acid and dimethylamine

Produces N,N-dimethylbutanamide.

Dipeptides from amino acids

Lys-Val and Val-Lys.

Primary protein structure

Consists of peptide bonds.

Secondary protein structure

Includes alpha helices and beta sheets formed by hydrogen bonding.

Tertiary protein structure

Stabilized by R group interactions and various bonding types.

Quaternary protein structure

Combination of two or more protein subunits.

Denaturation

Process of changing the shape of a protein without breaking its amide bonds.

Effects of denaturation

Affects secondary, tertiary, and quaternary structures; primary structure remains unaffected.

Bonds affected by heat and organic compounds

Hydrogen Bonds and Hydrophobic Interactions.

Bonds affected by acids and bases

Salt Bridges (Ionic Bonds) and Hydrogen Bonds between Polar R Groups.

Bonds affected by heavy metal ions

S-S bonds and Hydrogen Bonds.

Disulfide bond

A bond joining distant parts of a peptide.

Hydrophilic side chains

Interacting with water in tertiary structure.

Hydrophobic side chains

Forming a nonpolar center in tertiary structure.

Amine bond formation

The amine group on an amino acid bonds to the carboxylic acid group on another amino acid, forming an amide bond.

Hydrogen bonds in peptides

Form between the backbone of a peptide in secondary structure.

Proteins during digestion in stomach

HCl denatures the protein into its primary structure, and all of the peptide bonds are hydrolyzed.

Proteins during digestion in small intestine

Proteases in the small intestine catalyze this reaction, and the enzymes trypsin and chymotrypsin help further hydrolyze the remainder of the amine bonds.

Type of enzyme that catalyzes hydrolysis of peptide bonds in small intestine

Proteases

Class of enzyme for urease

Hydrolase

Substrates of urease

Urea and water

Optimal temperature of urease

Approximately 35-40°C

Effect of temperature rise to 55° on urease reaction rate

Decrease; once the temperature is past the optimal temperatures the enzyme starts to denature.

Type of inhibitor for acetohydroxamic acid

Reversible, competitive inhibitor

Effect of adding urea when inhibitor is present

It is a reversible inhibitor - there is no covalent modification occurring.

Effect of aspirin on cyclo-oxygenase (COX)

The acetyl group on aspirin covalently bonds to a serine residue in the active site of the COX enzyme.

Type of inhibitor aspirin is

Competitive Inhibitor

Reversibility of aspirin interaction with COX

IRREVERSIBLE: Covalent bond to active site.

Active site rigidity

False. In the induced fit model, the structure of enzyme is flexible.

Enzyme activation at any temperature and pH

False. Enzymes mostly have an optimum temperature and pH.

Vitamins as cofactors

True

Enzyme effect on reaction equilibrium

False. The enzyme lowers the activation energy to increase the reaction rate.

Enzyme effect on reaction spontaneity

False. Spontaneity of a reaction is determined by the energy of reactants and products and temperature at which the reaction occurs.

Enzyme ability to increase or decrease reaction rate

False. Enzymes can only increase the reaction rate.

Effect of temperature decrease on enzyme activity

True

Competitive inhibitor binding

True. A competitive inhibitor can enter and bind to the same active site as a substrate.

Reversible inhibitors binding to enzymes

False. Reversible inhibitors can leave, and when they do enzyme activity is restored.

Noncompetitive inhibitor effect on enzyme

True. A noncompetitive inhibitor cannot permanently deactivate an enzyme.

Need for vitamins in the body

False. Vitamins can be reused many times. Only a small amount is needed.

Coenzyme acting as oxidizing agent

False, reducing agent(s) lose H+ and e-.

Reducing agents in reduction reactions

True

NAD+ effect on alkane bonds

False, FADH2.

FAD

FAD and FADH2 are used to oxidize and reduce bonds between two carbons.

Coenzyme

A coenzyme is an organic molecule used so an enzyme-catalyzed reaction can occur.

Fat-soluble vitamins

Fat-soluble vitamins are not a coenzyme, but many water-soluble vitamins are coenzymes.

Enzymes

Enzymes are important biological catalysts because they increase the rate of chemical reactions in the body by lowering the activation energy of a reaction.

Zymogens

Zymogens are the inactive form of an enzyme that can be converted to the active form by removing small peptide sections.

Rubisco

The most abundant protein on earth is called Rubisco, which acts as an enzyme in photosynthesis in all plants.

Induced fit model

The induced fit model describes how Rubisco adds CO2 to RuBP.

Protease

A protease can remove a tripeptide section of Rubisco.

Hydrolysis of tripeptide

It takes 2 water molecules to hydrolyze a tripeptide into amino acids.

Irreversible competitive inhibition

This type of inhibition occurs when an inhibitor mirrors the quaternary structure of Rubisco and forms covalent bonds in the active site.

Quaternary structure forces

Rubisco relies on salt bridges, hydrogen bonding between backbones and between R-groups, and hydrophobic interactions to stay in its quaternary structure.

Reversible non-competitive inhibition

This type of inhibition occurs when an inhibitor temporarily binds to somewhere else than the active site.

Oxidoreductases

Catalyze oxidation-reductions reactions.

Hydrolases

Catalyze hydrolysis of chemical bonds.

Ligases

Catalyze a bond formation coupled to ATP hydrolysis to provide energy.

Isomerases

Catalyze isomerization of a substrate.

Lyases

Catalyze a group elimination to form a double bond, or addition of a group to a double bond.

Transferases

Catalyze transfer of functional groups.

Temperature effect on enzyme activity

As you decrease temperature, enzyme activity decreases.

Optimum temperature

As you increase temperature, enzyme activity increases until you hit the optimum temperature. If you go past the optimum temperature, the enzyme would denature.

pH effect on enzyme activity

As you decrease the pH, becoming more acidic, the enzyme will denature past its optimum pH.

Basic pH effect

As you increase the pH, becoming more basic, the enzyme denatures past the optimum pH.

Substrate Concentration

An increase in substrate concentration increases the rate of reaction (with excess enzyme). However, eventually, the enzyme is saturated with substrate and will reach a level of maximum activity.

Enzyme Concentration

As you increase the enzyme concentration, the rate of reaction increases (as long as there is excess substrate). If you decrease the enzyme concentration, the rate of reaction will slow down, as there is only so much enzyme for the substrate to bind to.

Reduction

Reduction is best defined as the decrease of C-O bonds or increase of C-H bonds, or the overall gain of electrons.

IUPAC Name: 3,3,4-trimethylhexan-2-one

IUPAC name for a specific ketone compound.

IUPAC Name: pentan-2-one

IUPAC name for a specific ketone compound.