Protein Structure and Function, Acid-Base Reactions, and Enzymes

Flashcards covering key concepts from the lecture notes on acid-base reactions, protein structure and function, and enzymes, in a question and answer format.

What is the role of an acid in chemical reactions?

Acids are substances that give up protons, increasing the hydronium ion concentration of water.

How do bases function in chemical reactions?

Bases are molecules or ions that acquire protons, lowering the hydronium ion concentration of water.

What is the formula for calculating pH?

pH = −log[H₃O⁺]

How does a higher concentration of hydronium ions ([H₃O⁺]) relate to pH and acidity?

A higher [H₃O⁺] results in a lower pH value, indicating a more acidic solution.

Why is the concentration of hydronium ions ([H₃O⁺]) considered the same as the concentration of hydrogen ions ([H⁺]) in aqueous solutions?

A hydronium ion is a proton (H⁺) that has attached to a water molecule (H₂O).

What percentage of the dry weight of cells do proteins account for?

More than 50% of the dry weight of cells.

What is the function of enzymatic proteins?

They selectively accelerate chemical reactions, such as digestive enzymes catalyzing the hydrolysis of bonds in food molecules.

Give an example of a defensive protein and its function.

Antibodies inactivate and help destroy viruses and bacteria, providing protection against disease.

What is the primary function of transport proteins like hemoglobin?

Transport proteins move substances, for example, hemoglobin transports oxygen from the lungs to other parts of the body.

What are the building blocks (monomers) of proteins?

Amino acids.

What are the four major components of an amino acid?

A carboxyl group, an amino group, a hydrogen atom, and a side chain ('R-group'), all linked to an ɑ-carbon.

What part of an amino acid determines its unique characteristics?

The side chain (R-group).

How do peptide bonds form between amino acids?

Peptide bonds form between the carboxyl group of one amino acid and the amino group of another via a condensation (dehydration) reaction.

What is the difference between a polypeptide and a protein?

A polypeptide is a polymer of amino acids. A protein is a functional molecule consisting of one or more polypeptide chains folded and coiled into a specific 3D conformation.

What is the N-terminus and C-terminus of a polypeptide chain?

The N-terminus is the end with a free amino group, and the C-terminus is the end with a free carboxyl group, defining the polypeptide's directionality.

What is the principle 'function follows form' in the context of proteins?

A protein's specific 3D structure determines how it works, often by recognizing and binding to other molecules.

What is the primary structure of a protein?

The unique sequence of amino acids in a polypeptide chain, determined by genetic information.

How can a slight change in a protein's primary structure affect its function, using sickle cell disease as an example?

A single amino acid substitution (e.g., glutamate for valine in hemoglobin) can lead to protein crystallization, causing red blood cells to sickle and reducing oxygen-carrying capacity.

What is the secondary structure of a protein, and what type of interaction is primarily responsible for it?

Secondary structure consists of coils (alpha helices) and folds (beta-pleated sheets) in sections of the polypeptide chain, resulting from hydrogen bonds between atoms in the polypeptide backbone.

What is the tertiary structure of a protein, and what types of interactions are involved?

Tertiary structure refers to irregular contortions superimposed on the secondary structure, resulting from interactions between amino acid side chains or between side chains and the backbone, including hydrogen bonds, ionic bonds, disulfide bridges (covalent between S atoms), and hydrophobic interactions.

What role do hydrophobic interactions play in forming the tertiary structure of a protein?

Hydrophobic amino acids cluster at the core of the protein, away from water, held together by van der Waals interactions, contributing to protein folding stability.

What is the quaternary structure of a protein?

The overall structure that results when a protein consists of two or more polypeptide chains (subunits), held together by interactions between side chains and/or polypeptide backbones of different chains.

Give two examples of proteins with quaternary structure.

Collagen (three helical subunits) and Hemoglobin (four subunits: two alpha and two beta chains).

What is protein denaturation, and what factors can cause it?

Denaturation is the process where a protein unravels and loses its functional 3D shape, caused by changes in pH, temperature, or salt concentration.

What are chaperonins (chaperone proteins) and what is their function?

Chaperonins are proteins that assist in the proper folding of other proteins, and can speed the refolding of denatured proteins.

What is an enzyme, and what is its role in biological reactions?

An enzyme is a protein catalyst used by living organisms to speed up and control biological reactions by lowering the activation energy without being consumed.

What is the 'induced fit' hypothesis regarding enzyme-substrate binding?

The 'induced fit' hypothesis states that when a substrate binds to an enzyme's active site, the enzyme undergoes a slight change in shape, resulting in tighter binding of the substrate.

What are cofactors, and what types are there?

Cofactors are non-protein helpers that bind to the active site of an enzyme and play a key role in stabilizing the transition state of a reaction. They can be inorganic (e.g., Zn, Mg, Fe) or organic (coenzymes, often derived from vitamins).

Explain competitive inhibition in enzyme regulation.

Competitive inhibition occurs when a regulatory molecule (inhibitor) binds directly to the active site of an enzyme, preventing the substrate from binding.

Explain allosteric regulation in enzyme activity.

Allosteric regulation occurs when a regulatory molecule binds to a site on the enzyme other than the active site, inducing a shape change that either makes the active site available (activation) or unavailable (inactivation) to the substrate.

List four factors that affect the rate of enzyme catalysis.

Substrate concentration, affinity of enzyme for substrate, temperature, and pH.