CB - T1 W4 Molecular Interactions

What determines the 3D shape of biological compounds?

Interactions within the molecule or between different molecules

What physiological processes do chemical interactions influence?

Cell signaling, enzyme catalysis, and the therapeutic mechanisms of drugs

What are the 5 major types of biological molecules outlined?

Proteins, nucleic acids, lipids, carbohydrates, and small molecules

What are proteins made of, and what are their primary functions?

Long chains of 20 kinds of amino acids; function as structural components and enzymes

What are the primary functions of nucleic acids?

Information storage (DNA, RNA), structure, catalysis (enzymes), and energy transfer

What is the general structure and function of lipids?

A charged head with a long hydrocarbon tail; used for energy storage, insulation, cushioning, and membranes

What are carbohydrates composed of and used for?

Long and short chains of sugar molecules (e.g., glucose, fructose); used for energy sources, energy storage, and structure

What is the primary function of small molecules in biology?

Mostly sending signals (e.g., hormones, vitamins, neurotransmitters)

What are intramolecular bonds?

Strong bonds within a molecule (such as covalent and ionic bonds) that are generally disrupted only by chemical reactions

What are intermolecular forces?

Weaker forces between molecules that provide cumulative strength and binding specificity (e.g., hormone-receptor binding)

What role do chemical bonds play in proteins?

They determine the 3D structure through primary, secondary, tertiary, and quaternary folding

What forces stabilize the DNA double helix structure?

Hydrogen bonds between complementary base pairs and disulphide bonds

How do enzymes interact with substrates?

Substrates enter the active site, the enzyme changes shape slightly to form a complex, converts substrate to products, and releases them

What are the main non-covalent chemical interactions?

Dispersion forces, permanent dipolar interactions, steric repulsion, hydrogen bonds, ionic interactions, and hydrophobic forces

What is a polar covalent bond?

A covalent bond where electrons are shared unequally, resulting in partial positive and negative charges (electronegativity difference of 0.4–1.7)

What is a dipole moment?

The separation of positive and negative charge, calculated as charge multiplied by distance

Why is carbon dioxide (CO

2

​

) non-polar despite having polar bonds?

It is linear (180

∘

); its symmetrical polar bonds pull in opposite directions and cancel each other out

Why is water (H

2

​

O) a polar molecule?

It has a bent shape (104.5

∘

) with a net dipole pointing toward the more electronegative oxygen atom

What are van der Waals interactions?

The sum of non-covalent forces including attractive dispersion forces, dipolar interactions, and repulsive steric forces

How does water affect electrostatic and van der Waals forces compared to a vacuum?

Water is an aqueous medium that significantly decreases forces of attraction (e.g., by 80x for ionic interactions)

What causes dispersion (London dispersion) forces?

Random electron motion creating temporary, uneven electron distributions and induced dipoles between atoms

What factors increase the strength of dispersion forces?

Larger molecular size and flatter shapes that allow closer contact

What is steric repulsion?

The repulsive force that occurs when electron clouds of two molecules come too close together at very short distances

What is the van der Waals radius?

The distance between atom centers where total potential energy is at a minimum (balance of attraction and repulsion)

Which atoms are typically involved in hydrogen bonding?

Highly electronegative atoms like Nitrogen (N), Oxygen (O), and Fluorine (F)

What is a hydrogen bond donor?

A hydrogen atom covalently bonded to an electronegative atom (N, O, F), creating an unshielded, acidic proton

What is a hydrogen bond acceptor?

An electronegative atom with a non-bonding pair of free electrons that electrostatically attracts the hydrogen proton

When are hydrogen bonds strongest?

When the nuclei of the donor, hydrogen, and acceptor are aligned in a straight line

How does temperature affect hydrogen bonds and molecular stability?

Higher temperature increases thermal energy and molecular motion, making bonds less stable and easier to break; lower temperature increases stability

What specific base pairing occurs via hydrogen bonds in DNA?

Adenine pairs with Thymine (A-T), and Guanine pairs with Cytosine (G-C)

What is the difference between transcription and translation in protein synthesis?

Transcription copies DNA into mRNA in the nucleus; translation uses ribosomes and tRNA to decode mRNA into a growing amino acid chain

What causes secondary protein structures like α-helices and β-sheets?

Hydrogen bonding along the peptide backbone combined with specific bond angles and amino acid types

What are the three main types of hydrogen bonds found in proteins?

Bonds between atoms of two peptide bonds, between a peptide bond and an amino acid side chain, or between two amino acid side chains

How are amino acids categorized based on their side chains?

Nonpolar, polar, and electrically charged (acidic or basic)

What is an ionic bond (salt bridge) in proteins?

An electrostatic attraction between oppositely charged amino acid side chains (e.g., basic lysine and acidic aspartic/glutamic acid) that stabilizes protein structure

What drives hydrophobic interactions?

The thermodynamic behavior of nonpolar molecules when exposed to water, causing them to cluster away from the aqueous environment

What is the difference between hydrophilic and hydrophobic molecules?

Hydrophilic molecules are polar and associate readily with water; hydrophobic molecules are non-polar and avoid water

Where are hydrophobic pockets commonly found in proteins?

Inside the protein core or acting as active sites for binding ligands and substrates

What structures are formed by phospholipids in aqueous environments?

Micelles, liposomes, and lipid bilayer sheets

What is hydration (solvation)?

The process where water molecules form a stabilizing "shell" around charged ions or polar solute molecules via dipolar interactions

How do drugs pass through the gut and travel in the bloodstream?

They must be lipophilic enough to cross cell membranes, yet slightly polar/soluble enough to undergo hydration and travel through aqueous blood

What are liposomes used for in drug delivery?

As spherical vesicles with a lipid bilayer to transport both hydrophilic (inside) and hydrophobic (in the membrane) drugs

How does increasing non-covalent interactions affect molecular association?

It creates tighter, more stable associations between molecules

What dictates the physical state (solid, liquid, gas) of a substance?

The balance of intermolecular non-covalent interactions and thermal energy (temperature)

Why do polar molecules have higher melting and boiling points than non-polar molecules?

Because breaking their stronger intermolecular interactions requires a large input of energy

What is an agonist drug?

A drug that binds to a receptor and activates a cellular response

What is a competitive inhibitor?

A drug that competes with the agonist for the same binding site on a receptor, decreasing the response curve

What is an allosteric activator?

A molecule that binds to a separate (allosteric) site on a receptor, increasing its affinity or efficacy for the agonist

What is an allosteric inhibitor?

A molecule that binds to a separate site on a receptor, decreasing the response to the agonist

What is catabolism?

Cellular pathways that break down food molecules into energy, heat, and cellular building blocks

What is anabolism?

Cellular pathways that use energy and building blocks to synthesize complex macromolecules

What role do enzymes play in chemical reactions?

They act as biological catalysts that speed up reactions without being consumed

What does lipase break down?

Fats into glycerol and fatty acids

What does protease break down?

Proteins into amino acids

What does amylase break down?

Starch into simple sugars

What is the enzyme sucrase's specific substrate and products?

Substrate is sucrose; products are glucose and fructose

What is electronegativity?

An atom's ability to attract shared electrons in a chemical bond

Which element has the highest electronegativity on the Pauling scale?

Fluorine (F, value of 4.0)

What electronegativity range classifies a pure covalent bond?

A difference of 0 to 0.4

What electronegativity range classifies an ionic bond?

A difference greater than 1.7

What is a permanent dipole?

A permanent separation of partial positive and negative charges within a molecule due to stable electronegativity differences

What is a cation-pi interaction?

A non-covalent interaction between a positive charge (cation) and the electron-rich π-system of an aromatic ring

What is a CH-π interaction?

A weak non-covalent bond between a C-H donor and the π-cloud of an aromatic ring

What is a halogen bond?

A non-covalent interaction formed when a halogen atom acts as an electrophile and interacts with an electron donor

What is denaturation in DNA or proteins?

The disruption of non-covalent bonds (like hydrogen bonds) causing the loss of 3D structure, usually caused by high heat or pH changes

What is renaturation?

The re-formation of hydrogen bonds and 3D structure when conditions (like temperature) return to normal

What is cooperativity in molecular binding?

When binding of one molecule to a multi-subunit protein or DNA strand makes binding of subsequent molecules easier (zippering effect)

What is the primary cellular environment for biochemical reactions?

An aqueous (water-based) environment

Why are weak intermolecular forces biologically advantageous over covalent bonds for signaling?

They allow for rapid, reversible binding and dissociation, essential for dynamic processes like cell signaling and enzyme action

What is the significance of multivalency in intracellular biomolecules?

Multiple binding sites allow weak individual interactions to sum together, driving phase separation and formation of physiological granules

What are pathological aggregates?

Abnormal, highly stable clumps of misfolded biomolecules resulting from unmanaged intermolecular interactions (e.g., in neurodegenerative diseases)

What is the relationship between bond number and bond strength?

Single bonds are weaker than double bonds, which are weaker than triple bonds

What is the general strength ranking of bond types from strongest to weakest?

Covalent bonds > Ionic bonds > Hydrogen bonds > Van der Waals / Dispersion forces

How does molecular shape influence biological activity?

It ensures precise lock-and-key or induced-fit complementarity between molecules, such as drugs fitting into receptor sites or substrates into enzyme active sites

What is the overarching theme of molecular interactions in biology?

Structure dictates function, and all biological processes rely on a delicate balance of diverse chemical forces working together