S01 Water and Noncovalent Bonds

Learning Objective 1: Define hydrogen bonding, hydrogen bond donors and hydrogen bond acceptors

What is a hydrogen bond?

An interaction between an electron-rich atom with a lone pair of electrons and an electron-deficient hydrogen.

Which atoms commonly participate as electron-rich atoms in hydrogen bonding?

Nitrogen and oxygen.

What does an electron-rich atom possess that allows it to participate in hydrogen bonding?

A lone pair of electrons.

What is the typical source of the electron-deficient hydrogen in a hydrogen bond?

A hydrogen covalently bound to an electronegative atom such as N or O.

What is the typical charge characteristic of the hydrogen involved in hydrogen bonding?

It has a partially positive charge.

How many hydrogen bonds can one nitrogen accept according to the lecture?

One.

Why can nitrogen accept one hydrogen bond?

Nitrogen has one lone pair of electrons.

How many hydrogen bonds can one oxygen accept according to the lecture?

Two.

Why can oxygen accept two hydrogen bonds?

Oxygen has two lone pairs of electrons.

How strong can hydrogen bonds be?

Weak to moderate in strength.

What is a unique characteristic of hydrogen bonding?

An interaction of orbitals takes place.

What is a hydrogen bond donor (HBD)?

A group in which X-H is covalently bound and X is an electronegative atom with a higher attraction for electrons.

What happens to the hydrogen in a hydrogen bond donor?

The hydrogen gains a partially positive charge.

What is a hydrogen bond acceptor (HBA)?

A functional group that provides an electron-rich atom to participate in a hydrogen bond.

What type of atom does a hydrogen bond acceptor provide?

An electron-rich atom.

Can some functional groups act as both hydrogen bond donors and acceptors?

Yes.

Which OH-containing functional group can act as both an HBD and HBA?

OH.

Which NH2-containing functional group can act as both an HBD and HBA?

NH2.

How can a functional group that is both an HBD and HBA interact at a binding site?

It can bind to one ligand as a hydrogen donor and another as a hydrogen acceptor.

Why can water form hydrogen bonds with other polar molecules?

Water is dipolar because its electrons are unevenly distributed between hydrogen and oxygen.

What property of water allows it to act as a solvent?

Its dipolar nature allows it to form hydrogen bonds with other polar molecules.

Learning Objective 2: Define amphipathic, hydrophilic (lipophobic), hydrophobic (lipophilic) and hydrophobic effect

What does hydrophilic mean?

Water loving.

What does lipophobic mean?

Lipid hating.

What does lipophilic mean?

Lipid loving.

What does hydrophobic mean?

Water hating.

What is an amphipathic molecule?

A molecule containing both hydrophobic and hydrophilic portions.

What type of molecule are phospholipids?

Amphipathic molecules.

What can phospholipids self-associate to form?

Lipid bilayers.

What is the biggest component of cell membranes according to the lecture?

Lipid bilayers.

What is the typical hydrophobic portion of a phospholipid?

Two long-chain fatty acids.

How many carbons are typically present in the fatty acid chains of phospholipids?

16-22 carbons.

What is the hydrophilic portion of a phospholipid?

A head group containing negatively charged phosphate attached to a hydrophilic molecule such as choline or inositol.

What happens when water is mixed with a hydrophobic molecule such as oil?

The hydrophobic molecules interact with each other instead of interacting with water.

Why do hydrophobic molecules interact with each other instead of water?

They lack ionic groups or dipoles that can interact with water.

Why are hydrophobic molecules excluded from water?

Water wants to form hydrogen bonds, but hydrophobic molecules cannot form them.

What is the hydrophobic effect?

The separation of hydrophobic molecules from water.

What happens to oil when mixed with water?

It separates from the water and forms its own layer.

What type of molecule is most likely to interact with water through hydrogen bonding?

A polar molecule.

Learning Objective 3: List the factors that affect water solubility of biological molecules and describe how the properties of water affect the interactions among biomolecules

What is one factor that affects the water solubility of biological molecules?

The ability to form hydrogen bonds.

What is another factor that affects the water solubility of biological molecules?

Ionization of one or more functional groups.

What happens to water solubility when a molecule has the ability to form hydrogen bonds?

Its ability to interact with water is increased.

What happens when one or more functional groups of a molecule become ionized?

Ionization affects the molecule's water solubility.

Why does water act as a solvent for polar molecules?

Water forms hydrogen bonds with other polar molecules.

Where is water distributed in the body according to the lecture?

Between intracellular and extracellular fluids.

What are examples of extracellular fluids listed in the lecture?

Interstitial fluid, blood, and lymph.

What is a biomolecule?

A molecule involved in biological systems.

What holds the atoms of a molecule together?

Covalent bonds.

What are small biomolecules defined as by molecular weight in the lecture?

Compounds with molecular weight less than 1000 g/mol.

What are some functions of small biomolecules?

They function as nutrients, cofactors, fuels, precursors, and building blocks of macromolecules.

What are macromolecules?

Large molecules that are polymers of smaller molecules.

What are polysaccharides?

Polymers of carbohydrates.

What is glycogen?

A polymer of glucose.

What is the function of glycogen?

It functions as a storage form of glucose between meals.

What is a polymer of glucose?

Glycogen.

What are starch and cellulose?

Polymers of glucose.

What are glycosaminoglycans?

Polymers of modified carbohydrates.

What is heparin?

An example of a glycosaminoglycan.

What are proteins?

Polymers of amino acids.

What is one structural role of proteins?

They contribute to structures such as bones, teeth, hair, and skin.

What role can proteins have in signaling pathways?

They can function as receptors.

What catalytic role can proteins have?

They can function as enzymes that catalyze bond breakage and formation of biomolecules.

What are nucleic acids?

Polymers of nucleotides.

Why is the term nucleic acid used?

Nucleic acids are major constituents of the nucleus.

What is the function of DNA and RNA?

They convey genetic information.

What are the major precursors to macromolecules?

Sugars, amino acids, and nucleotides.

Learning Objective 4: Define covalent bonds, ionic bonds and Van der Waals bonds and describe how they occur

What is a covalent bond?

A bond formed when two atoms with half-filled orbitals overlap and their electrons align with opposite spins, leading to energy stabilization.

What happens to the orbitals during covalent bond formation?

Half-filled orbitals overlap.

What happens to the electrons during covalent bond formation?

Their spins align in opposite directions.

What is the result of covalent bond formation?

Energy stabilization.

What is an ionic bond?

An attraction between two ions with opposite charges.

What is another name for ionic interactions?

Electrostatic interactions or salt bridges.

What causes ionic bonding?

Attraction between oppositely charged ions.

What are Van der Waals interactions?

Very weak interactions that occur between hydrophobic regions of different molecules.

What are Van der Waals interactions also called?

London forces.

Where do Van der Waals interactions occur?

Between hydrophobic regions of different molecules.

Is the electronic distribution in neutral, non-polar regions completely even or symmetrical?

No.

What exists in neutral, non-polar regions because electronic distribution is not completely even or symmetrical?

Areas of high and low electron density.

What do areas of high and low electron density form temporarily?

Temporary dipoles.

What can a dipole in one molecule do to a neighboring molecule?

It can induce a dipole in the neighboring molecule.

What results when a dipole induces a dipole in a neighboring molecule?

A weak Van der Waals interaction.

What type of electron-density region attracts a high-electron-density region on another molecule?

A low-electron-density region.

What determines the strength of Van der Waals interactions?

The distance between the molecules.

What happens to Van der Waals interactions when molecules are farther apart?

The interactions become less significant.

Why must a drug be close to a binding site for Van der Waals interactions to be significant?

The strength of the interactions depends on the distance between molecules.

Learning Objective 5: Define the important parameters of thermodynamics (enthalpy, entropy and free Gibbs energy) and describe how ΔG can be used to predict whether a reaction will occur spontaneously or not

What does thermodynamics study?

The spontaneity of a chemical reaction, including the direction and extent to which it proceeds.

What does kinetics study?

The speed of a chemical reaction.

What is the difference between thermodynamics and kinetics?

Thermodynamics concerns reaction spontaneity, whereas kinetics concerns reaction speed.

What is free energy (G)?

A thermodynamic variable used to explain whether a chemical reaction proceeds to the right or left as written.

What two variables determine free energy?

Enthalpy and entropy.

What is the equation for free energy?

G = H − TS.

What does T represent in the free energy equation?

Temperature in degrees Kelvin.

What does H represent?

The heat of the reaction.

What does S represent?

Randomness.

What happens to heat in a favorable reaction?

Heat is given off.

What happens to the energy of the products in a favorable reaction?

The products have less energy.

What happens to the randomness of products in a favorable reaction?

The products become more random.

What does ΔG < 0 indicate?

The reaction proceeds to the right as written.

What type of reaction has ΔG < 0?

Exergonic.

What does ΔG > 0 indicate?

The reaction proceeds to the left as written.

What type of reaction has ΔG > 0?

Endergonic.