S01 WATER AND COVALENT BONDS

What is biochemistry?

The study of the molecular basis of life.

What holds atoms together in a molecule?

Covalent bonds.

What is the molecular weight cutoff for small biomolecules?

Less than 1000 g/mol.

What are five functions of small biomolecules?

Nutrients, cofactors, fuels, precursors to other molecules, and building blocks of macromolecules.

What molecular weight can biomolecules reach as large macromolecules?

Greater than 10^10 g/mol.

What are macromolecules structurally?

Polymers of smaller molecules.

What are polysaccharides?

Polymers of carbohydrates.

What is the primary function of glycogen?

Storage form of glucose between meals.

Glycogen, starch, and cellulose are all polymers of which monomer?

Glucose.

What type of biomolecule is heparin?

Glycosaminoglycan (a polymer of modified carbohydrates).

What are proteins?

Polymers of amino acids.

What are three main biological roles of proteins?

Structural roles, receptors in signaling pathways, and enzymes.

What is the role of enzymes in the body?

Catalyzing bond breakage and formation of biomolecules.

What are nucleic acids?

Polymers of nucleotides.

Why were nucleic acids named 'nucleic'?

Because they are major constituents of the nucleus.

What are the two types of nucleic acids that convey genetic information?

DNA (deoxyribonucleic acid) and RNA (ribonucleic acid).

What are phospholipids?

Amphipathic molecules that can self-associate to form lipid bilayers.

What is the major constituent of cell membranes?

Lipid bilayers formed by phospholipids.

What constitutes the hydrophobic portion of a phospholipid?

Long-chain (16-22 carbons) fatty acids, typically two.

What constitutes the hydrophilic head group of a phospholipid?

Negatively charged phosphate attached to a hydrophilic molecule such as choline or inositol.

Where is water distributed in the human body?

Intracellular and extracellular compartments (interstitial fluids, blood, and lymph).

Why is water classified as a dipolar molecule?

It has an uneven distribution of electrons between the hydrogen and oxygen atoms.

How does water act as a solvent?

By forming hydrogen bonds with other polar molecules due to its dipolar nature.

What does the term 'hydrophilic' mean?

Water loving.

What does the term 'lipophobic' mean?

Lipid hating.

What does the term 'lipophilic' mean?

Lipid loving.

What does the term 'hydrophobic' mean?

Water hating.

Between which types of atoms does hydrogen bonding occur?

An electron-rich atom with a lone pair of electrons (N or O) and an electron-deficient hydrogen.

To what type of atom is an electron-deficient hydrogen usually covalently bound?

An electronegative atom (e.g., N or O).

How many hydrogen bonds can nitrogen accept and why?

One, because it has one lone pair of electrons.

How many hydrogen bonds can oxygen accept and why?

Two, because it has two lone pairs of electrons.

What is the strength range of a hydrogen bond?

Weak to moderate.

What is a unique characteristic feature of hydrogen bonding?

An interaction of orbitals takes place.

What is a Hydrogen Bond Donor (HBD)?

A group in which X-H are bound covalently where X is an electronegative atom.

Why does the hydrogen atom in a Hydrogen Bond Donor participate in hydrogen bonding?

It gains a partial positive charge.

What is a Hydrogen Bond Acceptor (HBA)?

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

Which functional groups can act as both a hydrogen donor and a hydrogen acceptor?

Functional groups such as OH or NH2.

What two main factors affect the water solubility of biological molecules?

Ability to form hydrogen bonds and ionization of one or more functional groups.

Why do hydrophobic molecules interact with each other when mixed with water?

They lack ionic groups or dipoles to interact with water.

Why are water molecules excluded from hydrophobic layers like oil?

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

What is the hydrophobic effect?

The separation of hydrophobic molecules from water.

How is a covalent bond formed?

When two atoms with half-filled orbitals overlap and their electrons align with opposite spins.

What outcome occurs when electrons align with opposite spins during covalent bond formation?

Energy stabilization.

How do ionic interactions (salt bridges) form?

When two ions with opposite charges are attracted to form a bond.

What are Van der Waals interactions (London forces)?

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

What creates temporary dipoles in neutral, non-polar regions of molecules?

Non-symmetrical electron distribution causing areas of temporary high and low electron densities.

How do temporary dipoles lead to Van der Waals interactions?

A dipole in one molecule induces a dipole in a neighboring molecule, attracting areas of high and low electron density.

What factor determines the strength of Van der Waals interactions?

Distance between molecules.

What does thermodynamics study?

The spontaneity of a chemical reaction (the direction and extent to which a reaction proceeds).

What does kinetics study?

The speed of a reaction (how fast a reaction takes place).

Which thermodynamic variable determines whether a chemical reaction proceeds to the right or left?

Free energy (G).

What is the mathematical equation for Gibbs free energy?

G = H - TS.

What does H represent in the Gibbs free energy equation?

Enthalpy (heat of the reaction).

What does S represent in the Gibbs free energy equation?

Entropy (randomness).

In the free energy equation, what scale is temperature (T) measured in?

Degrees Kelvin.

What two energy conditions characterize a thermodynamically favorable reaction?

Heat is given off (exothermic/lower energy products) and products become more random/less complex.

What direction does a reaction proceed when ΔG < 0?

To the right (spontaneous/exergonic).

What term describes a reaction with ΔG < 0?

Exergonic.

What direction does a reaction proceed when ΔG > 0?

To the left (non-spontaneous/endergonic).

What term describes a reaction with ΔG > 0?

Endergonic.

What state is a system in when ΔG = 0?

Equilibrium.