Biological Macromolecules and Chemical Principles

The spontaneity of a reaction—whether it will occur naturally without a continuous input of energy—is determined by the change in Gibbs Free Energy ($\Delta G$).

• A spontaneous reaction has a negative $\Delta G$ ($\Delta G < 0$).
• A nonspontaneous reaction has a positive $\Delta G$ ($\Delta G > 0$).

One critical concept in biology is entropy ($\Delta S$), which measures disorder. Many life processes, such as polymerization (the building of large molecules from smaller ones), are nonspontaneous because they decrease entropy, making the system more ordered.

Biological Macromolecules

Carbohydrates and Lipids

Carbohydrates serve as primary energy sources. For example, glycogen is a highly branched polysaccharide that releases energy more readily than starch because its frequent $\alpha$-1,6 glycosidic branches provide more "ends" for enzymes to act upon.

Lipids, such as triacylglycerides, are excellent for long-term energy storage. They are synthesized via dehydration reactions, where fatty acids are linked to a glycerol backbone, releasing a water molecule in the process. Because fats contain many nonpolar covalent bonds, they possess high potential energy. In cell membranes, cholesterol plays a vital role by interacting with the polar heads and nonpolar tails of phospholipids to regulate membrane fluidity.

Proteins: Structure and Function

Proteins are polymers of amino acids linked by peptide bonds. The function of a protein is entirely dependent on its three-dimensional shape, which is organized into levels:

1. Primary structure: The linear sequence of amino acids.
2. Secondary structure: Local folding patterns, such as $\alpha$-helices and $\beta$-pleated sheets, which are stabilized by hydrogen bonds.
3. Tertiary structure: The overall three-dimensional shape of a single polypeptide.

Enzymes are specialized proteins that catalyze reactions. They do this by providing an active site that precisely orients substrate molecules, lowering the activation energy required for the reaction to proceed. Some drugs act as competitive inhibitors, meaning they mimic the substrate and bind to the active site, preventing the actual substrate from reacting.

Nucleic Acids: The Blueprint of Life

DNA and RNA are the molecules responsible for storing and transmitting genetic information. DNA is generally more stable than RNA because its sugar (deoxyribose) contains one less oxygen atom than the sugar in RNA (ribose).

A fundamental feature of nucleic acids is directionality (polarity). A single strand has a 5' phosphate end and a 3' hydroxyl end. This polarity is essential for complementary base pairing, where specific nitrogenous bases pair together (A with T/U, C with G), allowing DNA to replicate accurately. The RNA world theory suggests that RNA may have preceded DNA in evolution because RNA can both store information and act as a catalyst (ribozymes).

Membrane Transport and Cell Environment

Cells must regulate what enters and exits their boundaries. The plasma membrane is selectively permeable. Small, nonpolar molecules can often pass through via simple diffusion, but larger or charged molecules require help.

Facilitated diffusion uses integral membrane proteins to allow specific solutes to move down their concentration gradient without using energy. For example, aquaporins are specialized protein channels that facilitate the rapid movement of water molecules across the membrane.

Another critical process is osmosis, the movement of water across a membrane. Water moves from areas of low solute concentration (hypotonic) to areas of high solute concentration (hypertonic). This is why a plant cell in fresh water becomes rigid (turgid), while a cell in a salty solution may shrivel.

Worked Example: Calculating Peptide Bonds If a polypeptide is composed of 100 amino acids, how many peptide bonds are present?

Solution: In a linear chain, the number of bonds is always $n - 1$, where $n$ is the number of monomers. $100 - 1 = 99 \text{ peptide bonds}$ (Reference:)