Introduction to Biochemistry: Macromolecules, Functional Groups, and Thermodynamics Ch 1

General Structure of Biological Macromolecules

Polymers and Directionality

Biological macromolecules such as proteins, nucleic acids, and polysaccharides are polymers, meaning they are composed of repeating monomeric units. These polymers exhibit directionality, which is crucial for their biological function.

• Polymer: A large molecule made up of repeating subunits (monomers).

• Directionality: Refers to the distinct ends of a polymer chain, such as the N-terminus and C-terminus in proteins, or the 5' and 3' ends in nucleic acids.

• Examples:

  • Amino acids → Proteins

  • Nucleotides → Nucleic acids

  • Monosaccharides → Polysaccharides

  • (Glycerol + 3 fatty acids) → Lipids

Additional info: Directionality is essential for processes such as DNA replication and protein synthesis, where enzymes recognize specific ends of the polymer.

Important Chemical Groups in Biochemistry

Functional Groups

Functional groups are specific groups of atoms within molecules that are responsible for the characteristic chemical reactions of those molecules. Understanding these groups is fundamental in biochemistry.

• Definition: A functional group is an atom or group of atoms that imparts specific chemical properties to a molecule.

• Examples: Hydroxyl, carboxyl, amino, sulfhydryl, phosphate, and methyl groups.

Class of Compound	General Structure	Characteristic Functional Group	Name of Functional Group
Alkenes	RCH=CH2	Double bond	CH2=CH-
Alcohols	RCH2OH	Hydroxyl group	-OH
Amines	RNH2	Amino group	-NH2
Carboxylic acids	RCOOH	Carboxyl group	-COOH
Phosphoric acid esters	ROPO3H2	Phosphoric ester group	-OPO3H2
Phosphoric acid anhydrides	ROPO2OH	Phosphoric anhydride group	-OPO2OH

Additional info: Functional groups determine the solubility, reactivity, and interaction of biomolecules.

Abundance of Important Elements in Biochemistry

Relative Abundance in Organisms vs. Universe

Biological systems are composed of a limited set of elements, with carbon, hydrogen, oxygen, and nitrogen being the most abundant. Their abundance in living organisms differs significantly from their abundance in the universe.

Element	Abundance in Organisms (per 1000 C atoms)	Abundance in Universe (per 1000 C atoms)
Hydrogen	80–250	10,000,000
Oxygen	1,000	1,000
Nitrogen	60–300	1,600
Phosphorus	8–50	3
Sulfur	6–40	80
Calcium	25–50	10
Iron	0.25–0.8	1

Additional info: The selective enrichment of certain elements in organisms reflects their essential roles in biological processes.

Primary Structure of Macromolecules

Sequence and Directionality

The primary structure of macromolecules refers to the linear sequence of monomers. This sequence determines the molecule's properties and function.

• Proteins: Sequence of amino acids from N-terminus (amino end) to C-terminus (carboxyl end).

• Nucleic acids: Sequence of nucleotides from 5' phosphate end to 3' hydroxyl end.

• Directionality: Each macromolecule has chemically distinct ends, which are critical for biological recognition and function.

Example: In DNA, the 5' end has a free phosphate group, while the 3' end has a free hydroxyl group.

Classification of Structural & Functional Biomolecules

Roles in Cells

Biomolecules are classified based on their structure and function. Proteins and nucleic acids are central to cellular processes, while lipids and carbohydrates play structural and energy storage roles.

• Structural biomolecules: Form cellular membranes, cytoskeleton, and extracellular matrix.

• Functional biomolecules: Enzymes (catalysts), signaling molecules, and transporters.

• Hybrid structures: Some biomolecules combine protein and nucleic acid components for specialized functions.

Example: Ribosomes are complexes of proteins and RNA that synthesize proteins.

Thermodynamics in Biochemistry

Classes of Thermodynamic Systems

Thermodynamics describes energy changes in biochemical processes. Systems are classified based on their ability to exchange energy and matter with their surroundings.

• Open system: Exchanges both energy and matter (e.g., living cell).

• Closed system: Exchanges only energy, not matter.

• Isolated system: No exchange of energy or matter.

Additional info: Most biological systems are open, allowing for nutrient uptake and waste removal.

Free Energy, Enthalpy, and Entropy

Biochemical reactions are governed by changes in free energy (G), enthalpy (H), and entropy (S).

• Free energy (G): The energy available to do work.

• Enthalpy (H): The heat content of a system at constant pressure.

• Entropy (S): A measure of molecular disorder or randomness.

Gibbs Free Energy Equation:

$\Delta G = \Delta H - T \Delta S$

• Spontaneous (exergonic) reaction: $\Delta G < 0$ (energy released)

• Equilibrium: $\Delta G = 0$

• Nonspontaneous (endergonic) reaction: $\Delta G > 0$ (energy required)

Example: Hydrolysis of ATP to ADP and phosphate is a spontaneous reaction with $\Delta G^\circ = -30.5$ kJ/mol.

Thermodynamics of Biochemical Processes

Understanding the thermodynamics of biochemical reactions is essential for predicting reaction direction and energy requirements.

• Enthalpy change ($\Delta H$): Reflects the number and type of bonds formed and broken.

• Entropy change ($\Delta S$): Indicates the change in disorder; positive $\Delta S$ means increased randomness.

• Temperature (T): Affects the balance between enthalpy and entropy contributions.

Additional info: Spontaneity does not imply reaction speed; enzymes are required to increase reaction rates in cells.