Introduction to Biochemistry: Macromolecules, Functional Groups, and Thermodynamics

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 refers to the distinct ends of the polymer chain that confer specific chemical properties and biological functions.

• Proteins: Polymers of amino acids, with an amino (N-) terminus and a carboxyl (C-) terminus.

• Nucleic acids: Polymers of nucleotides, with a 5' phosphate end and a 3' hydroxyl end.

• Polysaccharides: Polymers of monosaccharides, often with reducing and non-reducing ends.

• Lipids: Typically formed from glycerol and fatty acids, though not true polymers.

Example: The primary structure of a protein is its unique sequence of amino acids, which determines its function.

Important Chemical Groups in Biochemistry

Functional Groups

Functional groups are specific atoms or groups of atoms within molecules that are responsible for the characteristic chemical reactions of those molecules. Understanding these groups is essential for studying biochemical processes.

• Alcohols: Contain a hydroxy group (-OH).

• Amines: Contain an amino group (-NH2).

• Carboxylic acids: Contain a carboxyl group (-COOH).

• Phosphates: Contain phosphate groups (-PO4).

• Others: Aldehydes, ketones, esters, amides, thiols, etc.

Example: The carboxyl group in amino acids imparts acidic properties and participates in peptide bond formation.

Class of Compound	General Structure	Characteristic Functional Group	Name of Functional Group
Alcohols	R-OH	Hydroxy group	OH
Amines	R-NH2	Amino group	NH2
Carboxylic acids	R-COOH	Carboxyl group	COOH
Phosphates	R-PO4	Phosphate group	PO4
Esters	R-COOR'	Ester group	COOR'
Amides	R-CONH2	Amide group	CONH2
Thiols	R-SH	Sulfhydryl group	SH
Aldehydes	R-CHO	Carbonyl group	CHO
Ketones	R-CO-R'	Carbonyl group	CO

Abundance of Important Elements in Biochemistry

Elemental Composition of Organisms

Living organisms are primarily composed of a few key elements, with their abundance differing significantly from their occurrence in the universe. This reflects the unique requirements of life.

Element	Abundance in Organisms (per 1000 C atoms)	Abundance in Universe (per 1000 C atoms)
Hydrogen	80–250	10,000,000
Nitrogen	1,000	1,000
Oxygen	60–300	1,600
Sodium	10–20	12
Magnesium	8–50	8
Phosphorus	8–50	3
Sulfur	6–40	80
Potassium	25–50	10
Calcium	0.25–0.8	1
Iron	0.25–0.8	100
Copper	0.1–0.4	0

Example: Carbon, hydrogen, oxygen, and nitrogen are the most abundant elements in living organisms, forming the backbone of biomolecules.

Macromolecules: Structure and Function

Monomers and Polymers

Biological macromolecules are assembled from smaller units called monomers. The type of monomer determines the class of macromolecule and its function.

• Amino acids → Proteins

• Nucleotides → Nucleic acids

• Monosaccharides → Polysaccharides

• Glycerol and fatty acids → Lipids

Example: Proteins serve as enzymes, structural components, and signaling molecules in cells.

Primary Structure and Sequence

The primary structure of a macromolecule refers to the linear sequence of its monomeric units. This sequence determines the molecule's higher-order structure and biological activity.

• Proteins: Sequence of amino acids from N-terminus to C-terminus.

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

Example: The genetic code in DNA is determined by the sequence of nucleotides.

Functional Groups in Biomolecules

Role in Chemical Reactivity

Functional groups confer specific chemical properties to biomolecules, influencing their reactivity, solubility, and interactions.

• Hydroxyl (-OH): Found in alcohols and carbohydrates; increases solubility.

• Carboxyl (-COOH): Found in amino acids and fatty acids; acidic properties.

• Amino (-NH2): Found in amino acids; basic properties.

• Phosphate (-PO4): Found in nucleotides; involved in energy transfer.

Example: The phosphate group in ATP is critical for energy storage and transfer in cells.

Structural and Functional Biomolecules

Organization and Hybrid Structures

Biomolecules can form complex structures such as cellular membranes and hybrid protein/nucleic acid assemblies. Enzymes, which are primarily proteins, act as biological catalysts to accelerate chemical reactions.

• Cellular membranes: Composed of lipids and proteins, forming barriers and compartments.

• Enzymes: Catalyze biochemical reactions with high specificity and efficiency.

• Hybrid structures: Protein-nucleic acid complexes are essential for processes like transcription and replication.

Example: Ribosomes are ribonucleoprotein complexes that synthesize proteins.

Thermodynamics in Biochemistry

Classes of Thermodynamic Systems

Thermodynamic 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 cells).

• Closed system: Exchanges energy but not matter.

• Isolated system: No exchange of energy or matter.

Example: A cell is an open system, constantly exchanging materials and energy with its environment.

Free Energy, Enthalpy, and Entropy

Biochemical reactions are governed by changes in free energy (G), enthalpy (H), and entropy (S). The spontaneity of a reaction is determined by the change in free energy ($\Delta G$).

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

• Enthalpy ($H$): Heat content of a system at constant pressure.

• Entropy ($S$): Measure of disorder or randomness.

Key Equation:

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

• If $\Delta G < 0$: Reaction is spontaneous (exergonic).

• If $\Delta G = 0$: Reaction is at equilibrium.

• If $\Delta G > 0$: Reaction is nonspontaneous (endergonic).

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

$\text{ATP} + \text{H}_2\text{O} \rightarrow \text{ADP} + \text{Phosphate ion}$

$\Delta G^\circ = -30.5 \text{ kJ mol}^{-1}$

Spontaneity and Reaction Rates

Spontaneous reactions are those that can occur without external energy input, but this does not imply they are fast. Enzymes are required to accelerate many spontaneous biochemical reactions.

• Spontaneous: $\Delta G < 0$; reaction can proceed as written.

• Nonspontaneous: $\Delta G > 0$; reaction requires energy input.

• Equilibrium: $\Delta G = 0$; no net change occurs.

Example: The breakdown of glucose in cellular respiration is spontaneous but requires enzymes to proceed at a biologically relevant rate.

Additional info: The notes above expand on the brief points and images provided, adding definitions, examples, and context for a comprehensive introduction to biochemistry suitable for college students.