Lecture 6

Biomolecules: Proteins, Carbohydrates, Lipids, and Nucleic Acids

Key Terms and Concepts

• Protein, Polypeptide, Peptide bond, Amino acid, Conformation, Primary/Secondary/Tertiary/Quaternary structure, Denaturation, Carbohydrate, Monosaccharide, Disaccharide, Polysaccharide, Glycogen, Cellulose, Lipids, Fatty acid, Phospholipid, Steroid, Nucleotide, DNA, RNA, Purine, Pyrimidine, Deoxyribose, Ribose

Proteins

General Structure of Amino Acids

Amino acids are the building blocks of proteins. Each amino acid consists of a central (α) carbon atom bonded to an amino group, a carboxyl group, a hydrogen atom, and a unique side chain (R group) that determines its chemical properties.

• Central carbon (α-carbon): The main carbon atom to which all groups are attached.

• Amino group (-NH2): Acts as a base.

• Carboxyl group (-COOH): Acts as an acid.

• R group (side chain): Determines the identity and properties of the amino acid.

Importance of Side Chains: The side chain affects the amino acid's polarity, charge, and reactivity, influencing protein folding and function.

Type of R Group	Examples
Nonpolar	Glycine, Alanine
Polar	Serine, Threonine
Acidic	Aspartic acid, Glutamic acid
Basic	Lysine, Arginine

Levels of Protein Structure

Proteins have four levels of structure, each contributing to their function and diversity.

Level of Protein Structure	Explanation
Primary	Sequence of amino acids in a polypeptide chain.
Secondary	Local folding into α-helix or β-pleated sheet, stabilized by hydrogen bonds.
Tertiary	Three-dimensional folding due to interactions among R groups (hydrophobic, ionic, hydrogen bonds, disulfide bridges).
Quaternary	Association of multiple polypeptide chains into a functional protein.

• Examples: Hemoglobin (quaternary), myoglobin (tertiary).

Bonding Interactions in Tertiary Structure

• Hydrogen bonds: Between polar side chains.

• Ionic bonds: Between charged side chains.

• Disulfide bridges: Covalent bonds between cysteine residues.

• Hydrophobic interactions: Nonpolar side chains cluster away from water.

• van der Waals interactions: Weak attractions between all atoms, significant when many are present.

Protein Denaturation

Denaturation is the loss of a protein's native structure due to external stress (heat, pH, chemicals), resulting in loss of function.

• Consequences: Enzyme inactivation, loss of structural integrity, disease (e.g., prion diseases).

• Chaperone proteins: Assist in proper folding and prevent misfolding.

Functions of Proteins

• Enzymatic catalysis

• Structural support

• Transport

• Cell signaling

• Defense (immune response)

Polypeptide vs. Protein: A polypeptide is a single linear chain of amino acids; a protein may consist of one or more polypeptides folded into a functional shape.

Carbohydrates

Atoms and Ratios

Carbohydrates are composed of carbon (C), hydrogen (H), and oxygen (O), typically in a ratio of 1:2:1 (C:H:O).

Monosaccharides, Disaccharides, and Polysaccharides

• Monosaccharides: Simple sugars (e.g., glucose, fructose, galactose).

• Disaccharides: Two monosaccharides joined by a glycosidic bond (e.g., sucrose, lactose, maltose).

• Polysaccharides: Long chains of monosaccharides (e.g., starch, glycogen, cellulose).

Disaccharide	Formed from Which Two Monosaccharides?	Found Where?
Sucrose	Glucose + Fructose	Plants
Lactose	Glucose + Galactose	Milk
Maltose	Glucose + Glucose	Germinating seeds

Type of Polysaccharide	Examples (Plants/Animals)
Energy storage	Starch (plants), Glycogen (animals)
Structural building block	Cellulose (plants), Chitin (animals)

Formula for Monosaccharides: $C_nH_{2n}O_n$ (e.g., glucose: $C_6H_{12}O_6$)

Lipids

Types and Structure

Lipids are hydrophobic molecules including fats, phospholipids, and steroids. They are not polymers and are characterized by their insolubility in water.

• Fats (triglycerides): Composed of glycerol and three fatty acids joined by ester linkages.

• Phospholipids: Glycerol backbone, two fatty acids, and a phosphate group; major component of cell membranes.

• Steroids: Four fused carbon rings; includes cholesterol and hormones.

Saturated vs. Unsaturated Fatty Acids:

• Saturated: No double bonds; solid at room temperature; found in animal fats.

• Unsaturated: One or more double bonds; liquid at room temperature; found in plant oils.

Phospholipid Bilayer: Hydrophilic heads face outward toward water; hydrophobic tails face inward, forming the plasma membrane.

Nucleic Acids

Components of a Nucleotide

• Phosphate group

• Pentose sugar: Ribose (RNA) or deoxyribose (DNA)

• Nitrogenous base: Purines (adenine, guanine) or pyrimidines (cytosine, thymine, uracil)

DNA vs. RNA

Feature	DNA	RNA
Sugar	Deoxyribose	Ribose
Bases	A, T, G, C	A, U, G, C
Strands	Double	Single
Function	Genetic information storage	Protein synthesis, gene regulation

Central Dogma of Molecular Biology:

• DNA → RNA → Protein

Genetic information flows from DNA to RNA via transcription, and from RNA to protein via translation.

Summary Tables

Protein Structure Levels

Level	Key Features
Primary	Linear sequence of amino acids
Secondary	α-helix, β-pleated sheet (hydrogen bonds)
Tertiary	3D folding (R group interactions)
Quaternary	Multiple polypeptides assembled

Important Formulas

• Monosaccharide formula: $C_nH_{2n}O_n$

• Peptide bond formation (dehydration synthesis): $\text{Amino acid}_1 + \text{Amino acid}_2 \rightarrow \text{Dipeptide} + H_2O$

Additional info:

• Chaperone proteins help prevent misfolding and aggregation of polypeptides.

• Enzymes are proteins that catalyze biochemical reactions, increasing reaction rates without being consumed.

• Cellulose is indigestible to humans due to lack of appropriate enzymes; some organisms (e.g., cows, termites) digest cellulose with the help of symbiotic microbes.