Chapter 3: Macromolecules of the Cell

Proteins

Proteins are essential biological macromolecules composed of amino acids. Their structure and function are determined by the sequence and chemical properties of their constituent amino acids.

• Amino Acids:

  • There are 20 standard amino acids, each with a unique side chain (R group) and standard 3-letter or 1-letter abbreviations.

  • The generic structure of an amino acid includes:

    • A central (alpha) carbon atom

    • An amino group (-NH2)

    • A carboxyl group (-COOH)

    • A hydrogen atom

    • A variable R group (side chain)

  • The alpha carbon is chiral (except in glycine), resulting in L- and D-isomers; only L-isomers are found in proteins.

  • Amino acids can be classified as nonpolar (hydrophobic), polar (hydrophilic), or charged (acidic/basic). The properties of the R group determine the amino acid's behavior in water.

• Peptide Bonds:

  • Peptide bonds link amino acids via a condensation reaction between the carboxyl group of one amino acid and the amino group of another, releasing water.

  • Polypeptides have an N-terminus (amino end) and a C-terminus (carboxyl end).

• Levels of Protein Structure:

  • Primary Structure: The linear sequence of amino acids in a polypeptide, determined by DNA sequence.

  • Secondary Structure:

    • Regular folding patterns stabilized by hydrogen bonds within the polypeptide backbone.

    • Common types:

      • Alpha-helix: Stabilized by intramolecular hydrogen bonds.

      • Beta-sheet: Formed by hydrogen bonds between polypeptide regions; can be parallel or antiparallel.

  • Tertiary Structure:

    • Overall 3D shape of a single polypeptide chain, stabilized by interactions between R groups (hydrogen bonds, ionic bonds, disulfide bridges, van der Waals interactions, hydrophobic interactions).

    • Nonpolar R groups tend to cluster inside the protein, while polar and charged R groups are exposed to the aqueous environment.

  • Quaternary Structure: (Additional info: Not explicitly mentioned, but refers to the assembly of multiple polypeptide chains into a functional protein complex.)

Nucleic Acids

Nucleic acids, including DNA and RNA, are polymers of nucleotides that store and transmit genetic information.

• Nucleotide Structure:

  • Each nucleotide consists of a 5-carbon sugar, a phosphate group, and a nitrogenous base.

  • Numbering of the sugar carbons is important for understanding nucleotide structure.

  • Nitrogenous bases:

    • Pyrimidines: Cytosine (C), Thymine (T, in DNA), Uracil (U, in RNA)

    • Purines: Adenine (A), Guanine (G)

  • DNA contains deoxyribose; RNA contains ribose (RNA has an extra OH group at the 2' position).

• DNA as a Polymer:

  • Nucleotides are joined by phosphodiester bonds between the 5' phosphate and 3' hydroxyl groups.

  • DNA and RNA have directionality: 5' to 3' ends.

  • DNA is double-stranded, forming a double helix stabilized by complementary base pairing:

    • Adenine pairs with Thymine (A-T) via 2 hydrogen bonds.

    • Guanine pairs with Cytosine (G-C) via 3 hydrogen bonds.

  • Chargaff's rule: In double-stranded DNA, the amount of A equals T, and G equals C.

Carbohydrates: Polysaccharides

Carbohydrates are energy-rich biomolecules composed of monosaccharide units. They serve as energy sources and structural components in cells.

• Monosaccharides:

  • Simple sugars such as trioses (3C), pentoses (5C), and hexoses (6C).

  • Glucose (C6H12O6) is the most common hexose; exists in dynamic equilibrium between straight-chain and ring forms.

  • D-glucose is the most common isomer in biology.

• Polysaccharides:

  • Formed by condensation reactions between monosaccharides, creating glycosidic bonds.

  • Glycosidic bonds can be α or β, depending on the orientation of the linkage.

  • Storage Polysaccharides:

    • Starch: Found in plants; composed of α-glycosidic bonds.

    • Glycogen: Found in animals, fungi, and bacteria; also α-glycosidic bonds.

  • Structural Polysaccharides:

    • Cellulose: Found in plant cell walls; composed of β-glycosidic bonds. Most animals cannot digest cellulose; digestion requires bacterial enzymes.

Lipids

Lipids are a diverse group of hydrophobic molecules, including fats, phospholipids, and steroids, that play key roles in energy storage, membrane structure, and signaling.

• Fatty Acids:

  • Long hydrocarbon chains with a carboxyl group at one end; amphipathic molecules (hydrophobic tail, hydrophilic head).

  • Can be saturated (no double bonds; higher melting point) or unsaturated (one or more double bonds; kinks in chain, lower melting point).

• Triglycerides (Triacylglycerols):

  • Formed by condensation of glycerol with three fatty acids.

  • Function as energy storage molecules.

  • Saturated triglycerides are solid at room temperature (fats); unsaturated are liquid (oils).

• Phospholipids:

  • Major component of cell membranes; amphipathic molecules.

  • Typical structure: 2 fatty acids + glycerol + phosphate group + small polar "R" group.

• Steroids:

  • Characterized by a 4-ring hydrophobic structure.

  • Cholesterol is important for membrane fluidity and is a precursor for steroid hormones.