Comprehensive Guide to Biological Molecules and Carbon Carbohydrates Lipids Proteins and Nucleic Acids

Elements and the Basis of Organic Compounds

• Atomic Composition of Cells: Approximately $99\%$ of the mass of most cells is composed of four primary elements:

  • Hydrogen

  • Nitrogen

  • Carbon

  • Oxygen

• Organic vs. Inorganic Compounds:

  • Organic Compounds: Generally defined as molecules containing carbon atoms. Millions of different organic compounds exist, nearly all of which also contain hydrogen and frequently oxygen.

  • Inorganic Compounds: Pure carbon or carbon compounds lacking hydrogen, such as carbon dioxide ($CO_2$) and calcium carbonate ($CaCO_3$), are classified as inorganic. Despite this, they are integral to life. Water ($H_2O$), for instance, is an inorganic compound that acts as a solvent and transport medium within and between cells.

Carbon: The Framework of Biological Macromolecules

• Atomic Structure and Versatility:

  • Carbon is the fundamental element for life on Earth.

  • In its stable state, carbon has two energy levels; the second level contains four valence electrons.

  • This configuration allows a carbon atom to form covalent bonds with up to four other atoms, primarily hydrogen, oxygen, nitrogen, phosphorus, sulfur, and other carbon atoms.

  • The ability to bond with itself allows for various geometric structures: straight chains, branched chains, and rings.

• Macromolecules: These are large structures formed when smaller compounds, called monomers, join together in long chains to form polymers. The four major biological macromolecules are carbohydrates, lipids, proteins, and nucleic acids.

Making and Breaking Biological Molecules

• Dehydration Reaction (Synthesis):

  • Also known as a condensation reaction.

  • It joins two monomers by forming a covalent bond.

  • This involves the removal of a hydroxyl group ($-OH$) from one monomer and a hydrogen atom ($H$) from the other, effectively removing one water molecule ($H_2O$) for every subunit added.

  • Catalysis: This process requires reactants to be held close and specific bonds to be stressed, a role performed by enzymes.

• Hydrolysis Reaction (Degradation):

  • This is the reverse of dehydration, used to disassemble macromolecules into subunits.

  • A molecule of water is added. A hydrogen atom attaches to one subunit and a hydroxyl group attaches to the other, breaking the covalent bond.

Carbohydrates: Energy and Structure

• General Properties:

  • Molecules containing carbon, hydrogen, and oxygen in a molar ratio of $1:2:1$.

  • Empirical formula: $(CH_2O)_n$, where $n$ is the number of carbon atoms.

  • Rich in carbon-hydrogen ($C-H$) bonds, making them ideal for energy storage.

• Monosaccharides (Simple Sugars):

  • Single sugar units that cannot be further digested.

  • Highly soluble in water; can pass through cell membranes.

  • Classification by Carbon Number: Central energy storage sugars usually contain six carbons.

  • Classification by Functional Group:

    • Aldoses: Contain a terminal aldehyde group ($-CHO$) on the first carbon.

    • Ketoses: Contain a carbonyl group ($C=O$) or a ketone within the skeleton.

  • Examples: Glucose ($C_6H_{12}O_6$), Fructose, and Galactose.

• Disaccharides (Transport Sugars):

  • Formed by linking two monosaccharides via a dehydration reaction.

  • Function as transport molecules (e.g., sucrose in plant phloem sap) because they are less readily metabolized during transport.

  • Function as nutrition in animals.

• Polysaccharides (Complex Sugars):

  • Long polymers of monosaccharides.

  • Insoluble in water, ensuring they do not affect a cell's water potential.

  • Large size prevents them from diffusing out of the cell.

  • Easily hydrolyzed into glucose for tissue respiration.

  • Examples: Starch, Glycogen, Cellulose, and Chitin.

• Biological Roles of Carbohydrates:

  • Primary energy source and substrate for respiration to produce ATP.

  • Supporting structures (e.g., plant cell walls).

  • Precursors for other organic compounds like amino acids and fats.

  • Building blocks for nucleic acids (e.g., DNA).

  • Synthesis of lubricants (mucus) and nectar to attract insects.

Lipids: Hydrophobic Molecules

• General Properties:

  • Composed of carbon, hydrogen, and oxygen, but with significantly less oxygen relative to hydrogen compared to carbohydrates.

  • Hydrophobic (water-fearing) and vary greatly in structure.

• Fatty Acids:

  • Long-chain hydrocarbons with a hydrophobic tail and a hydrophilic carboxylic acid head ($-COOH$).

  • Saturated Fatty Acids: Single bonds between carbons; solid at room temperature; common in animals.

  • Unsaturated Fatty Acids: One or more double bonds in the chain; liquid at room temperature; common in plants and fish.

• Triglycerides:

  • Consists of one glycerol (a three-carbon polyalcohol with three $-OH$ groups) attached to three fatty acids.

  • Fatty acid chains typically vary from 14 to 20 carbons in length.

• Phospholipids:

  • Similar to triglycerides but the third fatty acid is replaced by a polar phosphate group.

  • They have hydrophilic heads and hydrophobic tails.

  • In water, they form a bilayer "sandwich" with heads facing outward and tails inward, creating the primary component of plasma membranes.

• Steroids:

  • Skeletons consists of four fused carbon rings.

  • Cholesterol: Provides physical stability to animal cell membranes and serves as a precursor for sex hormones.

  • Sex Hormones: Testosterone (primarily formed in testes) and Estrogen (primarily formed in ovaries) differ only by functional groups attached to the same carbon skeleton.

• Waxes:

  • Long-chain fatty acids connected to carbon chains containing alcohol functional groups.

  • Solid at normal temperatures due to a high melting point.

  • Functions:

    • Plants: Forms a protective cuticle to prevent water loss.

    • Animals: Fur/skin maintenance and earwax (cerumin), which repels or kills insects and traps dirt.

    • Honeybees: Produce beeswax for honeycomb cells.

Proteins: Structure, Function, and Organization

• Molecular Composition:

  • Linear polymers of 22 different amino acids.

  • Amino Acid Structure: Contains an amino group ($-NH_2$), a carboxyl group ($-COOH$), a hydrogen atom, and a variable R (side) group all bonded to a central carbon.

  • Peptide Bonds: Covalent bonds linking amino acids into a polypeptide chain.

• Types of Proteins:

  • Structural: Provides support (e.g., keratin in hair and horns).

  • Storage: Provides amino acids for growth (e.g., seeds and eggs).

  • Contractile: Enables movement (e.g., muscle contraction).

  • Transport: Moves substances (e.g., hemoglobin transporting oxygen in red blood cells).

  • Regulatory: Control cell processes and gene regulation.

  • Enzymes: Catalyze chemical reactions and aid digestion.

  • Antibodies: Detect and inactivate antigens.

  • Hormones: Act as chemical messengers.

  • Albumin: Regulates fluid balance in blood plasma; low levels cause pulmonary edema (fluid in lungs) or ascites (fluid in the abdomen).

• Levels of Protein Organization:

  1. Primary Structure: The specific order or sequence of amino acids in the polypeptide strand.

  2. Secondary Structure: Three-dimensional folding into patterns like alpha helices and beta sheets.

  3. Tertiary Structure: Polypeptide folding resulting from the hydrophobic effect (positioning of polar vs. non-polar amino acids), e.g., myoglobin in striated muscles.

  4. Quaternary Structure: A complex grouping of two or more polypeptide chains, e.g., keratin and hemoglobin.

Nucleic Acids: The Genetic Code

• General Properties:

  • Composed of Carbon, Hydrogen, Oxygen, Nitrogen, and Phosphorus ($C-H-O-N-P$).

  • Provide directions for building proteins and hold genetic information.

• Nucleotides (Monomers):

  • Consist of three parts: a five-carbon sugar, a negatively charged phosphate group ($PO_4^-$), and a nitrogenous base (one or two rings).

  • Polynucleotides: Chains formed by dehydration reactions linking the sugar of one nucleotide to the phosphate of the next, creating a sugar-phosphate backbone.

• Deoxyribonucleic Acid (DNA):

  • Double-stranded "double helix" structure.

  • Sugar: Deoxyribose.

  • Nitrogenous Bases: Adenine (A), Thymine (T), Guanine (G), and Cytosine (C).

  • Resides in cells as long fibers called chromosomes.

  • Genes: Specific stretches of DNA that program amino acid sequences, requiring translation from "nucleic acid language" to "protein language."

• Ribonucleic Acid (RNA):

  • Usually single-stranded.

  • Sugar: Ribose.

  • Nitrogenous Bases: Adenine (A), Uracil (U), Guanine (G), and Cytosine (C).

Questions & Discussion

• Servings and Nutrition: How many servings are in a container, and is this amount reasonable for a single consumption session?

• Calories and Fats: What is the total food calorie ($C$) count? How much fat and what specific kind of fat is in one serving? Why is dietary fat consumption important?

• Carbohydrates: How much and what kind of carbohydrates are in a serving, and what is their dietary importance?

• Evaluation: Based on nutritional content, should a specific food sample be eaten often or sparingly, and what is the justification?