Biochemistry of Organic Compounds

Chemical Level of Organization

• Organic Compounds

  • Definition: All organic compounds contain carbon and hydrogen atoms.

  • Characteristics:

  • Always contain carbon and hydrogen.

  • Generally also contain oxygen.

  • Carbon atoms readily bond to form long chains that can carry a variety of functional groups.

Functional Groups

• Definition: Functional groups are attached groupings of atoms that occur commonly in many organic molecules.

• Importance:

  • Influence the properties of the overall molecule.

  • Enable cells to transfer and capture energy as high-energy compounds.

Categories of Organic Molecules

• Biochemists classify the organic molecules of life into four primary categories:

  1. Carbohydrates

  2. Lipids

  3. Proteins

  4. Nucleic Acids

Important Functional Groups of Organic Compounds

• Amino Group (-NH₂):

  • Structure: R-NH₂.

  • Importance: Acts as a base accepting H⁺ depending on pH; can form bonds with other molecules.

  • Examples: Amino acids.

• Carboxyl Group (-COOH):

  • Structure: R-COOH.

  • Importance: Acts as an acid, releasing H⁺ to become R-COO⁻.

  • Examples: Fatty acids.

• Hydroxyl Group (-OH):

  • Structure: R-OH.

  • Importance: May link molecules through dehydration synthesis; hydrogen bonding between hydroxyl groups and water affects solubility.

  • Examples: Alcohols, fatty acids, carbohydrates, and amino acids.

• Phosphate Group (-PO₄²⁻):

  • Structure: R-OPO₄²⁻.

  • Importance: May link other molecules to form larger structures; may store energy.

  • Examples: Nucleic acids, high-energy compounds.

Carbohydrates

• Definition: Carbohydrates are organic molecules containing carbon, hydrogen, and oxygen, typically in a ratio near 1:2:1.

• Importance:

  • They are a major source of energy (approximately 1.5% of total body weight).

  • Examples include sugars and starches.

Types of Carbohydrates

1. Monosaccharides:

   • Definition: Simple sugars containing three to seven carbon atoms.

   • Examples: Glucose (the most important fuel in the body), fructose.

2. Disaccharides:

   • Definition: Two monosaccharides joined together through dehydration synthesis.

   • Examples: Sucrose, lactose, maltose.

   • Significant aspect: Must be broken down into monosaccharides before absorption.

3. Polysaccharides:

   • Definition: Complex carbohydrates formed from multiple monosaccharides.

   • Examples: Starch (from plants), glycogen (from animals), cellulose (a structural polysaccharide in plants).

   • Function: Digested carbohydrates convert to glucose which is used to produce ATP.

Hydrolysis of Carbohydrates

• Hydrolysis Process:

  • Hydrolysis breaks disaccharides into their monosaccharide components.

  • Reaction representation:
    ext{Sucrose} + ext{Water}
    ightarrow ext{Glucose} + ext{Fructose}

Lipids

• Definition: Lipids (from Greek 'lipos' meaning fat) contain carbon, hydrogen, and oxygen, with a higher carbon-to-hydrogen ratio (approximately 1:2).

• Characteristics:

  • Much less oxygen compared to carbohydrates.

  • May include small quantities of phosphorus, nitrogen, or sulfur.

• Examples: Fats, oils, waxes.

  • Insoluble in water and require special transport mechanisms in the blood.

Major Lipid Classes

1. Fatty Acids:

   • Structure: Long carbon chains with hydrogen atoms.

   • Types:

   • Saturated fatty acids: All carbon atoms are bonded to the maximum number of hydrogen atoms.

   • Unsaturated fatty acids: Contain one or more double bonds in the fatty acid tail, leading to reduced hydrogen attachments.

2. Glycerides:

   • Types formed through dehydration synthesis:

     • Monoglycerides (1 fatty acid), Diglycerides (2 fatty acids), Triglycerides (3 fatty acids also known as neutral fats).

   • Hydrolysis breaks glycerides down into fatty acids and glycerol.

3. Phospholipids:

   • Structure: Diglycerides with a phosphate group attached.

   • Function: Major component of cell membranes.

4. Steroids:

   • Structure: Large molecules composed of four carbon rings.

   • Function: Serve as hormones (e.g. cholesterol, estrogen, testosterone).

Eicosanoids

• Definition: Lipids derived from arachidonic acid.

• Examples: Prostaglandins (involved in cellular signaling) and leukotrienes (inflammatory response).

Proteins

• Definition: Proteins are the most abundant organic molecules in the body, typically comprising 20% of body weight.

• Composition: Contain carbon, hydrogen, oxygen, nitrogen, and sometimes sulfur and phosphorus.

• Structure: Long chains of amino acids; typically, a protein contains about 1000 amino acids.

Amino Acids

• Structure: Composed of a central carbon atom bonded to:

  • A hydrogen atom,

  • An amino group,

  • A carboxyl group,

  • An R group (variable side chain).

• Molecular Charge: Molecule has both positive and negative charges, resulting in a net charge of zero.

Peptides

• Formation: Amino acids are linked through dehydration synthesis to form peptide bonds.

• Types:

  • Dipeptides: Two amino acids linked together.

  • Polypeptides: Three or more amino acids linked together.

  • Proteins: Peptides containing more than 100 amino acids.

Protein Structure

1. Primary Structure: Sequence of amino acids in a polypeptide chain.

2. Secondary Structure: Resulting from hydrogen bonds; can form alpha-helices or beta sheets.

3. Tertiary Structure: Coiling and folding giving the protein its final 3D shape; interactions among R groups and water.

4. Quaternary Structure: Interaction among multiple polypeptide chains forming a functional complex.

   • Examples: Hemoglobin (globular protein), Collagen (fibrous protein).

Denaturation

• Definition: Any change in tertiary or quaternary structure that leads to loss of function.

• Causes: Extreme conditions such as high temperature (above 43ºC).

Enzymes

• Definition: Enzymes are specialized proteins that catalyze biochemical reactions in the body.

• Active Site: Specific point where substrates bind; shape determined by enzyme structure.

• Substrates: Reactants transformed during enzymatic reactions.

• Reaction Process:

  1. Substrate binds to the active site, forming an enzyme-substrate complex.

  2. The active site undergoes a reversible shape change, leading to product formation.

  3. The product detaches, allowing enzyme to recycle.

• Saturation Limit: Maximum rate of reaction occurs when enzyme is saturated with substrate.

High-Energy Compounds

• Definition: Compounds such as ATP that donate energy during enzymatic reactions.

• Structure of ATP: Composed of adenosine with three phosphate groups.

• Function: ATP formation from ADP is reversible; energy is stored and released through hydrolysis.

• Uses: Essential for muscle contraction, protein synthesis, and metabolic processes.

Nucleic Acids

• Definition: Large organic molecules composed of nucleotides containing carbon, hydrogen, oxygen, nitrogen, and phosphorus.

• Types:

  1. Deoxyribonucleic acid (DNA)

  2. Ribonucleic acid (RNA)

Nucleotide Components

• Composition:

  • Phosphate group,

  • Pentose sugar (deoxyribose in DNA; ribose in RNA),

  • Nitrogenous base (purines: adenine and guanine; pyrimidines: cytosine, thymine, and uracil).

Nucleic Acid Structure

• DNA:

  • Structure: Composed of two complementary nucleotide chains forming a double helix.

  • Base Pairing:

  • Adenine pairs with Thymine (A–T).

  • Cytosine pairs with Guanine (C–G).

• RNA:

  • Structure: Single chain of nucleotides.

  • Types:

  1. Messenger RNA (mRNA)

  2. Transfer RNA (tRNA)

  3. Ribosomal RNA (rRNA)

  • Function: Translates and transfers genetic information for protein synthesis.

Comparison of DNA and RNA

• DNA:

  • Sugar: Deoxyribose.

  • Bases: A, G, C, T.

  • Structure: Double helix, stores genetic information.

  • Length: More than 45 million nucleotides.

• RNA:

  • Sugar: Ribose.

  • Bases: A, G, C, U.

  • Structure: Varies, performs protein synthesis based on DNA instructions.

  • Length: Varies from fewer than 100 to about 50,000 nucleotides.