Chemical Level of Organization

Chemical Level of Organization

Organic Compounds

• Definition: Organic compounds are molecules that always contain carbon and hydrogen, and generally oxygen.

  • Key Properties:

  • Carbon atoms readily bond to each other to form long chains.

  • These chains can carry a variety of functional groups.

Functional Groups

• Definition: Attached groupings of atoms that occur commonly in many organic molecules and influence the properties of the overall molecule.

  • Importance: Many functional groups allow cells to transfer and capture energy as high-energy compounds.

  • Examples of Functional Groups:

  • Amino group (-NH2): Acts as a base by accepting H+, depending on pH; can form bonds with other molecules.

  • Carboxyl group (-COOH): Acts as an acid, releasing H+ to become R-COO-.

  • Hydroxyl group (-OH): May link molecules through dehydration synthesis; affects solubility due to hydrogen bonding with water.

  • Phosphate group (-PO4²-): Links other molecules to form larger structures; may store energy.

Classification of Organic Molecules

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

  1. Carbohydrates

  2. Lipids

  3. Proteins

  4. Nucleic acids

Carbohydrates

Basic Characteristics

• Composition: Composed of carbon, hydrogen, and oxygen, usually in a 1:2:1 ratio.

• Functions: Primarily serve as energy sources, accounting for roughly 1.5 percent of total body weight.

Types of Carbohydrates

1. Monosaccharides

• Definition: Simple sugars containing 3 to 7 carbon atoms.

• Types:

  • Triose (3 carbon)

  • Tetrose (4 carbon)

  • Pentose (5 carbon)

  • Hexose (6 carbon) - primary energy source (e.g., glucose)

  • Heptose (7 carbon)

• Examples: Glucose, Fructose

2. Disaccharides

• Definition: Formed from two monosaccharides joined together through dehydration synthesis.

• Example: Sucrose (table sugar), lactose (milk sugar), maltose (malt sugar).

• Characteristics: Soluble in water and can be broken down into monosaccharides through hydrolysis.

3. Polysaccharides

• Definition: Complex carbohydrates formed from multiple disaccharides and/or monosaccharides.

• Examples: Starches, glycogen, cellulose.

• Function: Digested carbohydrates are converted to glucose which is then utilized for ATP production.

Specific Polysaccharides

• Starches: Formed by plants from glucose; a major dietary energy source.

• Glycogen: Animal starch; made and stored in muscle cells; broken down when glucose is needed.

• Cellulose: Structural polysaccharide in plants; source of dietary fiber; associated with health benefits including reducing risks of certain diseases.

Lipids

General Characteristics

• Contain carbon, hydrogen, and oxygen with a carbon to hydrogen ratio of approximately 1:2.

• Composition includes much less oxygen compared to carbohydrates with similar numbers of carbon atoms.

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

• Examples include fats, oils, waxes; most are insoluble in water.

Types and Functions of Lipids

1. Fatty Acids

• Characteristics: Long carbon chains with attached hydrogen atoms, hydrophilic head (carboxyl group) and hydrophobic tail.

• Classification:

  • Saturated Fatty Acid: No double bonds; each carbon has four attached hydrogens.

  • Unsaturated Fatty Acids: One or more double bonds; classified as monounsaturated (one double bond) and polyunsaturated (more than one double bond).

2. Glycerides

• Definition: Fatty acid chains attached to a glycerol molecule.

• Types:

  • Monoglyceride: Glycerol + one fatty acid.

  • Diglyceride: Glycerol + two fatty acids.

  • Triglyceride: Glycerol + three fatty acids (also known as triacylglycerols).

• Function: Energy sources and storage.

3. Other Lipids

• Eicosanoids: Derived from arachidonic acid.

  • Examples: Prostaglandins (involved in inflammation) and leukotrienes (immune response).

• Steroids: Large molecules with four carbon rings; examples include cholesterol and sex hormones.

• Phospholipids and Glycolipids: Components of cell membranes; structure involves amphipathic properties (hydrophobic tails and hydrophilic heads).

Proteins

Overview

• Proteins are the most abundant organic molecules in the body and account for approximately 20% of total body weight.

• Composition: Consist of long chains of amino acids with diverse structures and functions.

Amino Acids

• Structure: Contains a central carbon atom attached to four groups: a hydrogen atom, an amino group, a carboxyl group, and a variable R group (side chain).

• Charges: Molecule has both positive and negative charges but a net charge of zero.

Peptide Formation

• Peptides are formed when amino acids are linked through dehydration synthesis, creating peptide bonds.

  • Types of Peptides:

  • Dipeptide: Two amino acids linked.

  • Polypeptide: Three or more amino acids linked; peptides over 100 amino acids termed proteins.

Protein Structure

Primary Structure

• Definition: The specific sequence of amino acids in a protein.

Secondary Structure

• Definition: Bonds formed between different parts of the polypeptide chain, likely leading to alpha-helices or beta-pleated sheets.

Tertiary Structure

• Definition: The 3D folding of the protein due to interactions among R groups and water.

Quaternary Structure

• Definition: Interaction between multiple polypeptides forming a protein complex; example includes hemoglobin and collagen.

Protein Denaturation

• Definition: Alteration of protein structure due to extreme conditions (e.g., temperature exceeding 43ºC or 110ºF), leading to loss of function and potential tissue damage.

Enzymes

Overview

• Enzymes are proteins that catalyze most biochemical reactions in the body.

• Structure of an enzyme includes an active site where substrates bind, determined by its tertiary/quaternary structure.

Mechanism of Action

• Enzyme specificity: Each enzyme binds only to substrates with a corresponding shape and charge.

• Process:

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

  2. Temporary shape change occurs.

  3. Product detaches, and enzyme can repeat the process.

Reaction Control

• Control of reaction rates relies on environmental conditions and enzyme activation.

• Saturation limit refers to substrate concentration needed for maximum reaction rate.

High-Energy Compounds

Overview

• High-energy compounds store and transfer energy released during enzymatic reactions.

• Adenosine Triphosphate (ATP): The most common high-energy compound.

Formation of ATP

• ATP is formed from adenosine, which consists of adenine and ribose, and the steps are:

  1. Adenosine + Phosphate = Adenosine Monophosphate (AMP)

  2. AMP + Phosphate = Adenosine Diphosphate (ADP)

  3. ADP + Phosphate = Adenosine Triphosphate (ATP)

Energy Transfer via ATP

• ATP formation is reversible; energy stored in ATP is released upon breakdown to ADP, useful for:

  • Muscle contraction

  • Synthesis of proteins, carbohydrates, and lipids.

Nucleic Acids

General Characteristics

• Nucleic acids are large organic molecules composed of carbon, hydrogen, nitrogen, oxygen, and phosphorus.

• Types include DNA and RNA, serving the primary function of storing and transferring genetic information for protein synthesis.

Nucleotide Components

• Each nucleotide consists of a phosphate group, a pentose sugar (either ribose or deoxyribose), and a nitrogenous base.

• Bases include:

  • Purines: Adenine, Guanine

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

Structure of Nucleic Acids

• In DNA, two nucleotide chains (complementary strands) twist to form a double helix; held together by hydrogen bonds between complementary bases (A-T and C-G pairs).

• RNA is a single chain of nucleotides, with its shape and function reflecting the sequence of its nucleotides. Types of RNA include mRNA, tRNA, and rRNA.

Comparison of DNA and RNA