Introduction to Organic Chemistry

Chapter 4 - Introduction to Organic Chemistry

Historical Context

  • Periodic Table: Dates back to around 450 B.C., early formulations laid the groundwork for modern chemistry.

Chapter 4 Outline

  • Organic Molecules

  • The Carbon Atom

  • Chemical Formulas & Drug Isomerism

  • Important Functional Groups

  • Macromolecules (Macros)

    • Carbohydrates

    • Proteins

    • Nucleic Acids

    • Lipids

Section 4.1 - What Are Organic Molecules?

Types of Molecules

  • Inorganic Molecules:

    • Characteristics:

    • Do not contain both carbon and hydrogen.

    • Typically small in size.

    • Often contain ionic bonds; most are soluble.

    • Examples include salts, acids, bases, and water.

  • Organic Molecules:

    • Characteristics:

    • Contain carbon and hydrogen (often with oxygen).

    • Typically complex in structure.

    • Contain covalent bonds; solubility can vary.

    • Examples: carbohydrates, proteins, lipids, nucleic acids.

Organic Chemistry vs. Biochemistry

  • Organic Chemistry:

    • Focused on the study of organic molecules, their structure, and synthesis.

  • Biochemistry:

    • Involves the study of the chemistry of life, focusing on chemical processes within living organisms.

Section 4.2 - Carbon: The Central Atom

Carbon Atoms

  • All organic molecules contain carbon and hydrogen and most include oxygen.

  • Carbon features:

    • Has four valence electrons allowing it to form four single covalent bonds.

    • Can also form double and triple bonds.

    • Capable of creating complex linear or ring structures.

  • Example:

    • Methane ( ext{CH}_4) is the simplest organic molecule.

Chemical Formulas

  • Molecular Formulas:

    • Indicate the number and ratio of atoms in a molecule (considered as a recipe).

  • Structural Formulas:

    • Demonstrate the actual arrangement of atoms within a molecule (considered as layout).

Drug Isomerism

  • Definition of Isomers:

    • Molecules that have the same molecular formula but different structural formulas.

  • Types:

    • Right-handed isomer (D form) designated as “es” or “dextro”.

    • Left-handed isomer (L form) designated as “ar” or “levo”.

  • Racemic Mixtures:

    • Many drugs exist as mixtures of D and L forms.

  • Thalidomide Tragedy:

    • One isomer acts as a sedative, while the other is teratogenic, leading to severe birth defects.

Section 4.3 - Carbon Skeleton and Important Functional Groups

Carbon Skeleton

  • The backbone structure of organic molecules form the carbon skeleton.

  • Carbons are numbered to assist in identifying different isomers.

  • Functional Groups:

    • Attached to the carbon skeleton and help determine the family name and chemical reactivity of the molecule.

  • Examples of Hydrocarbons:

    • Comprise large numbers of carbon and hydrogen atoms.

Functional Groups to Know for Exam 2

  • Methyl (–CH₃)

  • Hydroxyl/Alcohol (–OH)

  • Carboxyl (–COOH)

  • Phosphate (–PO₄³⁻)

  • Amine (–NH₂)

Methyl Group

  • Methyl Groups (–CH₃):

    • Bound to another atom, regulating gene expression through methylation (adding) and demethylation (removing) of methyl groups.

Hydroxyl (Alcohols)

  • Composed of a hydroxyl group (–OH) bonded to carbon.

  • Example: Ethyl alcohol or ethanol, commonly found in alcoholic beverages.

Carboxyl Groups

  • Also known as carboxylic acid.

  • Created from a combination of carbonyl (C=O) and hydroxyl (-OH) groups, abbreviated as -COOH.

  • Characteristically acidic due to the ability to lose an H⁺ ion.

  • Examples include acetic acid, alpha hydroxy acids (AHAs), and citric acids.

Amino Group

  • Contains nitrogen bonded to two hydrogens (–NH₂).

  • Functions as a base that can accept H⁺ to form ammonia (NH₃).

  • Ammonia is toxic; the liver converts it to urea for elimination through urine and sweat.

  • Additionally, plants use amino acids in defense mechanisms (e.g., anesthetics, antidepressants).

Phosphate Groups

  • Represent a polyatomic ion (–PO₄³⁻); this alters to –PO₄²⁻ upon attachment to the carbon skeleton.

  • Significant component of key biological molecules such as DNA, RNA, ATP, and phospholipids.

  • The negative charge facilitates interactions with other positively charged molecules.

Section 4.4 - Organic Compounds Critical for Life

Macromolecules

  • Organic compounds can be large macromolecules, characterized by:

    • Polymers: Formed from repeated smaller units known as monomers.

    • Hydrolysis: A catabolic process breaking down macromolecules.

    • Dehydration Synthesis: An anabolic process building macromolecules by removing water (H₂O).

Carbohydrates

  • Composition: Contains carbon (C), hydrogen (H), and oxygen (O).

  • Indicative naming: Suffix ‘-ose’ identifies sugars.

  • Sugar types:

    • Monosaccharides: Simple sugars, e.g., glucose, fructose, galactose (with the molecular formula ext{C}6 ext{H}{12} ext{O}_6).

    • Disaccharides: Composed of two monosaccharides, e.g., maltose, lactose, and sucrose.

    • Polysaccharides: Comprised of more than two monosaccharides, e.g., starch (plant storage) and glycogen (animal storage).

  • Structural Roles:

    • Cellulose supports plant structures; chitin supports in fungi and arthropods.

The Glycemic Index (GI)

  • Carbohydrates are vital for survival.

  • Purpose of GI: Rates foods based on the speed they increase blood glucose levels:

    • Scale: 0 – 100 with high GI foods rapidly absorbed causing quick spikes followed by crashes.

    • Benefits of low GI foods: They are absorbed more slowly, promoting satiety.

    • Example: Fiber, critical for balanced nutrition.

    • Nutrition advocates balance; no specific food is inherently bad.

  • Applicability for Diabetics: GI serves as a helpful classification.

Proteins

  • Described as the most versatile biological molecules, with both structural and functional roles.

  • Elements: Composed of carbon (C), hydrogen (H), oxygen (O), and nitrogen (N).

  • Structural Proteins:

    • Linear and robust, providing support (e.g., collagen in skin, bones, and muscles; keratin in skin/hair/nails); myosin and actin in muscle structure.

  • Functional Proteins:

    • Exhibit complex shapes essential for processes such as enzymatic reactions, hormone regulation (e.g., insulin, glucagon), and immune response (e.g., antibodies).

    • Includes transport proteins (e.g., lipoproteins, albumin) and membrane proteins.

Polypeptides and Amino Acids

  • Polypeptides: Chains of amino acids joined by peptide bonds.

  • Monomers: Amino acids.

  • Amino Acid Structure: Contains a carboxyl group, an amino group, and a variable R group that dictates chemical behavior.

  • Essential vs Non-Essential Amino Acids:

    • Essential: Must be obtained through diet.

    • Nonessential: Can be synthesized by the body.

  • Peptide Bonds: Formed by connecting carboxyl groups of one amino acid to the amino group of another amino acid.

A Guide to the Twenty Common Amino Acids

  • Overview:

    • Proteins are constituted from twenty common amino acids, while over 500 occur in nature.

    • This chart only shows the amino acids encoded directly by the human genetic code.

  • Quotes:

    • "Essential' amino acids must be acquired through food, while non-essential can be synthesized by the body.

Chart Structure for Amino Acids

  • Chemical structure with single-letter code, three-letter code, and corresponding DNA codons.

    • Various classifications include aliphatic, aromatic, acidic, basic, hydroxylic, sulfur-containing, amidic.

Protein Structure

  • Levels of Structure:

    • Primary: Sequence of amino acids.

    • Secondary: Interactions between R groups producing structures like alpha helices and beta sheets.

    • Tertiary: The final folded and functional shape of a protein.

    • Quaternary: Interactions between multiple polypeptide chains.

Denaturation of Proteins

  • Proteins are denatured when they lose their functional shape.

  • Factors causing denaturation include changes in temperature and pH levels.

  • Notably, proteins can unfold at approximately 104 °F.

Nucleic Acids

  • Overview: Deoxyribonucleic Acid (DNA) and Ribonucleic Acid (RNA).

  • DNA: Hereditary material that encodes for proteins.

  • RNA: Facilitates the transfer of genetic code from DNA for protein synthesis.

  • Monomers: Comprised of nucleotides, which include:

    • Pentose sugar

    • Negative phosphate group

    • Nitrogenous base.

Nitrogenous Bases

  • Bases are paired complementarily:

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

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

Structure of DNA and RNA

  • DNA: Double-stranded, contains thymine (T).

  • RNA: Single-stranded, contains uracil (U).

  • Both have a phosphate-sugar backbone leading to complementary base pairing.

Lipids

  • Defined as fats, waxes, and oils.

  • Characteristics: Not true polymers; lack traditional monomer subunits; all are nonpolar and hydrophobic.

  • Comprised mostly of carbon, hydrogen, and some oxygen.

Important Classes of Lipids

  • Neutral Fats (Triglycerides):

    • Predominantly energy-producing organic molecules; most abundant fats in diets.

    • Structure: One glycerol bonded to three fatty acid chains.

  • Fatty Acids:

    • Saturated: Contain only single bonds, remain solid at room temperature (e.g., whole milk, cream, pork).

    • Unsaturated: Have double bonds, remain liquid at room temperature (e.g., nuts, olive oil).

    • Hydrogenation can convert unsaturated fats to saturated fats.

Phospholipids

  • Function: Primary structural component of cell membranes; similar to triglycerides, with a charged phosphate group and two fatty acid chains.

  • Structural Divisions: Polar head (hydrophilic) due to phosphate group and non-polar tails (hydrophobic) due to fatty acid chains.

Steroids

  • Composed of a four carbon-ring structure, include cholesterol, produced from the liver, found only in animals.

  • Functions: Integral in cell membranes, synthesis of bile salts, and vitamin D; also produced as steroid hormones such as testosterone and estrogen.

Dietary Fats

  • Cholesterol:

    • Low-Density Lipoprotein (LDL): Often referred to as bad cholesterol.

    • High-Density Lipoprotein (HDL): Known as good cholesterol.

  • Triglycerides (Tgs) can contribute to conditions such atherosclerosis when combined with LDLs and fatty acids.