Chapter 3: The Organic Molecules of Life
3.1 Organic Molecules
Organic molecules contain carbon and hydrogen; inorganic molecules do not contain a combination of carbon and hydrogen (e.g., ext{H}_2 ext{O} and ext{NaCl}).
Carbon atom basics:
Total of six electrons; four in the outer shell.
Almost always shares electrons with elements such as hydrogen, nitrogen, and oxygen.
Can bond with as many as four other elements.
Most often shares electrons with other carbon atoms.
Hydrocarbons: chains of carbon atoms bonded only to hydrogen atoms.
Isomers: same number and kinds of atoms (same molecular formula) but different arrangements; may have different properties.
When discussing isomers, several types are introduced:
Constitutional (structural) isomers: different connectivity.
Stereoisomers (spatial isomers): same connectivity, different spatial arrangement.
Diastereomers: stereoisomers that are not mirror images.
Enantiomers: non-superimposable mirror images.
Conformers (rotamers): different shapes due to rotation around single bonds; cis-trans isomerism is a type of stereoisomerism for double bonds.
Figure 3.2 highlights that carbon chains can vary in:
Length, presence of double bonds, and branching.
Carbon rings can form in different sizes and have double bonds.
The carbon skeleton size/shape and attached functional groups determine molecule behavior; functional groups are a key determinant of reactivity.
Functional group defined: a specific bonded set of atoms that imparts characteristic properties and reactions to the molecule.
Often use R to represent the remainder of the molecule attached to the functional group.
Figure 3.3: Common Functional Groups (structure and examples at a glance)
Hydroxyl group: structure R–OH; Found in alcohols and sugars.
Carboxyl group: structure R–C(=O)–OH; Found in fatty acids and amino acids.
Amino group: structure R–NH_2; Found in amino acids and proteins.
Sulfhydryl group: structure R–S–H; Found in cysteine and proteins.
Phosphate group: structure O ext{–}P(=O)(OH)_2 (often bound via an ester linkage); Found in ATP and nucleic acids.
Other notes: functional groups determine the chemical properties and reactivity of organic molecules; their presence and combination explain diversity of biomolecules.
3.2 Carbohydrates and Lipids overview:
There are four categories of biological molecules: Carbohydrates, Lipids, Proteins, Nucleic Acids.
Digestion breaks these molecules into subunits to build macromolecules.
Building complex molecules:
Monomers: subunits.
Polymers: monomers joined together.
Dehydration synthesis (condensation): joins monomers to form polymers with removal of a water molecule;
ext{Monomer} + ext{Monomer}
ightarrow ext{Polymer} + ext{H}_2 ext{O}Hydrolysis: adding water to break polymer bonds; OH from water attaches to one monomer, H attaches to the other.
ext{Polymer} + ext{H}2 ext{O} ightarrow ext{Monomer}1 + ext{Monomer}_2
Monosaccharides and disaccharides and polysaccharides are the carbohydrates.
3.3 Proteins and Nucleic Acids are addressed later in this unit with details on structure and function.
3.2 Carbohydrates and Lipids (in detail)
Carbohydrates are mainly used for immediate energy; they are enzymatically broken down to release energy used to make ATP. They can also serve structural roles (e.g., cellulose in plant cell walls).
Carbohydrate classification:
Monosaccharides: a single sugar molecule; simple sugars.
Disaccharides: two monosaccharides linked together.
Polysaccharides: long chains of monosaccharides; can be energy storage or structural.
Monosaccharides specifics:
Carbon backbone ranges from 3 to 7 carbons; general formulas vary by size.
Glucose: ext{C}6 ext{H}{12} ext{O}_6; two isomers—fructose and galactose.
Ribose: ext{C}5 ext{H}{10} ext{O}_5; found in RNA.
Deoxyribose: ext{C}5 ext{H}{10} ext{O}_4; found in DNA (lacks one O).
Glycose variants include triose (e.g., glyceraldehyde, dihydroxyacetone), pentose (e.g., ribose), and hexose (e.g., glucose).
Simple carbohydrate definitions:
Simple carbohydrates (sugars) are readily digested and provide rapid energy.
Monosaccharide examples and structures (brief):
Glyceraldehyde, dihydroxyacetone (trioses).
Ribose (pentose), glucose (hexose).
Structural diagrams depict linear and ring forms; note that sugars can cyclize to rings in solution.
Disaccharides:
Maltose: glucose–glucose; yeast fermentation for energy in beer; hydrolysis of maltose yields two glucose molecules.
Sucrose: glucose + fructose (table sugar).
Lactose: galactose + glucose.
General hydrolysis: disaccharide + water → two monosaccharides (e.g., maltose + water → 2 glucose).
Maltose fermentation: maltose + H₂O → 2 glucose; yeast fermentation converts glucose to ethanol and CO₂ (beer production).
Polysaccharides: many are used as energy storage molecules or structural components.
Plant storage: starch (amylose, amylopectin) made of α-glucose; storage in plants.
Animal storage: glycogen; highly branched polymer of glucose.
Structural roles: cellulose (plant cell walls) and chitin (exoskeletons of crustaceans and insects).
Most abundant organic molecule overall is cellulose; digested mainly by specific microbes.
Figure references summarize structure and function of starch, glycogen, and cellulose.
Carbohydrate structures (summary):
Amylose vs amylopectin in starch; branching patterns differ (1→4 vs 1→6 glycosidic bonds).
Glycogen is highly branched; cellulose is unbranched with parallel chains; hydrogen bonding holds cellulose chains together.
Lipids overview:
All lipids are insoluble in water; composed of long nonpolar hydrocarbon chains; low hydroxy group content; highly diverse in structure and function.
Primary roles: long-term energy storage; waterproofing effects on skin, hair, and feathers; membrane components (phospholipids).
Fats and oils are triglycerides: three fatty acids attached to glycerol.
Glycerol: ext{C}3 ext{H}8 ext{O}_3 with three —OH groups.
Fatty acid: long carbon chain with a carboxyl group at one end; general formula for saturated or unsaturated hydrocarbon chains; energy-dense molecules.
A triglyceride forms when the carboxyl portions of three fatty acids react with the three –OH groups of glycerol, releasing 3 H₂O in the process (dehydration synthesis).
Fatty acids details:
Unsaturated fats have double bonds in the carbon chain; fewer hydrogens than two per carbon atom.
Trans fats are unsaturated fats with trans orientation around the double bond.
Saturated fatty acids have no double bonds (fully saturated with hydrogens).
Examples with typical formulas (illustrative):
Arachidic: ext{C}{20} ext{H}{40} ext{O}_2
Stearic: ext{C}{18} ext{H}{36} ext{O}_2
Palmitic: ext{C}{16} ext{H}{32} ext{O}_2
Oleic: ext{C}{18} ext{H}{34} ext{O}_2
Linoleic: ext{C}{18} ext{H}{32} ext{O}_2
Common fat sources and terms shown: canola oil (unsaturated), butter (saturated).
Phospholipids: membrane components
Form the bulk of the plasma membrane.
One end is water-soluble (polar head); the other end is nonpolar (nonpolar tails).
Polar head typically includes a phosphate group; nonpolar tails are fatty acid chains connected via glycerol.
They form a bilayer that lines the inside and outside of the cell membrane; the inside is hydrophobic while the outside interacts with water.
Example components: phosphatidylcholine (PC), phosphatidylserine (PS), phosphatidylethanolamine (PE), phosphatidylinositol (PI), phosphatidylglycerol (PG), sphingomyelin, cholesterol as membrane components.
Steroids: four fused rings
Lipids made of four fused rings; no fatty acids; insoluble in water; derived from cholesterol.
Differ by functional groups; examples include cholesterol, testosterone, estrogen.
Example overview of steroid synthesis: cholesterol is converted through a series of enzyme-catalyzed steps (e.g., pregnenolone, progesterone, 17α-hydroxylase, 17,20-lyase, 3β-HSD) leading to various steroids including glucocorticoids, mineralocorticoids, and sex steroids (androgens, estrogens).
Cellular locations of enzymes may include mitochondria and smooth endoplasmic reticulum.
3.3 Proteins and Nucleic Acids
Proteins: many roles including support, metabolism, transport, defense, regulation, and motion.
Proteins are polymers of amino acid monomers.
Each amino acid has a central (α) carbon bonded to a hydrogen atom, an amino group, a carboxyl group, and a side chain (R group).
There are 20 standard amino acids; the R group defines the identity and properties (polar vs nonpolar, acidic/basic).
Amino acids and peptides:
Peptide: two or more amino acids covalently linked.
Peptide bond: formed by a dehydration reaction between amino acids.
Polypeptide: a chain of many amino acids joined by peptide bonds.
The sequence of amino acids (primary structure) determines the final three-dimensional shape and function of the protein.
Examples of amino acids (selected from diagrams):
Valine (Val): nonpolar.
Glutamate (Glu): ionized (negative charge at physiological pH).
Cysteine (Cys): nonpolar; contains a thiol group (—SH).
Tryptophan (Trp): nonpolar; complex ring structure.
Figure 3.18 Synthesis and Degradation of Peptide
Dehydration synthesis builds a dipeptide from two amino acids, releasing a water molecule.
Hydrolysis breaks a dipeptide into two amino acids by adding water.
Protein structure organization (levels):
Primary structure: amino acid sequence (polymeric chain);
Example sequence includes various amino acids (e.g., Val, Asn, Ala, Lys, Ser, Val, Leu, Cys, His, etc.).
Secondary structure: alpha helix and beta-pleated sheet; hydrogen bonds stabilize the structure.
Tertiary structure: overall three-dimensional globular or fibrous shape resulting from interactions among R groups (hydrophobic interactions, hydrogen bonds, ionic/salt bridges, disulfide bonds, etc.).
Quaternary structure: more than one polypeptide chain interact to form a functional protein.
Protein denaturation:
Denaturation is the loss of structure and function, often due to changes in pH or temperature.
Example: native albumin can denature under heat or chemical exposure; crosslinking (disulfide bonds) can also alter structure.
Nucleic Acids: DNA and RNA
DNA: deoxyribonucleic acid; stores genetic information.
RNA: ribonucleic acid; helps to make proteins.
Nucleotides: the monomer units of nucleic acids; composed of a phosphate group, a five-carbon sugar, and a nitrogenous base.
Nitrogenous bases: Adenine (A), Guanine (G), Cytosine (C), Thymine (T) in DNA; Uracil (U) replaces thymine in RNA.
Structure of DNA: deoxyribose sugar, nitrogenous bases, and a phosphate backbone forming a double helix; base pairing rules: A pairs with T (two hydrogen bonds), C pairs with G (three hydrogen bonds).
DNA structural variants: A-DNA, B-DNA, Z-DNA; distinct forms with different sugar-phosphate geometries.
RNA structure: single-stranded; ribose sugar; uses uracil instead of thymine; bases include A, G, C, U; backbone consists of sugar-phosphate linkages.
Comparing proteins and nucleic acids:
The sequence of bases in DNA determines the sequence of amino acids in a protein.
The sequence of amino acids determines a protein’s three-dimensional structure and function.
Small changes in the DNA can cause large changes in a protein, illustrating the tight coupling between genotype and phenotype.
Sickle-cell disease example: a single amino acid substitution—valine replaces glutamate at position 6 in the β-globin chain—leading to sickle-shaped red blood cells and disease phenotype.
Practical and real-world implications:
Understanding the link between DNA sequence and protein structure helps explain genetic diseases and informs approaches in medicine and biotechnology.
The study of nucleic acids underpins modern genetics, sequencing, and gene editing debates and ethics.
Ethical and philosophical notes (implicit in content):
Knowledge of DNA structure and sequence has profound implications for privacy, genetic testing, and potential gene therapies.
The ability to alter proteins and genes raises questions about safety, equity, and responsible use of biotechnology.
Summary of key formulas and notations
General polymerization (dehydration synthesis):
ext{Monomer} + ext{Monomer}
ightarrow ext{Polymer} + ext{H}_2 ext{O}
Hydrolysis (bond cleavage):
ext{Polymer} + ext{H}2 ext{O} ightarrow ext{Monomer}1 + ext{Monomer}_2
Carbohydrate formulas (examples):
Glucose: ext{C}6 ext{H}{12} ext{O}_6
Ribose: ext{C}5 ext{H}{10} ext{O}_5
Deoxyribose: ext{C}5 ext{H}{10} ext{O}_4
Sucrose (disaccharide): ext{C}{12} ext{H}{22} ext{O}_{11}
Fatty acids and lipids (examples):
Saturated fatty acid: ext{C}{18} ext{H}{36} ext{O}_2
Unsaturated fatty acid: ext{C}{18} ext{H}{34} ext{O}_2
Trans fat note: trans configuration around a double bond; still unsaturated overall.
Lipid components (triglyceride): glycerol + three fatty acids; general glycerol formula: ext{C}3 ext{H}8 ext{O}_3
DNA structure and base pairing (high level):
Base pairs: ext{A} ext{ pairs with } ext{T}, ext{ two hydrogen bonds}
ext{C} ext{ pairs with } ext{G}, ext{ three hydrogen bonds}
Nucleotide composition (DNA vs RNA):
DNA sugar: deoxyribose (no 2' OH); bases A, G, C, T.
RNA sugar: ribose (with 2' OH); bases A, G, C, U.
Note: The above notes summarize the content from the provided transcript, including major and minor points, definitions, structures, examples, and the numerical/formula references given (formatted in LaTeX). The organization follows the lecture's order: organic molecules and isomers, carbohydrates and lipids, proteins and nucleic acids, with emphasis on structure–function relationships, biochemical processes (synthesis and hydrolysis), and real-world relevance such as energy storage and genetic information.