Chapter 2 Part 2 - Organic Molecules

Overview of Organic Molecules

• Organic molecules always contain carbon and hydrogen; carbon atoms can bond with each other to form long chains (hydrocarbons).
• Carbon typically forms four bonds, reflecting the octet rule: a carbon atom can bond to 4 other atoms, and can form single or double bonds in various arrangements.
• Carbon–carbon bonding leads to saturated and unsaturated structures; saturated fats have no C=C double bonds and form straight, compact tails; unsaturated fats have one or more C=C bonds that introduce kinks, keeping tails bent and typically liquid at room temperature.
• Functional groups sat at the ends of carbon chains determine how organic molecules behave in reactions (structure at the end tells you reactivity). Examples: hydroxyl group (-OH) and carboxyl group (-COOH, with C=O and -OH). These groups influence solubility, acidity/basicity and reaction pathways.
• Functional groups remind us of electron shell considerations in atoms: outward groups influence overall behavior of molecules in reactions, similar to how electron arrangements influence atomic reactivity.

Dehydration and Hydrolysis: how polymers form and break apart

• Polymer vs. monomer:
  • Polymer: many monomers linked together.
  • Monomer: a single unit.
  • Formation via dehydration (dehydration synthesis): remove water to join monomers into a polymer.
  • Breaking polymers via hydrolysis: insert water to split polymers into monomers.
• Simple schematic equations:
  ext{Monomer}1 + ext{Monomer}2
  ightarrow ext{Polymer} + H2O \ ext{Polymer} + H2O
  ightarrow ext{Monomer}1 + ext{Monomer}2
• Why it matters:
  • After a meal, glucose monomers can be joined by dehydration to store energy as a polymer (e.g., glycogen in the liver) or as fat.
  • When energy is needed (e.g., the next morning), hydrolysis breaks down stored polymers into glucose monomers for ATP production.
  • Energy yield: one glucose can produce about ext{≈} 36 ext{ ATP} molecules, enabling cellular work.
• Practical implication: without dehydration/hydrolysis, you would need to eat every time you wanted to do work in the body.

Categories of organic biomolecules (biomolecules essential for life)

• Bio means life; main categories: carbohydrates, lipids, proteins, nucleic acids.
• Each category consists of monomers (small units) that link to form polymers (larger molecules).
• Monomers → Polymers:
  • Monosaccharide → Carbohydrates (polymer: polysaccharide)
  • Fatty acid tails + glycerol → Lipids (polymer conceptually, e.g., triglycerides)
  • Amino acids → Proteins (polymer: polypeptides, eventually folded into proteins)
  • Nucleotides → Nucleic acids (polymer: DNA/RNA)

Carbohydrates

• Monomer: monosaccharide (e.g., glucose). Can have five or six carbons:
  • Five-carbon sugars form the backbone for nucleic acids in DNA/RNA.
  • Six-carbon sugars form many carbohydrates.
• Glucose is a key human body monosaccharide; used to store energy as ATP after breakdown.
• Disaccharides (two monosaccharides joined by dehydration):
  • Maltose = glucose + glucose
  • Sucrose = table sugar (glucose + fructose)
  • Lactose = milk sugar
  • Most disaccharides are easy to break down, though lactose requires the enzyme lactase; lactose intolerance results from lacking lactase.
• Polysaccharides (many sugars linked):
  • Glycogen: stored energy in liver; highly branched polymer of glucose used for quick energy release.
  • Starch: plant storage polysaccharide (e.g., in potatoes, wheat) to store energy for plants.
  • Cellulose: structural carbohydrate in plants; extensive hydrogen bonding creates rigid fibers; humans cannot digest cellulose; dietary fiber aids intestinal health by helping mechanical digestion.
• Visual note: structural similarity between starch and glycogen; both are digestible glucose polymers, while cellulose is not digestible by humans due to different linkages.

Lipids

• Lipids are not true polymers like carbohydrates or proteins; they are a broad group with nonpolar, hydrophobic characteristics.
• Core layout: glycerol head with fatty acid tails.
• Fatty acid tails can be saturated or unsaturated:
  • Saturated fats: no C=C bonds; straight tails; typically solid at room temperature (e.g., butter).
  • Unsaturated fats: contain C=C bonds causing kinks; tails stay bent and liquids in many contexts; generally considered healthier for cardiovascular health because they don’t pack tightly into plaques.
• Phospholipids (two tails, one glycerol head) are essential for cell membranes:
  • Form a phospholipid bilayer with hydrophilic heads facing outward and hydrophobic tails inward, creating a barrier between inside and outside of the cell.
  • Without fats, you would not have enough phospholipids to form membranes.
• Steroids (four fused rings) have distinct roles:
  • Cholesterol: a steroid component within cell membranes; contributes to membrane rigidity and fluidity; essential for membrane structure.
  • Hormones like testosterone and estrogen are steroids that influence development and meiosis.
• Practical takeaway: fats are essential in the diet to supply components for membranes (phospholipids) and hormones (steroids).

Proteins

• Monomer: amino acids (the building blocks of proteins); each amino acid has an amino group, a carboxyl group, a hydrogen, and a distinctive side chain (R-group).
• Peptide bonds connect amino acids via dehydration reactions, forming dipeptides, tripeptides, and polypeptides:
  • Di-peptide: two amino acids joined by a peptide bond.
  • Polypeptide: several amino acids linked; proteins are polypeptides that have folded into functional forms.
• Proteins have a wide range of functions:
  • Structural: collagen (skin support), keratin (hair and nails).
  • Enzymes: speed up chemical reactions (most enzyme names end with -ase; e.g., sucrase breaks down sucrose).
  • Hormones: signaling molecules (e.g., insulin is a peptide hormone).
  • Transport: proteins can bind and transport molecules in the blood.
  • Antibodies: immune defense; antibodies target foreign pathogens.
  • Membrane channels: allow substances to cross membranes.
• Protein structure and function depend on folding into specific shapes:
  • Primary structure: linear sequence of amino acids (beads on a string).
  • Secondary structure: local folding patterns; alpha helix or beta sheet.
  • Tertiary structure: overall 3D shape combining helices and sheets.
  • Quaternary structure: assembly of multiple folded subunits into a larger protein (e.g., collagen has multiple subunits).
• The final shape determines function; amino acid sequence is important, but correct folding is essential. If folding is disrupted, function is lost (denaturation): for example, heating an egg denatures egg proteins, preventing normal biological function.
• Denaturation factors: extreme heat, pH changes can unfold proteins, destroying function.

Nucleic Acids

• Two main types: DNA (deoxyribonucleic acid) and RNA (ribonucleic acid).
• Nucleotide: the monomer unit of nucleic acids; composed of a phosphate group, a five-carbon sugar, and a nitrogenous base.
• DNA vs RNA differences:
  • Sugar: DNA uses deoxyribose (missing one oxygen); RNA uses ribose.
  • Bases: DNA has adenine (A), guanine (G), thymine (T), cytosine (C); RNA has adenine (A), guanine (G), uracil (U), cytosine (C).
  • Structure: DNA is typically double-stranded and forms a twisted helix; RNA is usually single-stranded.
• Base-pairing rules in DNA:
  • A pairs with T via two hydrogen bonds; C pairs with G via three hydrogen bonds.
  • Represented as:
    A-T ext{ (two hydrogen bonds)},
    C-G ext{ (three hydrogen bonds)}.
• A detailed view of DNA’s complementary bases shows how the two strands run antiparallel and are held together by hydrogen bonds between bases; the sequence of bases encodes genetic information.
• ATP (adenosine triphosphate) is a nucleotide that functions as the cell’s energy currency:
  • It consists of a sugar (ribose), a phosphate group(s), and a nitrogenous base.
  • Energy storage resides in the phosphate-phosphate bonds; energy is released upon hydrolysis of a phosphate group, enabling cellular work.
  • ATP acts as an energy shuttle, moving energy from where it is produced (e.g., from glucose metabolism) to where it is consumed.
• Relationship between nucleic acids and proteins:
  • DNA is transcribed into RNA, which is translated into a sequence of amino acids to form a polypeptide, which folds into a functional protein.
  • Nucleic acids and proteins are interdependent in gene expression and cell function.
• Summary of the flow:
  • DNA (gene) → transcription → RNA → translation → polypeptide → folding → functional protein.

Connections to foundational principles and real-world relevance

• Functional groups determine reactivity just as electron arrangement guides atomic behavior; small changes at the end of a molecule can drastically alter its interactions and outcomes.
• The dehydration/hydrolysis balance enables organisms to store energy and mobilize it on demand, underpinning metabolism and energy homeostasis.
• The distinction between saturated and unsaturated fats has health implications; unsaturated fats tend to stay liquid and are generally better for cardiovascular health compared to saturated fats.
• The phospholipid bilayer is fundamental to cell membranes, controlling what enters and leaves cells and enabling cellular compartmentalization.
• Protein folding is essential for function; misfolding or denaturation disrupts biological activities and can cause disease.
• The central dogma (DNA → RNA → Protein) links genes to function, underscoring how genetic information directs cellular processes.

Key terms to remember

• Monomer, Polymer, Dehydration (synthesis), Hydrolysis
• Carbohydrates, Lipids, Proteins, Nucleic Acids
• Monosaccharide, Disaccharide, Polysaccharide
• Saturated fat, Unsaturated fat
• Phospholipid bilayer, Cholesterol, Steroids
• Amino acids, Peptide bond, Dipeptide, Polypeptide, Primary/Secondary/Tertiary/Quaternary structure
• DNA, RNA, Nucleotide, Complementary base pairing (A-T, C-G; A-U in RNA)
• ATP and energy transfer