AJ

Chapter 2: Inorganic and Organic Compounds (Lecture Notes)

Inorganic vs Organic compounds

  • Inorganic compounds: no carbon; small, simple molecules
    • Examples:
    • Water: H$_2$O
    • Oxygen: O$_2$
    • Salts, acids & bases
  • Organic compounds: Large, structurally complex; always contain carbon; held together by covalent bonds
  • The 4 most common elements in organic compounds:
    1. Carbon
    2. Hydrogen
    3. Oxygen
    4. Nitrogen
    • Often contain a carbon skeleton (chain of carbon atoms)
  • Functional groups
    • Groups of atoms that can bind to the carbon skeleton
    • Adding different functional groups → different kinds of organic compounds
    • Examples of functional groups:
    • Hydroxyl group: –OH
    • Amino group: –NH$_2$
    • Carboxyl group: –COOH
    • Phosphate group: –PO$4$H$2$
  • Building up vs. breaking down of molecules
    • Building up (anabolic): dehydration synthesis (lose H$_2$O)
    • Several small monomers combine to form one large polymer
    • Forms covalent bonds (example: O–O–O–O chain represents polymer linkage)
    • Breaking down (catabolic): hydrolysis (input H$_2$O)
    • One large polymer breaks down into several small monomers
    • Break covalent bonds
    • Example: OH + H break a bond to form monomers

The Major Organic Compounds: overview

  • For each organic compound, know:
    • Building blocks (what they are composed of)
    • Any group/category types
    • Key function(s)
    • Examples
  • The 4 major organic compounds: Carbohydrates, Proteins, Lipids, Nucleic acids

1. Carbohydrates

  • Building blocks: carbon, hydrogen, oxygen
  • Also known as “carbs” or sugars
  • Usually end in the suffix “-ose”
  • Classified into 3 major groups by size: 1) Monosaccharides
    • Simple sugars containing 3-7 carbon atoms
      ightarrow quick energy sources
    • Sweet and water soluble
    • Provide quick source of energy for living cells (e.g., glucose for humans)
    • Examples: glucose, deoxyribose (DNA sugar), fructose
      2) Disaccharides
    • Formed when two monosaccharides form a covalent bond called a glycosidic bond via dehydration synthesis
    • Provide structural component for bacterial cell walls
    • Examples: sucrose, lactose
      3) Polysaccharides
    • Tens to hundreds of monosaccharides joined via dehydration synthesis
    • Function: long-term energy storage and structural components for plant cell walls (cellulose)
    • Examples: starch (plants; long-term energy), glycogen (animals; long-term energy), cellulose (plant cell wall) – all polymers of glucose

2. Proteins

  • Building blocks: carbon, hydrogen, oxygen, nitrogen and sometimes sulfur
  • Essential in cell structure and function (structure ⇄ function)
  • Most diverse among organic compounds; many shapes → many functions
  • Key protein types and functions:
    • Structural proteins: keratin (reinforces skin; barrier to infection)
    • Transporter proteins: in cell membranes (e.g., channels and carriers)
    • Enzymes: speed up chemical reactions
    • Antibodies: immune response
    • Bacterial toxins: poisonous proteins made by some bacteria
  • Amino acids (building blocks):
    • Each amino acid has a central carbon that binds to four groups:
    • Amino group
    • Carboxyl group
    • Hydrogen
    • Side chain (R group) – varies
    • There are 20 different amino acids
    • Two sulfur-containing amino acids exist (discussed as the ones causing bends in the chain)
  • Peptide bonds
    • Two amino acids linked by a covalent bond called a peptide bond via dehydration synthesis
    • Bond forms between the amino group and the carboxyl group
    • Mechanism: OH from carboxyl and H from amino are removed to form H$_2$O
  • Protein structure determines function
  • Denaturation
    • Proteins can lose/change shape (structure) and thus lose/change function
    • Denaturation occurs under harsh/hostile environments (e.g., high temperature, low pH); may be permanent
  • Levels of protein structure (from simple to complex): 1) Primary: sequence of amino acids; a polypeptide chain (linear) 2) Secondary: folding/coil into a helix or pleated sheet (stabilized by hydrogen bonds)
    • Examples: hair protein (alpha-helix), skin protein (beta-pleated sheet)
      3) Tertiary: irregular folding into 3D shape; stabilized by disulfide bridges, hydrogen bonds, ionic bonds
    • Not limited to neighboring amino acids
    • Disulfide bonds can form between sulfur-containing AAs that are far apart
      4) Quaternary: two or more polypeptide chains bound together; multiple tertiary subunits
    • Bulky and complex
    • Examples: hemoglobin (4 subunits), antibodies (4 subunits), some enzymes (several subunits)

3. Lipids

  • Building blocks: carbon, hydrogen, oxygen
  • Subunits/buiding units: triglycerides (glycerol + 3 fatty acids)
  • Key function: major component of cell membranes (phospholipid bilayer)
  • Classes of lipids: i. Simple lipids (fats or triglycerides)
    • Structure: 1 glycerol + 3 fatty acid chains linked by ester bonds via dehydration synthesis
    • Saturation:
      • Saturated: no double bonds in fatty acids (all single bonds)
      • Unsaturated: one or more double bonds in fatty acids
    • Function: energy source when carbohydrates are not available
      ii. Complex lipids (membrane lipids)
    • Phospholipids: contain 1 glycerol and 2 fatty acids
    • Regulate transport; maintain homeostasis
    • Have polar regions (polar head) and nonpolar regions (nonpolar fatty acid tails)
      • Polar = charged; nonpolar = uncharged
    • Examples include waxes, glycolipids (lipids with attached carbs), mycolic acid (waxy lipid in the cell wall of Mycobacterium tuberculosis)
      iii. Steroids and Sterols
    • Form when three 6-carbon rings (A, B, C) attach to one 5-carbon ring (D)
    • When an –OH group attaches to one of the 6-carbon rings, it is called a sterol
    • Examples: cholesterol, plant/phytosterols, ergosterol (fungal membranes)
    • Function: structural component of eukaryotic cell membranes
  • Note: Steroids/sterols provide rigidity and signaling roles in membranes; cholesterol is a key membrane component

4. Nucleic Acids

  • Building blocks: carbon, hydrogen, oxygen, nitrogen (and phosphorus in the backbone, though the transcript lists nitrogen and mentions protein) and phosphate groups; also ATP is a nucleic acid-related molecule
  • Building blocks: nucleotides linked by covalent bonds called phosphodiester bonds via dehydration synthesis
  • Nucleotides consist of: i. Sugar: a 5-carbon pentose sugar ii. Phosphate group iii. Base: nitrogen-containing base from Purine or Pyrimidine families
    • Purines: Adenine (A), Guanine (G)
    • Pyrimidines: Cytosine (C), Uracil (U) in RNA, Thymine (T) in DNA
  • DNA
    • Double-stranded molecule; double helix
    • Sugar-phosphate backbone
    • Base pairing: A pairs with T via hydrogen bonds; C pairs with G via hydrogen bonds
    • Thymine is present in DNA (not in RNA)
  • RNA
    • Usually single-stranded
    • Sugar-phosphate backbone
    • No universal base pairing like DNA; includes Uracil instead of thymine
    • Three main types: mRNA, tRNA, rRNA
    • Function: protein synthesis
  • ATP (Adenosine Triphosphate)
    • A nucleic acid-like molecule that remains as a single nucleotide
    • High-energy compound
    • Stored chemical energy released by hydrolysis/breaking of bonds between phosphate groups

Connections and implications

  • How dehydration synthesis and hydrolysis relate to metabolism
    • Building macromolecules requires energy input and removal of water
    • Breaking macromolecules releases energy when bonds are hydrolyzed
  • Structure–function relationships across macromolecules
    • Protein shape determines function; conformational changes impact activity
    • Lipid bilayer structure determines permeability and transport; membrane fluidity depends on lipid composition
    • Nucleotide sequence in DNA encodes genetic information; sequence variations drive diversity of proteins
  • Real-world relevance
    • Carbohydrates provide quick energy (glucose) vs. storage forms (starch, glycogen) and structural support (cellulose in plants)
    • Lipids provide long-term energy reserves and form membranes; steroids influence signaling
    • Proteins underpin virtually all cellular processes, from catalysis (enzymes) to immunity (antibodies) to structure (keratin)
    • Nucleic acids store and transfer genetic information; ATP is the energy currency of the cell

Key terms recap (quick reference)

  • Dehydration synthesis: monomers join, releasing a molecule of water
  • Hydrolysis: polymers broken down by addition of water
  • Glycosidic bond: covalent bond linking monosaccharides
  • Peptide bond: covalent bond linking amino acids
  • Phosphodiester bond: bond linking nucleotides in nucleic acids
  • Primary/Secondary/Tertiary/Quaternary structures: levels of protein folding and organization
  • Saturated vs. unsaturated fats: presence/absence of double bonds in fatty acids
  • Phospholipid bilayer: fundamental architecture of cell membranes
  • Purines vs. Pyrimidines: two-base families in nucleotides
  • A–T and C–G pairing: hydrogen-bonded base pairs in DNA
  • Denaturation: loss of protein structure and function due to environment