AJ

Chapter 2: Inorganic and Organic Compounds (Notes)

Inorganic vs Organic Compounds

  • Inorganic compounds: no carbon; small, simple molecules that usually lack carbon. Examples: H₂O, O₂, salts, acids & bases.
  • Organic compounds: large, structurally complex; always contain carbon (minimum requirement); held together by covalent bonds.
  • Four most common elements in organic compounds: C (carbon), H (hydrogen), O (oxygen), N (nitrogen).
  • Carbon skeleton: usually a chain of carbon atoms; forms the backbone for building more complex molecules.
  • Functional groups: groups of atoms that can bind to the carbon skeleton; adding different functional groups yields different kinds of organic compounds. Examples of functional groups:
    • Hydroxyl or alcohol (-OH)
    • Amino group (-NH₂)
    • Carboxyl group (-COOH)
    • Phosphate group (-PO₄³⁻)
  • Building up vs breaking down of molecules:
    • Building up (anabolism): dehydration synthesis (condensation) to assemble polymers from monomers, releasing water. General form:
      \text{Monomer}1 + \text{Monomer}2 \rightarrow \text{Polymer} + H_2O
    • Breaking down (catabolism): hydrolysis to break polymers into monomers, requiring water input. General form:
      \text{Polymer} + H2O \rightarrow \text{Monomer}1 + \text{Monomer}_2
  • Covalent bonds: formation/breaking involves sharing of electrons between atoms.

The Major Organic Compounds

  • For each organic compound, know the building blocks, group/category types, key functions, and examples.
  • The 4 major organic compounds: Carbohydrates, Proteins, Lipids, Nucleic Acids.

1) Carbohydrates (carbs or sugars)

  • Building blocks: carbon, hydrogen, oxygen.
  • Often end with the suffix "-ose".
  • Classified by size into three major groups:
    1. Monosaccharides
    • Simple sugars containing 3–7 carbon atoms.
    • Sweet-tasting and water soluble.
    • Provide quick source of energy for living cells (e.g., glucose for humans).
    • Examples: glucose, deoxyribose (DNA sugar), fructose.
    1. Disaccharides
    • Formed when two monosaccharides covalently bond via a glycosidic bond through dehydration synthesis.
    • Provide structural components for bacterial cell walls.
    • Examples: sucrose, lactose.
    1. Polysaccharides
    • Consist of tens to hundreds of monosaccharides joined through dehydration synthesis.
    • Function: long-term energy storage and structural components for plant cell walls (cellulose/fiber).
    • Examples: starch (plant long-term energy), glycogen (animal long-term energy), cellulose (plant fiber).
    • Note: All three (starch, glycogen, cellulose) are polymers of glucose.

2) Proteins

  • Building blocks: carbon, hydrogen, oxygen, nitrogen, and sometimes sulfur.
  • Essential roles: cell structure and function; they are structurally and functionally the most diverse group of organic compounds, so there are many protein shapes and functions.
  • Key protein categories and functions:
    • Structural proteins: keratin — reinforces skin and provides a physical barrier to infection.
    • Transporter proteins: present in cell membranes (protein channels and carriers).
    • Enzymes: speed up chemical reactions.
    • Antibodies: immune response.
    • Bacterial toxins: poisonous proteins produced by some bacteria.
  • Amino acids: building blocks/subunits of proteins.
  • Chemistry of amino acids:
    • Each amino acid has a central carbon (the alpha carbon) that binds to four groups: an amino group, a carboxyl group, a hydrogen, and a side chain (R group).
    • There are 20 different amino acids with distinct R groups.
    • Only two amino acids contain sulfur, and they can form disulfide bonds which contribute to protein folding.
  • Peptide bonds:
    • Two amino acids are linked by a covalent peptide bond formed via dehydration synthesis.
    • The bond forms between the amino group of one amino acid and the carboxyl group of the next.
    • Water (H₂O) is released in the process.
  • Protein structure and function relationship:
    • The three-dimensional shape of a protein determines its function.
    • Denaturation: if a protein loses or changes its shape, it loses or changes function. Denaturation can occur in harsh/hostile environments (e.g., high temperature or low pH).
  • Levels of protein structure (from simple to most complex): 1) Primary structure: sequence of amino acids; a polypeptide chain; linear, no folds. 2) Secondary structure: folding/coil into an α-helix or a β-pleated sheet held together by hydrogen bonds.
    • Examples: hair protein (keratin) forms a helix; skin proteins often form pleated sheets.
      3) Tertiary structure: global 3D folding of the secondary structures, stabilized by disulfide bridges, hydrogen bonds, and ionic bonds between amino acids.
    • Result: a three-dimensional shape; interactions can occur between non-adjacent amino acids (not just neighboring ones).
      4) Quaternary structure: assembly of two or more polypeptide chains into a functional protein; composed of subunits.
    • Examples: hemoglobin (4 subunits), antibodies (multiple subunits), some enzymes (multiple subunits).
  • A note on terminology used in class: AMINO ACIDS are the building blocks; there are 20 types, each defined by its unique R-group.

3) Lipids

  • Building blocks: carbon, hydrogen, oxygen.
  • Core building blocks: triglycerides (formed from one glycerol molecule and three fatty acids).
  • Primary function: major components of cell membranes and energy storehouse; lipids provide energy when carbohydrates are scarce.
  • Lipid classes:
    1. Simple lipids (fats or triglycerides)
    • Structure: 1 glycerol + 3 fatty acids linked by an ester bond via dehydration synthesis.
    • Saturated fatty acids: no double bonds in the fatty acids (all single bonds).
    • Unsaturated fatty acids: one or more carbon–carbon double bonds.
    1. Complex lipids
    • Cell membranes are made of complex lipids called phospholipids.
    • Structure: glycerol, 2 fatty acids, and a phosphate-containing group.
    • Properties: polar head region (phosphorylated, polar) and nonpolar tails; polar region is charged, nonpolar region is uncharged.
    • Functions: regulate transport and contribute to membrane homeostasis.
    • Examples of other complex lipids: waxes, glycolipids (lipids with attached carbohydrate), mycolic acid (a waxy lipid in the cell wall of Mycobacterium tuberculosis).
    1. Steroids and sterols
    • Structure: three six-carbon rings (A, B, C) fused to one five-carbon ring (D).
    • An -OH group attached to one of the six-carbon rings yields a Sterol.
    • Examples: cholesterol (animal membranes), phytosterols (plants), ergosterol (fungi membranes).
    • Function: structural component of eukaryotic cell membranes.

4) Nucleic Acids

  • Composition: carbon, hydrogen, oxygen, nitrogen (also phosphorus is implied by backbone chemistry in real biology, but the transcript notes focus on these elements); examples include DNA, RNA, and ATP.
  • Building blocks: nucleotides; linked together by covalent bonds in dehydration synthesis to form nucleic acids via phosphodiester bonds.
  • Nucleotides consist of:
    • Sugar: a five-carbon pentose sugar.
    • Phosphate group.
    • Base: a nitrogen-containing base that comes from either the Purine family or the Pyrimidine family.
    • Purines: adenine (A) and guanine (G).
    • Pyrimidines: cytosine (C), uracil (U), thymine (T).
  • DNA (Deoxyribonucleic Acid)
    • Structure: double-stranded molecule with a sugar–phosphate backbone.
    • Bases pair via hydrogen bonds: A pairs with T; C pairs with G.
    • Base pairing specifics: A–T (two hydrogen bonds) and C–G (three hydrogen bonds).
    • Thymine is found only in DNA.
    • Function: stores genetic information.
  • RNA (Ribonucleic Acid)
    • Structure: usually single-stranded with a sugar–phosphate backbone.
    • Bases: includes uracil (U) instead of thymine.
    • Base pairing is not described as a defining feature in this content, but RNA includes regions that may pair within the molecule.
    • 3 main types of RNA and their roles in protein synthesis:
    • mRNA (messenger RNA)
    • tRNA (transfer RNA)
    • rRNA (ribosomal RNA)
  • ATP (Adenosine Triphosphate)
    • Structure: adenosine (sugar + base) attached to three phosphate groups.
    • It is a nucleic acid that remains as a single nucleotide.
    • Function: high-energy compound; stores chemical energy.
    • Energy release: energy is released by hydrolysis/breaking of phosphate bonds, enabling cellular work.
    • General hydrolysis form:
      \text{ATP} \rightarrow \text{ADP} + \text{P_i} + \text{energy}

Connections to foundational principles and real-world relevance

  • Dehydration synthesis vs hydrolysis underpins how macromolecules are built and broken down in all living systems.
  • The concept of functional groups explains why molecules with the same carbon skeleton can have very different chemical properties and biological roles.
  • The idea that protein function is determined by structure highlights the importance of environmental conditions (temperature, pH) on enzyme activity, immune function, and overall metabolism; denaturation has practical implications in cooking, sterilization, and disease.
  • Carbohydrates serve as immediate energy sources (monosaccharides), energy storage (starch/glycogen), and structural components (cellulose in plants).
  • Lipids provide long-term energy storage, form cellular membranes, and contribute to signaling; membrane composition (phospholipids, sterols) is crucial for membrane fluidity and function.
  • Nucleic acids carry genetic information (DNA) and direct protein synthesis (RNA), while ATP provides energy for cellular processes; these molecules are central to heredity, metabolism, and regulation of cellular activities.

Quick recap of the main concepts

  • Dehydration synthesis forms polymers; hydrolysis breaks polymers into monomers, both releasing or consuming water respectively.
  • The four major organic compounds (Carbohydrates, Proteins, Lipids, Nucleic Acids) each have distinctive building blocks, functions, and examples.
  • Proteins exhibit hierarchical structure (primary to quaternary) that determines function; denaturation disrupts function.
  • Lipids are diverse (simple triglycerides, complex phospholipids, and steroids) and are key to membranes and energy storage.
  • Nucleic acids store information (DNA), participate in protein synthesis (RNA), and high-energy carriers (ATP).

Key terms to memorize

  • Dehydration synthesis (condensation)
  • Hydrolysis
  • Glycosidic bond
  • Peptide bond
  • Amino acids; R groups; disulfide bonds
  • Primary, Secondary, Tertiary, Quaternary structure
  • Saturated vs Unsaturated fatty acids
  • Phospholipid; lipids in membranes
  • Steroid/sterol; cholesterol, phytosterol, ergosterol
  • Nucleotide; phosphodiester bond
  • Purines vs Pyrimidines
  • A–T and C–G base pairing
  • mRNA, tRNA, rRNA
  • ATP and hydrolysis energy