Foundations of Biology Study Notes

The Chemical and Physical Foundations of Biology

Foundations of Biology Overview

Part I: Chemistry

  • Atomic Structure

  • Electronegativity

  • Types of Bonds

  • Water

  • pH

Part II: Biochemistry

  • Macromolecules

  • Biological Molecules – Organic Chemistry

  • Chains, Branches, and Rings

  • Functional Groups

  • Dehydration Synthesis and Hydrolysis Reactions

  • 4 Types of Biological Macromolecules
      - Polysaccharides
      - Lipids
      - Proteins
      - Nucleic Acids

Biological (Organic) Molecules

  • Framework of Biological Molecules
      - Composed primarily of carbon bonded to other carbon atoms or different types of atoms

  • Carbon's Characteristics
      - Valence: 4 (tetravalent)
      - Capable of forming four covalent bonds, allowing complexity and three-dimensional shapes in large molecules

  • Hydrocarbons
      - Composed of carbon and hydrogen

  • Energy Storage
      - Covalent bonds in hydrocarbons store significant energy
      - Generally have low electronegativity and limited solubility in water due to nonpolar covalent bonds

Building with Carbon

  • Organic Chemistry and Diversity
      - Potential forms include length of carbon skeleton, branching, presence of double bonds, and ring formation

  • Functional Groups
      - Modifications to properties of molecules via functional groups, often including polar elements due to electronegative atoms

Functional Groups

  • Hydroxyl
      - Highly reactive, forms hydrogen bonds

  • Carbonyl
      - Two types; both can undergo oxidation reactions:
        - Aldehyde: carbonyl at end of molecule
        - Ketone: carbonyl within molecule

  • Carboxyl
      - Weak acid capable of losing protons and forming hydrogen bonds

  • Amino
      - Weak base capable of gaining protons, forming hydrogen bonds

  • Phosphate
      - Highly electronegative, stores energy, acts as a weak acid upon proton release

  • Sulfhydryl
      - Capable of forming covalent disulfide bonds

Macromolecules are often Polymers

  • Definition
      - Long molecules (polymers) composed of linked monomer subunits

  • Synthesis and Breakdown
      - Dehydration Synthesis: removal of OH- and H+ to synthesize and form H2O
      - Hydrolysis: breaks covalent bonds by adding H2O (OH and H are added)

Types of Biological Macromolecules

  • Carbohydrates

  • Lipids

  • Nucleic Acids

  • Proteins

Carbohydrates (Sugars)

  • Definition
      - Sugars consist of carbon, hydrogen, and oxygen in a 1:2:1 ratio represented as (CH2O)n

  • Structure
      - Common monosaccharide: Glucose

  • Cellulose Structure
      - Composed of long chains (microfibrils) providing structural support in plant cell walls

Simple Sugars (Monosaccharides)

  • Classification
      - Defined by the number of carbons and placement of functional groups
        - Triose: Glyceraldehyde (3 carbons)
        - Pentose: Ribose (5 carbons)
        - Hexose: Mannose (6 carbons)

  • Isomers
      - Position changes of –H and –OH groups lead to different properties
      - Glucose and Mannose: structural isomers, same formula, different arrangements

  • Carbonyl Group Reaction
      - Forming linear vs ring structures through interactions with other parts of the molecule

Ring Structures in Monosaccharides

  • Formation Process
      - Covalent bond between carbonyl group and -OH facilitates ring closure

  • Configurations
      - Two conformations: α (down position) and β (up position) affecting digestibility

Disaccharides and Polysaccharides

  • Disaccharide Formation
      - Two monosaccharides connected by glycosidic bonds (dehydration synthesis)
      - α Bonds: e.g., Maltose and Sucrose
      - β Bonds: e.g., Lactose

  • Polysaccharides
      - Composed of multiple monosaccharide units, can be branched or linear
      - Storage Polysaccharides:
        - Starch (plants) and Glycogen (animals) with α glycosidic bonds
      - Structural Polysaccharides:
        - Cellulose (plants), Chitin (arthropods) having β glycosidic bonds

Lipids

  • Characteristics
      - Generally non-polar, water-insoluble, and form a significant component of cell structures

  • Classification
      - Includes fats, oils, sterols, and phospholipids

Fats (Triglycerides/Triacylglycerols)

  • Composition
      - Comprised of three fatty acids linked to glycerol (3-carbon molecule with –OH groups)

  • Energy Density
      - Yield more energy per gram than carbohydrates due to C-H bonds

  • Storage Considerations
      - Hydrophobic nature: fats do not require water for storage, enhancing energy density

Fatty Acids

  • Variability
      - Lengths and saturation levels vary
        - Saturated: No double bonds; solid at room temperature (animal sources)
        - Unsaturated: One or more double bonds; liquid at room temperature (plant sources)
      - Monounsaturated: one double bond
      - Polyunsaturated: multiple double bonds

Phospholipids

  • Structure
      - Composed of glycerol, two fatty acids (hydrophobic), and a phosphate group (hydrophilic)

  • Properties
      - Amphipathic: having both hydrophilic and hydrophobic characteristics

Sterols

  • Cholesterol
      - Structure: Four interlocking hydrocarbon rings with a polar –OH group
      - Functionality
      - Maintains membrane fluidity, vital for synthesizing Vitamin D, steroid hormones, and bile salts

Proteins

  • Definition
      - Highly diverse macromolecules, functionally arranged polypeptides

  • Polypeptide Structure
      - Linear chain of amino acids
      - Proteins perform biological roles

Amino Acids

  • Structure
      - Composed of an amino group (-NH2), carboxyl group (-COOH), and a hydrogen atom bound to a central carbon
      - R represents variable side chains; 20 different amino acids classified into groups:
        - Nonpolar amino acids
        - Uncharged polar amino acids
        - Charged amino acids

Peptide Bonds

  • Definition
      - Linkage between two amino acids, created through a dehydration synthesis reaction between -COOH and –NH2 groups

Levels of Protein Structure

Primary Structure

  • Linear sequence of amino acids determined by covalent peptide bonds

Secondary Structure

  • Formation of α-helices and β-sheets stabilized by hydrogen bonds

Tertiary Structure

  • Three-dimensional shape of polypeptides, stabilized by various bonds (H-bonds, ionic, disulfide bridges)

Quaternary Structure

  • Assembly of multiple polypeptides; not all proteins have this level of structure

Chaperones

  • Role in protein folding and refolding of denatured proteins
      - Denaturation leads to loss of function; some structures resist denaturation
      - Chaperones can assist in renaturation

Nucleic Acids

DNA

  • Function
      - Encodes information for protein assembly

RNA

  • Function
      - Reads DNA information to guide protein synthesis

Nucleic Acid Structure

  • Made from nucleotides:
      - Five-carbon sugars (ribose or deoxyribose)
      - 1-3 phosphate groups
      - Nitrogenous bases (purines: adenine, guanine; pyrimidines: cytosine, thymine, uracil)
        - Ribose: C2’ has -OH
        - Deoxyribose: C2’ has -H

DNA Helix Structure

  • Double-stranded, formed via hydrogen bonding

  • Complementary base pairing rules: A-T and C-G

Polymerization of Nucleotides

  • Nucleotides linked via dehydration synthesis (phosphodiester bond)
      - Strands oriented 5’ to 3’ with two strands running anti-parallel

Central Dogma of Biology

  • Explores relationships among DNA, RNA, and proteins

  • Understanding structure is critical to grasp biological activity

Practice Questions

  • Identify complementary strand given a DNA sequence

  • Example: 5' ATTCGCGT 3' has complementary sequence 3' TAAGCGCA 5'