Bio II Honors Notes

Chemistry and Biology Connection

1) Elements and Molecules

  • Chemistry provides the foundational understanding of elements and molecules fundamental to biological systems.

2) The pH Scale

  • The pH scale measures acidity and alkalinity, crucial for biochemical reactions.

3) Chemical Bonding

a) Ionic Bonds

  • Ionic bonds involve the transfer of electrons, resulting in charged atoms (ions) that attract each other.

b) Covalent Bonds

  • Covalent bonds involve the sharing of electrons between atoms.

4) Chemical Reactions

  • Chemical reactions are ubiquitous in biological processes.

a) Photosynthesis Process

  • The equation for photosynthesis is:
    6CO<em>2+6H</em>2O+extLight=C<em>6H</em>12O<em>6+6O</em>26CO<em>2 + 6H</em>2O + ext{Light} = C<em>6H</em>{12}O<em>6 + 6O</em>2

b) Understanding Enzymes and Catalysts

  • Enzymes are catalysts that speed up biochemical reactions. Understanding these is essential for grasping how reactions facilitate biological processes.

c) Importance of Chemical Reactions

  • Understanding chemical reactions is critical as all biological processes occur through biochemical reactions that allow for energy acquisition, metabolism, and homeostasis.

  • Biological systems, such as cellular respiration and photosynthesis, rely on biochemical reactions that involve equilibrium and reversible reactions.

  • Without a grasp of chemical reactions, explaining energy acquisition and the maintenance of internal conditions crucial for life becomes impossible.

5) Polarity (Polar vs. Nonpolar)

a) Electron Sharing and Partial Charges

  • In polar molecules, atoms do not share electrons equally, resulting in partial electric charges.

b) Effects of Polarity

  • Polarity leads to slight attractions, affecting properties like surface tension, adhesion, and cohesion.

6) The Polarity of Water / Properties of Water

a) Importance of Water's Polarity

  • Water's unequal charge distribution enables hydrogen bonding between water molecules.

b) Cohesion and Adhesion

  • These properties support capillary action and nutrient transport in plants.

c) High Specific Heat and Heat of Vaporization

  • Water has a high specific heat, stabilizing internal temperatures necessary for homeostasis.

d) Universal Solvent Characteristics

  • Water’s polarity allows it to dissolve polar substances, facilitating biochemical reactions.

e) Hydrogen Bonding and Density

  • The hydrogen bonding in water makes ice less dense than liquid water, allowing survival of marine life in cold environments.

7) Organic Molecules in Biology

a) Definition and Overview

  • Organic molecules contain carbon and usually hydrogen, forming the basis of biological structure and function.

b) Biomolecules of Cells

  • Main biomolecules include carbohydrates, lipids, proteins, and nucleic acids.

    • Monomer: The basic unit (e.g., amino acids for proteins).

    • Polymer: Larger molecules formed by monomers (e.g., proteins from amino acids).

    • Example: Amino acids (monomers) combine to form proteins (polymers).

c) Carbohydrates

  • Monomer: Monosaccharide

  • Polymer: Polysaccharide

  • Elements: Carbon, Hydrogen, Oxygen (CHO) in a 1:2:1 ratio

  • Shape: Carbon rings

  • Examples: Grains

  • Major Functions: Energy source, structural roles in cells.

8) Carbohydrate Varieties

a) Types of Carbohydrates

  • Monosaccharides: Single sugar units, also called simple sugars (e.g., pentose vs. hexose).

  • Disaccharides: Comprise two monosaccharides joined via dehydration synthesis.

    • Examples:

    1. Lactose (galactose + glucose)

    2. Sucrose (glucose + fructose)

    3. Maltose (two glucose molecules)

  • Polysaccharides: Multiple monosaccharide units.

    • Examples:

    1. Starch: Energy storage in plants

    2. Glycogen: Energy storage in animals

    3. Cellulose: Structural component in plant cell walls

    4. Chitin: Structural component in fungi and exoskeletons of some animals.

9) Lipids

a) Definition and Composition

  • Monomer: No true monomer, primarily glycerol and fatty acid chains.

  • Polymer: Not applicable.

  • Elements: Carbon, Hydrogen, Oxygen (CHO)

  • Shape: Long carbon chains.

  • Characteristics: Large, nonpolar, insoluble in water.

  • Major Functions:

    • Long-term energy storage

    • Structural components of cell membranes

    • Heat and insulation

    • Cell communication and regulation

    • Protection

b) Varieties of Lipids

  • Types include:

    • Fats

    • Oils

    • Phospholipids

    • Steroids

    • Waxes

  • Triglycerides: A form of long-term energy storage, composed of three fatty acids.

c) Fatty Acids

  • Saturated: No double bonds between carbons; typically solid at room temperature (e.g., butter, lard).

  • Unsaturated: One or more double bonds between carbons, generally liquid at room temperature (e.g., plant oils).

10) Phospholipids

a) Structure

  • Similar to triglycerides but composed of one glycerol molecule linked to two fatty acids and a modified phosphate group.

b) Properties

  • Fatty acid tails are nonpolar and hydrophobic while the phosphate group head is polar and hydrophilic.

c) Function

  • Essential for forming plasma membranes of cells.

11) Proteins

a) Definition

  • A protein is a polypeptide fold into a specific shape essential for its function.

b) Composition and Structure

  • Monomer: Amino acids

  • Polymer: Polypeptides

  • Elements: Carbon, Hydrogen, Oxygen, and Nitrogen (CHON)

  • Shape: 4 Levels of structures involved in protein folding: Primary, Secondary, Tertiary, Quaternary.

c) Formation and Function

  • Proteins are polymers linked by peptide bonds (covalent bonds between amino acids).

  • Peptides consist of two or more amino acids; polypeptides are longer chains.

  • Denaturation occurs when proteins lose their shape due to chemicals, changes in pH, or high temperatures, impairing their function.

d) Levels of Protein Structure

  1. Primary Structure

  2. Secondary Structure

  3. Tertiary Structure

  4. Quaternary Structure

e) Function

  • Proteins serve various functions, including:

    • Enzymatic activity (metabolism)

    • Structural support (keratin, collagen)

    • Transport (membrane proteins, hemoglobin)

    • Defense mechanisms (antibodies)

    • Regulation (hormonal functions)

    • Motion and movement (microtubules)

12) Amino Acids

a) Overview

  • There are 20 common amino acids, differing by their R (variable) groups, which can vary in complexity.

b) Protein Synthesis

  • Proteins undergo dehydration synthesis where water is removed to form dipeptides, leading to polypeptide chains (proteins).

13) Nucleic Acids

a) Definition

  • Monomer: Nucleotide

  • Polymer: DNA and RNA

  • Elements: Carbon, Hydrogen, Oxygen, Nitrogen, and Phosphorus (CHONP)

b) Function and Structure

  • Functions: Storage and transmission of genetic information.

  • Examples: DNA (Deoxyribonucleic acid) & RNA (Ribonucleic acid)

c) Composition of Nucleotides

  • Each nucleotide consists of three components:

    • A phosphate group

    • A pentose sugar

    • A nitrogen-containing (nitrogenous) base

d) Nucleotide Structure

  • Nucleotides link through dehydration synthesis to form a linear molecule (strand) of nucleotides.

e) ATP

  • ATP is an example of nucleotide structure with significant roles in energy transfer.

14) Functional Groups

a) Definition

  • Functional groups are clusters of specific atoms bonded to the carbon skeleton, determining the chemical reactivity and polarity of organic molecules.

b) Examples

  • The R group in amino acids varies and alters the properties of the molecule.

15) Isomers

a) Definition

  • Isomers are molecules that share the same chemical formula but have different atomic arrangements.

b) Types of Isomers

  1. Structural Isomers: Different covalent arrangements of their atoms.

  2. Geometric Isomers: Same covalent arrangements but differing spatial arrangements.

  3. Enantiomers: Isomers that are mirror images of one another.

c) Note

  • Diastereomers, Stereoisomers, conformers, and rotamers are less critical for basic understanding.