02/12 Lecture Chemistry and Carbon Chemistry

Introduction

  • Discussion ties into forthcoming checkpoint exam questions.

  • Introducing chemistry, specifically carbon chemistry, using a unique analogy involving snakes and skincare products.

Overview of Snake Venom and Its Properties

  • Snake Venom:

    • Containing proteins and enzymes designed to target prey.

    • Analogy used: Snake venom consists of components that break down moisture in the skin.

    • Hyaluronic Acid (HLA): Moisturizing agent found in skincare products.

    • Tightens skin, making it feel softer and less saggy.

    • Venom contains an inhibitor that breaks down hyaluronic acid, causing skin to become cracked and dry, which facilitates the penetration of venom.

Biological and Chemical Components of Venom

  • Key components of snake venom:

    • Proteases: Enzymes that break down proteins.

    • Phospholipases: Enzymes that break down cell membranes.

    • Neurotoxins: Affect nerve function.

    • Cardiotoxins: Affect heart function.

Connection to Carbon Chemistry

  • Venom's properties segue into the study of carbon chemistry, particularly its application in biological systems.

Review of Food Ingredients

  • Presentation of three food items: a peach, banana, and strawberry.

    • Misconception: Consumers often prefer foods with fewer ingredients labeled.

    • Actual strawberries consist of numerous components beyond sugar and water, including preservatives and omega fatty acids.

  • Concept of Chemophobia: Fear or mistrust of chemicals in everyday life.

    • Example: Potatoes contain solanine, but the quantity is negligible and generally safe.

    • Dosage Principle: Toxicity depends on quantity versus presence of a chemical.

    • Arsenic in rice: A high volume (50 grams) needed to be lethal, clients requiring 7 million servings highlight misconception.

Interactive Questions for Self-Assessment

  • Visual representation of atomic structure:

    • Atomic number of Element X: 13

    • Atomic mass: 30

    • Protons (p): 13, Electrons (e): 13, Neutrons (n): 17 (calculated as 30 - 13).

Electron Configuration and Ions

  • Electron configuration in shells:

    • 1st shell: 2 electrons

    • 2nd shell: 8 electrons

    • Remaining 3 electrons in the outer shell (3rd shell).

  • Discussion on Ions: Positive ions (cations) formed by losing electrons and negatively charged ions (anions) from gaining electrons.

Types of Chemical Bonds

  • Covalent Bonds: Sharing of electrons between atoms.

    • Non-polar covalent bond: Equal sharing of electrons.

    • Polar covalent bond: Unequal sharing due to one atom being more electronegative (e.g., water).

    • Oxygen has a strong pull on electrons, creating a bent molecular structure.

  • Ionic Bonds: Electrons transferred from one atom to another, resulting in charged ions.

Weak Bonds

  • Classification of weak bonds:

    • Hydrogen Bonds: Weak attractions between hydrogen atoms and electronegative atoms (e.g., in water).

    • Van der Waals Forces: Weak intermolecular forces between neutral molecules.

Interaction of Chemistry and Biology

  • Example: Drug development that mimics biological molecules (e.g., endorphins and morphine) showing the interrelation between chemistry and biological effects.

Water Properties

  • Water's Structure:

    • Polar molecule with strong covalent bonds within and weak hydrogen bonds between.

  • High Heat Capacity: Water changes temperature slowly; requires significant energy to alter temperature.

    • Example: Boiling water vs. heating metal pot.

  • Solvent Properties: Water as a solvent, crucial for biological reactions.

  • Cohesion and Adhesion: Water molecules sticking together (cohesion) and to other substances (adhesion), enabling processes like capillary action in plants.

Introduction to pH

  • pH scale definition: Represents the concentration of hydrogen ions (H+).

  • pH values in bodily fluids:

    • Stomach: pH 2 (acidic)

    • Small intestine: pH 7-8 (neutral to slightly basic).

  • Review of calculating pH: Using formulas for hydrogen and hydroxide concentrations.

    • Example calculation provided without specifics due to interactive teaching nature.

Buffer Systems

  • Buffers: Substances that maintain the pH levels in biological systems by absorbing excess acids or bases.

    • Example: Bicarbonate/carbonic acid buffer role in human blood.

    • Processes analogous to absorbing spills in real life:

    • Base spills neutralized by buffering acids.

    • Acid spills neutralized by buffering bases.

  • Conceptual Framework: Understanding how buffers operate without excessive technical jargon.

Transition to Carbon Chemistry

  • Recognition of the necessity of mastering carbon chemistry in the underpinning of biological macromolecules (proteins, lipids, carbohydrates, and nucleic acids).

  • Plan to explore various functional groups associated with carbon compounds.

Functional Groups in Carbon Chemistry

  • Importance of identifying and understanding the main functional groups:

    1. Hydroxyl Group (Alcohol): -OH; polar; general occurrence in alcohols.

    2. Carbonyl Group: C=O; exists in two forms:

    • Ketone: carbonyl is flanked by two carbon atoms.

    • Aldehyde: carbonyl is at the end of a carbon chain.

    1. Carboxyl Group: -COOH; acidic properties; acts similarly to COOH.

    2. Amino Group: -NH2; basic because it can gain a proton, forming a positive ion.

    3. Sulfhydryl Group: -SH; stabilizes proteins via disulfide bonds.

    4. Methyl Group: -CH3; nonpolar and bulkier, involved in hydrophobic interactions.

    5. Phosphate Group: -PO₄³⁻; negatively charged; linked to energy carriers like ATP.

  • Understanding the practical implications and functionalities of each group is essential for studying biological systems.