Biological Molecules: Water Structure and Properties Lecture Notes

Reference Materials and Recommended Textbooks

• Core References:
  • Biology by Stephen Nowick.
  • Modern Biology.
  • Biology: 11th Edition.
  • Biology: AP Edition.
  • Biology (8th Edition) by Solomon, E.P., L.R. Berg, and D.W. Martin, published by Thomson Learning, Inc., 2002 (International Student Edition).

Course Etiquette and Professional Reminders

• Punctuality: Students are expected to arrive on time.
• Handphone Policy: Mobile phones must be switched OFF or set to SILENT during lectures.
• Focus: Complete attention is required during instruction.
• Attendance: Attendance at lectures is mandatory/compulsory.
• Preparedness: Students must bring their books to every session.

Effective Lecture Note-Taking Strategies

• Fundamental Goal: The objective of a student is to be able to listen to the professor effectively while capturing critical points.
• The Cornell Two-Column System:
  • Keywords: Left column for main topics or terms (e.g., "Solids", "Liquids", "Gases").
  • Notes: Right column for specific details (e.g., "Gases do not have a definite shape or volume").
  • Summary: A section at the bottom to insert a synthesis of the lecture after the class ends.
• Selection and Analysis:
  • Only record the most important points.
  • Highlight references mentioned by the lecturer for future follow-up.
  • Listen for case studies and identifying complementary examples.
  • Document all words or technical terms not immediately understood for later research.
• Organization:
  • Maintain a dedicated file for each module.
  • Use a lecture notes cover sheet to keep materials organized.
  • Rewrite or "write up" notes after the lecture if the original version is messy or incomplete.
  • Develop a personal shorthand system using abbreviations.
• Value of Note-Taking:
  • Useful Record: Retains important points and identifies information sources for future use.
  • Writing Assistance: Helps ideas flow; assists in planning by showing available information; allows for renumbering and reorganizing.
  • Conceptual Understanding: Focusing on info selection forces you to think about how concepts fit together.
  • Memory Retention: Briefly summing things up aids long-term memory; the physical act of writing aids motor memory; visual patterns are more memorable.
  • Exam Revision: Material is well-organized and easier to recall if more info is already in memory.

Layout Typology

• Picture Window: Uses a large dominant piece of art on top, followed by a headline, body copy, and finally the product signature. It is noted as the simplest layout.
• Other Layout Styles:
  • Copy Heavy
  • Frame
  • Bleed
  • Grid
  • Mondrian
  • Panel
  • Mortice
  • Silhouette
  • Angular
  • Jumble

Chapter 1: Biological Molecules Overview

• Chapter Outlines:
  • 1.1 Water
  • 1.2 Carbohydrates
  • 1.3 Lipids
  • 1.4 Proteins
  • 1.5 Nucleic Acids

1.1 The Physical and Chemical Structure of Water ($H_2O$)

• Abundance: Water is a very common compound in living organisms. In the human body, water accounts for approximately $75\%$ of total body weight.
• Atomic Composition: A water molecule consists of one oxygen atom and two hydrogen atoms.
• Intramolecular Bonding:
  • The atoms are held together by strong covalent bonds formed through the sharing of electrons.
  • Specifically, the two hydrogen atoms share electrons with the oxygen atom.
• Molecular Geometry:
  • The three atoms form a triangle (V-shape) rather than a straight line.
  • The bond angle between the two hydrogen atoms is exactly $104.5^\circ$.
• Polarity and Electronegativity:
  • Electronegativity: Oxygen is more electronegative than hydrogen, meaning it attracts the shared electrons more strongly.
  • Charge Distribution: The water molecule is electrically neutral overall, but because the hydrogen atoms are on the same side, charge is not evenly distributed.
  • Partial Charges: The oxygen atom has a net partial negative charge ($\delta-$), and the hydrogen atoms have a net partial positive charge ($\delta+$).
  • Polarity: Because of the unequal sharing of electrons, water is defined as a polar molecule.
• Intermolecular Bonding (Hydrogen Bonds):
  • The $\delta+$ hydrogen atoms of one water molecule are attracted to the $\delta-$ oxygen atoms of adjacent water molecules.
  • These attractive forces are called hydrogen bonds.
  • Strength: Hydrogen bonds are weaker than covalent bonds but strong enough to hold water molecules together collectively.
  • Capacity: Each water molecule can form a maximum of four hydrogen bonds with surrounding water molecules.

1.2 Chemical Interactions: Hydrophilic vs. Hydrophobic

• Hydrophilic (Water-loving): Polarity allows water to attract other polar molecules or ionic substances. Examples include sugar and salt ($NaCl$).
• Hydrophobic (Water-hating): Water repels non-polar molecules. An example is oil, which does not mix with water.

1.3 Essential Properties of Water and Physiological Roles

1. Universal Solvent

• Mechanism: Water is a powerful solvent for polar and ionic substances. Its ability to form hydrogen bonds allows it to surround ions (hydration) and dissociate them (e.g., separating $Na^+$ and $Cl^-$ ions in a salt crystal).
• Physiological Roles:
  • Acts as a medium for chemical reactions.
  • Functions as a transport solvent in animal blood and plant vascular tissues (xylem and phloem).
  • Provides substrates for metabolic reactions like the photolysis of water in photosynthesis and hydrolysis in digestion.
  • Interacts with hydrophobic macromolecules like proteins and nucleic acids to maintain lipoprotein membrane structures.

2. Low Viscosity

• Mechanism: Small molecular size allows molecules to slide over each other easily. Hydrogen bonds are continuously forming and breaking.
• Physiological Roles:
  • Lubrication: Found in mucus (snail/earthworm movement), tears (eye protection), saliva, and amniotic fluid.
  • Transport: Enables blood plasma, lymph, and plant sap (xylem/phloem) to flow easily.
  • Diffusion: Acts as an efficient medium for the diffusion of substances.

3. High Specific Heat Capacity

• Definition: The amount of heat required to raise the temperature of $1\,kg$ of water by $1\,K$.
• Value: $4200\,kJ\,K^{-1}\,kg^{-1}$ (also cited as $4.2\,kJ\,K^{-1}\,kg^{-1}$ in some contexts).
• Mechanism: Significant energy is required to break the hydrogen bonds that restrict molecular movement.
• Physiological Roles:
  • Allows organisms to maintain a stable internal body temperature despite environmental fluctuations.
  • Protects life from rapid, damaging temperature changes.

4. High Latent Heat of Vaporization

• Definition: The heat energy required to transform liquid water into vapor.
• Value: $2260\,kJ\,kg^{-1}$.
• Mechanism: High energy is needed to break the hydrogen bonds linking individual molecules for evaporation to occur.
• Physiological Roles:
  • Cooling Effect: Evaporation of sweat cools body surfaces. For example, evaporating just $1\,g$ of water can cool $540\,g$ of the body by $1^\circ C$.
  • Moisture Retention: Helps cells preserve water by resisting excessive evaporation.
  • Alternative Cooling: Animals that do not sweat may bathe or wet themselves to utilize this cooling property.

5. Maximum Density at $4^\circ C$

• Mechanism: Water reaches its highest density at $4^\circ C$. As it cools toward $0^\circ C$ to freeze, the molecules form a crystalline lattice where they are spaced further apart.
• Behavior of Ice: Ice is less dense than liquid water and floats on the surface.
• Physiological Roles:
  • Floating ice acts as an insulating layer for the water below.
  • Prevents lower depths from freezing, allowing aquatic organisms in ponds and lakes to survive winter in liquid water.

6. High Surface Tension (Cohesion and Adhesion)

• Cohesion: Attraction between like molecules (water attracting water). This creates high surface tension.
• Adhesion: Attraction between different substances (water attracting polar surfaces).
• Capillary Action: Water adheres to the surfaces of narrow tubes (like xylem) and is drawn up in long, continuous columns without breaking.
• Physiological Roles:
  • Enables the transport of water from roots to the tops of tall trees against gravity.
  • Supports "surface skimmers" (e.g., insects like the water strider); the insect's waxy cuticle prevents wetting, and its mass is insufficient to break the surface tension reinforced by hydrogen bonding.

Questions & Discussion

• Question: Why is water a polar molecule?
  • Answer: It is due to the difference in electronegativity between hydrogen and oxygen, leading to a slight negative charge on oxygen and a slight positive charge on hydrogen.
• Revision Exercise:
  • Task 1: Draw the structure of a water molecule.
  • Task 2: How many maximum numbers of water molecules can attach to one water molecule?
    • Answer: 4.
  • Task 3: Draw and label the structure showing these attachments.
    • Requirement: Must label covalent bonds ($104.5^\circ$ angle) and hydrogen bonds.