BSC1005 Lecture #3

Essential Chemistry for Biology

Chapter 2 Overview

  • Elementary concepts and terminologies in chemistry relevant to biology.

Chemistry Terminology

  • Element: Substance that cannot be broken down or converted to another substance by chemical means.

  • Atom: Basic structural unit of matter.

  • Molecule: Two or more atoms joined by chemical bonds (can be similar or different); examples include:

    • Water: H₂O

    • Oxygen gas: O₂

  • Compound: A molecule where the types of atoms are different; examples include:

    • Carbon dioxide: CO₂

    • Propane: C₃H₈

Basic Components of an Atom

  • Elements determined by the number of protons (referred to as the atomic number).

  • Atomic weight of an atom is the sum of its protons and neutrons.

  • In a neutral atom, the number of protons is equal to the number of electrons. Atoms can form ions (charged atoms) during chemical reactions.

  • Protons and neutrons are located in the nucleus, while electrons surround the nucleus in shells.

Periodic Table of Elements

  • The periodic table categorizes elements based on their atomic number and properties.

    • Example Elements:

    • Lithium (Li): Atomic Number 3, Mass 6.941

    • Sodium (Na): Atomic Number 11, Mass 22.990

    • Carbon (C): Atomic Number 6, Mass 12.011

    • Oxygen (O): Atomic Number 8, Mass 15.999

  • Importance of certain elements in biological molecules: Carbon (C), Hydrogen (H), Oxygen (O), Nitrogen (N), Phosphorus (P), Sulfur (S).

Isotopes

  • Isotope: Variants of a given element that differ in their number of neutrons while having the same number of protons.

  • Carbon Isotopes Example: All carbon isotopes have 6 protons but differ in neutrons.

  • Radioactive Isotopes: Some isotopes (like Carbon-14) are radioactive and decay over time, known as their half-life. Useful in radiocarbon dating.

Elemental Composition of the Human Body (by Weight)

  • Oxygen (O): 65.0%

  • Carbon (C): 18.5%

  • Hydrogen (H): 9.5%

  • Nitrogen (N): 3.3%

  • Calcium (Ca): 1.5%

  • Trace Elements: < 0.01% including Boron (B), Manganese (Mn), etc.

Health Implications of Trace Elements

  • Deficiencies of trace elements can lead to various health conditions. Example symptoms of anemia:

    • Skin: Pallor, Coldness, Yellowing

    • Respiratory: Shortness of breath

    • Muscular: Weakness

    • Central Nervous System: Fatigue, Dizziness

    • Blood Vessels: Low blood pressure

    • Heart: Palpitations, Rapid heart rate

Chemical Behavior of Elements

  • Electron configuration affects chemical behavior. Electrons are organized in shells.

  • Octet Rule: Atoms prefer 2 or 8 electrons in their outer shell for stability.

  • Noble Gases: Do not react; each has a full outer shell (Exceptional elements: He (2 e-), Ne, Ar, Kr, Xe, Rn (8 e-)).

Chemical Reactions

  • Thousands of reactions occur in cells necessary for life. Metabolism is the sum of all these reactions.

Electron Configuration Example: Nitrogen (N)

  • Atomic Mass: 14.0067

  • Electron configuration: 2,5

    • Protons: 7

    • Neutrons: 7

    • Electrons: 7 (neutral atom)

Atoms and Chemical Bonds

  • Atoms strive for a stable electronic configuration, achieving this by forming chemical bonds.

    • Types of Bonds:

    1. Ionic Bonds: Formed through electron transfer resulting in charged ions.

    2. Covalent Bonds: Atoms share one or more pairs of electrons; stronger than ionic bonds. Example: water formation (H₂O).

Polar and Non-Polar Covalent Bonds

  • In a non-polar covalent bond, electrons are shared equally (e.g. O₂).

  • In polar covalent bonds, electrons are shared unequally due to differences in electronegativity (e.g. H₂O).

    • Electronegativity: The tendency of an atom to attract shared electrons when forming a bond.

Hydrogen Bonds and Water Properties

  • Water molecules attract one another, forming hydrogen bonds, contributing to:

    • Cohesion: Water molecules sticking to one another.

    • Adhesion: Water sticking to other polar surfaces.

  • Water has a high degree of surface tension.

  • Water as a universal solvent: Dissolves numerous substances due to its polarity.

pH Scale and Biological Relevance

  • Water can dissociate into hydroxide ions (OH⁻) and hydrogen ions (H⁺).

  • The pH scale measures acidity/basicity, ranging from 0 (acidic) to 14 (basic), with water approximately neutral at 7.

  • Biological processes are sensitive to pH changes; optimal pH varies for different enzymes.

Ocean Acidification and Its Effects

  • The ocean absorbs atmospheric CO₂, forming carbonic acid which affects carbonate ion concentrations critical for marine life.

  • Increased CO₂ leads to lower carbonate ion concentrations, impacting organisms requiring calcium structures to survive.

Temperature Moderation by Water

  • Water has a high specific heat, allowing it to absorb significant energy without large temperature changes, crucial for moderating global temperatures.

Density of Ice vs Water

  • Ice is less dense than liquid water due to the hydrogen bonding structure, which causes it to float.

  • If ice sank, water bodies would freeze from the bottom up, significantly disrupting aquatic ecosystems.

Potential Causes of Sea Level Rise

  1. Glacier and Icecap Melting: Potential rise of 0.5m.

  2. Thermal Expansion of Oceans: Major contributor to 20th-century sea level rise.

  3. Melting of Ice Sheets: Could result in significant sea level increases (e.g. East Antarctic ice sheet could raise levels by 64m).

Conclusion and Upcoming Topic

  • Next class will cover "Chapter 3: The molecules of Life".