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IB DP Biology Study Notes

1.1.2 Molecular Structure and Bonding

The essence of many chemical and biological phenomena lies in molecular structure and bonding. A prime exemplar is the humble water molecule, which due to its unique bonding character, governs a myriad of life-sustaining properties.

Covalent Bonding in Water Molecules

Water, represented as H₂O, is an intriguing molecule with fascinating properties attributed to its specific molecular bonding.

Understanding Covalent Bonding

  • Covalent bonds arise when two atoms pool their electrons to ensure both have a full outer electron shell, facilitating stability.
  • In the case of water:
    • The oxygen atom needs two more electrons to complete its outer shell.
    • Each hydrogen atom offers one electron, leading to two covalent bonds being formed in one water molecule.
  • It's crucial to differentiate between ionic bonds (where electrons are transferred) and covalent bonds (where electrons are shared).
Diagram of a water molecule showing covalent bonding.

Image courtesy of Daviewales

Delving into Polarity

  • Atoms involved in covalent bonding are not always equal partners.
  • Electronegativity is a measure of how strongly an atom can attract shared electrons in a bond.
    • Oxygen, being more electronegative than hydrogen, exerts a stronger pull on the shared electrons.
  • The unequal sharing results in a polar covalent bond.
    • Oxygen becomes slightly negatively charged (δ-).
    • Hydrogen becomes slightly positively charged (δ+).
  • Consequently, water has a distinct molecular polarity – one end of the molecule is more positive, while the other is more negative.
Diagram of water molecule showing polar covalent bond.

Image courtesy of Pradana Aumars

Unpacking Polarity's Consequences

The inherent polarity in water molecules dictates a series of remarkable behaviours and properties.

Cohesion and Surface Tension

  • Water molecules attract one another, a phenomenon termed cohesion.
    • This gives rise to a high surface tension, making it difficult for small organisms to break the water surface.
    • It also leads to the formation of droplets when water is placed on certain surfaces.

Adhesion and Capillary Action

  • The attraction of water molecules to other substances is known as adhesion.
    • For instance, water adhering to glass causes menisci to form in graduated cylinders.
    • This adherence causes capillary action, allowing water to move through narrow spaces against gravity, facilitating processes like the ascent of water in plants.
Cohesion, adhesion and surface tension.

Image courtesy of Quizlet

Solvent Properties

  • Water's polarity renders it an "universal solvent".
    • It can dissolve a vast array of substances, especially ionic compounds and other polar molecules.
    • In biological systems, this enables various chemical reactions and processes vital for life.

Hydrogen Bonds: A Special Attraction

The story of water's uniqueness doesn't end with its polarity; the intrigue continues with hydrogen bonding.

Nature of Hydrogen Bonds

  • Arising due to water's polarity, the δ+ hydrogen of one molecule is magnetically drawn to the δ- oxygen of another.
  • They're classified as intermolecular forces, i.e., forces between different molecules, as opposed to intramolecular forces within a molecule.
  • Though they're weaker than covalent bonds, hydrogen bonds are still remarkably robust compared to other intermolecular forces.
Diagram of water molecules with covalent and hydrogen bonds labelled.

Image courtesy of CNX OpenStax

Impacts on Physical Properties

  • Melting and Boiling Points: Water's relatively high melting and boiling points are a direct consequence of hydrogen bonding. Considerable energy is required to break multiple hydrogen bonds when changing states.
  • Anomalous Expansion: Unlike most substances, water expands when it freezes. This is because the formation of hydrogen bonds creates a hexagonal lattice in ice, making it less dense than liquid water. Hence, ice floats.

Biological Significance of Water's Properties

Water's unique molecular structure and bonding translate to numerous biologically significant properties.

Cellular Context

  • The polar nature of water makes it an excellent medium for biochemical reactions within cells. Enzymes, substrates, and cellular machinery all function optimally in aqueous environments.

Transportation

  • Water's cohesiveness and adhesive properties assist in the movement of blood in animals and sap in plants, ensuring nutrients and waste materials are efficiently transported.

Thermoregulation

  • Given its high specific heat capacity, water acts as a thermal buffer. This means water can absorb or release a substantial amount of heat without undergoing significant temperature changes. This property is crucial for maintaining homeostasis in living organisms.

FAQ

The viscosity, or "stickiness", of a liquid refers to its resistance to flow. In water, the presence of hydrogen bonds causes molecules to "stick" together more than they would in the absence of such bonds. However, because hydrogen bonds are transient and continually breaking and reforming, water remains relatively less viscous than many other liquids with strong intermolecular attractions. This balance ensures that water flows easily, yet with enough viscosity to support capillary action. It's this property that facilitates efficient transportation of water in plant xylem and blood in animal capillaries.

Water's high heat of vaporisation means that it requires a significant amount of energy to transform it from liquid to gas. For living organisms, especially larger animals like mammals, this property is crucial for thermoregulation. When animals perspire, the water in sweat requires a substantial amount of heat to evaporate. This heat is taken from the animal's body, leading to a cooling effect. For plants, the high heat of vaporisation helps in maintaining cell turgor and structure. It also ensures that plants don't lose excessive amounts of water during transpiration, supporting their survival in varying conditions.

Cell membranes are primarily composed of phospholipids, which have a hydrophilic (water-attracting) head and two hydrophobic (water-repelling) tails. The polarity of water influences how these molecules organise themselves. In an aqueous environment, the hydrophilic heads face outwards, interacting with the water, while the hydrophobic tails orient themselves inwards, away from the water. This results in the formation of a bilayer, with the tails protected inside and the heads exposed outside. This bilayer structure serves as a barrier, regulating the passage of substances in and out of the cell, and is fundamental to the integrity and functionality of cells.

Yes, substances that do not form hydrogen bonds can still dissolve in water. While hydrogen bonding is one of the primary reasons many substances dissolve in water, other types of interactions, like dipole-dipole and ion-dipole interactions, can also promote solubility. For instance, alcohols with short carbon chains, like methanol and ethanol, don't primarily dissolve due to hydrogen bonding with water but rather due to their polar nature, which allows them to mix well with water. However, as the carbon chain lengthens in alcohols, their solubility in water decreases, illustrating that while hydrogen bonding is influential, it isn't the sole determinant of a substance's solubility in water.

When water interacts with ionic compounds, its polarity plays a pivotal role in the dissolution process. The positive and negative ions in the ionic compound are attracted to the polar ends of the water molecules. The partially negative oxygen atoms surround and solvate the positive ions, while the partially positive hydrogen atoms surround and solvate the negative ions. This process is called hydration. It helps to stabilise the ions in solution and counteracts the ionic bond holding them together, leading to the ionic compound dissolving in water. This exceptional ability of water to dissolve various ionic compounds is central to its role as a solvent in biological systems.

Practice Questions

Describe the significance of polarity in water molecules and explain how this leads to hydrogen bonding.

Water molecules have inherent polarity due to the unequal sharing of electrons between the oxygen and hydrogen atoms. Oxygen, being more electronegative than hydrogen, attracts the shared electrons more closely. This results in a partial negative charge on the oxygen end and a partial positive charge on the hydrogen ends. This polarity causes the partial positive hydrogen of one water molecule to be attracted to the partial negative oxygen of another molecule, leading to the formation of hydrogen bonds. These hydrogen bonds, although weaker than covalent bonds, are significant because they influence many of water's unique properties, including its solvent abilities and high heat capacity.

Elaborate on how the properties of water resulting from hydrogen bonding affect its biological significance.

Hydrogen bonds give water several distinctive properties that have profound biological implications. Firstly, water's high boiling and melting points, relative to other molecules of its size, are due to the energy required to break these bonds. This allows water to remain in a liquid state in most environments on Earth, serving as a universal medium for biochemical reactions. Secondly, the lattice structure formed by hydrogen bonds in ice makes it less dense than liquid water, ensuring ice floats, which plays a pivotal role in aquatic ecosystems by insulating the water below. Additionally, the cohesive and adhesive properties of water, stemming from hydrogen bonding, are vital for the transportation of nutrients and waste in organisms.

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