Chemistry Chapter 5: Chemical Bonding

Hands-On Summer-Break Research

• The Dobbie Smith Prizes offer a £1000 bursary for a 6-8 week summer research experience.
• Open to first-year natural sciences and related studies students at the University of Glasgow.
• Students must consult with a suitable member of staff, agree on a project, and then submit an application letter to the Undergraduate School.
• Details are available on the MOODLE site or from Prof. M. Blatt ([email protected]).
• The deadline for applications is 12:00 noon on Friday, 28th March 2025.

Atoms, Bonds, Water, and Membranes

• What are atoms?
  • Atoms are the smallest particles that retain the properties of an element (e.g., carbon, oxygen).
  • Atoms are made up of subatomic particles: protons, neutrons, and electrons.
  • Elemental properties are determined by the atomic number (number of protons).
  • Most atoms have equal numbers of protons and neutrons, but some isotopes may have additional neutrons (e.g., carbon-14).
• What are bonds?
  • Bonds form when atoms share or exchange electrons to achieve more stable (full) electron shells.
  • Different bonds (ionic, covalent) form depending on how atoms transfer or share electrons.
• Why is water a 'universal solvent'?
  • Water is a polar molecule (due to uneven electron distribution), meaning it has partial charges.
  • This polarity allows water to interact with other polar and charged molecules.
• What are membranes?
  • Membranes are phospholipid polymers (made of fatty acids, glycerol, phosphate, and a terminal group).
  • Phospholipids are amphipathic molecules, meaning they have both hydrophilic and hydrophobic parts. This leads to spontaneously assembling monolayers and bilayers in water.
  • Membranes are crucial for compartmentalization within cells, protecting components, and enabling signal transduction.

What Determines Chemical Bonding?

• The physical chemistry of an atom is determined by its electronic complement and the distribution of electrons around the nucleus.
• Electrons are arranged in electron shells and orbitals, which define the probability distribution of that electron within shells and orbitals.
• Electrons can move between shells, requiring an input or release of energy.

What Determines Bond Formation?

• Bonds form when atoms share or exchange electrons to achieve stable or filled electron shells.
• Stable atomic states possess paired electrons and filled electron shells.
• Atoms with unpaired electrons or partially-filled outer shells react to fill or empty their shells.
  • Examples are given using the Lewis-dot representation.

Electron Shells Define the Periodic Table of Elements

• Electron shells determine an elements position on the Periodic Table.
• Elements with similar electron configurations share similar chemical properties and reactivity.

Which Bonds are Important for Life?

• Ionic Bonds:
  • Form when atoms exchange electrons.
  • Result in oppositely charged ions that attract each other forming an ionic bond, like in sodium chloride.
  • Crucial in biological processes, such as forming crystals and for transporting ions within the cell.
  • Atomic valence differs from ionic valence.
• Covalent Bonds:
  • Form when atoms share electrons.
  • Examples are given, including hydrogen, water, and methane.
  • Different covalent bond types (single, double, triple bonds) are defined by the number of electrons shared.
• Hydrogen Bonds:
• Partial charge interactions between polar molecules.
  • Important for interactions between water molecules.
• Van der Waals Interactions:
  • Interactions that arise between atoms with locally induced dipoles, very close together.

Why is Water a 'Universal Solvent' for Life?

• Water molecules are polar; they possess a partial positive charge on hydrogen, and a partial negative charge on oxygen.
• These interactions allow water to readily dissolve polar (charged) and ionic compounds, creating hydration shells around them.
• This high polarity and tendency to form hydrogen bonds also explains water's cohesive and adhesive properties, high specific heat, and role as a good insulator.

Adhesive/Cohesive Forces in Wetting and Capillary Action

• Cohesion refers to the attraction between water molecules.
• Adhesion refers to the attraction between water molecules and other molecules.
• These forces are crucial for water transport and plant transpiration.
• Cohesive tension limits tree size due to how water moves upward through the stem

Biological Membranes Hold Charge

• Diffusion of Ions:
  • Driven by chemical and electrical gradients.
• Selective Diffusion:
  • Across semi-permeable membranes creates a small ion imbalance.
• The Nernst Equation:
  • Describes the equilibrium between chemical & electrostatic forces on charged molecules (ions).
• Electrode Use:
  • Microelectrodes can be used to measure membrane voltage.

Organelles and Their Locations

• A variety of organelles is present to separate different roles and protect various components, and include:
  • Nucleus
  • Rough endoplasmic Reticulum
  • Smooth endoplasmic Reticulum
  • Golgi
  • Mitochondria
  • Chloroplasts
  • Lysosomes
• These organelles are membrane-bound and contribute to both structural and functional compartmentalization.

What Are Membranes?

• Membranes are phospholipid bilayers.
• Phospholipids are amphipathic (hydrophilic head, hydrophobic tails).
• These molecules spontaneously form monolayers and bilayers in water.
• Simple detergents function as amphipathic molecules and are able to dissolve other polar and organic compounds in water.

Why Are Membranes Important?

• Membranes compartmentalize metabolic activities.
• Membranes separate and protect cellular components.
• Membranes provide a scaffold for signalling components.
• Membranes act as a medium for cellular energy generation (e.g., electron transport chain).
• Diffusion across membranes is important for transporting molecules between the inside and outside of cells.

What Do Diffusion Rates Mean?

• Diffusion rates across membranes are influenced by factors like distance, concentration gradients, and the size of the diffusing molecules.
• Diffusion is slower in thicker membranes than thinner ones.
• Limits cell & membrane size in biological materials.

Fluorescence - A New Window on the Cell

• Fluorescence occurs when a molecule absorbs light, causing electrons to move to an excited state.
• Energy is then released when the electrons return to their ground state, resulting in the emission of light at a longer wavelength.
• This enables cell analysis and is used to investigate details of cell structure and function

Green Fluorescent Protein (GFP)

• GFP is a protein that fluoresces when exposed to light.
• Genetically engineered GFP can be used to visualize cell processes and structures in plants and animals.

Endoplasmic Reticulum

• ER is a network of membranes within cells involved in protein synthesis and processing and other tasks. This network is highly mobile within the cell.
• ER is interconnected by membranes.

Golgi

• Golgi is organized in stacks and/or networks of membrane sacs that process, modify, and transport proteins.
• Similar to ER, the Golgi also appears to be highly mobile within the cell.
• Both plant and animal cells have similar Golgi structures.

Chloroplasts

• Chloroplast are plant organelles that carry out photosynthesis.
• Chloroplasts and mitochondria have double membranes, suggesting a symbiotic origin.
• Chloroplasts have their own independent division and replication mechanisms.
• Chloroplasts can communicate within cells by creating structures called Stromules.

Membrane Structure and Function

• Membranes are phospholipid polymers that spontaneously form monolayers and/or bilayers in water.
• Membranes function as physical barriers and support structures within the cell.
• Organelles, including ER, Golgi, mitochondria and chloroplasts are membrane-enclosed compartments crucial for eukaryotic cell function.