Chapter 1-6: Chemistry of Life, Water, and Macromolecules
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Today’s topic: the chemistry of life
Focus on atoms, molecules, and the natural biomolecules essential to life.
We’ll connect to prior content about atoms forming molecules and the types of bonds that hold things together.
Atoms, elements, and the periodic table in biology
Not all elements are equally relevant to life; we commonly focus on a subset of elements essential for biology.
The instructor uses a class activity about identifying charges of subatomic particles to reinforce atomic structure and bonding.
Important charge facts observed in the activity:
Subatomic particles carry charges: protons are positive, neutrons are neutral, electrons are negative.
An atom’s nucleus contains protons and neutrons; electrons form the electron cloud around the nucleus.
Basic atomic structure and how atoms form matter
Atoms are the most basic units of elements; atoms combine to form molecules and compounds.
Bonds between atoms can be covalent, ionic, or interactions such as hydrogen bonds and Van der Waals forces.
Covalent vs ionic bonds; polarity concepts
Covalent bonds involve sharing electrons between atoms; they can be nonpolar (even sharing) or polar (unequal sharing).
Polar covalent bonds create partial positive and negative regions within a molecule (e.g., water).
Nonpolar covalent bonds have an overall net neutral charge distribution (no distinct positive/negative ends).
Ionic bonds: atoms transfer electrons to form ions (cation vs anion) which then attract each other.
Cation: positively charged ion (loss of electrons).
Anion: negatively charged ion (gain of electrons).
Intermolecular forces (not true bonds): hydrogen bonds and Van der Waals interactions help hold molecules together without sharing electrons.
Water as a central example of biology chemistry
Water is polar due to uneven electron distribution between hydrogen and oxygen.
Water formula: \mathrm{H_2O}
Key properties of water discussed:
Ice is less dense than liquid water, allowing ice to float in liquid water.
Water is an excellent solvent, dissolving many substances (e.g., sugars, salts).
Water has high heat capacity and a high heat of vaporization, helping regulate temperature and energy storage.
Water exhibits cohesion (water–water attractions) and adhesion (water–other surfaces), largely due to hydrogen bonding.
Hydrogen bonds vs covalent bonds:
Hydrogen bonds are transient attractions between polarized molecules (e.g., between water molecules) and are not covalent bonds.
Visualizing water behavior and surface phenomena
Surface behavior of water can allow certain organisms to traverse water surfaces (e.g., small insects) due to cohesion at the surface.
Water’s polarity enables dissolving and transporting substances (e.g., sugars) in biological fluids like blood plasma.
Water’s heat capacity contributes to climate stability by moderating temperature changes in oceans and bodies of water.
Recap of key water-related terms and concepts
Cohesion: water molecules sticking to each other.
Adhesion: water molecules sticking to other substances.
Surface tension: a consequence of cohesive forces at the air–water interface.
Solvent properties: water surrounds solutes, enabling transport (e.g., sugar in blood).
Carbon and the backbone of biomolecules
Carbon’s bonding versatility is central to life: it can form up to four covalent bonds, enabling long chains and complex structures.
Carbon–carbon bonds can be single, double, or triple bonds, influencing molecular strength and geometry.
The small size and bonding flexibility of carbon allow the formation of large macromolecules with diverse functions.
Macromolecules: overview and key examples
Macromolecules are large, often polymeric molecules built from repeating monomer units.
Major classes discussed: carbohydrates, lipids, proteins, and nucleic acids.
Carbohydrates
Structure and roles:
Made up of carbon, hydrogen, and oxygen in various arrangements; often ring-shaped in biological contexts.
Functions include short-term energy storage, structural roles, and signaling.
Examples mentioned: glucose-based polymers such as glycogen (animal storage) and cellulose (structural in plants).
Relationship to energy and signaling: carbohydrates help provide quick energy and participate in cell signaling and membrane structure.
Lipids
General features:
Lipids are hydrocarbons and are typically nonpolar, making them hydrophobic.
Principal lipid types mentioned include cholesterol, steroid hormones, waxes, triglycerides, and phospholipids.
Amphipathic nature of phospholipids:
Phospholipids have hydrophobic (water-fearing) tails and hydrophilic (water-loving) heads.
Arrangement in membranes: the hydrophobic tails face inward (inside the bilayer), while the hydrophilic heads face outward, creating a selective barrier.
Implications for cell membranes: this amphipathic organization explains selective permeability and membrane structure.
Proteins
Diversity and roles:
Humans express tens of thousands of different proteins with diverse functions (enzymatic activity, protection, signaling, structural roles, etc.).
Protein structure levels:
Primary structure: the linear sequence of amino acids (polypeptide chain).
Secondary structure: local folding patterns within the chain (e.g., alpha helices, beta sheets).
Tertiary structure: the overall three-dimensional shape of a single polypeptide (often described as a folded, noodle-like form).
Quaternary structure (mentioned as another possible level): arrangement of multiple polypeptide chains into a functional protein complex.
Bonding in proteins:
The peptide bonds between amino acids are covalent bonds (sharing of electrons along the backbone).
Nucleic acids
Nucleotides and polymers:
Nucleotides are the monomer units that covalently bond to form nucleic acids.
DNA and RNA are polymers built from nucleotides.
Components of a nucleotide:
Phosphate group, a sugar, and a nitrogenous base.
The backbone of nucleic acids is formed by covalent linkages between phosphate groups and sugars.
Polymer concept:
A polymer is a long chain composed of repeating monomer units (n monomers).
Connecting ideas and broader context
This lecture builds on prior content about atoms, bonds, and the idea of macromolecules as essential to life processes.
Carbohydrates, lipids, proteins, and nucleic acids are the four main classes of biomolecules that underpin energy flow, structure, signaling, and heredity.
The physical-chemical properties of water and carbon’s bonding versatility are foundational to understanding how biomolecules behave in biological systems.
Practical and ethical implications
Understanding the chemistry of life informs nutrition, health, medicine, environmental science, and climate-related biology (e.g., how oceans regulate heat via water properties).
A solid grasp of biomolecule structure and function supports evidence-based approaches in biology, pharmacology, and biotechnology.
Quick takeaways for exam prep
Distinguish covalent vs ionic bonds and their impact on molecular structure.
Explain polarity and how it drives water’s solvent properties, cohesion/adhesion, and hydrogen bonding.
Describe water’s key physical properties: density of ice vs liquid, heat capacity, solvent ability, cohesion, adhesion, and surface tension.
Recall the four biomolecule classes and their basic roles: carbohydrates (energy/structure), lipids (membranes/energy storage), proteins (enzymes/structure/signaling), nucleic acids (genetic information and protein synthesis).
Understand protein structure levels (primary, secondary, tertiary; possibly quaternary) and the role of covalent bonds in nucleic acids forming DNA/RNA polymers.
Final note
The lecturer emphasized that today’s material is dense; future lectures will continue to build on these foundations with additional depth on these macromolecules and their roles in cells.