Biology Chapter: Water and Organic Molecules

Biology 1 - Cells, Molecular Biology and Genetics (Biol 1000)

• Course offered by Dr. Michael Cardinal-Aucoin in Winter 2025 at York University
• Course covers cells, molecular biology, and genetics

Building Blocks of Life

• Chemistry of Life is a fundamental concept in the course.
• Biological macromolecules are crucial elements.
• Polymers, carbohydrates, lipids, proteins, and nucleic acids are discussed as key biological macromolecules.

Review Chapter 2

• Matter, elements, and atoms are building blocks.
• Atoms consist of protons, neutrons and electrons.
• Atomic mass and number are important concepts.
• Isotopes have different neutron numbers.
• Valence electrons and ions are described.
• Ionic and covalent bonds are discussed.
• Non-polar, polar covalent bonds, and electronegativity are explored.
• Hydrogen and Van der Waals forces are introduced.
• Chemical reactions include reactants, products, reversible reactions, equilibrium, and specificity.
• Water properties – polarity, cohesion, adhesion, high specific heat are discussed.
• Functional groups are covered.

The Molecules of Life

• All cells comprise four main biological macromolecules—carbohydrates, lipids, nucleic acids, and proteins.
• These molecules share a carbon backbone.
• The diversity of ways these molecules are built and combined is explored.

The Chemistry of Life

• 20-25% of the 92 elements are essential for life.
• Carbon, hydrogen, oxygen, and nitrogen together account for 96% of all living matter.
• Other important elements like calcium, phosphorus, potassium, sulfur, sodium, chlorine, and magnesium make up the remaining 4%.

Table 2.1 Elements in the Human Body

• A table detailing the percentage of each element present in the human body, including the percentage of water.

Water and Life

• Water is the fundamental biological medium on Earth, where life originated.
• All living organisms rely on water more than any other substance.
• Most cells comprise 70-95% of water.
• Water is vital for dissolved molecules in cells.
• Water's abundance on Earth contributes to its habitability.

Summary (Water)

• Water’s key properties result from polarity and hydrogen bonding.
• Expansion upon freezing, cohesion/adhesion, moderation of temperature, and versatility as a solvent are discussed.
• pH of water is tightly regulated by living organisms.

Water

• Polarity, simplicity and complexity, and the importance of water as the birthplace of life are addressed.
• Hydrogen as a fundamental element is discussed.
• Oxygen's significance as the most abundant component of water.

The Backbone of Life

• All living organisms primarily consist of carbon-based molecules.
• Carbon's ability to form complex, large molecules.
• The vast abundance of carbon in the cosmos is noted.
• Proteins, DNA, and carbohydrates fundamentally distinguish living matter.

A Note about Formulae

• Aspartic acid, a building block of proteins, is detailed.
• Chemical and condensed structural formulae and the Lewis diagram for the molecule are presented.
• The various chemical bonds in the molecule are described.

Diversity of chemical functional groups

• Chemical functional groups constructed with carbon are diverse.

The Molecules of Life (Summary)

• Key functions of carbohydrates, lipids, nucleic acids, and proteins are described.

Polymers

• Polymers are formed from repeating monomer units joined by covalent bonds.
• Proteins consist of amino acid subunits.

Building polymers

• Polymer formation occurs via dehydration synthesis (condensation).
• Dehydration removes a water molecule to form a bond.

Breaking down polymers

• Polymer breakdown occurs through hydrolysis.
• Hydrolysis adds a water molecule to break a bond. 

Polymers (Summary)

• Biological macromolecules, such as carbohydrates, lipids, proteins, and nucleic acids, are generally polymers made from monomer subunits.

Carbohydrates

• Carbohydrates are used as sources of energy by organisms.
• Carbohydrates are essential structural components of some organisms.
• Carbohydrates consist of chains of simple monosaccharides.

Simple sugars (carbohydrates)

• Simple sugars contain a 1:2:1 ratio of C, H and O.
• Simple sugars are called monosaccharides, ending in '-ose', and are named based on the number of carbons

Carbohydrates (Simple sugars)

• Monosaccharides are categorized by the number of carbons in the carbohydrate skeleton (e.g., triose, tetrose, pentose, or hexose).
• They are classified based on the location of the carbonyl group (aldehyde or ketone).

Carbohydrates (Glucose - chain to ring)

• Glucose often depicted as a linear chain in diagrams, but actually forms a ring structure in solution.
• Functional groups, like aldehyde and alcohol can be involved in forming the reactive ring structures.

Carbohydrates (Glycosidic bonds)

• Disaccharides and polysaccharides are formed when monosaccharides are linked together via glycosidic bonds.
• Glycosidic bonds occur between the carbon-1 of one monosaccharide and a hydroxyl group on another monosaccharide.

Sugars (carbohydrates - Disaccharides)

• Disaccharides are composed of two monosaccharides bound together—examples include sucrose, lactose, and maltose.
• They vary in their glycosidic linkage (alpha vs. beta), which impact their function.

Carbohydrates (Polysaccharides)

• Polysaccharides are lengthy chains of monosaccharides linked by glycosidic bonds.
• Examples include starches (i.e., amylose, amylopectin) used for energy storage in plants, and glycogen for energy storage in animals.
• Structural polysaccharides such as cellulose in plants and chitin in fungi.

Carbohydrates (Energy storage in plants)

• Plants store starch in chloroplasts.
• Starch consists of amylose and amylopectin (branched).
• A 1-4 glycosidic bond forms the linear amylose component.

Lipids

• Lipids are significant biological macromolecules that are not derived from repeating monomers.
• Lipids are distinguished by their hydrophobic property, defined by their chemical structure.
• Principal categories include neutral fats, phospholipids, and steroids.

Lipids (Neutral Fats)

• Neutral Fats, like triglycerides, have crucial roles in biological systems, such as energy storage.
• They are crucial for insulation from cold temperatures and protecting internal organs.

Lipids (Phospholipids)

• Phospholipids are constituents of cell membranes.
• These lipids exhibit both hydrophilic and hydrophobic properties.
• These properties lead to the formation of a bilayer structure in biological membranes.

Lipids (Steroids)

• Steroids are components of cell membranes, vitamins and hormones.
• Examples include cholesterol and hormones like cortisol.

Nucleic Acids

• Nucleic acids are constructed from nucleotides, which then comprise nitrogenous bases, pentose sugars, and phosphate groups.
• These biomolecules have prominent roles in information storage, including DNA and RNA. 

DNA

• In cells, DNA is typically a double helix composed of two nucleotide strands.

The "Central Dogma"

• DNA acts as a blueprint for protein synthesis.
• The process of transcription translates DNA sequences into mRNA.
• mRNA carries instructions to build proteins, which then involves the process of translation.

Proteins

• Proteins are complex polymers designed from amino acid subunits.
• Proteins are essential components of living organisms performing numerous life functions.

Proteins (Enzymatic proteins)

• Enzymatic proteins accelerate chemical reactions.
• Examples include digestive enzymes.

Proteins (Defensive proteins)

• Antibodies fight against diseases.

Proteins (Storage proteins)

• Storage proteins, such as casein and ovalbumin are responsible for storing amino acids.

Proteins (Transport proteins)

• Proteins known as transport proteins carry substances throughout the body.
• Examples include hemoglobin that carries oxygen in blood.

Proteins (Hormonal proteins)

• Hormones, such as insulin, coordinate bodily functions regulating glucose concentrations and other bodily processes, such as blood sugar levels.

Proteins (Receptor proteins)

• Receptors respond to chemical signals.
• Receptors may be membrane bound molecules that initiate cellular responses in response to molecules such as growth hormones. 

Proteins (Contractile proteins)

• Example is actin and myosin that facilitates cellular movement. 

Proteins (Structural proteins)

• Proteins that form the structural component of hair, feathers, and other external appendages. 

Proteins (Amino acid substitution)

• Genetic mutations in the DNA sequences change the amino acid sequence in the resultant protein molecules.
• This has an impact on the proteins' function.

Proteins (Quaternary structure)

• Proteins' quaternary structure occurs when two or more polypeptide chains come together to form larger functional complexes.
• Examples of such proteins are hemoglobin that carries oxygen in the circulation system. 

Protein: Form and Function

• Structure determines protein function.
• Different levels of protein structure (primary, secondary, tertiary, and quaternary) contribute to protein function

Proteins (Denaturation)

•   Tertiary structure is crucial for protein function.
• Denaturation disrupts bonds causing proteins to lose function.

Proteins (Types of R-Groups)

• Hydrophobic and hydrophilic types of amino acid R-groups exist.
• These properties determine how specific segments of the protein interact
• These interactions are also crucial for how various levels of protein structure form. 

Proteins (Special amino acids)

• Specific amino acids may contain specific reactive groups.
• For instance, glycine is very small and proline creates a bend in the protein chain.
• Cysteine residues can bind via a disulfide bond to create strong and stable bridges in the three dimensional conformation of the protein molecules. 

Proteins (Essential amino acids)

• Some amino acids need to be obtained via external sources because they cannot be produced by the body.

Proteins (Peptide bonds)

• Peptide bonds connect amino acids to create polypeptide chains.
• These bonds are formed by dehydration synthesis.

Proteins (Polypeptide chain)

• Polypeptide chains have directionality (polarity) with an amino terminus and a carboxyl terminus.

Proteins (Primary structure)

• The sequence of amino acids is the primary structure of a protein.
• The primary structure is unique for each specific protein.

Proteins (Secondary structure)

• Interactions influence alpha-helices and beta-sheets.
• Secondary structures form parts of larger protein structures via interactions between amino acids. 

Proteins (Tertiary structure)

• The tertiary structure is the three-dimensional arrangement of a peptide chain.
• R-Group interactions, and chemical bonds (i.e. hydrogen bonds, disulfide bridges, ionic bonds, Van der Waals forces, and hydrophobic interactions) contribute to the protein’s unique three dimensional form. 

Proteins (Quaternary structure)

• Individual units come together to create various and new complexes.
• Proteins like hemoglobin consist of multiple polypeptide subunits.

Proteins (Pathogens: Prions)

• Prions are misfolded proteins.
• They induce other proteins to misfold resulting into prion diseases.

Proteins (Summary)

• A summary of the key concepts about proteins is given.