• Unit 3: Biological Molecules

    Biological molecules are the essential molecules needed for life. These molecules can be organic or inorganic. Organic chemistry is the study of carbon, which is an element that forms strong covalent bonds essential for the foundational structures of all living things. Water, salts, acids, and bases are mostly essential inorganic molecules that facilitate many biological processes.

    All organisms contain organic biological molecules – carbohydrates, proteins, lipids, and nucleic acid – that are essential to life. This unit will help you understand the structures and functions of these organic molecules and how our body needs them to function properly.

    Completing this unit should take you approximately 5 hours.

    • Upon successful completion of this unit, you will be able to:

      • list the characteristics of water that make it important to life as we know it;
      • describe the role of acids, bases, and buffers in biological systems;
      • define pH and the role of hydrogen ions in living systems;
      • recognize the structure of the four major biological macromolecules;
      • describe the functions of the four major biological macromolecules;
      • indicate the monomers and polymers of carbohydrates, proteins, and nucleic acids; and
      • describe the four levels of protein structure.

    • 3.1: Water and Organic Molecules

      The important molecules of life include water, salts, acids, bases, and organic compounds. Water is the solvent of life. Living organisms survive because of chemical reactions that occur in the presence of water. Molecules that are dissolved by water (salts, acids, and bases) are hydrophilic, while organic molecules that are nonpolar and unable to form hydrogen bonds with water are hydrophobic. Each type of substance has an important role in the chemical reactions of life.

      • Water is one of the most important compounds on earth – no living organism can survive without it. A water molecule is made up of one oxygen atom that is simultaneously bonded to two hydrogen atoms. The covalent bonds between the oxygen and each hydrogen are polar because the sharing of electrons between oxygen and hydrogen is not equal. Because of this unequal sharing, the oxygen atom is partially negatively charged, and each hydrogen atom is partially positively charged, making the overall water molecule polar. This gives water several special characteristics:

        • Water molecules can form hydrogen bonds with other polar molecules, including other water molecules.
        • Water is less dense in the frozen state than in the liquid state. Because of this, bodies of water freeze from the top down and thaw during seasonal warming.
        • Water has a high specific heat capacity, requiring more energy than most substances to change its temperature. This stabilizes the temperature of bodies of water more than landmasses.
        • Water has high cohesion, allowing for capillary attraction that can lift water through vessels to the tops of the tallest trees.
        • Water is an excellent solvent, and the chemistry of life is mostly aqueous solution chemistry.
        • Water has high surface tension, allowing small organisms to walk on the surface of water.
        • Water has a high latent heat of vaporization, requiring much energy to change its state from liquid to gas. This allows for effective evaporative cooling by sweating.
        • Water exists in all three states (solid, liquid, and gas) within a comparatively narrow range of temperatures that organisms can tolerate.

        Because of these special characteristics, it is no surprise that life evolved in the ocean and that we can view every living cell as a tiny bag of water and biological molecules.

      • Water Page

        Read this chapter to learn about the four unique properties of water. After you read, you should be able to explain why water is an excellent solvent, describe water molecules that are polar and capable of hydrogen bonding with four neighboring water molecules, and distinguish between a solute, solvent, and solution.

      • The Properties of Water Page

        Watch this lecture, which reviews the special chemical properties of the water molecule.

    • 3.2: Acids and Bases

      pH is the measure of the very reactive hydrogen ion. We use the pH scale to measure the hydrogen ion concentration of biological systems. An imbalance of the level of hydrogen ions can be damaging to life. Acids are molecules that, when dissolved by water, increase the levels of hydrogen concentration in the solution. Bases are molecules that, when dissolved by water, decrease the hydrogen concentration in the solution. Buffers work to maintain pH by regulating levels of hydrogen ions in living things.

      • Acids, Bases, and the pH Scale Page

        Watch these short videos, which give an overview of acids, bases, and the pH scale.

      • pH, pOH, and pKw Page

        Watch this lecture to learn how the pH scale affects biological systems. Remember that acids are proton donors, while bases are proton acceptors.

      • Electrolytes and pH Page

        As you review this section, notice the difference between a strong and weak acid and base. How do the pH measurements of acidic and basic solutions affect living organisms? Different foods have different amounts of hydrogen ions, which is also known as proton concentration.

      • Hydrogen Atoms in Acids and Bases Page

        Watch this lecture, which describes how acids and bases relate to the concentration of hydrogen ions in a solution. You should be able to explain how acids and bases alter the hydrogen ion concentration of a solution directly and indirectly.

    • 3.3: Biological Macromolecules

      Living things are mainly composed of organic or carbon-based molecules. Carbon has four valence electrons, a quality that gives it the ability to form strong covalent bonds in large, complex, and diverse molecules. Living things need this molecule diversity to provide the many structures that have so many different functions. These biological macromolecules of life are carbohydrates, lipids, proteins, and nucleic acids. All organisms have four major classes of large biological molecules (also called macromolecules):

      1. Lipids comprise a diverse set of hydrocarbon molecules (containing hydrogen and carbon). This makes them largely non-polar because the covalent bonds in hydrocarbons (between two carbon atoms or between a carbon atom and a hydrogen atom) feature equal sharing of electrons.

      2. Polysaccharides are complex carbohydrates made up of carbon, hydrogen, and oxygen in a 1:2:1 ratio, giving them an empirical formula generalized as (CH2O)n.

      3. Proteins are enormously diverse in structure and function, yet they all feature the substructure of amino acids. Each amino acid features a central carbon atom simultaneously connected to a hydrogen atom, an amino group, a carboxyl group, and a variable R group.

      4. Nucleic acids are informational molecules with a basic structure. Each of their subunits includes a five-carbon sugar (either ribose or deoxyribose) attached to a phosphate group and a nitrogenous base.


      Knowing the chemical structure that underlies these essential biomolecules not only allows you to recognize them. It allows you to understand how they are constructed within cells and how they chemically interact with each other in metabolism and to give rise to the structural component of organisms.

      • A polymer is a particular category of macromolecule that is built by connecting many smaller subunits, called monomers (poly- means many). Of the four biological macromolecules that you have been studying, only three are polymers. Lipids are not polymers, but the others are.

        • Polysaccharides are macromolecular carbohydrates. Be careful with the words polysaccharide and carbohydrate. They are sometimes used interchangeably, but should not be. Carbohydrates include both small molecules and large molecules (macromolecules). Polysaccharides are a type of carbohydrates, but not all carbohydrates are polysaccharides. As the name implies, polysaccharides are polymers made up of multiple monosaccharides. Monosaccharides are monomers, and they can be connected in a linear or branched arrangement.
        • Proteins are polymers that are made up of monomers called amino acids. Unlike polysaccharides, which may be branched, a protein must be a linear (or end-to-end) arrangement of amino acids. Organisms use 20 different kinds of amino acids (in an unlimited number of combinations and orders) to construct their proteins.
        • We can also call a nucleic acid a polynucleotide. That alternative name indicates it is a polymer made up of many nucleotides. In the case of DNA, the monomers are nucleotides containing the pentose (five-carbon sugar) called deoxyribose. For RNA, the nucleotides contain ribose instead of deoxyribose. Although there are only four commonly used DNA nucleotides (and four commonly used RNA nucleotides), a typical DNA molecule contains millions of nucleotides, so there is an unlimited number of sequences of such nucleotides.


        Be sure you can match each type of monomer to the type of polymer that can be made from such monomers. You should also know how polymers are constructed using dehydration reactions and deconstructed using hydrolysis reactions.

      • Biological Polymers Page

        Watch this lecture to review biological macromolecules and their role in biological organisms. Identify their building blocks and how they form polymers. Also, understand the structures and how they relate to the function of each macromolecule's role in organisms. After watching, you should be able to list the four major classes of macromolecules, distinguish between monomers and polymers, and define the terms dehydration synthesis and hydrolysis.

      • Carbohydrates Page

        Carbohydrates are classified into three subtypes: monosaccharides, disaccharides, and polysaccharides. Some polysaccharides (like cellulose and chitin) are important for their structural strength, whereas other polysaccharides (like starch and glycogen) are important for storing energy. Polysaccharides also serve as important identity markers on the surfaces of cells, so they play a role in immunity.

        A carbohydrate is an organic compound such as sugar or starch, which plants use to store energy. Read this text, which discusses the role of carbohydrates in cells and in the extracellular materials of animals and plants. When you finish, make sure you can describe the function and structure of carbohydrates.

      • Lipids Page

        Lipids are important for storing energy, thermal insulation, and providing protective padding. Phospholipids form the infrastructure of all cell membranes. Lipids also make up natural waxes and oils and many hormones. Read this section to learn more about lipids. When you have finished reading this section, make sure you can describe the function and structure of lipids.

      • Proteins Page

        Proteins perform an impressively long list of biological functions. They function as enzymes, structural elements, chemical signals, transporters, and receptors. They also play important roles in cell-to-cell adhesion and immunity. As you read this section, make sure you can describe the four levels of protein structure.

      • Nucleic Acids Page

        Nucleic acids include various DNA and RNA molecules. They serve informational purposes. DNA stores the genetic code, and various types of RNA help in the process of interpreting that code to build proteins. Certain RNAs can also function as catalysts.

      • After you have read this section, try to respond to the following review questions:

        1. Why are biological macromolecules considered organic?
        2. What role do electrons play in dehydration synthesis and hydrolysis?
        3. Describe the similarities and differences between glycogen and starch.
        4. Why is it impossible for humans to digest food that contains cellulose?
        5. Explain at least three functions that lipids serve in plants and/or animals.
        6. Why have trans fats been banned from some restaurants? How are they created
        7. Explain what happens if even one amino acid is substituted for another in a polypeptide chain. Provide a specific example.
        8. Describe the differences in the four protein structures.
        9. What are the structural differences between RNA and DNA?
        10. What are the four types of RNA and how do they function?

    • Unit 3 Assessment

      • Unit 3 Assessment Quiz
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        Take this assessment to see how well you understood this unit.

        • This assessment does not count towards your grade. It is just for practice!
        • You will see the correct answers when you submit your answers. Use this to help you study for the final exam!
        • You can take this assessment as many times as you want, whenever you want.