Unit 3 Notes Isomers, Carbon, Water, Macromolecules and Enzymes


Unit 3 Notes Isomers, Carbon, Water, Macromolecules and Enzymes


  1. Chemical Bonds
  • I will assume that you already know atomic structure, covalent bond, ionic bond, double and triple bonds, writing molecular formulas, writing and balancing chemical equations and not planning to discuss these in this course. If you have issues with these concepts, you need to come to after school tutoring.
  • Electronegativity describes an atom’s attraction for an electron. This is an artificially assigned value that can be easily obtained from a data table. The general rule is that atoms with higher electronegativities attract the electrons more than atoms with lower electronegativities. So if you have two atoms with different electronegativities bind, the one with higher En will attract the electrons more in the bond – polar covalent bond. If two atoms in a covalent bond have the same En the electrons are shared equally so the bond is nonpolar covalent.
  • Hydrogen bonding – weak attraction between MOLECULES of polar covalent compounds. The positive end of one molecule attracts to the negative end of another molecule.
  • Van der Waals attraction – very weak attraction between nonpolar molecules. This attraction results from the temporary asymmetric distribution of electrons on the outer shells of atoms. These attractions reinforce molecular shapes. Molecular shapes are vital for proper receptor or enzyme substrate binding.
  1. Organic Chemistry
  • Organic chemistry studies the characteristics and reactions of carbon containing (organic) compounds. Organic compounds rely on the unique characteristics of carbon. These are:
  • 4 covalent bonds
  • Able to bind with other atoms
  • Able to form long chains and rings
  • Able to form double and triple bonds
  1. Isomers
  • Isomersare compounds with the same number and type of atoms but different arrangements of these atoms. However, in biology, it is important to know the proper arrangement of the atoms, because binding of molecules to receptors and enzymes will depend on it.
  • There are three basic types of isomers:
  • Structural isomers – different arrangements, side chains of the same molecule.
  • Cis/trans isomers – Side chains of the same molecules can be arranged on the same plain or on opposite plains.
  • Enantiomers – different arrangement of atoms or side chains around asymmetric carbon atoms.
  • Functional groups – parts of molecules that are directly involved in a chemical reaction.

You don’t need to memorize these for now, but eventually as we are learning the molecules you will learn them.

  1. How Do Polymers Form?

Review the Miller-Urey experiment, forming polymers and the RNA world hypothesis from Unit 1. You will be quizzed on these topics again.

  • Polymer – a long molecule consisting of many similar or identical building blocks linked together by covalent bonds.
  • Monomer – the single repeating units of a polymer
  • Dehydration synthesis – chemical reactions that form polymers from monomers by releasing water from the monomers and binding the remaining groups of atoms together.
  • Hydrolysis – chemical reactions that form monomers from polymers by breaking the original monomer-monomer covalent bonds and adding water to separate these monomers.


  1. The Chemical Properties of Water
  1. The Physical Properties of Water
  2. Specific Heat
  1. Cohesion and Adhesion
  1. Universal solvent
  1. Density
  1. Viscosity
  1. Color
  1. Surface Tension
  1. The Biological Role of Water


  1. Understanding Hydrogen Ions
  • Water can dissociate to OH- and H+ ions (or more precisely H3O+ ions)
  • In pure water the concentration of these two ions is about the same, 10-7moles/L. So the product of the concentrations of these two ions:

[H+] [OH-] = 10-14

  • To measure pH, we use the negative logarithmic expression of the H+ ion concentration:

pH = -log [H+]

  • Because an acid adds hydrogen ions into a solution, it will have more [H+] than water, so its pH is going to be less than 7, while a base adds OH- ions and removes HHhHHHH+ ions from the solution so its pH is higher than 7.
  • All compounds that release hydrogen ions are considered acids. Strong acids completely break down to hydrogen ions and negative ions. Weak acids have a combination of molecular and ionic forms of the acid.
  • Bases are substances that decrease the hydrogen ion concentration in a solution by bonding OH- ions to free hydrogen ions in solutions. Strong bases also dissociate completely to their ionic form and weak bases also have a mix of the molecular and ionic forms.
  1. The Effects of Changes in pH on Living Things
  • Cells are very sensitive to changes in pH and can only exist within very narrow pH ranges.
  • pH changes can destroy the structure of organic molecules, so organisms have a system of buffers to prevent changes in pH.
  • Buffers are substances that minimize changes in H+ ion and OH- ion concentrations in a solution. Buffers accept hydrogen ions when there are too many and release them when there are too few of them. These substances are usually weak acids with corresponding weak bases.
  • An example of a buffer is CO2 in blood where it reacts with water:

H2CO3 ↔ HCO3- + H+

  1. Changes In Environmental pH Affect Ecosystems
  • Many pollutants (CO2, SO2, N2O) in the atmosphere can react with water and form acids. These acids alter the pH of rain, so acid precipitation forms. Acid precipitation changes the pH of lakes, rivers, reacts with the chlorophyll of leaves, breaks down the shells and other hard structures of animals, changes the soil composition and ruins human-made buildings, bridges etc.
  • Ocean Buffering System -- As atmospheric CO2 levels increase, this gas dissolves more in the oceans and forms carbonic acid. The high level of CO2 ultimately decreases the available CaCO3 for organisms to use building their shells and also affect their ability to reproduce.

Skills exercise

  • Ocean acidification can be stopped by decreasing the CO2 levels in the atmosphere.


  1. Overview
  • Carbohydrates are compounds formed from carbon, hydrogen and oxygen in a 1:2:1 ratio.
  • All carbohydrates have major functions in energy release and storage of living organisms. They can also act as raw materials for making other molecules, as structural materials and can help with cell identification.
  • Three basic types of carbohydrates are:
  • Monosaccharides
  • Disaccharides
  • Polysaccharides
  1. Monosaccharides
  • They are the simplest carbohydrates
  • They typically provide quick energy for chemical reactions when they are broken down during cellular respiration or fermentation. They also participate in forming larger polymers of carbohydrates and nucleic acids.
  • Each monosaccharide is made up of a carbonyl group (C=O) (Remember functional groups? This in one of them) and several hydroxyl groups (-OH) (another functional group).
  • Monosaccharides are classified by:
  • The location of the carbonyl group (can be aldehydes or ketones)
  • The length of the carbon chain/ring (trioses, tetroses, pentoses and hexoses)
  • The arrangement of hydroxyl groups around asymmetric carbon atoms (remember enantiomers)
  • The long chain of monosaccharides frequently closes up to form a ring, according to the closing of the ring, there are two versions of glucose, an α-glucose and a β-glucose.

Figures 2 and 3 – Module 9

  • The shape and structure of the molecules determine how they participate in chemical reactions. For example, monosaccharides are used during cellular respiration. While they are broken down, their energy is trapped in ATP molecules. They are also raw materials for making amino acids and nucleic acids.
  1. Disaccharides and Polysaccharides
  • To make long-term storage more efficient, monosaccharides are combined together into long chains of disaccharides and polysaccharides by using dehydration synthesis.
  • The simplest conversion is forming disaccharides. Glycosidic linkage (a covalent bond) forms between two monosaccharides to form a disaccharide. During this bonding, a –OH is released from the first carbon atom of one monomer and a –H is broken down from the 4th carbon atom of the second monomer. This results in the release of a water molecule.

Figure 6 – Module 9

  • Important disaccharides include:
  • Maltose – a disaccharide that is a dimer of starch, used in beer brewing
  • Sucrose – everyday table sugar
  • Lactose – milk sugar
  • Organisms can use polysaccharides for energy storage and for structural support. As energy storage molecules (glycogen in animals and starch in plants) they can release the energy as they are broken down to monosaccharide units and then used during cellular respiration. Both glycogen and starch are made up of α-glucose molecules. Plants can use starch for long-term storage while animals usually use glycogen for shorter term energy storage and can deplete it in a couple of days.
  • Polysaccharides that are used for structural support include cellulose, chitin and peptidoglycan. Cellulose is built up of β-glucose monomers. It is highly unsoluble in water and nonreactive. Its fibrous structure builds cell walls of plants.
  • Chitin occurs in the cell walls of fungi, some algae and in insect exoskeletons. The structure of chitin is similar to cellulose in its sturdy, nonreactive nature but contains N-containing monosaccharides.
  • Peptidoglycan is also a sturdy polysaccharide that also contains amino acids besides the usual monosaccharide units. Peptidoglycan builds up the cell wall of bacteria.

Good summary on Figure 10 – Module 9

  • Smaller segments of polysaccharides (also called oligosaccharides) are also used for cell recognition. These segments are joined to proteins on the outer surface of cell membranes. These segments of glycoproteins are unique to the cell type and to the species or individual and used for identification by other cells of the organism.


  1. What Are Lipids?
  • A diverse group of macromolecules that have a wide range of structures and functions, however they are generally nonpolar and do not mix well in water.
  • They are not strictly speaking polymers, because they are not composed of multiple repeating units.
  • The three main groups of lipids are:
  • Simple lipids
  • Phospholipids
  • Sterols
  1. Simple Lipids
  • Simple lipids are also called triglycerides are lipids that are composed of 1 glycerol and 3 fatty acid monomers. These monomers combine by dehydration synthesis.
  • Fatty acids are carboxylic acids with a carboxyl functional group on one end and a long carbon chain with 16-18 carbon atoms on the other end of the molecule. The fatty acid carbon chain can be saturated if the chain only has single bonds among the carbon atoms. These saturated fatty acids are long, linear molecules. Mammalian fat, lard, butter etc. is this kind of fat.
  • Unsaturated fatty acids have one or more double bonds between the carbon atoms. The carbon chains naturally always take on the cis isomeric form. Oils are formed from unsaturated fatty acids. Because of the double bonds, the carbon chain has a kink in the molecule. It is hard to line up these bent chains next to each other in an organized manner, this is the reason why oils are liquid on room temperature.
  • Trans fats – trans isomers of unsaturated fatty acids. These don’t have the kink in their chain, so they are solids on room temperature. They are harder for us to digest and can have harmful health effects.
  • Essential fatty acids – fatty acids that cannot be synthesized by the liver but are necessary to build important molecules (omega-3 and omega-6 fatty acids)
  • Simple lipids form when 3 fatty acids combine with 1 glycerol molecule by dehydration synthesis.
  • Simple lipids are generally used as stored energy sources in animals and some nuts. They can build up under the skin and provide insulation, protection and dissolve fat soluble vitamins, such as A, D, E and K.

A fat or triacylglycerol molecule is composed of one glycerol molecule and three fatty acid molecules A fatty acid is a carboxylic acid with a hydrocarbon chain that is usually 16 to 18 carbon atoms long Recall that a carboxyl group is formed by a terminal carbon that is double bonded to oxygen and single bonded to a hydroxyl group O H Glycerol is an alcohol molecule composed of a chain of three carbon atoms each with a hydroxyl group

  1. Phospholipids
  • A type of lipid composed of two fatty acids, 1 glycerol and 1 phosphate combined by dehydration synthesis.
  • The fatty acid tails remain nonpolar while the phosphate head of the molecule is polar. As a result, phospholipids can dissolve partially both in polar and in nonpolar substances.
  • They can form single layered micelles or two layered phospholipid bilayers in water or in oil.
  • Phospholipid bilayers form the main component of cell membranes and many cell organelles. This bilayer also controls what enters and leaves the cell. The hydrophobic interior of the membrane is impermeable for polar (hydrophilic) molecules, but permeable for hydrophobic molecules.

When a phospholipid bilayer forms phospholipids line up to keep the hydrophobic tails from the aqueous surroundings The hydrophilic heads face outward toward the aqueous environment and the hydrophobic tails of each layer face each other

  1. Steroids (sterols)
  • A highly nonpolar lipid that is composed of four fused rings with various functional groups attached to it.
  • Sterols are important for forming sex hormones, vitamin D, cholesterol, bile salts.
  • Sex hormones are important in determining secondary sex characteristics and the gender of a person.
  • Vitamin D is important for the Ca2+ metabolism of the body and to enhance the immune system.
  • Cholesterol is an important building block of the cell membrane of animals. It makes the cell membrane more resistant to temperature changes.
  • Bile salts help to dissolve fats before enzymes can digest them.


  1. The Levels of Protein Structure
  • Proteins are macromolecules that are made up of one or more polypeptide chains. The polypeptide chains form from amino acid monomers.
  • Primary structure: formed by amino acids combining with each other during dehydration synthesis. The amino acids join by peptide bonds. Every amino acid has the following parts:
  • Amino group (another functional group)
  • Side chain or R-group
  • Carboxyl group
  • All amino acids differ in their side chain (R-group). According to the types of R-groups there are 20 amino acids in every living organism. The type of the side chain is important because its polarity will determine the polarity of the protein and the binding of the side chains to each other.

See activity

  • Secondary structure: A coiled and folded shape that forms when hydrogen bonding connects the remaining carbonyl and –NH groups of different amino acids to each other. The hydrogen bonding can form among distant amino acids or can form among amino acids that are close by:
  • α – helix develop from the hydrogen bonds between nearby amino acids
  • β-pleaded sheet forms when the hydrogen bond forms between distant amino acids
  • Tertiary structure: Interactions between the side chains of amino acids to form the 3D structure of a polypeptide. These interactions occur between the R groups of amino acids. The types of interactions include:
  • Hydrophobic effect – clustering nonpolar side chains inside of the polypeptide when water is present
  • Hydrogen bonding – attraction of hydrogen atoms of R groups to O or N atoms of other side chains.
  • Covalent bonding – two sulfur atoms can bond together covalently to form a disulfide bridge
  • Ionic bonding – attraction between positively and negatively charged side chains
  • Van der Waals attractions – weak forces between nonpolar side chains.
  • Quaternary structure: When associations of multiple polypeptides form a functional protein. The multiple polypeptides may be the same type or different types of polypeptides joined. This level of protein structure uses the same type of bonds as the tertiary structure.

Figures 5 and 6 in Module 11 are great review animations

  1. Protein Function

Proteins perform a wide range of functions in living organisms. Here is a collection of some of their functions:

  • Enzymes – act as biological catalysts, lower the activation energy of reactions
  • Receptors – surface proteins in cell membranes can detect signals coming from outside of the cell
  • Hormones – signal molecules that regulate cell function
  • Transport – these proteins can carry substances across cell membranes or to larger distances in the body
  • Structural support – hard structures of living organisms frequently have tough protein components such as in hair, finger nails, claws, horns, hooves etc.
  • Motor proteins – move cells or entire organisms – muscle fibers are made up of proteins, also cilia and flagella of cells have protein components
  • Defense proteins – antibodies, parts of the immune system are also proteins.
  1. Denaturation of Proteins
  • Proteins are very sensitive to their environment. Various environmental factors, if they change too far from the ideal conditions, collapse or interfere with the structure of proteins. If the structure of proteins is distorted, they are not able to perform their functions any more.


  1. The Role of Enzymes in Metabolism
  • Chemical reactions don’t happen fast enough in living organisms. Enzymes are biological catalysts that speed up the chemical reactions by lowering their activation energy.
  • Enzymes are usually proteins but some can also be composed of RNA – ribozymes.
  • Enzymes can only bind specific molecules – substrates. These substrates are the reactants of the reaction that enzymes catalyze. Enzymes get their name after the specific substrate that they catalyze by using the substrate name + ase suffix.
  • The part of the enzyme that binds with the substrate is called the active site, this is formed by the tertiary and quaternary structure of the enzyme. The active site wraps around the substrate and forms the enzyme-substrate complex. This structure forms by using the R-groups of amino acids.
  • Activation energy is the energy needed to overcome the energy barrier of breaking old chemical bonds and forming new ones. Enzymes act as biological catalysts because they lower the energy requirements of the reaction without being used up by the reaction.

Two graphs compare the energy barrier for a reaction to proceed in the absence and presence of enzymes Each plots total energy over time The graph on the left shows an uncatalyzed reaction where the activation energy is high The graph on the right shows an enzyme catalyzed reaction where the activation energy is lower made low by the presence of an enzyme