3.1: Lab 3 Background

Learning Objectives

• Explain the functions of the four main groups of biomolecules.
• Identify the monomers of biomolecules.
• Explain how enzymes catalyze chemical reactions between specific substrates.
• Design experiments to test for the presence of biomolecules and enzymatic reactions.
• Describe and graph the results of experiments.

Introduction: Biomolecules

The large molecules necessary for life that are built from smaller molecules are called biological macromolecules, or biomolecules for short. The four major classes of biomolecules are carbohydrates, lipids, proteins, and nucleic acids. Each is an important component of the cell and performs a wide array of functions. They typically contain carbon, hydrogen, oxygen, nitrogen, as well as phosphorus, sulfur, and other minor elements. Most biomolecules are called polymers and are built from repeating segments called monomers (the prefix mono means one and the prefix poly means many). We can think of monomers as legos and polymers as the structure built from legos, like a castle or spaceship. Today, we will explore the four classes of biomolecules and figure out how to determine whether the biomolecules are in a solution.

Carbohydrates

Carbohydrates are a diverse class of macromolecules with which we are probably rather familiar. One of the most common examples of a carbohydrate is glucose, which can be found in just about every cell in every organism. Glucose is a simple sugar that can be broken down easily to provide energy for the organism. There are many other examples of energy-providing carbohydrates, as well as others with different functions.

Carbohydrates consist of carbon, hydrogen, and oxygen in a 1:2:1 ratio, meaning that for every one carbon atom, a carbohydrate has two hydrogen and one oxygen atoms. It is helpful that the name carbohydrate itself reminds us of this ratio. Think of carbo- as referring to a carbon atom and hydrate as in water, or H2O (two hydrogens and one oxygen).

Broadly, carbohydrates are classified into three subtypes: monosaccharides, disaccharides, and polysaccharides.

Monosaccharides (mono = one; sacchar = sweet) are simple sugars whose names end with the suffix “-ose”, the most common of which is glucose. The chemical formula for many monosaccharides, including glucose, is \(\ce{C6H12O6}\) (which matches the 1:2:1 ratio described above). In most living species, glucose is an important source of energy. During cellular respiration, energy is released from glucose and that energy is used to help make adenosine triphosphate (ATP). During photosynthesis, energy from sunlight converts carbon dioxide and water into glucose. Other example monosaccharides include fructose (as in high fructose corn syrup) and galactose.

Disaccharides (di = two) form when two monosaccharides are covalently bonded together. Common disaccharides include lactose, maltose, and sucrose. Lactose, the sugar found in milk, is a disaccharide consisting of the monomers glucose and galactose. The most common disaccharide is sucrose, or table sugar, which is composed of the monomers glucose and fructose.

Polysaccharides (poly = many) are long chains of monosaccharides linked by covalent bonds. Polysaccharides may be very large molecules, including starch, glycogen, cellulose, and chitin. Plants store sugar in the form of starch, which is made up of many molecules of glucose monomers. Similarly, animals, including humans, store sugar in the form of glycogen, which is also made up of many glucose monomers. Glycogen is a highly branched molecule usually stored in liver and muscle cells. Whenever glucose levels decrease, glycogen is broken down to release glucose. Also, when animals consume plants or other animals, the starch or glycogen gets broken down into the glucose building blocks. Cellulose is one of the most abundant natural biopolymers, built from many glucose monomers. The cell walls of plants are mostly made of cellulose, which provides structural support to the cell. In fact, wood and paper are mostly cellulose.

Lipids

Lipids are a diverse group of biomolecules that include fats, oils, waxes, phospholipids, and steroids. Lipids are not true polymers because there is not one kind of monomer that bonds together to make all lipids (unlike how all polysaccharides are made up of many monosaccharides). Lipids are nonpolar molecules, which makes them hydrophobic (“water-fearing”) and insoluble in water. Lipids perform many different functions in a cell.

For example, fats are a common lipid that store energy for long-term use. In fact, fats are far more efficient at storing energy than sugars, containing about twice the energy in only one-sixth the volume of equal weight of carbohydrate! A fat molecule, such as a triglyceride, consists of two main components—glycerol and fatty acids. Fatty acids are commonly mistaken as a monomer because they are found in many different kinds of lipids. All fatty acids have a carbon “backbone” with several carbon atoms bonded together along the middle of the molecule. Depending on the chemical structure of the fatty acid, it is classified as either saturated or unsaturated.

Saturated fatty acids tend to have a straight chain of carbon atoms, each of which only have single bonds between neighboring carbons. They are saturated with hydrogen; in other words, the molecule has the most hydrogen atoms it could possibly hold. Because of this, saturated fatty acids are tightly packed and tend to be solid at room temperature, such as animal fats contained in meat and the fat contained in butter.

Unsaturated fatty acids contain at least one double bond between carbons. The double bond causes a bend or a “kink” that prevents the fatty acids from packing tightly, keeping them liquid at room temperature. Fish oil is one example, but most unsaturated fatty acids are plant-based, including vegetable oils such as olive oil, corn oil, and canola oil.

Phospholipids are the main component of cell membranes. One property that allows them to make an effective plasma membrane is that they have both hydrophobic and hydrophilic regions. They have fatty acid chains that are hydrophobic and a phosphate group that is hydrophilic. Cells are surrounded by a phospholipid bilayer, where the fatty acids face each other, away from water, whereas the phosphate groups can face either the outside environment or the inside of the cell, which are both aqueous.

Unlike the phospholipids and fats discussed earlier, sterols, such as cholesterol, steroids, and hormones, have a ring structure. This ring structure separates them from the other lipids, though they are still hydrophobic. Cholesterol is mainly synthesized in the liver and is the precursor of many steroid hormones, such as testosterone and estradiol. It is also the precursor of vitamins E and K.

Waxes are made up of a hydrocarbon chain with an alcohol (–OH) group and a fatty acid. Examples of animal waxes include beeswax and cerumen (earwax). Plants also have waxes, such as the coating on their leaves that helps prevent them from drying out.

Proteins

Proteins are one of the most abundant molecules in living systems and have the most diverse range of functions of all macromolecules. Proteins may be structural, regulatory, contractile, or protective; they may serve in transport, storage, or membranes; or they may be toxins or enzymes. Enzymes are a common kind of protein, which we will explore later on in this lab. Each cell in a living system may contain thousands of different proteins, each with a unique function. Their structures, like their functions, vary greatly. They are all, however, polymers of amino acids (which are the monomers).

While there are many tens of thousands of proteins that exist, there are just 20 different amino acid monomers! We can think of the amino acids like the 26 letters of the English alphabet and proteins like the many thousands of words the letters (or amino acids) make. Each amino acid has the same fundamental structure, which consists of a central carbon atom bonded to an amino group (–NH2), a carboxyl group (–COOH), and a hydrogen atom. However, what sets them apart from each other is a variable group bonded to the central carbon atom known as the R group. The R group is the only difference between the 20 amino acids; otherwise, the amino acids are identical.

The sequence and number of amino acids ultimately determine a protein’s shape, size, and function (like the sequence and number of letters differentiating words). Each amino acid is attached to another amino acid by a covalent bond, known as a peptide bond. Thus, the polymer is called a polypeptide chain. Before a protein becomes fully functional, the polypeptide chain needs to fold into a unique shape. To understand how the protein gets its final shape, or conformation, we need to understand the four levels of protein structure: primary, secondary, tertiary, and quaternary.

The primary structure is the unique sequence and number of amino acids in a polypeptide chain. The unique sequence for every protein is ultimately determined by the gene that encodes the protein. The secondary structure describes local folding, including the β-sheet (β = “beta”), and the α-helix (α = “alpha”). The tertiary structure describes global folding, where distant sides of the polypeptide chain interact to produce a unique three dimensional shape. Some proteins are fully functional after the tertiary structure takes shape, but others have a quaternary structure where multiple polypeptide chains bond together. When proteins are exposed to high temperatures, high salt concentrations, or extreme pH, their three dimensional shape breaks down, or denatures. Proteins cannot recover from being denatured and will no longer function.

Nucleic acids

Nucleic acids are key macromolecules in the continuity of life. They carry the genetic blueprint of a cell and instructions for the functioning of the cell. Nucleic acids are made up of monomers called nucleotides. Each nucleotide is made up of three components: a nitrogenous base attached to a sugar molecule, which is attached to a phosphate group. The nucleotides bond to each other to form the polynucleotides deoxyribonucleic acid (DNA) or ribonucleic acid (RNA). DNA is the genetic material found in all living organisms, from single-celled bacteria to multicellular mammals. RNA is mostly involved in protein synthesis. The DNA molecules never leave the nucleus, but instead use an RNA intermediary to communicate with the rest of the cell.