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25.5: Biochemical Molecules

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Lesson Objectives

The student will:

  • describe the basic structure of fatty acids, monosaccharides, and proteins.
  • identify the chemical purpose fulfilled by lipids, carbohydrates, and enzymes.
  • describe the biological function of hemoglobin and DNA.

Vocabulary

  • amino acid
  • biochemistry
  • carbohydrate
  • dipeptide
  • DNA
  • enzyme
  • fatty acid
  • lipids
  • phospholipid
  • polymer
  • polypeptide
  • protein
  • steroid

Introduction

Biochemistry is the study of the structure and properties of molecules in living organisms. In a full course in biochemistry, you would study how those molecules are made, changed, and broken down. Examples of the types of molecules important to biochemistry are proteins, hormones, and nucleosides.

This video details the discovery of organic molecules on extrasolar planets (1l I&E): http://www.youtube.com/watch?v=Lxs9Pmxy5MA (5:04).

Lipids

Otherwise known as fats and oils (triglycerides), lipids are produced for the purpose of storing energy. One of the best known lipids is cholesterol, which is used in the body to construct cell membranes and as a building block for some hormones. High levels of cholesterol are linked to coronary disease.

There are many categories of lipids, but the three main categories are:

  1. fatty acids
  2. steroids
  3. phospholipids

Fatty acids are molecules with a carboxylic acid group at one end, while the remainder of the molecule is a hydrocarbon chain having anywhere from four to thirty-six carbon atoms. They can be saturated or unsaturated, and they generally occur as unbranched chains. As with all biochemical molecules, there are good fatty acids as well as bad.

Omega-3 fatty acid (linolenic acid) is a beneficial fatty acid, cited as slowing the buildup of atherosclerotic plaques. Omega-3 fatty acids have been shown to regulate the immune system and to lower blood pressure. The structure of omega-3 is shown below. It is found in seed oils, fish, and in egg yolks. Since the body cannot produce these particular fatty acids, food is the only source of this type of lipid. Therefore, omega-3 is known as an essential fatty acid.

Notice that omega-3 fatty acid has a carboxylic acid functional group on one end and a terminal methyl group on the other end. It also has three double bonds, one at carbon 9, one at carbon 12, and one at carbon 15, giving this fatty acid its unique structure.

Steroids are compounds where four carbon rings are bounded together with branches and functional groups bounded to the rings. Depending on the combinations of the rings, branches, and functional group, different steroids can be formed with different functions in the body. The diagram below shows the structures of lanosterol and corticosterone. In lanosterol, notice that the four rings, the hydroxyl group, and the number of branches from the carbon rings. Lanosterol has 30 carbon atoms in total and acts as the basic building block for all steroids. Corticosterone is a steroid hormone important in mobilizing the immune system to fight infection. Notice the similarity in the structures to lanosterol.

Phospholipids are a combination of fatty acids, glycerol, and a phosphate group joined together. Phospholipids play a major role in cell membranes. The figure below shows phosphatidyl choline, which is the major component of lecithin. Lecithin is present in egg yolk and soy beans, among other foods. Notice the position of the links between the amine, the phosphate group, the glycerol, and the fatty acids.

Carbohydrates

Carbohydrates supply the necessary energy living systems need to survive. All carbohydrates contain carbon, hydrogen, and oxygen and have the general formula \mathrm{C}_x(\mathrm{H}_2\mathrm{O})_y. These molecules are also known as sugars or sugar chains that perform specific functions depending on their structure. Carbohydrates can be classified into three different categories:

  1. monosaccharides
  2. disaccharides
  3. polysaccharides

Monosaccharides and disaccharides are also known as simple sugars. Refined white sugar commonly found in the home is an example of a simple sugar. More precisely, refined white sugar is the simple sugar sucrose. Sucrose is a disaccharide formed when two monosaccharides (glucose and fructose) join. A monosaccharide is a single sugar unit whereas a disaccharide has two sugar units. Illustrations of sucrose, glucose, and fructose are shown below. Notice that the bond joining the two monosaccharide units in sucrose. The molecule on the left in sucrose is a glucose molecule, while the molecule on the right is a fructose molecule. As the two monosaccharides join, both glucose and fructose will lose a hydrogen atom and one of the molecules will also lose an oxygen atom when they join to form the disaccharide.

Sucrose: a disaccharide

Glucose: a monosaccharide

Fructose: a monosaccharide

Within polysaccharides, there are numerous individual sugar units. Starches, for example, are polymers where a large number of glucose monosaccharides join together. Starches have the general formula (\mathrm{C}_6\mathrm{H}_{10}\mathrm{O}_5)_n, where n is dependent on the type of starch formed. For example, glycogen is an animal starch that is made up of approximately 60,000 glucose units. Glycogen is important as a source of energy storage in both the liver and in muscles. When an organism needs that energy, degradation enzymes release the glucose units. Notice in the diagram below how the glucose molecules are linked together in glycogen.

Proteins

A polymer is a large organic molecule that contains hundreds or even thousands of atoms. Amino acids are molecules that contain an amine group (-\mathrm{NH}_2) and a carboxylic acid group (-\mathrm{COOH}). There are twenty different naturally occurring amino acids that differ only in the R group that separates the amino group from the carboxyl group. When amino acids join together, the link that joins them is called a peptide bond. The diagram below shows the formation of the dipeptide bond.

Two amino acids joining is a dipeptide. When many amino acids combine together, a polypeptides will form. A protein is a combination of these polypeptides or long chains of amino acids. Proteins are essential to the structure and function of all biological cells. Figure below shows a 3D model of the protein myoglobin, which is a marker for damaged muscle tissue. It is released when the muscle tissue is damaged. It is a polypeptide made from a chain of 153 linked amino acids.

Representation of a 3D model of a protein.

Representation of a 3D model of a protein.

Other proteins that are essential to our life include keratin, collagen, actin, myosin, and hemoglobin. Hair and nails contain keratin, tooth enamel and bones are made from collagen, and muscle tissue contains actin and myosin. Hemoglobin is the most complex of the human proteins and is used to transport oxygen in the blood.

There are four different types of structures that proteins form in the body:

  1. primary (1^\circ) structures
  2. secondary (2^\circ) structures
  3. tertiary (3^\circ) structures
  4. quaternary (4^\circ) structures

Primary (1^\circ) structures are linear chains of amino acids where the peptide bonds link the amino acids together in long chains or sheets. An example of the primary structure of protein is shown in Figure below.

Primary structure of a protein

Primary structure of a protein.

Secondary (2^\circ) structures can form pleated sheets where hydrogen bonds are formed between the amine groups and the carboxylic acid groups of the amino acids in the peptide link (see Figure below).

Secondary structure of a protein.

Pleated Sheet of the Secondary Structure

These structures can also form alpha-helix formations where hydrogen bonds connect the amino acids in the peptide link and the carboxylic acid groups in amino acids further down the protein chain. The diagram below shows the structure for the alpha helix. Notice the coiled structure versus the more straightened structure of the pleated sheet.

Tertiary (3^\circ) structures form helical structures as pleated sheets and alpha-helices join together in the same molecule. The structure of myoglobin shown above (in Figure above) shows the strings of the pleated sheets and the coils of the alpha-helix structures. There is hydrogen bonding between amino hydrogen atoms and carbonyl oxygen atoms with the secondary structures, as well as bonding between the amino acids.

Lastly, quaternary (4^\circ) structures occur when two or more polypeptides join together. The quaternary structure of hemoglobin, (Figure below) the principal oxygen-carrying protein found in red blood cells, is a combination of four structural units similar to the tertiary structure of myoglobin.

Hemoglobin

Hemoglobin

This video shows an animation of the formation of a protein (10a, 10c; 1l I&E Stand.): http://www.youtube.com/watch?v=w-ctkPUUpUc (4:00).

This video explains how amino acids form the polypeptide backbone structure of proteins (10f; 1l I&E Stand.): http://www.youtube.com/watch?v=0_WaQniUU-g (2:22).

Enzymes

Proteins are essential to life, and there are over 10,000 different kinds of proteins in the body. Enzymes are a subset of proteins. They are a specific type of protein that speed up chemical reactions, thus acting as biological catalysts. Recall that a catalyst is a substance which accelerates the rate of a chemical reaction without itself undergoing any net change. There are more than 4,000 enzyme reactions that occur in biological systems. One of the earliest known enzymes, known as amylase, was first identified by Anselme Payen in 1833. This enzyme is used in digestion to convert starch to sugar in the body. If you were to chew on a cracker, you would notice that after a while it would start to taste a little sweet in the mouth. This is the enzyme in the saliva beginning to do its job. Figure below shows an illustration of amylase. Notice the similarity in structure between enzymes and proteins.

Amylase

Amylase

DNA

After a discussion of proteins, the next logical step is to learn about nucleic acids. DNA (short for deoxyribonucleic acid), is a polynucleotide found primarily in the nucleus of the cell that maintains our genetic coding. Its function is to direct the body in the synthesis of proteins. The DNA molecule is a large polynucleotide with a molecular weight in the range of 6 million amu. Ribonucleic acids, like RNA, are smaller with molecular weights in the realm of 20,000 to 40,000 amu. A DNA nucleotide consists of one sugar (deoxyribose), a phosphate group, and one of four nitrogen bases. These four nitrogen bases are:

  1. adenine (A)
  2. thymine (T)
  3. guanine (G)
  4. cytosine (C)

Looking at the structure for deoxyribose (the sugar in the DNA molecule, structure shown in Figure below), the phosphate will react and form a link with the hydroxyl groups, forming an outer layer of phosphate-deoxyribose chains. The inner structure of the DNA molecule contains the nitrogen bases. Each nitrogen base has linked to the deoxyribose via a hydroxyl group on the sugar unit, and through hydrogen bonding, these nitrogen bases have complementary linkages to each other (A exclusively links to T, and C connects only to G).

Deoxyribose

Deoxyribose

It is interesting to note that the two strands form a double helix (see Figure below), which adds flexibility to the structure, easy storage, and availability of genetic material in addition to ease in the integrity of replication. In order to copy the DNA in cell replication, the double helix unwinds, resulting in two complementary strands, each of which can construct a daughter double helical DNA structure of its own.

DNA Illustration as a double helix

Illustration of DNA as a double helix.

Lesson Summary

  • Lipids are used for the storage of energy.
  • Carbohydrates are also known as sugars or sugar chains, and they supply the necessary energy for living systems.
  • Amino acids are building blocks for proteins.
  • Enzymes are a special type of protein that speed up chemical reactions and thus act as catalysts.
  • DNA contains our genetic coding, its function is to direct the body in synthesizing proteins.

Further Reading / Supplemental Links

The learner.org website allows users to view streaming videos of the Annenberg series of chemistry videos. You are required to register before you can watch the videos but there is no charge. The website has one video that relates to this lesson called “Proteins: Structures and Function.”

This video is a ChemStudy film called “Synthesis of an Organic Compound.” The film is somewhat dated but the information is accurate.

Review Questions

  1. Fill in the following table (Table below).
Compound Main Purpose
Carbohydrate
Lipid
Protein
Enzyme
DNA
  1. For which biochemical molecule do the triglycerides belong?
    1. carbohydrates
    2. lipids
    3. proteins
    4. enzymes
  2. A primary structure is most likely part of what biochemical molecular classification?
    1. carbohydrates
    2. lipids
    3. proteins
    4. enzymes
  3. This biochemical molecule is considered a subset of a larger group of molecules?
    1. carbohydrates
    2. lipids
    3. proteins
    4. enzymes
  4. Starch is a member of what biochemical molecular group?
    1. carbohydrates
    2. lipids
    3. proteins
    4. enzymes
  5. The structure for ribose is shown below. What is the difference between this sugar and the sugar commonly found in DNA?

All images, unless otherwise stated, are created by the CK-12 Foundation and are under the Creative Commons license CC-BY-NC-SA.

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