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Organic molecules – molecules which contain carbon.


Organic molecules – molecules which contain carbon.

We will consider four classes of organic molecules that are important is living things:

Carbohydrates, lipids, proteins, and nucleic acids.


The central role of carbon

The element carbon forms the backbone of organic molecules. A carbon atom has six protons and six electrons, two electrons in its first energy level and four in its second energy level. Thus carbon can form four covalent bonds with four other atoms.


For example, Carbon joined to four hydrogen atoms forms Methane (CH4), which is natural gas.


Carbon can also form bonds with other carbon atoms forming chains. Ethane (C2H6), for example, contains two carbons; propane, three; and butane (C4H10), four.


Ethane C2H6


Propane C3H8


Butane C4H10

In the examples shown above including methane (CH4), ethane (C2H6), and butane (C4H10) the carbon atoms are joined either to each other or to hydrogen atoms. Such compounds, consisting of only carbon and hydrogen, are known as hydrocarbons.

hydrocarbon is an organic molecule that is composed of only carbon and hydrogen.

Hydrocarbons are important because they form fuels, including gasoline, diesel fuel, and heating oil, that are burned to produce energy.

Covalent Bonds

The molecules shown above have atoms that are joined by covalent bonds. A covalent bond is the sharing of a pair of valence electrons by two atoms. This is also considered a single covalent bond. The bonds in the molecules above, for example, between the carbons and the hydrogens are examples of single covalent bonds. They are represented by drawing a single line between the two atoms. Atoms may also be joined by double covalent bonds. A double covalent bond is the sharing of two pairs of valence electrons by two atoms. An example of a molecule containing a double covalent bond, ethene, is shown below.


Ethene C2H4

Functional groups

In addition to bonding to other carbon atoms or hydrogen atoms, carbon atoms can also join to groups of atoms known as functional groups. Functional groups determine the specific chemical properties of an organic molecule.

Hydroxyl Group

A hydroxyl group (―OH), consists of a hydrogen atom bonded to an oxygen atom. Do not confuse this functional group with the hydroxide ion, (OH−).

Hydroxyl groups are found in alcohols. Some examples are methanol, or wood alcohol (CH3OH), and ethanol, or grain alcohol (C2H5OH), which is present in all alcoholic beverages. Hydroxyl groups are found in Glycerol, C3H5(OH)3, which forms the backbone of triglycerides (fats and oils). Hydroxyl groups are also common in sugars.

Carbonyl Groups

“The carbonyl group (CO) consists of a carbon atom joined to an oxygen atom by a double bond (Campbell, 2009).” Carbonyl groups include aldehyde groups and ketone groups.

Aldehyde Groups

An aldehyde group is a carbonyl group that is located at the end of the organic molecule.

Ketone Groups

A ketone group is a carbonyl group that is located in the interior of the organic molecule.

Aldehyde and ketone groups are commonly found in sugars. The aldehyde group is found in glucose and galactose, for example. The ketone group is found in fructose.

Carboxyl Group

The carboxyl group, ―COOH, consists of a carbon atom double bonded to an oxygen atom and single bonded to a hydroxyl group.

Carboxyl groups are found in organic acids.

The carboxyl group can release a hydrogen ion from the hydroxyl group into the solution. In this way it acts as an acid.

The carboxyl group (-COOH), is a functional group that gives a molecule the properties of an acid.

An example of an acid that contains a carboxyl group is acetic acid.


Amino Groups

The amino group (−NH2) consists of a nitrogen atom joined to two hydrogen atoms.

The amino group is found in amino acids and proteins.


Sulfhydryl Groups

The sulfhydryl group (―SH) consists of a sulfur atom joined to a hydrogen atom.

Sulfhydryl groups are found in certain amino acids such as cysteine. It is also found in proteins. In proteins, sulfhydryl groups can join together to link chains of the protein. This is important in bending the protein into a particular shape that is important in enabling the protein to perform its function.

Phosphate Groups

Phosphate groups (PO4−) a phosphorus atom is bonded to four oxygen atoms. Two oxygens carry negative charges. Phosphate groups are found in high-energy molecules such as ATP (adenosine triphosphate).

Methyl Groups

A methyl group consists of a carbon atom joined to three hydrogen atoms.

Methyl groups are structural components of many organic molecules.

“Addition of a methyl group to DNA, or to molecules bound to DNA, affects the expression of genes (Campbell, 2009).”


Macromolecules such as polysaccharides, fats, or proteins are composed of subunits or monomers. The monomers are linked together by a reaction known as dehydration synthesis or condensation. In this process a molecule of water is removed between the monomers and a chemical bond is formed between the two molecules.

Macromolecules are broken down in the reaction known as hydrolysis. Hydrolysis is the breaking down of a large molecule into smaller ones through the addition of a molecule of water. A hydrogen is attached to one subunit and a hydroxyl to the other, breaking the covalent bond.


Carbohydrates – organic molecules that contain carbon, hydrogen, and oxygen. In a carbohydrate, the hydrogen and oxygen are found in a 2:1 ratio. Their empirical formula (a list of the atoms in a molecule with a subscript to indicate how many of each) is (CH2O)n, where n is the number of carbon atoms. In this type of formula we can see that a carbohydrate consists of carbon combined with two hydrogens and oxygen (H2O) or water, forming a molecule with the formula C(H2O)n. Therefore carbohydrates are “hydrates of carbon”.

Carbohydrates are the primary energy-storage molecules in most living things. Carbohydrates also serve as structural elements.

Because they contain many carbon-hydrogen (C-H) bonds, which release energy when they are broken, carbohydrates are well suited for energy storage.

There are three kinds of carbohydrates, including

1. Monosaccharides (simple sugars) such as ribose, glucose, and fructose, contain only one sugar molecule.

2. Disaccharides (double sugars) consist of two sugar molecules joined together. Some examples are sucrose (table sugar), maltose (malt sugar), and lactose (milk sugar).

3. Polysaccharides are made up of many sugar molecules (monosaccharides) linked together. Examples are cellulose and starch.


Monosaccharides or simple sugars can be described by the formula (CH2O)n, where n may be as small as 3, as in C3H6O3, or as large as 8, as in C8H16O8.


Monosaccharides are metabolized to release energy. The primary energy source of cells is glucose, a six-carbon sugar.

The 5-carbon sugars ribose and deoxyribose are units used to build the structure of nucleic acids. Ribose found in RNA; deoxyribose is found in DNA.

Hydroxyl groups and an aldehyde or ketone group characterize monosaccharides. Monosaccharides also contain hydroxyl groups.

Examples of Monosaccharides


Glucose has the formula C6H12O6.


“Sugars can exist in a straight-chain form, but in water solution, they almost always form rings (Raven and Johnson).”



Isomers – forms of a molecule which have the same numbers and kinds of atoms but which differ in the arrangement of those atoms.

Glucose is not the only sugar with the formula C6H12O6. Among the other monosaccharides that have this same empirical formula are fructose and galactose. They are isomers of glucose. Both contain carbonyl groups, but in glucose the carbonyl group is an aldehyde group attached to the end of the molecule. In fructose it is a ketone group in the interior of the molecule. Galactose differs from glucose in the orientation of one hydroxyl (-OH) group.


Breakdown of monosaccharides to release energy

Monosaccharides are burned, or oxidized to yield carbon dioxide and water:

(CH2O)n + nO2 → (CO2)n + (H2O)n

This is the reaction for cellular respiration that releases energy to power cellular work. Cellular work includes building large molecules, transport of substances through cell membranes, muscle contraction, other forms of cellular movements, etc.

“As measured in a calorimeter, the oxidation of a mole of glucose releases 673 kilocalories (Curtis and Barnes, 1989)”:

C6H12O6 + 6O2 → 6CO2 + 6H2O

ΔH˚ = -673 kcal


Disaccharide – carbohydrates that are composed of two monosaccharides chemically joined together. (A double sugar)

Importance of Disaccharides:

1. Disaccharides are metabolized to release energy.

2. Disaccharides are used to transport sugars particularly in plants.

Although vertebrates transport sugar in the form of glucose, other organisms often use disaccharides for the same purpose.

Disaccharides are formed by linking two monosaccharides. In the synthesis of a disaccharide molecule from two monosaccharide molecules, a molecule of water is removed from the molecules and a chemical bond forms linking the two monomers. This reaction is an example of dehydration synthesis or condensation.

When a molecule of glucose is joined to another molecule of glucose, the resulting molecule is maltose:

glucose + glucose → maltose


When glucose combines with fructose, the resulting disaccharide is sucrose:

glucose + fructose → sucrose

Sucrose is cane sugar or table sugar. Sucrose is the form in which most plants transport glucose.

The disaccharide lactose is formed by combining the monosaccharides glucose and galactose.

glucose + galactose → lactose

Lactose is a sugar that occurs only in milk. It is known as milk sugar. Lactose is found in the breast milk used to supply energy to infants. Utilizing lactose for supplying food to the baby has the effect of reserving energy for the child, since many adults, including virtually all non-white humans, lack the enzyme required to cleave the disaccharide into its two monosaccharide components. Since they lack this enzyme, adults cannot metabolize lactose (Raven and Johnson).

“When a disaccharide is split into its monosaccharide units, which happens when it is used as an energy source, a molecule of water is added. This splitting is known as hydrolysis, from hydro, meaning “water”, and lysis, meaning “breaking apart” (Curtis and Barnes)”.

“Hydrolysis is an energy-releasing reaction. The hydrolysis of sucrose, for example, releases 5.5 kilocalories per mole. Conversely, the formation of sucrose from glucose and fructose requires an energy input of 5.5 kilocalories per mole of sucrose (Curtis and Barnes)”.



Polysaccharides – carbohydrates that are made up of monosaccharides linked together in long chains.

Functions of polysaccharides: polysaccharides are used for the storage of carbohydrate energy. They are also used for building the structure of organisms and for protection.

Storage polysaccharides


Starch is the principal form in which glucose is stored in plants.


In animals glucose is stored in the form of glycogen, or animal starch. Glycogen differs from starch in that the average chain length is longer and that there are more branches in the chain. In glycogen the branches occur every eight to ten glucose units.

structural polysaccharides

Certain polysaccharides are important in building the structural components of living organisms. Cellulose makes up the cell walls of plants. It is the most common organic compound in the biosphere (Curtis and Barnes, 1989).

Cellulose is composed of long chains of monomers of glucose, just as starch and glycogen are.

Most animals do not have the enzyme that is necessary for the digestion of cellulose. Humans cannot digest cellulose; however, it is a source of fiber and necessary for the proper functioning of the digestive system. Certain microorganisms can digest cellulose. Cattle and other ruminants that live on vegetation, also lack the enzyme required to break down cellulose. However, they have a stomach that is composed of several parts. In the stomach there is a population of microorganisms. They break down the cellulose, making it possible for the animal to live on their diet of vegetation. Termites feed on rotting wood. They also lack the enzyme required for the digestion of cellulose. However, they have entered into a symbiotic relationship with a flagellate known as Trichonympha. This tiny protozoan lives within the intestine of the termite. It does have the enzyme that breaks down the cellulose, and makes the food energy available for the termite. In return, the protozoan has a protected location in which to live, and is provided with a steady source of food.


Chitin is a polysaccharide that makes up the shell of arthropods such as lobsters, crabs, or insects. As such it forms a protective coat of armor around the animal. It also makes up the cell walls of fungi.


Lipids – organic molecules that contain carbon, hydrogen, and oxygen. In a lipid, the hydrogen and oxygen are not in a 2:1 ratio, the ratio is much higher.

The major function of lipids in living organisms is to store energy. When organisms have excess glucose they usually convert some of it into lipids and store it for when it is needed. In our bodies we have adipose tissue or fat which contains stored food. Some plants also store food energy as oils, especially in seeds and fruits. Lipids are also used for other purposes, phospholipids, glycolipids, and waxes are used for structural purposes. Some lipids serve as chemical messengers such as lipid hormones. Other lipids provide waterproof coverings for plant organs.

Lipids are a general group of organic substances that are insoluble in polar solvents, such as water, but that dissolve readily in nonpolar organic solvents, such as chloroform, ether, and benzene (Curtis and Barnes, 1989).

fat or oil consists of three molecules of fatty acids joined to one glycerol molecule. Glycerol is a three-carbon alcohol that contains three hydroxyl groups. “A fatty acid consists of a long hydrocarbon chain that terminates in a carboxyl group (-COOH); the nonpolar chain is hydrophobic, whereas the carboxyl group gives one portion of the molecule the properties of an acid (Curtis and Barnes, 1989).”

Because there are three fatty acids joined to a molecule, the resulting molecule is called a triglyceride. “The three fatty acids of a triglyceride do not have to be identical, and often differ markedly from one another (Raven and Johnson).” “Fatty acids vary in length. The most common are even-numbered chains of 14 to 22 carbons (Raven and Johnson).”

The fatty acids are joined to the glycerol by the removal of a molecule of water. This is a dehydration synthesis or condensation reaction.


Saturated and Nonsaturated Fats

Saturated fats – fats that contain all the hydrogen that they can possibly hold. Saturated fats do not contain any double chemical bonds.

Unsaturated fats – unsaturated fats contains one or more double chemical bonds. As a result, hydrogen atoms can be added by opening up the double bond.

Saturated fats tend to be solid at room temperature. Many of these are animal fats such as butter and lard. They usually have high melting temperatures.

Unsaturated fats tend to be liquid. Their chains bend at the double bonds. They also have low melting points. Unsaturated fats commonly are oils, such as olive oil, peanut oil, and corn oil.

“It is possible to convert an oil into a hard fat by adding hydrogen. The peanut butter that you buy in the store has usually been hydrogenated to convert the peanut fatty acids to hard fat and thus to prevent them from separating out as oils while the jar sits on the store shelf.”

“Fats and oils contain a higher proportion of energy-rich carbon-hydrogen bonds than carbohydrates do and, as a consequence, contain more chemical energy. On the average, fats yield about 9.3 kilocalories per gram as compared to 3.79 Kcal per gram of carbohydrate, or 3.12 Kcal per gram of protein (Curtis and Barnes, 1989).”

“As you might expect, the more highly saturated fats are richer in energy than less saturated ones. Animal fats contain more calories than do vegetable fats. Human diets that contain relatively large amounts of saturated fats appear to upset the normal balance of fatty acids in the body, a situation that may lead to heart disease (Raven and Johnson).”

Insulators and Cushions

Large masses of fatty tissue surround mammalian kidneys and serve to protect these organs from physical shock (Curtis and Barnes, 1989).”

Another mammalian characteristic is a layer of fat under the skin, which serves as thermal insulation. This layer is particularly well developed in seagoing mammals (Curtis and Barnes, 1989).”

Among humans, females characteristically have a thicker layer of subdermal (“under the skin”) fat than males. This serves as a reserve food supply that nourishes the woman, but, more importantly the unborn child and the nursing infant (Curtis and Barnes, 1989).”


Phospholipids are composed of a molecule of glycerol joined to two molecules of fatty acids. The third carbon of the glycerol molecule is occupied by a phosphate group to which another polar group is usually attached.

The phosphate end of the molecule is hydrophilic (Greek hydros “water” and philos “loving”). This means that it is attracted to water. The fatty acid portion is hydrophobic (Greek hydros phobos “water-fearing or hating”), which means that it is repelled by water.

Phospholipid molecules make up the middle layer of the cell membrane. In the cell membrane, the phospholipid molecules form a double molecular layer. One layer is arranged so that the hydrophilic “heads” (polar ends) of the molecules face the outside of the cell. They do so, because they are attracted to water, and water is found on the outside of the cell. Similarly, in the inner layer of phospholipid molecules, the hydrophilic “heads” all face toward the inside. This is because once again they are attracted to water and there is water inside the cell in the cytoplasm. The fatty acid tails of the phospholipid molecules in both layers face inward. Because the fatty acid portion of the molecule is hydrophobic, or repelled by water, the tails swing inward to get as far away from the water as possible.



Steroids are a group of lipids, which are composed of ring of carbon atoms.

“Although steroids do not resemble the other lipids structurally, they are grouped with them because they are insoluble in water (Curtis and Barnes, 1989).”

The steroids form one of two major groups of hormones, the other being a group of hormones made of protein.

Significance of lipids: As can be seen by considering their role in forming hormones, the lipids are important in regulating and controlling body function.

The male sex hormone testosterone and the female sex hormone estrogen are steroids. Testosterone regulates the growth and development of the male sexual organs and regulates the process of spermatogenesis. Estrogen regulates the growth and development of the female reproductive organs and controls the menstrual cycle.

Other steroid hormones include the hormones produced by the adrenal cortex. They are important in controlling the reaction to stress.



Prostaglandins are modified fatty acids. In a prostaglandin, two nonpolar tails are attached to a five-carbon ring (Raven and Johnson).”

“Prostaglandins appear to act as local chemical messengers (Raven and Johnson).”

“Some stimulate smooth muscle to contract or to relax; others constrict or expand the diameter of small blood vessels (Raven and Johnson).” “Prostaglandins have been shown to be involved n many aspects of reproduction, and in the inflammatory response to infection (Raven and Johnson).”

Aspirin works by inhibiting prostaglandin synthesis. As a result, it reduces pain, inflammation, and fever.


Cholesterol, like the other lipids, is composed of carbon-containing rings.

Cholesterol is a component of cell membranes. Cholesterol is also a major component of the myelin sheath, the membrane that surrounds nerve axons. It helps to speed up nerve impulses.

Cholesterol is synthesized by the body. The site of synthesis is the liver. Dietary sources rich in cholesterol include meat, cheese, and egg yolks.

Cholesterol has been implicated in atherosclerosis (also known as “hardening of the arteries”) and in heart disease.

Cholesterol is transported in the blood in particles composed of a core of cholesterol surrounded by a coating of lipoproteins. There are two principal forms of the lipoproteins: low-density lipoproteins (LDLs) and high-density lipoproteins (HDLs).

LDLs carry cholesterol to various destinations in the body, including the liver as well as hormone-synthesizing organs. HDLs function to dispose of excess cholesterol by carrying it to the liver where it is degraded and prepared for excretion.


Waxes form waterproof coverings on the surfaces of plant organs such as leaves. In this way they prevent the excessive loss of water from the plant. They also form protective coverings on the skin, fur, or feathers of animals. The exoskeleton of insects is often covered by a layer of wax (Curtis and Barnes, 1989).


Proteins are organic molecules which contain carbon, hydrogen, oxygen, nitrogen, and sulfur.

Proteins are composed of long chains of amino acids.

Generalized formula for an amino acid:


The amino acids are linked by peptide bonds to form polypeptides. Example:


This reaction is an example of a dehydration synthesis reaction.

The sequence of the amino acids in a polypeptide chain is determined by DNA in the nucleus of the cell.

Functions of proteins

1. Proteins form the structure of living things.

Proteins make up much of the form of the human body. For example most of the substance of our muscles is composed of proteins.

2. Proteins are found in the cell membrane

Proteins, along with lipids, form the structure of the cell membrane. Proteins are found in the outer and inner layers of the cell membrane.

Proteins control transport through the cell membrane

Some proteins extend through the cell membrane from the outside to the inside. These proteins, which are known as transport proteins, contain pores or channels. They control the transport of substances into and out of the cell. They are involved in transport functions such as active transport and facilitated diffusion.

Proteins serve as receptors that combine with hormones and neurotransmitters and help to convey their message to the cell

On the surface of the cell, proteins form molecular binding sites or receptors. These are locations at which chemical messengers, such as hormones or neurotransmitters combine.

Proteins form markers on cell surfaces that give the cell a particular identity

We have unique proteins and glycoproteins on the surfaces of our cells which give these cells particular molecular identities. In defending our body, it is important for our immune system to be able to distinguish between the cells and tissues which belong in our body (“self”), from those that do not (“non-self”). Being able to make this distinction allows the immune system to target the non-self agents or antigens so that they can be attacked and eliminated.

3. Proteins form enzymes that control metabolic reactions in living organisms.

Metabolic reactions in living organisms typically occur in a series of many steps. A particular enzyme catalyzes each step. The presence of absence of a particular enzyme may determine whether a particular reaction or even the entire metabolic sequence can take place. Enzymes are crucial for many vital metabolic functions. For example, the reactions of digestion depend upon enzymes. In the stomach, the enzyme pepsin begins the breakdown of proteins. In the intestine there are enzymes which carry out the breakdown of carbohydrates, proteins, fats, and nucleic acids. The breakdown of glucose to release energy consists of many individual reactions. Again, a particular enzyme controls each reaction.

4. Proteins form hormones that control and regulate body function.

Protein hormones make up a major group of hormones. (The other major group of hormones is made of lipid).

A hormone is a chemical substance that is produced in one part of the body, but which functions somewhere else in the body.

Examples of Protein hormones: Growth hormone controls the rate of growth in living organisms. Thyroxine controls metabolic rate. ACTH controls reactions to stress. Insulin controls the transport of glucose into cells.

5. Proteins regulate the action of genes.

Proteins regulate the action of genes. They form repressors which regulate transcription.

6. Proteins produce movement in living organisms.

Muscle Contraction

The contraction of muscle is produced by the interaction of proteins. The mechanism of muscle contraction is explained by the sliding filament hypothesis. According to this hypothesis, muscle tissue is composed of contractile units known as sarcomeres. In the center of this unit is a dark band called the A band. This is made of two proteins called actin and myosin. The myosin molecules make up thick myofilaments. The actin molecules make up thin myofilaments. In a sarcomere that is not in a contracted state, the actin filaments fit in between the myosin filaments. They come in from each side of the A band but do not meet in the middle. When the muscle contracts, the actin filaments slide inward between the myosin myofilaments.

Beating of Cilia and Flagella

The beating of cilia and flagella is caused by the interaction of proteins.

Cell Motility

Axoplasmic transport

Cytoplasmic streaming

Amoeboid movement

7. Proteins perform important functions in the blood and body fluids.

Transport of oxygen and carbon dioxide

Hemoglobin in the blood transports oxygen and carbon dioxide. In the lungs, hemoglobin combines reversibly with oxygen. This oxygenated blood is returned to the heart to be pumped to the cells and tissues. As the blood travels through the tissues, it gives up its oxygen to the cells and picks up the waste product carbon dioxide. The carbon dioxide is transported back to the heart and then to the lungs where the carbon dioxide can be eliminated in the exhaled breath.

Transport of Hormones

Hormones, such as thyroid hormone are transported in combination with proteins.

As Antibodies, Proteins Protect the Body against Disease

Antibodies are proteins. These are Y-shaped molecules which combine with disease-causing agents and lead to their destruction.

Protein molecules are involved in the clotting of blood

Proteins take part in the reactions leading to the blood clot. The protein fibrin is a major component of the blood clot.

Proteins help to maintain the proper osmotic composition of the blood

As plasma proteins, proteins help to maintain a balance of forces that act at the capillary membrane. Plasma proteins in the blood create a force that draws fluid into the capillary. This force tends to counteract the force of blood pressure that acts to force fluid out of the capillary. If the concentration of protein is reduced to levels that are below normal, the balance of forces is upset, and fluid begins to move from the blood into the tissues. This abnormal buildup of fluid produces swelling or edema.

Proteins regulate acid-base balance in the blood and body fluids

Because proteins contain both acid and basic groups, they can neutralize either acid or base. In this way, they function as buffers to maintain the pH of the blood or body fluids within a certain range.

8. Proteins function in storage

Proteins in egg white or in seed function in the storage of nutrition. Ferritin stores ions. Casein stores ions in milk. Calmodulin binds calcium ions.

Structure of Proteins

Proteins are composed of long chains of amino acids.

There are 20 kinds of amino acids.

Generalized formula for an amino acid

An amino acid has a central carbon atom. Like all carbon atoms, this carbon atom has four bonds extending from it. A hydrogen atom is connected to one of these bonds. An amino group (NH2) is attached to a second bond. The third bond is attached to a carboxyl group (COOH). The fourth bond is attached to various groups. This is the group that determines which specific amino acid is produced. In the generalized formula, this group is represented by the symbol R. Substituting a specific group in this position produces a specific amino acid, one of the 20 different kinds.

The NH2 group (amino group) can function as a base. It can accept a hydrogen ion from the solution, becoming NH3+. The COOH can function as an acid. It can release a hydrogen ion (H+) into the solution. Because proteins have both acidic and basic groups, they can function as acid-base buffers. They can neutralize either acid or base.

In a protein, the amino acids are joined by peptide bonds. This bond is formed between the amino group of one amino acid and the carboxyl group of an adjacent amino acid. The peptide bond is formed between the two amino acids as a molecule of water is removed from between them. This is a dehydration synthesis reaction. Linking together two amino acids produces a dipeptide. Linking together several amino acids produces a polypeptide.

The DNA in the nucleus of the cell determines the sequence of the amino acids in the polypeptide chain. This sequence is very specific for particular proteins.

Example of the specificity of a protein – sickle cell anemia

The disease sickle cell anemia is caused by the presence of a defective hemoglobin molecule. “When oxygen is removed from them, these molecules change shape and combine with one another to form stiffened rod-like structures. Red blood cells containing large proportions of such hemoglobin molecules become stiff and deformed, taking on the characteristic sickle shape. The deformed cells may clog the smallest blood vessels (capillaries). This causes blood clots and deprives vital organs of their full supply of blood, resulting in pain, intermittent illness, and, in many cases, a shortened life span (Curtis and Barnes, 1989).” In the hemoglobin molecule, there are four polypeptide chains, two alpha chains and two beta chains. The defect that causes sickle cell anemia is a substitution of an incorrect amino acid in the sequence of amino acids in the beta chain of hemoglobin. The beta chain contains 146 amino acids. Sickle cell anemia results from a mistake in only one out of these 146 amino acids. In position 6 in the beta chain of hemoglobin, the amino acid valine replaces the normal glutamic acid.

essential amino acids

Humans can synthesize all but nine of the amino acids. The amino acids that must be supplied in the diet are called essential amino acids. These include the following amino acids: Histidine, Isoleucine, Leucine, Lysine, Methionine, Phenylalanine, Threonine, Tryptophan, and Valine.


The structure of proteins can be considered on four levels, going from the simplest to the most complex. These four levels are primary structuresecondary structuretertiary structure, and quaternary structure.


The primary structure of a protein is the sequence of amino acids along the length of the polypeptide chain.

In the polypeptide chain, the amino acids are linked together, like boxcars in a train.

DNA determines the amino acid sequence in the polypeptide chain.

“Each different protein has a different primary structure (Curtis and Barnes, 1989).”


There are two forms of secondary structure: the alpha helix and the beta pleated sheet.

In the alpha helix, the polypeptide chain is coiled into a spiral or helical structure. The coiling is caused by the formation of hydrogen bonds between the CO and NH groups of the main chain.

The beta-pleated sheet is formed by hydrogen bonding between several polypeptide chains. The hydrogen bonds connect the polypeptide chains between their NH and CO groups so that they come to lie side by side in a zigzag pattern.


Tertiary structure refers to the folding of helical (or randomly coiled) chains (Chemical Basis of Life, Sci. Amer.) to form proteins with a globular shape. This structure is determined by interactions between R groups. For example, a bond known as a disulfide bond may form between two cysteine molecules located along the polypeptide.


The quaternary structure is determined by the combination of several different polypeptides along with non-protein groups to form a functional protein.

The Hemoglobin Molecule as an Example of a Functional Protein with Quaternary Structure

Hemoglobin is a protein found in our red blood cells. It is the red pigment that is responsible for transporting oxygen in our blood. It combines reversibly with oxygen in the lungs. From the lungs, the blood is returned to the heart and then pumped to all parts of the body. As the blood travels through the tissues, hemoglobin releases the oxygen to the cells. It then combines reversibly with carbon dioxide. The blood carries this carbon dioxide to the heart and then to the lungs. In the lungs, the carbon dioxide is expelled from the body in the exhaled breath.

The hemoglobin molecule has a quaternary structure. It is made up of four polypeptide chains: two alpha chains and two beta chains. In addition there are four iron-containing, or heme groups.


An enzyme is an organic catalyst.

The term organic refers to a substance that contains carbon.

A catalyst is a substance that speeds up the rate of a chemical reaction.

Almost all known enzymes are proteins. Recently, an exception to this was discovered. It was found that RNA could function as an enzyme. This RNA is known as ribozyme.

Enzymes catalyze chemical reactions by bringing substrates together in an optimal orientation conducive to the formation or breaking of chemical bonds.

Many enzymes are named by adding the suffix –ase to the name of the substrate. For example, the enzyme sucrase works on sucrose, the enzyme lipase works on lipid, and so on. Not all enzymes are named this way. Pepsin and Trypsin, which act on proteins, are examples.

Some enzymes require one or more nonprotein components, called cofactors in order to be active. The cofactor may be a metal ion or an organic molecule called a coenzyme; some enzymes require both (Lehninger, 1975).

Coenzymes generally contain as part of their structure a vitamin, a trace organic substance required in the diet of certain species (Lehninger, 1975).


As an example of the action of an enzyme, consider the joining of carbon dioxide and water to form carbonic acid.

CO2 + H2O image19.jpg H2CO3

Carbon dioxide water Carbonic acid

The reaction may proceed in either direction. Without the enzyme the rate of the reaction is very slow. Perhaps 200 molecules of carbonic acid form in an hour.

In the presence of the enzyme carbonic anhydrase, the rate of the reaction is greatly increased. An estimated 600,000 molecules of carbonic acid form, not every hour, but every second. The enzyme has speeded the reaction rate about 10 million times.

“Enzymes accelerate reactions by factors of at least a million. Indeed, most reactions in biological systems do not occur at perceptible rates in the absence of enzymes (Stryer, 1995).”

How Enzymes Work

Enzymes combine with specific substrates. The reason enzymes combine with specific substrates is explained by the lock and key theory.

Enzymes combine with specific substrates. The substrate is the substance that the enzyme works on. The enzyme sucrase breaks down sucrose. It does not work on maltose or lactose. The enzyme pepsin breaks down protein into polypeptides. It breaks the protein at specific locations. Pepsin cleaves peptide bonds at the C-terminus of phenylalanine, leucine, tryptophan, and tyrosine.

“Trypsin is quite specific in that it catalyzes the splitting of peptide bonds on the carboxyl side of lysine and arginine residues only (Stryer, 1995).”

The enzyme combines with the substrate, forming an enzyme-substrate complex.

E + S ↔ ES → E + P

“The substrates are bound to a specific region of the enzyme called the active site.

The reason that the enzyme works on specific substrates is explained by the lock and key theory. The lock and key theory was developed by Emil Fischer in 1890 (see Stryer, 1995). This theory states that the enzyme has a specific shape. This shape fits into a corresponding shape on the substrate. The shape of the enzyme may be compared to the shape of a key designed to fit a particular lock. The shape of the substrate may be compared to that of the lock. The enzyme and substrate fit together like a key fits a particular lock.

A modification of the lock and key theory was postulated by Daniel E. Koshland, Jr. in 1958 (see Stryer, 1995). He pointed out that the binding of substrate markedly modifies the shapes of the active sites of many enzymes. “The active sites of these enzymes assume shapes that are complementary to that of the substrate only after the substrate is bound. This process of dynamic recognition is called induced fit (Stryer, 1995).”

Enzymes speed up chemical reactions by lowering the energy of activation for particular reactions.

The energy of activation is the energy required to get a reaction going.

For example, imagine that you wanted to start a fire in a fireplace. You obviously could not start the fire by holding a match to a large log. The amount of heat would not be great enough to start the log on fire. Another way of saying this is that the energy supplied by the match was not sufficient to supply the energy of activation required to start the reaction. To get the large log to burn, we would need to put paper in the fireplace, then some small twigs, then some small logs, and then finally place our large log on top of this. The energy supplied by the burning of the smaller items would then be great enough to start the log on fire. We would have supplied sufficient energy of activation to get the reaction going.

Enzymes speed up chemical reactions by lowering the energy of activation required to get the reaction going. This can be seen by examining two lines on the graph, one showing the energy of activation required for a reaction that is not catalyzed by an enzyme, and a second line showing a reaction catalyzed by an enzyme:


Enzymes lower the energy of activation by bringing substrates together. They can then react more efficiently. An enzyme can also work by bringing certain groups of the enzyme into close proximity to certain bonds of the substrate. This alignment makes it easier for the bonds to be broken, thereby lowering the energy of activation for the reaction.

Following the reaction, the enzyme has not been permanently altered, and can be recovered and used again. As a result, only tiny amounts of enzymes are required to catalyze reactions.


Among the factors that affect enzymes are temperature, pH, and the concentrations of the enzyme and the substrate.

1. Temperature

Temperature affects ordinary chemical reactions. Increasing the temperature increases the rate of a chemical reaction. For example, the rate of most chemical reactions is approximately doubled by a 10º C rise in temperature.

The rate of a chemical reaction that is catalyzed by an enzyme is also increased by temperature. However, because the enzyme is a protein, as the temperature is increased and reaches a certain point, the reaction behaves differently. If we look at the effect of temperature on the rate of a reaction catalyzed by an enzyme, (graph) we will see that as the temperature increases, the rate of the reaction also increases. This happens until a certain high temperature is reached. At this temperature the enzyme is inactivated. The enzyme is denatured. An example of this is seen when an egg is boiled. Prior to boiling, the egg white, which is the protein albumin, is a clear liquid. After the egg is boiled, the clear albumin turns into the solid egg white. The change that took place was permanent and irreversible. It is an example of a protein being denatured. The same thing happens to an enzyme subjected to a very high temperature. The enzyme is denatured. This inactivates or destroys the activity of the enzyme. As a result, the rate of the reaction catalyzed by the enzyme levels off and then drops.

“Although most enzymes are inactivated at temperatures above about 55 to 60º C, some are quite stable and retain activity at much higher temperatures, e.g., enzymes of various species of thermophilic bacteria inhabiting hot springs, which are still active at temperature exceeding 85º C (Lehninger, 1975).”




In order to function, enzymes must work within specific ranges of pH.

“Most enzymes have a characteristic pH at which their activity is maximal; above or below this pH the activity declines (Lehninger, 1975).”

For example, the enzyme pepsin, which functions to break down proteins in the stomach forming polypeptides, works best at a pH of 2 to 3 and is completely inactive at a pH above approximately 5 (Guyton, 1986).

The enzyme salivary amylase, which functions in the mouth cavity to break down starch into maltose and dextrins, works best at a pH of 6.8.

Other enzymes, which work in the small intestine, such as pancreatic lipase, work best at an alkaline pH of 8.0.



When the concentration of the enzyme is significantly lower than the concentration of the substrate, the rate of an enzyme-catalyzed reaction is directly dependent on the enzyme concentration.




We will examine the effect of the substrate concentration on the rate of an enzyme-catalyzed reaction. If the concentration of the substrate is increased, the rate at which the product is formed also increases, up to a maximum value. At that point the enzyme molecule is saturated with substrate (Alberts, et al. 1994).



Nucleic acids include deoxyribonucleic acid (DNA) and ribonucleic acid (RNA).

Nucleic acids constitute the genetic material. They make up the genes which are found on the chromosomes and which determine our genetic traits.


Deoxyribonucleic acid is made up of the following components:

1. Nitrogenous bases

There are four nitrogenous bases in DNA: adenine, thymine, cytosine, and guanine.

Adenine and guanine have a two-ring structure and are known as purines. Cytosine and thymine have a single-ring structure and are known as pyrimidines.

2. Deoxyribose sugar

Deoxyribose is a 5-carbon sugar.

3. Phosphate groups

The building unit of DNA is called a nucleotide. A nucleotide is composed of a nitrogenous base joined to a 5-carbon sugar, joined to a phosphate group. DNA is built of many repeating nucleotide units.

DNA contains the genetic code that directs the synthesis of protein. This code is present in the form of the sequences of nitrogenous bases that are found along the length of the DNA molecule.


Ribonucleic acid (RNA) is a nucleic acid that helps DNA to construct a protein.

RNA is a single-stranded molecule. It contains the following components:

1. Nitrogenous bases

RNA contains the nitrogenous bases adenine, uracil, cytosine, and guanine. Note that in RNA, the nitrogenous base uracil replaces the thymine found in DNA.

2. 5-carbon sugar

The 5-carbon sugar found in RNA is ribose (not Deoxyribose as in DNA).

3. Phosphate groups

Types of RNA

There are three main types of RNA:

1. Messenger RNA – carries the code for the construction of a protein from the DNA in the nucleus to the ribosomes in the cytoplasm.

2. Transfer RNA – picks up amino acids in the cytoplasm and brings them to the messenger RNA at the ribosomes.

3. Ribosomal RNA – makes up the structure of the ribosome.

Recently, additional forms of RNA have been discovered that have important roles in transcription and gene control. These include:

4. Small nuclear RNA (snRNA) – involved in the splicing (removal of noncoding regions) of messenger RNA molecules prior to transcription.

5. Signal recognition particle RNA (SRP RNA) – recognizes a signal sequence on a messenger RNA molecule and then attaches to a receptor protein in the endoplasmic reticulum to anchor the ribosome involved in translating the protein to the endoplasmic reticulum.

6. Micro-RNA (MiRNA) – involved in the control of gene expression.


When energy is needed in the cell, for example to make muscles contract or to transport molecules across cell membranes, or to synthesize large molecules etc., the energy is supplied by the breakdown of adenosine triphosphate (ATP).

The ATP molecule contains an enormous amount of energy within its chemical bonds. This energy is released when a phosphate group is removed from the molecule, forming adenosine diphosphate. The released energy is then used to power cellular work. Additional energy may be released by continuing the breakdown of the molecule. In this reaction a second phosphate group is removed from adenosine diphosphate forming adenosine monophosphate.

The Structure of ATP

The ATP molecule is made up of the following components: the purine base adenine, the five-carbon sugar ribose, and three phosphate groups. Adenine plus ribose comprise the molecule adenosine. Adenosine monophosphate is adenosine attached to one phosphate group. Adenosine diphosphate is attached to two phosphate groups. Adenosine triphosphate to three phosphate groups.

The first phosphate group is attached to the adenosine by a normal chemical bond. This is indicated in the diagram by a straight line between the two components. The bonds between the next two phosphate groups are high-energy bonds. Wavy lines indicate the high-energy phosphate bonds. These bonds contain most of the energy in ATP, energy that is released when the bonds are broken.

The Breakdown of ATP

The breakdown of ATP begins with the splitting off from the molecule of a phosphate group.

ATP → ADP + P + energy

Adenosine triphosphate → Adenosine diphosphate + phosphate + energy

The Building of ATP

When there is an excess of energy available, the cells produce ATP. For example, lets assume that you have recently eaten a meal such as lunch and that it was rich in sugars. When you are resting the food is digested, the nutrients are absorbed, and enter the bloodstream. The level of sugar in the blood is high. The sugars enter the cell and are broken down via glycolysis and the Citric Acid Cycle to produce energy. This energy is then used to produce ATP.

ATP is usually produced by starting with adenosine diphosphate (ADP). The energy from the breakdown of glucose is used to join a phosphate group to ADP, forming ATP.

ADP + P + energy → ATP

Adenosine diphosphate + phosphate + energy → Adenosine triphosphate

Study Guide Organic Molecules and their Importance in Living Things draft 9

Revised 10/12/2019



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