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The chemical Basis of Life
Organic molecules
1. Carbohydrates
Carbohydrates are made of the atoms: oxygen, hydrogen and carbon . They are soluble in water due to the presence of the following polar groups, which can make H-bonds with water:
• Hydroxyl group (OH)
• Aldehyde group (H-C=O) • Ketone group (-C=O)
Carbohydrates are divided into three groups according to their complexity:
• Monosaccharides : made of one sugar, examples on this include glucose, fructose, and ribose . The names of sugars end with the suffix ose, which means sugar. Monosaccharides can have 3, 4, 5, 6 or more carbon atoms in their structures. The following table shows the names of some sugars depending on the number of carbon atoms.
Number of carbon atoms |
General name of sugar |
3 |
Triose
Such as glyceraldehyde. In the Calvin cycle of photosynthesis , PGAL or GALP is glyceraldehyde phosphate, which is a three carbon sugar. |
5 |
Pentose
Such as ribose which is important in the structure of RNA. In DNA the pentose sugar is deoxyribose , which is a ribose missing one oxygen. |
6 |
Hexose
Such as glucose which is broken in respiration to release energy. |
In the process of respiration, glucose is broken down inside the cell to release energy in the form of ATP, as shown below:
C6H12O6 + 6O2  6CO2 + 6H2O + energy
Glucose is carried from the small intestine to all body cells by the circulation. Its level in blood is controlled by hormones including insulin and glucagon, which are secreted by the pancreas and work in the liver.
The structure of glucose can exist in the form shown below, which is known as
΅ - D- glucose.
The numbers show the carbon position in the structure.
2. Disaccharides: These are carbohydrates made by the condensation reaction of two monosaccharides as shown in the following example:
Glucose + Glucose Maltose + Water
The following diagram illustrates this reaction.
A condensation reaction builds up big molecules from smaller ones with the removal of water. Other examples of disaccharides are sucrose, which is formed from the condensation reaction of glucose and fructose, and lactose (the sugar of milk) is formed from the condensation reaction of glucose and galactose:
3. Polysaccharides: These are polymers made from the condensation reaction of three or more monosaccharides (monomers).
Starch (amylose) is a polysaccharide that functions as a storage substance in plant cells. It is made from 1,000 or more alpha-glucose units attached together by glycosidic bonds.
 A starch polymer can exist in the form of a helix. The shape of the helix is maintained by hydrogen bonds.
Starch is present in plant cells in structures called starch grains. These grains can be seen under the microscope in thin sections of potato tubers stained black with iodine (fig. 2.1). Other examples on plant structures containing high amounts of starch are cereal grains such as wheat, rice and maize. Starch is stored in these seeds to provide energy for the growth of the embryo during seed germination.
Glycogen is an animal storage polysaccharide, which is also made of many glucose units. The units are connected together in long chains that have side branches, so it is a branched molecule. In mammals it is mainly stored in the liver and muscles in the form of glycogen granules (fig. 2.2).
Diagram showing the branched structure of glycogen. Glycogen is a polymer of glucose. It is the storage carbohydrate in animal cells. In humans and other mammals it is mostly stored in the liver. Also it is stored in the muscles as a source of energy.
Both starch and glycogen can be broken down to produce glucose, which is then used in cellular respiration to release energy. The breakdown of polysaccharides to monosaccharides is called hydrolysis; one water molecule is needed for each bond to be broken (fig 2.3).
Hydrolysis is involved in the process of digestion of big molecules to smaller ones in the digestive tract by the action of specific enzymes.
Another important polysaccharide is cellulose, which is a polymer of glucose, and a constituent of plant cell walls. Cellulose is a structural polysaccharide; it is made of glucose chains attached together by H-bonds (Fig. 2.4), an arrangement that makes cellulose a tough structure.
Figure 2.1 : Appearance of starch grains in potato cells under the light microscope.
Figure 2.2 : Appearance of glycogen granules in liver cells under the light microscope.
Figure 2.3 : Hydrolysis of starch to glucose. Hydrolysis is a reaction that breaks down big molecules to smaller ones, with the addition of water. Condensation reaction builds smaller molecules into bigger ones with the removal of water molecules.
In hydrolysis of starch, each glycosidic bond (indicated by the arrow) is broken and a water molecule is used. A starch with 4 glucose units needs 3 water molecules for the hydrolysis of the 3 bonds.
How many water molecules are needed for hydrolyzing a polymer with 1000 glucose units?
The formula is:
Number of monomers = n
Number of bonds = n-1
Answer: 999 water molecules
What is the structural formula of a carbohydrate made of 10 glucose units?
Answer :
10 x (C6H12O6) = C60H120O60
When 10 glucose units are linked into a polymer, 9 water molecules (9xH2O) come out from the 9 bonds that link these molecules together, hence:
C60H120O60 minus 9H2O = C60H102O51
Hence, the general formula of a carbohydrate could be written as: CxH2yOy
Cellulose cell wall is fully permeable to water and other substances, and so it does not have much control on the passage of substances. It is the cell membrane with its various properties and channels that controls the entry and exit of substances. However, the cell wall is very important in counteracting water pressure that results from osmosis. Consequently, plant cells swell with the entry of water, but they do not burst. Swelling of plant cells results in turgidity and this is one of the factors that gives support and skeleton to plants.
The structure of cellulose is shown in figure 2.4
Figure 2.4 : Cellulose made of cellulose microfibrils; each made of a chain of glucose units. The chains are connected together by H-bonds giving cellulose its tough structure.
Plant cells are turgid (strong and tough) with water pressure and wall pressure due to the properties of cellulose. Cellulose is a tough elastic substance that allows the cell to swell but not burst. Support in grasses and other herbaceous plants is mainly due to the properties of cellulose. For humans, cellulose is an important source of dietary fiber. Having no cellulase in our digestive system, cellulose cannot be digested and it moves out of the digestive tract taking with it some harmful substances and facilitating the process of digestion and excretion. Moreover, research has proven that dietary fiber decreases the incidence of colon cancer. |
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2. Proteins
Proteins are organic compounds that contain the atoms, oxygen, carbon, hydrogen and nitrogen. In addition many proteins contain sulfur.
Proteins are polymers of amino acids, the building units. Each amino acid has a central carbon atom connected to the following groups
:
- A carboxyl group
- An amino group - NH2
- A hydrogen atom. H
- An R group, which is different in different amino acids. There are 20 different amino acids, so there are 20 different R groups.
Consequently an amino acid has the following structure:
The amino and carboxyl groups give amino acids and proteins their characters and properties and so they are called functional groups.
When amino acids are linked together to form proteins, the amino group of one amino acid links with the carboxyl group of another amino acid and form a bond called a peptide bond. A water molecule is removed from the formation of each peptide bond. The number of water molecules removed in polymerization of amino acids to polypeptides is always one less than the number of amino acids in the polypeptide. Hence in a polymer of 100 amino acid units 99 water molecules came out from the bonds between the amino acids.
Figure 2.5: Condensation of 2 amino acids into a dipeptide. The peptide bond forms between the carboxyl and the amino groups
When two amino acids connect together by condensation, a dipeptide results. The bond between the two amino acids is called peptide bond, it occurs between the carboxyl group of one amino acid and the amino group of the other amino acid, as shown in figure 2.5
.
Polypeptides are made by the condensation reaction of 3 or more amino acids, as shown in figure 2.6. Proteins are water soluble to some extent due to the presence of amino and carboxyl groups and other charged groups. Their solubility decreases with size.
Figure 2.6: a simple representation of a polypeptide made of the condensation of amino acids
3. Lipids
Lipids or triglycerides are organic substances containing oxygen, hydrogen and carbon. Each lipid molecule is made of three fatty acids and one glycerol by condensation reactions. They are hydrophobic due to the long neutral hydrocarbon chains in their structure.
There are two types of lipids: fats and oils. Fats contain saturated fatty acids in their structures, so they are solid at room temperature, e.g., butter and the animal fat which is found mostly in red meat. Unsaturated fat is mostly present in plants, e.g., olive oil, sunflower oil, corn oil and others.
Unsaturated fat is healthier in our diet, since saturated fat causes increased cholesterol levels in the blood which results in cardiovascular problems.
Phospholipids
Phospholipids are molecules made of one glycerol, 2 fatty acids and a phosphate group. 
phospholipids are major constituents of the cell membrane, which is made of a phospholipid bilayer. The phosphate head is negatively charged and the tails are neutral. This results in phospholipids being partly hydrophilic and partly hydrophobic, as shown in the diagram
Consequently, phospholipids maintain the integrity of the cell membrane. The fatty acid tails are always directed away from water and so they stick together, and this keeps the two layers intact in one unit. The heads on the other hand are hydrophilic and so they are always arranged in the water phase of the cytoplasm and the intercellular fluid (the fluid outside the cell), as shown below: 
Diagram showing the phospholipid bilayer which forms a major part of the cell membrane. The heads are immersed in the water of the cytoplasm and intercellular fluid, while the tails are stuck together away from water.
As shown in the above diagram the phosphate heads, which are polar, face the inner and outer sides of the membrane. The inside of the membrane is in contact with the cytoplasm, while the outer side is in contact with the intercellular fluid (the fluid outside the cell). The cytoplasm and the intercellular fluid contain mainly water and so the phosphate heads can be arranged in the manner shown above, since these heads are hydrophilic. The fatty acid tails on the other hand are hydrophobic so they are arranged in a way that keeps them away from water as shown above. This keeps the integrity and shape of the cell membrane, and so the two layers of the phospholipid bilayer stay attached together and they would not peel off each other.
Functions of lipids :
1. Energy production : lipids have about twice the energy content of both proteins and carbohydrates
2. Heat insulation : the layer of fat under the skin insulates the body against temperature changes. Arctic animals, such as whales have a thick layer of fat, called blubber.
3. Fat is a storage molecule, and because it is hydrophobic, it is stored without water. Therefore, it does not add much to the body weight, and this makes it very useful as a storage substance in birds, especially during migration. The bird needs storage of adequate amount of energy, with the least amount of weight.
4. Shock absorbent; there is a layer of fat surrounding some organs in the body, such as the kidneys, this protects them from shocks and knocks in the surrounding environment.
5. Some lipid derivatives act as hormones (testosterone, estrogen, and progesterone) and others as components of cell membranes (phospholipids). 4. Nucleotides Nucleotides are organic compounds made of a phosphate group, a nitrogen base and a pentose sugar (a pentose is a 5-carbon sugar), which could either be ribose or deoxyribose. A nucleoside is a nucleotide without the phosphate group (it is made of sugar and one of the nitrogen bases). The molecules are connected together by covalent bonds as shown in the diagram below: 
These nucleotides are important structures in the formation of: nucleic acids RNA and DNA, coenzymes, and the energy molecule ATP.
Nucleic acids : DNA and RNA are called nucleic acids because they were first discovered in the nucleus. Later it was found that DNA is part of the chromosomes in the nucleus and that it is also found in the mitochondria and the chloroplasts.
RNA, however can be found in the nucleus and in the cytoplasm. RNA (Ribonucleic acid)
RNA is a polymer of nucleotides in the form of a single chain. The nitrogen bases that occur in its structure are of 4 different types, as shown below:
A = Adenine
G = Guanine
C = Cytosine
U = Uracil
The pentose su
gar is ribose (a 5-carbon sugar). The structure of RNA is shown in figure 2.9.
RNA functions in protein synthesis and it occurs in the nucleus and the cytoplasm. There are 3 types of RNA; messenger RNA (mRNA), transfer RNA (tRNA) and ribosomal RNA (rRNA). The function of these molecules will be discussed in detail in a later chapter.
As shown in the diagram a ribose sugar is connected to a phosphate on one side and a nitrogen base on the other. Within the strand a phosphate molecule connects between two nucleotides by being connected to the sugars of the two nucleotides. A nitrogen base is only connected to the ribose sugar.
RNA is a polymer of nucleotides, the nitrogen bases can be A, C, G or U. The bonds connecting all the molecules and atoms together are covalent bonds. The phosphate of one nucleotide is connected to the sugar of the adjacent nucleotide. So the nucleotides are connected together through their phosphates. The nitrogen base is connected to the sugar of each nucleotide. The sequence of nitrogen bases characterizes an RNA.
Figure 2.9: Structure of RNA; it is a chain made of repeated units of nucleotides, so it is a polynucleotide.
A simple diagram of RNA can be drawn as shown below:
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A simple diagram of an RNA chain
S =sugar
P = phosphate
B = Nitrogen base
DNA (Deoxyribonucleic acid)
DNA, deoxyribonucleic acid, is a polymer of nucleotides. As in RNA, each nucleotide is made of a phosphate group, nitrogen base and a pentose sugar (fig. 2.10). However the pentose sugar here is deoxyribose instead of ribose (Deoxyribose has one less oxygen in its structure)
The following diagram shows the difference between ribose and deoxyribose (the numbers in the diagram refer to the carbon position in the ring):
As shown in the above diagram deoxyribose has one less oxygen than ribose. The numbers 1-5 indicate the carbon position in each molecule. Notice that carbon number 2 has OH in ribose and H in deoxyribose.
Figure 2.10: A diagram representing the structure of a nucleotide. There are 4 different types of nitrogen bases in DNA, these are:
A = Adenine G = Guanine C = Cytosine T = Thymine
The nucleotides are linked together by covalent bonds into a chain of repeated nucleotides. DNA is made of two such chains. It is a double helix (fig.2.11)
The two nucleotide chains are connected together by week H-bonds between their bases. Adenine is always attached to thymine (A-T), and guanine to cytosine (C-G). This is called the complementary base pair rule and it has a great importance in the function of DNA during cell replication and protein synthesis.
Figure 2.11 : Diagram representing the structure of DNA. Notice that the number of A nucleotides = the number of T nucleotides, and a similar relation exists between
Hence the ratio of C:G = 1 and A:T = 1
Question : If adenine represents 30% of a DNA molecule, what is the percentage of cytosine?
Solution:
A = T = 30%
A+T =60%
C+G=40%
C=G=20%
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Figure 2. 12: Diagram showing the DNA double helix. Each strand is made of nucleotides connected together into a giant polynucleotide chain. The two chains are twisted around each other like a twisted ladder The sequence of nitrogen bases in a DNA molecule is of great importance and it is called the genetic code. We will learn more about this in the Genetics section of this book.The structure of one chain of DNA can be represented more simply as shown in figure 2.13. Notice that the-S-P-S-P- makes the backbone of the structure and that the bases are connected to the sugar molecule. |
Figure 2.13 : A simple diagram of DNA double strand. The structure looks like a ladder, with the sides made of sugar and phosphate and the steps made of nitrogen bases
As shown in the diagram, in the DNA molecule a deoxyribose sugar is connected to a phosphate on one side and a nitrogen base on the other. Within the strand a phosphate molecule connects between two nucleotides by being connected to the sugars of the two nucleotides. A nitrogen base is covalently connected to the ribose sugar of the nucleotide of one strand, and it is connected by hydrogen bonds to the nitrogen base of the other strand.
Covalent bonds exist between all the atoms of each strand.
Hydrogen bonds are present only between the nitrogen bases of the two strands.
Comparison of RNA and DNA structures
The energy molecule
ATP
ATP is adenosine triphosphate. It is also made of nucleotides. The following molecules make one ATP structure:
Ribose sugar
Adenine (nitrogen base)
Three phosphate molecules.
A diagram representing the structure of ATP is shown below:
ATP is an energy molecule. The energy is stored in the bonds between the phosphate groups. To release the energy and use it in different functions, the bond between the first two phosphates is broken, and energy is released, as shown below:
As shown above ATP is broken to ADP to release energy. The reverse of this occurs in respiration when ATP is produced from ADP
The energy used for making an ATP molecule in respiration comes from glucose. When glucose is broken in respiration, energy which is stored in the bonds between the atoms of the molecule is released. This energy is used to phosphorylate ADP into ATP. ADP is a diphosphate molecule, when it takes another phosphate; it becomes a triphosphate molecule, an ATP. The energy needed to attach the phosphate group to the ADP molecule comes from breaking glucose. Hence, when glucose is broken, it produces ATP.
To form ATP, the cell needs ADP and phosphate. Cells use ATP as a direct energy source for processes such as, active transport, muscle contraction, cell division, movement of sperms, nerve impulse, DNA replication, protein synthesis and other energy requiring functions.
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