FED. SCHOOL OF DENTAL TECH.

AND THERAPY, ENUGU

LECTURE THREE NOTES

Introduction: - One of the most interesting chemical asymmetries associated with life on Earth is the mismatch between the composition of cells on the one hand and of inanimate matter on the other. Although, there are about 92 elements occurring naturally in nature, however, due to the rich and diverse metabolic process that make living cells work, living chemistry is largely built around Carbon, Oxygen, Nitrogen & Hydrogen, with these elemental components serving as the key building blocks making up the cells dry weight.
The Chemical composition

Chemical substances form the basis of all living organisms, from microbes to plants and mammals. These chemical substances are classified a chemical elements (i.e. micro molecules) and chemical compounds (i.e. macro molecules) from both the organic & inorganic world that appear in roughly the same proportions & perform the same general task.
Chemical Elements in Living Cells

There are about 92 elements occurring naturally in nature. From these 92 elements, only about 25 elements are needed to build living organisms, as not all these element found in all living cell. These elements are divided into major elements and minor or trace elements respectively.
Major elements

These includes Hydrogen H; Oxygen O; Nitrogen N; Carbon C; Phosphorus P & Sulphur S, that are most frequently found in the living cells. They make up more than 90% of the total body mass of a living cell and when combined in various ways, form virtually all known organic biochemicals that are utilized in the synthesis of small number of building blocks, which are in turn, used in the construction of a vast variety of vital macromolecules (including Carbohydrates; Proteins; Nucleic acids & Lipids). Each of these four biomolecules or macromolecules consists of some form of carbon, and when they're bonded together they form the basis of a living creature.
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These elements includes Sodium Na; Magnesium Mg; Calcium Ca; Potassium K; & Chlorine Cl, found in living cells in minute quantities, thus often referred to as trace elements. Trace-elements are the elements are found in small quantity in cells, but are important in biological processes. They make up about 4% total body mass of a living cell.

Trace element found in a living cell and their relative importance

Sodium (K) Magnesium (Mg) Calcium (Ca)

Controls osmotic pressure in the cells. Helps in the transmission of nerve impulses. Helps in protein synthesis. It is the main components of the bones & teeth. Triggers contraction of muscle cells. Promotes blood clotting. Needed in the synthesis of chlorophyll. Formation of cell walls (cellulose). Regulates semi-permeability of plasma membranes. Formation of carbohydrates. Activation of certain enzymes. Photolysis of water during photosynthesis.

Potassium (K) Chlorine (Cl)

Required in muscles contraction. Involves in transmission of nerve impulses. Formations of hydrochloric acid in the stomach. Maintains pH value of the stomach.

Chemical Compounds in Living Cells

A chemical compound is a substance (and a macromolecule) which consists of two or more chemical elements combined in a fixed ratio. Common elements such as Carbon (C); Oxygen (O); Hydrogen (H); Nitrogen (N); Sulphur (S) & Phosphorus (P) can combined with each other to form various chemical compounds in the living cells. The chemical compounds in the living cell can be divided into two major groups as organic (compounds that contain the element Carbon) and inorganic (compounds which do not contain carbon).
Organic compounds

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These are chemical compounds containing carbon element (exception are carbon monoxide, carbon dioxide, carbides and carbonates which are typically considered as inorganic). They are usually found in and originate from living organism. Organic compounds usually consist of macromolecules (large molecules) and are usually big and complex. These complex compounds found in a living cell are four which includes Carbohydrates, Lipids; Proteins & Nucleic acids.

Carbohydrates

A carbohydrate is any member of a widespread class of natural organic substances that includes sugars, starch and cellulose. The carbohydrates are made up of carbon, hydrogen and oxygen. The ratio of hydrogen to oxygen atoms in a molecule is usually 2:1. Carbohydrates are often isomers meaning, they have the same atomic composition but different structures. Many carbohydrates have the general formula CX(H2O)Y, where x is approximately equal to y. Three basic types of carbohydrates are monosaccharides (including glucose, fructose & galactose); disaccharides (including maltose, sucrose & lactose, galactose); oligosaccharides (including ---------) and polysaccharides (including glycogen and cellulose).

(A carbohydrate molecular structure)

(A schematic illustration of different types of carbohydrate)

Importance of Carbohydrates

The importance of carbohydrates in living cells are:1. 2. 3. 4. 5.

Is a main source of energy in the cells. Formation of the external skeletons of insects. Is an energy store in animal cells (in the form of glycogen) and in plants cells (in the form of starch). For building cell walls in plant cells. An important constituent of dietary fiber.

Monosaccharide

This is the basic building block of carbohydrates. They are reducing sugars and cannot be broken down further into smaller units of carbohydrates.
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Monosaccharide also called simple sugar containing 5-6 carbon atoms. The common monosaccharide is a six-carbon sugar with a molecular formula of C H O Three most common of monosaccharide are glucose (also called dextrose, grape sugar or corn sugar); fructose (fruit sugar) and galactose. Glucose is the most common monosaccharide and respiratory substrate. Monosaccharides are sweet-tasting crystalline substances which are soluble in water.
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Glucose: -

Glucose is a constituent of the two most widespread disaccharides, sucrose and lactose, and is the sole structural constituent of the polysaccharides cellulose, starch and glycogen. This is the most common monosaccharide in living cells. It is the monomer of most polysaccharides and the end product of digestion of starches and glycogen.

(A glucose molecular structure)

Fructose:-

This is the constituent of most sweet fruits & honey.

(A fructose molecular structure)

It is found in milk. Galactose is a common constituent of oligosaccharides and polysaccharides (e.g. agar, carrageenan), and also is found in carbohydrate-containing lipids called glycolipids located in brain and nerve tissue.

(A galactose molecular structure)

Disaccharides are complex sugars (sometimes often referred to as double sugar ), containing two monosaccharides joined together chemically with the elements of a molecule of water, through condensation chemical reaction process. All disaccharides taste sweet and are soluble in water.
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The general formula of a disaccharides is C H O Disaccharides also called double sugar. Disaccharides can be broken down to their constituent monosaccharide by a chemical reaction involving the addition of water. The reaction is known as hydrolysis.
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Examples of disaccharides are maltose, sucrose and lactose (milk sugar).

Types

Sucrose

Commonly found in sugar cane, sugar beets and sweet Made of glucose and fructose fruits. Generally extracted from sugar cane or sugar beets and then purified and crystallized to be used as a sweetener in beverages. Is the product of partial digestion of starch. Made of two glucose molecules Present in the milk. Consist of glucose and galactose.

Maltose Lactose

The figure below shows an illustrated examples of formation of disaccharides from the condensation reaction of monosaccharides.

Hydrolysis is a chemical reaction that breaks up large molecules of disaccharides by adding water to them.

The figure below is an illustration of a reversible breaking down

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disaccharides into monosaccharides.

NOTE:- Maltose and lactose are reducing sugars

(and can be tested directly by Benedicts solution i.e. when maltose or lactose is boiled with Benedicts solution, there will be a brick red precipitation produced which indicates the presence of a reducing sugar), while sucrose is a non-reducing sugar (and has no direct test, however, the monomers of sucrose i.e. glucose & fructose are reducing sugar, and can therefore be tested by breaking down sucrose into glucose and fructose through hydrolysis reaction heating sucrose solution with hydrochloric acid followed by the heating of the products with Benedicts solution, that will produce a brick red precipitate indicating the presence of reducing sugar and hence presence of sucrose in the solution).
Polysaccharides

Polysaccharides are much larger molecules of complex sugar, which comprise of to 10,000 monosaccharides joined together to form long chains of simple sugars called polymer.
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Many monosaccharide molecules join together in a condensation reaction (with the removal of water molecules) to form a large polysaccharides molecules. Polymerisation is the process of condensing many individual monosaccharide molecules to form large polysaccharides molecules. In polymerisation, the individual monosaccharide molecules are called monomers. Polymerisation of monosaccharide forms: glycogen (in humans and animals) and starch & cellulose (in plants) and these are the three most common forms of polysaccharides.

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The three classes of polysaccharides

Glycogen

Glucose

Humans and animals

The stored carbohydrate found in the muscles and liver of humans and many animals. It consists of a complex chain of glucose molecules. Molecules with many side branches. Major storage of carbohydrates in animals and fungi, for examples, in muscle cells and liver cells. A class of plant-based polysaccharides made up of units of glucose. Starches typically comprise a combination of two substances: amylose and amylopectin. Consists of two components. Unbranched, helical chains of glucose units. Branched chains of glucose units.

Starch

Glucose

Plants

Cellulose

Glucose

Plants

Major storage of carbohydrate in plants. The basic structural material in plants contains over 3,000 glucose molecules. Cellulose is in the form of insoluble dietary fiber. It is a Straight unbranched chain of glucose units in Plant cell wall.

Lipids

Lipids are diverse group of substances that contains carbon, hydrogen and oxygen. The proportion of oxygen is lower than that in carbohydrates. For example, the general formula of stearic acid is C H O . All lipids are insoluble in water and it also dissolve readily in other lipids and in organic solvent such as ether and ethanol. The main types of lipids are Fats & Oils; Waxes; Phospholipids & steroids (including cholesterol, testosterone, oestrogen and progesterone).
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Fats and oils

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Fats are solid at room temperature (20C), whereas oils are liquid. Each molecule of fats or oils is made up of one glycerol combining with three fatty acids which may be the same or may be different. Three molecule of water are removed in this condensation reaction. These molecules of fats and oils are known as triglycerides. Fats often contain only saturated fatty acids; while oils usually contain unsaturated fatty acids. In saturated fatty acids, the carbon atoms are bonded to the maximum number of other atoms, in a single bond and the hydrocarbon chain is relatively straight. However, in unsaturated fatty acids there exists a double bond in the form of CH=CH- in the hydrocarbon chain. The process is as diagrammatically illustrated in the next page.

The chemical formulae and examples of fatty acids found in living cells
Types of fatty acids Example Structural Formula

Saturated Unsaturated

Stearic acid Oleic acid

CH3(CH2)16COOH CH3(CH2)7CH=CH(CH2)7COOH

(A molecular structure of a saturated fatty acid)

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(A molecular structure of an unsaturated fatty acid)

(A molecular structure of fats & oil molecules in a living cell)

gram, while carbohydrates can provide only 17 kJ per gram. Animal fats such as lard, butter and cream are example of saturated fats; while vegetable oil such as olive oil and sunflower oil are example of unsaturated fats.

The similarities & differences between saturated and unsaturated fats

Saturated fats

Unsaturated fats

Both are triglycerides They yield 38 kJ per gram

Both are triglycerides They yield 38 kJ per gram

Their molecules congregate into globule because of their Their molecules congregate into globule because of their hydrophobic properties hydrophobic properties
Differences between Saturated and unsaturated fats Saturated fats Unsaturated fats

Higher melting point.

Lower melting point.

Most are solid at room temperature. More likely to cause disease of the heart and arteries.

Most are liquid at room temperature. Less likely to cause disease of the heart and arteries.

More stable at room temperature and less readily become Unstable at room temperature and less readily become rancid. rancid.
Waxes

Waxes are similar to triglycerides, but the fatty acids are bonded to long-chain alcohols rather than glycerol. Waxes are usually hard solids at room temperature. Waxes are used to waterproof the external surface of plants and animal. The cuticle of a leaf and the protective covering on an insects body are made of waxes. It is also a constituent of the honeycomb of bees
Phospholipids

Phospholipids have a similar structure to triglycerides but one of the fatty acids is replaced by a phosphate group. The end of the phospholipids molecule containing the phosphate group is hydrophilic, and also the other end containing the hydrocarbon chain of the fatty acids is as well hydrophobic. The hydrophilic end is soluble in water while hydrophobic is insoluble in water.
Steroids

A steroid molecule has a complex ring structure. Steroids occur in plants and animals. Examples of steroids are cholesterol, testosterone, estrogen and progesterone.

Functions of the three basic types of steroids found in living cells

Cholesterol. Testosterone. Estrogen and progesterone.

Strengthens the cell membrane at high body temperature. Male reproductive hormone. Female reproductive hormone.

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Proteins

Proteins are compounds of these elements: Carbon (C); Hydrogen (H): Oxygen (O); Nitrogen (N); Sulphur (S) and Phosphorus (P). The building block for protein are amino acid (monomer) which are joined together to form protein via condensation reaction. Amino Acids are the subunits of all proteins and each amino acids carries two functional group which includes:- a carboxyl group (- COOH) which is acidic and an amino group (-NH ) which is basic. The two amino acids can combine together to form a dipeptide via a condensation reaction between the carboxyl group of one and the amino group of the other, in which the resulting bond linking the two amino acids is called a peptide bond. This is a represented in the chemical equation below.
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long chains of amino acids are called polypeptides. And a polypeptide is formed by the condensation reaction of many amino acids, with the removal of water. Also a polypeptide chain can also be hydrolyzed, with the addition of water molecules to form individual amino acids.
NOTE: - That

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Types of amino acids:

There are basically two types of amino acid in living cells. These are essential amino acids (i.e. those not synthesized by body cells and are only obtained by food) and non-essential amino acids (i.e. those synthesized by body cells). There are 20 kinds of amino acids that support the body, each having their own functions. There are as many as one hundred thousand kinds of proteins that constitute the body and these comprise only twenty kinds of amino acid in various proportion. These twenty amino acids are essential to the body and in addition to being the materials for proteins; they are used as an energy source for the body cells when needed.

NOTE: - Food that contain all the essential protein are called 1
nd

class proteins (e.g. milks, meat, eggs); while those that lacks a few essential amino acids are referred to as 2 class proteins (e.g. plants such as corn etc.)
Structure of protein:

st

Protein is made of four basic structures as primary, secondary, tertiary and quaternary structures.
Primary Structure

In this structure, the amino acids are arranged in a linear sequence to form a long linear chain of polypeptide.
Secondary structure
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Here the polypeptide is coiled to form alpha helix i.e. a helixor pleated sheet.
Tertiary structure

This structural arrangement presents the helix or a pleated sheet folded in various ways to form globular proteins.
Quaternary structure

Here the folded protein chains are joined together to form a single protein molecule.
NOTE: - It can be seen that the basic structure of protein is the primary structure, and it is the primary structure that

yield credence to the formation of both the secondary, tertiary and quaternary structures of proteins as illustrated below.

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Enzymes
These are protein molecules act as biological catalysts. They speed up the rate of metabolic reactions and do not chemically changed at the end of the reaction. The substance whose reactivity is increased by enzymes is known as a substrate. General Characteristics of Enzyme proteins:
1. 2. 3. 4. 5. 6. 7.

Enzymes speed up the rates of biochemical reactions in cells. Only a small amount of enzymes is needed to catalyze a lot of substrate. Enzymes are very specific each class of enzymes will catalyze only one particular reaction. Enzymes are not used up or destroyed in the reactions that they catalyze, but can be reused again. Enzymes catalyze reversible reactions Many enzymes are only able to work with in presence of a coenzymes (or cofactor). Enzymes are effected by changes in temperature and pH

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Naming of Enzyme proteins:

An enzyme is named by taking its substrate name and adding the suffix -ase. Example here is a protease enzyme that catalyses the hydrolysis of protein. However it is important to note that the -ase rule does not apply to enzymes discover before the -ase idea was introduced, for instance as seen in such enzymes as pepsin, rennin, ptyalin and tripsin. The modern classification of enzymes was decided by the International Union of Biochemistry (IUB) in 1961
General classification of enzyme proteins:

Enzymes are generally classified as either intracellular or extracellular enzymes. In which the intracellular enzymes (are those that catalyses reaction within a cell and are formed by the free ribosome in the cytoplasm); while the extracellular enzymes (are those that leaves the cell and catalyses reaction outside the cell and synthesized by ribosome attached to the rough endoplasmic reticulum).
Mechanisms of action of enzyme proteins:

Each enzyme molecule has a region with very precise shape called active site. The substrate molecule fit into the active site of the enzymes like a key into a lock, forming an enzyme-substrate complex, a temporary structure. Reactions take place at active site to form a product. The products have a different shape from the substrate and therefore repelled from a active site.

Factors affecting enzyme proteins activities:

As each enzyme protein has an optimum pH at which its rate of reaction is the fastest; for instance pepsin at pH 2, (acidic); amylase pH 7 (neutral) and trypsin at pH 8-9 (alkaline). Nonetheless, the following under listed factors do have significant effects on the general activities of enzyme proteins in a living cell.
1. 2. 3. 4.

pH Temperature Concentration of enzyme Concentration of substrate

The effect of temperature on enzyme-proteins activity

These effects includes:

Maximum increase in the rate of reaction, known as optimum temperature.

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Sudden fall in the optimum temperature to around 37C-40C, due to the breakup of bonds maintaining enzyme proteins structures resulting in loose of shapes. Final stoppage of enzyme protein activity at 60C, due to the total denaturing of enzyme proteins.

The effect of substrate concentration on enzyme-proteins activity

These effects includes:

Increase in the substrate concentration will increase the chance of enzyme proteins-substrate collision, and the rate of reaction will increase. Addition of substrate will not increase the rate of reaction anymore because the constant enzyme proteins concentration becomes the limiting factor.

The effect of enzyme-proteins concentration on enzyme-proteins activity

These effects include:

When the concentrations of enzyme proteins increase, there is more chance enzyme proteins-substrate collision, resulting in the linear increase in the rate of reaction due to the lack of other limiting factors.

The uses of enzyme proteins:

These effects include:1. 2.

Enzyme can extracted from any living organism, and used either at home or in industry Enzymes that are commonly used in daily life are: a. Papain-found in papaya used to tenderise meat b. Protease-used to tenderise meat and remove hair from the skin etc.

Nucleic acids

Living organisms are complex systems. Hundreds of thousands of proteins exist inside each one of us to help carry out our daily functions. These proteins are produced locally, assembled piece-by-piece to exact specifications. An enormous amount of information is required to manage this complex system correctly. This information, detailing the specific structure of the proteins inside of our bodies, is stored in a set of molecules called nucleic acids. A nucleic acid is a polymer comprising numerous nucleotides (each composed of a phosphate unit, a sugar unit, and a "base" unit) linked recursively through the sugar and phosphate units to form a long chain with base units protruding
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from it. As found in biological systems, nucleic acids carry the coded genetic information of life according to the order of the base units extending along the length of the molecule. The connectedness of living organisms can be seen in the fact that such nucleic acids are found in all living cells and in viruses, and the flow of genetic information is essentially the same in all organisms.

Nucleic acids are biological molecules essential for life, and include DNA (deoxyribonucleic acid) and RNA (ribonucleic acid). Together with proteins, nucleic acids make up the most important macromolecules; each is found in abundance in all living things, where they function in encoding, transmitting and expressing genetic information. The term nucleic acid is the overall name for DNA and RNA, members of a family of biopolymers. All living cells and organelles contain both DNA and RNA, while viruses contain either DNA or RNA, but usually not both.
NOTE: -

Composition:

The basic component of biological nucleic acids is the nucleotide (a linear polymer). Each of which contains three basic components, a pentose sugar (ribose or deoxyribose), a phosphate group, and a pyrimidine nucleobase or purine (sometimes termed nitrogenous base or simply base). The substructure consisting of a nucleobase plus sugar is termed a nucleoside. However, it is important to note that nucleic acid types differ in the structure of the sugar in their nucleotides DNA contains 2'-deoxyribose while RNA contains ribose (where the only difference is the presence of a hydroxyl group). Also, the nucleobases found in the two nucleic acid types are different: adenine, cytosine, and guanine are found in both RNA and DNA, while thymine occurs in DNA and uracil occurs in RNA. Nucleic acid molecules are usually unbranched, and may occur as linear and circular molecules.

Nucleic acids are also generated within the laboratory, through the use of enzymes. (DNA and RNA polymerases) and by solid-phase chemical synthesis. The chemical methods also enable the generation of altered nucleic acids that are not found in nature, for example peptide nucleic acids.
NOTE: -

Types of nucleic acids:

The most common nucleic acids are deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) that form a team which together oversees and carries out the construction of the tens of thousands of protein molecules needed by living organisms according to the ever-changing context of each cell.
Deoxyribonucleic acid
DNA is often compared to a blueprint, since it contains instructions for constructing other components of the cell,

such as proteins and RNA molecules. Deoxyribonucleic acid is a nucleic acid that contains the genetic instructions used in
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the development and functioning of all known living organisms. The main role of DNA molecules is the long-term storage of information and the DNA segments that carry this genetic information are called genes, but other DNA sequences also have structural purposes, or are involved in regulating the use of this genetic information.
Ribonucleic acid

Ribonucleic acid (RNA) functions in converting genetic information from genes into the amino acid sequences of proteins. The three universal types of RNA include transfer RNA (tRNA), messenger RNA (mRNA), and ribosomal RNA (rRNA).

Messenger RNA: -- Acts to carry genetic sequence information between DNA and ribosomes, directing protein synthesis (i.e. it serves as the template for the synthesis of a protein). It carries information from DNA to the ribosome, a specialized structure where the message is then translated into a protein. Ribosomal RNA: -- Is a major component of the ribosome, and catalyzes peptide bond formation. The molecules are extremely abundant and make up at least 80 percent of the RNA molecules found in a typical eukaryotic cell. In the cytoplasm, rRNA molecules combine with proteins to perform a structural role, as components of the ribosome. Transfer RNA: -- Serves as the carrier molecule for amino acids to be used in protein synthesis, and is responsible for decoding the mRNA. It is a small chain of about 70-90 nucleotides that transfers a specific amino acid to a growing polypeptide chain at the ribosomal site of synthesis. It pairs the amino acid to the appropriate codon on the mRNA molecule.

Component structural parts of nucleic acid:

All nucleic acids are made of the same building blocks (monomersi.e. nucleotides/nucleobases), comprising of a five carbon sugar, a base that has a nitrogen ( N) atom and an ion of phosphoric acid. However, the most common nucleotide bases are the purines (comprising of adenine and guanine) and the pyrimidines ( made of cytosine and thymine or uracil in RNA).

Illustrated below is the molecular structural arrangement of these nucleobases

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Inorganic compounds in living cells

Chemical compounds that do not contain carbon Usually a smaller and simpler than organic compounds Are mostly associated with non-living things. Founds in cells water, acids, alkalis and mineral salts

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