The chemical constituents of cells (1)

The chemical constituents of cells

The chemical constituents of cells include carbohydrates, lipids, proteins, nucleotides, ions and

water.

A. Carbohydrates

It is a group of organic compounds containing carbon, hydrogen and water. The ratio of H:O

atoms is usually 2:1 as in water. The basic unit of carbohydrates is the single sugar called

saccharide. The general formula is Cx(H2O)y

Classification of carbohydrates

a. Monosaccharide

They are called simple sugars e.g. glucose, fructose, galactose because they cannot be

hydrolyzed (broken down) into any simpler carbohydrates. They are the building units for

the more complex carbohydrates.

They are sweet, soluble, crystalline molecules and can reduce the Benedict’s solution to an

insoluble red cuprous oxide, therefore they are also called reducing sugars.

The general formula is (CH2O)n.

When n =5, it is called 5-carbon sugars (pentoses) (CH2O)5;C5H10O5; e.g. ribose,

deoxyribose

When n = 6, 6-carbon sugars (hexoses) (CH2O)6;C6H12O6; e.g. fructose, galactose

Glucose produced in photosynthesis can be converted to starch for temporary storage. It can

also be converted to sucrose for transport. Glucose is the chief building unit for the structural

material for plants: cellulose, hemicellulose an pectin. It can be oxidized to release energy.

b. Disaccharide (= complex sugars/double sugars)

Disaccharidse are formed by two monosaccharide units combining together with the

elminiation of a molecule of water, a process called condensation. The two monosaccharides

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are joined by a covalent bond, the glycosidic bond.

They are sweet, soluble and crystalline, reducing except sucrose, examples: maltose (glucose

+ glucose), lactose (glucose + galactose), sucrose (glucose + fructose)

c. Polysaccharide

Monosaccharides may link by through glycosidic bonds to form a polysaccharide by

condensation reactions. They are not sweet, insoluble or slightly soluble in water, non-

crystalline. The compact insoluble structure makes it ideal as a storage carbohydrate because

they will not diffuse out of the cell nor exert an osmotic effect within the cell. In case of

demand, the polysaccharide can be hydrolyzed to release free sugars. These sugars can be

oxidized to release energy or are synthesized to new compounds.

(1) Starch

It consists of long chain of α-glucose and may have branches at places. It consists of 20-30%

amylose and 70-80% amylopectin. Amylose is an unbranched chain of 200-1500 glucose

residues linked byα-1,4-glycosidic bonds. The molecule takes the form of a helix.

Amylopectin contains from 1300-1500 glucose units. It a branched molecule with both theα-

1,4-glycosidic andα-1,6-glycosidic bonds.

The chain is colied into a helix forming a cylinder in which most of the hydroxyl group, OH,

capable of forming cross linkage projecting into the interior. Because no cross-linkage can

be formed between starch molecules, it lacks structural properties.

Since the starch chains are folded by the hydrogen bonds projected inwards, they are packed

together in spherical plastids to form starch grains for storage function in plants.

(2) Glycogen

It is the storage carbohydrate of animals. It consists chains ofα-glucose molecules linked by

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1-4 or 1-6 α-glycosidic bonds but are shorter and more branched. Glycogen is more stable

than starch and exists in the cytoplasn as tiny granules. It is particularly abundant in liver

and muscles.

(3) Cellulose

It is a polymer of long chains of β- glucose molecules linked by 1-4 glycosidic bonds. The

orientation of the molecule causes the OH-group to stick outward from the chain in all

directions. There chains form hydrogen bonds in between the parallel running chains thereby

establishing a 3-dimensional lattice. There help to give cellulose its considerable stability

which makes it a valuable structural material (in cell wall). The stability makes it difficult to

digest.

B. Lipid

They are organic substances containing C, H and O (O is in a smaller proportion). There are

4 types of lipids: fats and oils, phospholipids, waxes and steroids. They are insoluble in

water but are readily soluble in organic solvent e.g. ether, alcohol, acetone

a. Building up a lipid

Lipids are esters of fatty acids and an alcohol, of which glycerol is by far the most abundant.

Glycerol has three hydroxyl (-OH) groups and each hydroxyl group (-COOH) of a fatty acid,

forming a triglyceride. Triglycerid is formed by condensation reacion that 3 water molecules

are removed and 3 oxygen bonds (ester bonds) are established between the glycerol and the

3 fatty acids. Its basic structure is CH3-(CH2)n-COOH

b. Kinds of fatty acids

As most naturally lipids contain the same alcohol, namely glycerol, it is the fatty acids

which determine the characteristics of any particular lipid.

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1. All fatty acids contain a carboxyl group (-COOH) which is partially ionized and can

form ionic bonds. The carboxyl group is therefore polar and is hydrophilic i.e. they

attract water.

2. The remainder of the molecule is a hydrocarbon chain of varying length.

a. This chain may posses one or more double bonds in which case it is said to be

unsaturated. They have low melting point. They are oils or soft fats at room

temperature. Oils occur mainly in plants.

b. If, however, it possesses no double bonds, it is said to be saturated. They have

higher melting points and are solid at room temperature. They are fats which are

characteristics of animals.

3. The hydrocarbon chains may be very long. Within the fat they form long ‘tails’ which

extend from the glycerol molecule. These ‘tails’ are non-polar and are hydrophobic i.e. they

repel water.

c. Functions of lipids

1. As energy source

2. Storage (triglycerides)

3. Water proof

4. Insulation

5. Protection

6. Major components of cell membrane (phospholipid)

C. Protein

Proteins contain C, H, O, N (some has S, P). They are polymers of high relative molar mass.

a. Amino acids

Proteins are marco-molecules which consist of a large number of amino acids. It has a
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structural formula: NH2-R-CH-COOH. All amino acids contain both a basic structure: one

amino group (NH2) and one carboxyl group (COOH), thus amphoteric, act as buffer. There

are about 20 different amino acids can be commonly found in plant and animal proteins

1. Amphoteric property

i. Zwitterion

Amino acids are soluble in water to form ions. These ions are formed by the loss of a

hydrogen ion from the carboxyl group, making it negatively charged (-COO-). This

hydrogen ion associates with the amino group, making it positively charged (-NH3+).

The ion is therefore dipolar. An ion which has both positively charged and negative charged

regions is called zwitterions, i.e. exist as dipolar ions (zwitterions) in neutral aqueous

solutions. Amino acids are amphoteric because they have both acidic and basic properties.

Some are acidic (with more COOH group), some are basic (with more NH2 group)

ii. Buffer

Being amphoteric amino acids can act as buffer solutions. A buffer solution is one which

resists the tendency to change its pH even when small amounts of acids or alkali are added

to it. Such a property is esstenial in biological systems where any sudden change in pH

could adversely affect the function of enzymes.

The presence of amino (basic) and carboxyl (acidid) groups at the free ends of the

polypeptide chain makes it possible for the protein to combine with basic or acidic

substances. It is a very important feature that enables it to form the building materials of the

body.

b. Peptide linkage to form polypeptides

Protein is formed by having amino acids linked together by a chemical bond called a peptide

bond or peptide linkage. This bond is formed by condensation reaction of the amino group
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of one amino acid attaching to the carboxyl group of another amino acid. The union of 2

amino acids is called dipeptide. Further condensation reactions lead to the addition of further

amino acids to form a long chain called polypeptide.

c. Types of bonds in a polypeptide

The shape is important in the functioning of proteins (polypeptides), especially enzymes.

The shape of a polypeptide is due to 3 types of bonding which occur between various amino

acids in the chain.

1. Disulphide bond: bonding between 2 sulphur-containing amino acids.

2. Ionic bond: bonding between additional and NH2 (NH3+) and COOH (-COO-) group.

3. Hydrogen bond: bonding between positively charged H and negatively charged O atoms,

weak but responsible for maintaining the shape and stability of the polypeptide.

4. Hydrophobic interactions: interaction between non-polar R group.

d. Structural organization of proteins

Individual protein is determined by the sequence of amino acids comprising its polypeptide

chain, together with the pattern of folding and cross-linkage.

1. Primary structure

The primary structure of a protein is the linear sequence of amino acids in its molecule.

Proteins differ from each other in the variety, numbers and order of their constituent amino

acids. Knowing the sequence of amino acids in a protein is important because the sequence

determines practically all the properties of the protein. Many proteins contain more than one

polypeptide chain, a connection between them is held by a disulphide bond (S-S) on the

amino acid cysteine, e.g. insuline.

2. Secondary structure

Polypeptide chains may become folded or twisted in various ways. The most common ways
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are to coil to form a helix (α-helix) or to fold into sheets (β-sheets). These forms are referred

to as the secondary structure of the protein.

When the polypeptide molecule coils up or folds up on itself, some of the atoms form so-

called ‘weak bonds’: hydrogen bonds, ionic bonds and van der Waals forces. Whilst none of

these bonds is strong compared with covalent bonds, where many hundreds are formed they

act to maintain the characteristic shape of the polypeptide or protein.

Collagen forms a triple helical structure. The 3 polypeptide chains twisted together achieve

stability from the hydrogen bonds formed between the NH groups in one chain and the CO

groups in an adjacent chain.

3. Tertiary structure

It is due to the bending and twisting of the polypeptide helix into a complex molecular

(globular) shape. The shape is held by different types of bonding (disulphide, ionic any

hydrogen) between adjacent parts of the chain, e.g. myoglobin.

4. Quaternary structure

Many complex proteins exist as aggregations of polypeptide chains held together by the

various forms of bonding previously described. Their precise arrangement is described as

the quaternary structure of protein. An example is haemoglobin, which consists of four

separate polypeptide chains – two α-chains and two β-chains. Haemoglobin also contains

four haem groups within the molecules; proteins like this, which contain non-protein

material in their molecules, are called conjugated protein. The non-protein part is called the

prosthetic group.

e. Other classification

1. Fibrous proteins: primary and secondary structure

2. Globular proteins: tertiary structure

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3. Conjugated proteins: quaternary structure

4. Intermediate proteins: fibrous but soluble e.g. fibrinogen in blood

f. Functions

1. Structural components

e.g. collagen of connective tissues, in cell membrane and cytoplasm.

2. Homeostatic: soluble proteins act as buffers, stabilizing the pH wherever they occur in the

body.

3. Hormonal: insuline, glucagons (regulation of glucose metabolism)

4. Enzymatic: most enzymes are proteins e.g. digestive enzymes of gut

5. Transport: cell membrane protein and protein of membranes of cell organelles (involved in

transport of metabolites and ions across membranes), haemoglobin, myoglobin.

6. Protection: e.g. antibodies

7. Movement: acting, myosin (muscle contraction mechanism)

8. Storage: casein in milk, aleurone protein in seeds

g. Metabolism of proteins.

1. Denaturatin and renaturation of protein

Denaturation: loss of specific 3-D conformation of a protein molecule, change may be

temporary or permanent, but amino acid sequence remains unaffected. Denatured protein

unable to carry out their normal functions.

Cause of denaturation:

a) heat or radiation

b) strong acids and alkalis and high concentration of salts

c) heavy metals

d) organic solvents and detergents

Renaturation: a protein spontaneously refold into its original structure after denaturation,

providing conditions are stable. Tertiary structure can be determined purely by primary
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structure

2. Hydrolysis of proteins

The peptide bond can be broken by hydrolysis with dilute acids or by enzymes. An acid

hydrolyses all the peptide bonds in a polypeptide quite indiscriminately, so breaking it down

to its constituent amino acids. Some protease enzymes attack specific bonds, producing

shorter peptide chains; others hydrolyze any peptide linkage present.

D. Nucleotides and nucleic acids

Two types of nucleic acid are found in living cells: deoxyribonucleic acid (DNA) and

ribonucleic acid (RNA). Most of the DNA is in the nucleus, but while there is some RNA in

the nucleus most is in cytoplasm, particular in the ribosomes.

Nucleic acids are long, thread-like macromolecules build up of nucleotides. Nucleotides are

arranged to form extremely long molecules: polynucleotides

a. Structure of nucleotide

Hydrolysis of a nucleotide yield 3 components: a pentose sugar, nitrogenous bases and

phosphoric acid.

There are two types of nucleic acids, depending on the pentose they contain. Those

containing ribose C5H10O5 are called ribonucleic acid (RNA), those containing deoxyribose

C5H10O4 are called deoxyribonucleic acid (DNA).

Each nucleic acid (DNA, RNA) contains 4 different bases, 2 derived from purine and 2 from

pyrimidine. The nitrogen in the rings gives the molecules their basic nature. Purines has 2

rings (one hexagonal ring and one pentagonal ring) consists of adenine (A) and guanine (G)

while pyrimidines has one ring consisting cytosine (C) and thymine (T) in DNA or uracil

(U) in RNA. The bases are commonly represented by their initial letters A, G, C, T and U.

RNA contains uracil (U) in place of thymine (T) in DNA.

Phosphoric acid gives nucleic acids their acid character.

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b. Condensation reactions form nucleotides

The combination of a pentose sugar with a base by condensation forms nucleoside.

Nucleotide is formed by further condensation between nucleoside and phosphoric acid.

Different nucleotides are formed according to the sugars and base used.

c. Structure of dinucleotides and polynucleotides

2 nucleotides join to form a dinucleotide by condensation between the phosphate group of

one nucleotide (at C5) with the pentose sugar of the other nucleotide (at C3) to form a

phosphodiester bridge. The process is repeated up to several million times to make a

polynucleotide. An unbranched sugar-phosphate backbone to formed by phosphodiester

bridges between the 3’ and 5’ carbon atoms of the sugars. Phosphodiester linkages are

formed from strong covalent bonds and these confer strength and stability on the

polynucleotide chain. This is an important point in preventing breakage of the chain during

DNA replication.

d. Example of mononucleotides

Adenosine triphosphate (ATP) is energy-rich compound used to release energy for muscular

contraction or other metabolic. It consists of an adenine linked to a pentose sugar which in

turn linked to 3 phosphate groups.

e. Example of dinucleotides

Nicotinamide adenine dinucleotide (NAD) is a coenzyme to involve in enzymatic reactions.

It is formed by combining 2 nucleotides by condensation reaction. NAD acts as electron (H)

carrier in respiration or photosynthesis (refer to respiration for further details)

f. Example of polynucleotides
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1. DNA

A DNA molecule is made up of 2 parallel polynucleotide chains coil around each other to

form a double helix which is anti-parallel and right-handed. Each chain has a sugar-

phosphate backbone with bases which project at right angle and H-bond with the bases of

opposite chain across is constant and equal to width of a base pair (width of a purine and a

pyrimidine). The combination of the bases is: A=T, C≡G. The 2 chains are complementary,

the sequence in one chain determines the other (base pairing)

2. RNA

RNA is a single-stranded molecule. The pentose sugar of RNA is ribose and the organic

bases are A, G, C, U. There are 3 types: tRNA, rRNA, mRNA. It is involved in protein

synthesis (refer to genetics)

E. Water

Water due to its chemical and physical properties takes a very important role in the life of

organisms.

a. Chemical properties of water

1. Water is the reagent participating in many metabolic activities of protoplasm.

a) It provides reducing hydrogen which is in form of NADPH in photosynthesis of green

plants.

b) It is also essential to the hydrolytic reactions such as digestion in organisms.

2. Water is the principal solvent for many substances

Water is an excellent solvent for polar substance (salts) and some non-ionic substance

(sugars, single alcohol). The majority of cell’s chemical reaction takes place in aqueous

solutions. It acts as a transport medium (blood, lymphatic and excretory systems, and in

xylem and phloem).

3. The high dielectric constant of water allows the dissociation of substances dissolved in it.
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Hence affects their chemical and/or electrical activities that in turn affect the functioning of

the organisms e.g. osmotic concentration of ionized solution.

b. Physical properties of water

1. The high heat capacity of water minimize temperature fluctuations in cells. It provides a

very constant external environment for many cells and organisms

2. The high thermal conductivity of water allows good transfer of heat throughout the body that

will avoid the occurrence of destructive local ‘hot spots’.

3. The high density of water at 4oC enables ice to float on water. This saves the lives of many

aquatic organisms which have a viable habitat in cold winter. The inhabitants of aquatic

environment are not subject to the sudden freezing of the water throughout its bulk.

4. The low viscosity of water allows its rapid movement into and throughout cells. Moreover it

makes water a useful lubricant to reduce friction in places with constant movement, e.g.

mucus, synovial fluid

5. The high latent heat of vaporization of water makes it a good evaporative collant to remove

the excessive heat from many terrestrial organisms, e.g. sweating, panting of animals,

transpiration in plants

6. The strong cohesive force between water molecules takes a very important role in the

transport of water in plants. It accounts for its capillarity in soil and the capillarity in the

narrow xylem. All these help the plants absorb water from soil. It accounts for the

transpiration pull on the continuous water column in the xylem of the plants.

7. The incompressibility of water is a useful mean of support. It forms the hydrostatic skeleton

of many organisms to achieve support in the aqueous and vitreous humour of the eyeball, the

coelom of the earthworm, the erection of penis. Water also acts as a cushion for protection

e.g. amniotic fluid protects the embryo.

8. The high density of water provides the buoyancy support of aquatic organisms which do not

need a bulky skeletal system.

9. The fluid medium of water enables the male gametes swimming to achieve fertilization. It
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also aids the dispersal of spores and seeds. Thus water takes an important role in the

perpetuation of species.

10. The high surface tension of water allows surface dwelling organisms attaching to the water

surface to breathe, e.g. mosquito larvae hanging on the water surface. It also permits

movement on the water surface e.g. water boatman and water skater.

F. Inorganic ions

1. The occurrence of ions in cells

Important cations are: Na+, K+, Ca2+, Mg2+, Cu2+, Fe2+, Fe3+. Important anions are: Cl-, HCO3-,

NO3-, H2PO4-, SO42-, I-

2. The functions of ions

a. As constituents of various chemicals. Nitrogen and sulphur, obtained by plants as nitrates and

sulphates, enter into the composition of proteins some of which also contain phosphorous and

other elements. In addition phosphorous is found in ATP, and iodine occurs in thyroxine, the

thyroid hormone.

b. As constituents of structures. Many proteins form structural materials such as connective

tissue fibres in which nitrogen and sulphur are important elements. Nitrogen and

phosphorous, constituents of nucleic acids, are found in the chromosomes; phosphorous in

the cell membrane; calcium in the plant cell wall; and calcium and phosphorous in bones.

c. As constituents of enzymes. Enzymes are proteins all of which contain nitrogen. In addition,

certain enzymes contain metal ion such as copper or iron, e.g. catalase contains iron which is

believed to represent the catalytic center of the enzyme.

d. As metabolic activators. Certain ions activate enzymes, e.g. magnesium activates enzymes

in phosphate metabolism.

e. As constituents of certain pigments. The 2 best known biological pigments are haemoglobin

and chlorophyll, which contain iron and magnesium respectively. Iron is also found in the
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cytochromes, a group of pigments of great importance in energy release.

f. As determinants of the cation-anion balance in cells. Sodium, potassium and chloride ions

are particularly important in this regard, especially in nerves, muscles and sensory cells

where they are involved in the transmission of impulses.

g. As determinants of osmotic pressure. Mineral salts, together with other solutes, determine

the osmotic potential of cells and body fluids. In humans, for instance, the osmotic pressure

must not be allowed to fluctuate beyond narrow limits, and much of our physiology is

directed towards preventing this.