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Concepts in Biology by C.C.Divina 19

This module discusses the basic

concepts of Chemistry vital in the

understanding of biological principles. It

features the important compounds in

living systems like water, carbohydrates,

lipids, proteins and nucleic acids. It also

has a short discussion on the work of

enzymes.


Chemistry of Life

Chemical compounds make up living

things and they have specific functions

that contribute to the overall

performance of life activities. Within

a living system, these compounds

react with each other following the

principles of chemistry and physics.

Because Biology is a multi-science

discipline, it is helpful in

understanding the biological concepts

if you also understand the basic

principles of chemistry and. physics.

REVIEW OF BASIC CHEMISTRY

PRINCIPLES

The following are basic concepts in

Chemistry worth looking into to

facilitate your understanding of

Biology .

� Matters occupy space and have

weight.

� Elements are substances that cannot be broken into its simpler

component by ordinary means and

they are the simplest form of

matter. Most of these elements are

found in nature while others are

synthesized in the laboratory.


Each element is characterized by

its atomic name and represented

most often by the first letter of

its name. Examples of elements and

their symbols are Hydrogen (H),

Carbon ©, Nitrogen (N), Oxygen (O)

and Chlorine) The list of elements

and their symbols are found in the

Periodic Table.

� The smallest amount of an element

is the atom. It is composed of

three sub-atomic particles, - the

protons, neutrons and electrons.

The positively charged protons and

the neutral neutrons are found the

central nucleus of the atom and

the negatively charged electron

roam around the nucleus in the

different energy levels called

shells or orbitals.

� The atomic number of an element is determined by the number of

protons in the nucleus, that

atomic weight is equivalent to the

number of protons and neutrons.

Each of proton and neutron

particle weighs approximately 1

dalton while the election has

negligible weight. In some atoms

of the same element, additional

neutrons are found thereby

increasing the atomic weight.

� Atoms with the same atomic number

but different atomic weights are

called isotopes. Isotopes of


hydrogen are simple hydrogen (1H1),

deuterium (1H2) and tritium (1H

3).

The hydrogen atom

� Atoms are electrically neutral

because the number of protons in

the nucleus is equal to that of

the negatively charged electrons

in the orbital. The number of

electron in the outermost energy

shell determines largely the

physical and chemical properties

as well as the behavior of the

atoms. The valence of the atoms

determines the tendency to

combine with the other atoms in

a reaction to complete the

electrons in the outermost shell

and thus making the atom stable.


� The forces of attraction between

the reacting atoms are called

chemical bonds. The differences

in the electron activity n the

outermost shell orbital leads to

the formation f different kinds

of chemical bonding and examples

of which are the electrovalent

or ionic bonding and the

covalent bonding.

� In ionic or electrovalent

bonding, there is the process of

transfer of electrons from one

atom to another. This transfer

of electrons makes the atoms

stable by completing the

electrons in the outermost

energy shell, this particular

bonding forms ionic compound

which readily disassociate into

charged particles called ions in

aqueous solutions. An example of

this compound is table salt or

NaCl, which easily ionizes into

Na+ and Cl- ions.


� In covalent bonding, there is

the sharing of electron between

atoms, the shared electrons are

rearranged so that neither atom

loses or gains electrons. Carbon

with four electrons at its

outermost shell conveniently

forms covalent bonding with

other atoms, like hydrogen,

oxygen and nitrogen.

� When atoms in covalent bonding

do not share electrons equally,

the molecule produce behaves

like it has a positive and

negative end. This bonding is

known as polar covalent bonding

and produce a molecule called

dipoles, Water molecule (HOH)

is a dipole wherein, hydrogen

and oxygen share unequally the

electrons, so that the oxygen

end is slightly negative while

the hydrogen poles are slightly

positive.

� In chemical compounds, atoms

combine chemically in definite

proportions. Compounds are

classified into inorganic and

organic compounds. Inorganic

compounds do not usually contain

carbon but when present it is

not linked to hydrogen and

oxygen.


� Organic compounds have carbons

attracted to the hydrogen and

oxygen and are found a part of

product of living things. The

chemical properties of compounds

are affected u the kinds of

atoms involved the bonds formed

and the spatial arrangement of

the atoms.

� When molecules of various

compounds come in contract, they

may form chemical bonds and

undergo chemical reaction. The

major types of reactions are

synthesis, decomposition and

displacement and rearrangement.

In synthesis, molecules combine

to form a complex one. An

example of this reaction is the

formation of carbohydrates from

simple sugars. The complex

material may be decomposed to

its simpler component by

decompositions as in th4

breakdown of proteins into its

amino acid components thee is an

exchange of molecules in

displacement reaction and change

in the position of atom in the

molecule if the rearrangement

reaction.

� The rate of chemical reactions

is influence by factors like (1)

the nature of the reactant (2)

concentration of the reactants


(30 size of the reacting

molecule (4) temperature and (5)

presence of catalysts.

� Compounds vary in their

capability to react; some are

more reactive than the others do

some are inert. Faster moving

molecules have greater chance of

reacting because of collision.

Temperature increases kinetic

energy of the reacting molecules

thereby increasing the rate of

reaction catalyst increase the

rate of chemical reactions by

lowering the activation energy

of the reactions.

� Solutions may be acidic, basic

or neutral based on the presence

of hydrogen and hydroxyl ions or

other similar radical groups.

Acidity and alkalinity of the

solution is determined buy its

pH. Solutions with pH 7 is

neutral and those with lower pH

than 7 is acidic and those with

higher are basic. Buffers are

chemical systems that protect

solutions from changing to acid

or basic because of their

ability to neutralize the acid

or base introduced in the

system.


Chemical Basis of Life

A living organism is chemically

composed of organic and inorganic

compounds. The organic compounds in the

organism are carbohydrates, protein

lipids and nucleic acids are organic

macromolecules. The inorganic

components of the organism are water,

salts and other minerals.

The protoplasm of the plant or

animal cell contains 75 to85% water, 10

to 12 % protein, 2 –3 % lipid and 1%

carbohydrate, 1% other inorganic

materials. The amount of water vary

from one cell to the other but water is

the most common molecule in proteins

are the most prevalent organic compound

in the cell.

Questions to Answer

1. Draw the atom of hydrogen, carbon and

oxygen showing the protons, neutrons

and electrons in the orbitals or energy

shells.

2. Give the factors that may hasten

chemical reactions. Cite a practical

example to show how each factor may

affect chemical reactions.

3. What is the difference between an ionic

compound from a covalent compound


Water

Water is a solvent necessary for

life; it has a unique set of physical

and chemical characteristics that are

vital to the structure and functions of

cells as well the organisms. It is a

molecule composed of two atoms of

hydrogen and a molecule of oxygen

bonded covalently The electrons are

unequally shared wherein more are found

along the area of oxygen thereby

creating a negative pole and leaving

the hydrogen as positive pole. This

polar covalent bond of the water

molecule makes it most adapted to

performing its functions in living

systems.

Water is a dipole so that its

molecules tend to bond with each other

and form a lattice-like structure. The

bonds existing between these molecules

are hydrogen bonds. Each negative

oxygen pole is attracted to two or more

hydrogen ends of the other water

molecules thus forming a tetrahedron.

Because water is a polar covalent

compound it is highly cohesive and

adhesive, it has high specific heat and

heat of vaporization, strong tensile

strength and surface tension. All these

properties contribute to the role it

performs in living systems


Water is good thermoregulator. It

prevents sudden extreme temperature

changes because it has high melting and

boiling points, high heat of fusion and

vaporization, high specific heat and

high surface tension. It means that a

lot of energy is required to bring an

increase in the temperature of the

water molecule. This large amount of

energy is needed to break down the

hydrogen bonds that are found between

water molecules. (See figure above of

water molecules and the hydrogen bonds

between them).

Water is an excellent solvent. It

serves as a natural solvent for

minerals and other important biological

compounds in the body. It is in a

liquid state at physiological

temperature,that it serves as a

dispersion medium of the colloid system

of the protoplasm. Its kinetic and

A. Water molecule showing the polar covalent

bonding

B. Water molecules showing the hydrogen bonds

between molecules


Review Questions

1. Describe the molecular structure e of water. Relate its structure

with its properties.

2. Why is it better to say water is an “excellent solvent”

rather than it is a “universal solvent”? What do you think

will happen if everything is soluble in water?

3. Enumerate the different functions of water in living

systems and explain how water molecules are adapted in

performing these functions .Is it possible for the different life activities to proceed without water? Why or why not?

unique solubility properties both

result from the strong cohesive

characteristic of the water molecules.

Water does not readily

disassociate into ions so that the pH

of the cell or any living system is

maintained. Likewise water is used as a

transport system for the important

substances.

Water is very vital to living

things. The loss of water in living

system may mean death to the organisms.

It is although worth remembering that

water is not a source of energy in

living system.

The Organic Compounds

The organic macromolecules in

living systems are classified as


carbohydrates, proteins, lipids and

nucleic acids. The basic framework of

the organic compounds is the skeleton

of carbon atoms, which may appear in

chains, rings, networks, or

combinations of these forms. These

compounds are very diverse and

versatile, existing in vitally

unlimited number and possessing varied

properties. This diversity is due to

the valence of carbon, which is 4; thus

allowing it to form four bonds with

hydrogen, oxygen, and nitrogen or even

another carbon. It can form single,

double and triple bonds.

The combinations of the weak and

strong bonds in organic molecules

account for their stability and

flexibility. The stability of the

organic compounds is shown by their

sluggish reactions with another with

water molecules or molecular oxygen,

its stability is due to the presence of

weaker bonds like hydrogen bond, ionic

bond and van der Waals bond. These

bonds allow the rearrangement of

molecular atoms.

Carbohydrates

Carbohydrates are organic

compounds made up of atoms of carbon,

hydrogen and oxygen, wherein there

exists a distinct ratio of 2 hydrogen

atoms to 1 oxygen atom. The general


formula for carbohydrates is Cx(H2O)y, hydrates of carbons.

The simplest form of carbohydrates

are the simple sugars called

monosaccharides. Monosaccarese with

three carbons are called trioses, those

with five carbons like ribose and

deoxyribose are pentoses and those with

six carbons like glucose (blood sugar

or dextrose), fructose (fruit sugar)

and galactose are hexoses. These three

hexoses are isomers with the same

chemical formula of C6H12 O6.

Molecules of monoscaccharedes

react to form dissaccharides with the

removal of water molecule. This process

is called dehydration synthesis or

condensation (See figure below). The

bond formed between the two

monosaccharides is called glycosidic

bond. Examples of dissacharides are

maltose (glucose + glucose), sucrose or

table sugar (glucose + fructose ) and

lactose or milk sugar (glucose +

galactose).

Carbohydrates composed of many

monosacchareds are called

polysaccharides. Common examples of

these polymers of monosaccharedes are

starch, the storage form of

carbohydrates in plants, glycogen, the

storage form of carbohydrates in

animals and cellulose, the major

component of fibers and walls of plant

cell walls.


Some common examples of

carbohydrates in plants and animals

Carbohydrates play important roles

in the physiology of cell. They serve

as structural component of certain

organelles and are basically the source

of usable and reserved energy. Glucose

is the immediate substrate for cellular

respiration.


Lipids

Lipids are made up of carbon,

hydrogen and oxygen, howerver, there is

much less oxygen compared to carbon and

hydrogen. They are a large groups of

macromoleuces with common

characteristic of being soluble in non-

polar organic solvents, like alcohol

and ether but insoluble in water.

Lipids are stored in the cell

chiefly in the form of fat which cells

can synthesize from sugars. A fat

molecule consists of three fatty acid

molecules joined to one glycerol

molecule by condensation of dehydration

synthesis. The nature of the fat is

determined by the length of carbon

chain in the fatty acids and by whether

the acids are saturated or unsaturated.

Unsaturated fatty acids have

double bonds while the saturated fats

Review Questions

1. How would you know if the compound is a

carbohydrate given only it formula?

2. What do carbohydrates do in living systems?

3. Give other names of the following.

a. dextrose b. fruit sugar c. milk sugar

4. Identify the polysaccharides described

a. storage form of carbohydrates in plants

b. storage form of carbohydrates in animals

c. major component of fibers and plant cell wall

d. disaccharide from condensation of two

glucose.


contain single bonds. Unsaturated fatty

acids common in plants than animals.

Examples of unsaturated fatty acids are

olive oil, peanut oil and corn oil and

saturated fatty acids common animals

are butter and lard.

Lipids are storage form of energy

that maybe hydrolyzed to give off heat

in times of body needs. Also parts of

the organism is made up of fats.

Examples of lipids containing three

fatty acids attached to a glycerol

molecule are true fate like

triglycerides found as stored fats in

adipose tissues in animals and oils in

plants. Phospholipids which are

component of cell membrane have a

phosphate group and two fatty acids

attached to glycerol. Example of this

is phophatidylcholine, common component

of membranes. Waxes are also lipids

with fatty acids and alcohol, examples

of which are the bee wax and the ear

Formation of fats through dehydration synthesis


wax. Lipid without fatty acids are the

steroids. Examples of steroids are

cholesterol and sex hormones

testosterone, estrogen and

progesterone.

Proteins

Proteins are organic compounds

containing nitrogen aside from carbon,

hydrogen and oxygen. Phosphorus and

sulfur may also be present as

structural atoms. They are

macromolecules and are chains of

monomer compounds called amino acids.

Amino acids contain basic amino

group (-NH2) and acidic carboxyl group

(-COOH) but differ in their side

chains. See the figure below to show

some fo the amino acids. The presence

of both acidic and basic groups in the

amino acid molecules make them act as

buffers that maintain the pH of living

systems. Examples of amino acids are

lysine, glycine and glutamic acid.

Review Questions

1. Describe lipids and compare with carbohydrates.

2. Differentiate saturated from unsturated fats; fats from

sterols; glyceride from phospholipid.

3. Enumerate some examples of lipid compounds,

where they are found and what do they do?


Two amino acids unite through the

amino group of one molecule and the

carboxyl group of the other through

dehydration synthesis. The bond formed

between these two amino acids is the

peptide bond and the molecule produced

is a dipeptide. A chain of three of

more acids is polypeptide. Long chains

of polypeptides are proteins which are

folded forming a three dimensions

configuration.

There are only a few known amino

acids, yet there are very many

different kinds of proteins formed from

them. This is possible because the

sequential arrangement of the amino

acids of the protein chain determines

the type of protin compound formed.

Using analogy, the Filipino alphabet

has 28 letters only and yet can form

thousands of words.


Proteins are bonded by strong and

weak bonds. Thus, changes in

temperature, pH and other factors in

the environment easily denature protein

patterns. Denaturation is the loss of

the natural properties because of the

alteration of the structure of the

three dimensional protein molecule. A

good example to demonstrate

denaturation is the exposure of the egg

while or ova labumin to extreme change

in temperature, where a transparent,

sticky and almost colorless fluid is

altered to an opaque, white solid

state.

Proteins are the most abundant

organic material in living systems.

They are capable of storing energy in

the body which are released during the

body need. They are the basic

structural component of living things


and thy act as enzymes and hormones.

Examples of the structural protein are

keratin and hemoglobin, contractile

proteins are myosin and actin of the

muscles; enzymes are amylase and

lipase.

Review Questions

1. Explain the following statements

a. Proteins are highly specific.

b. Proteins easily denature.

2. Where do you find the following protein

compounds

a. hemoglobin,

b. keratin

c. myosin

d. albumin


Nucleic Acids

Nucleic acids are complex

molecules, larger than most proteins

and contain carbon, hydrogen, oxygen,

nitrogen and phosphorus which are

organized into compounds called

nucleotides. Nucleotides are made up of

three compounds, the nitrogenous base,

the pentose sugar and the phosphate

group.

There are two general

classification of nitrogenous bases –

the purines and pyrimidines. The

purines are the adenine and guanine and

the pyrimidines are the cytosine,

uracil and thymine. Adenine pairs with

uracil and thymine and guanine pairs

with cytosine. Nitrogeneous bases are

linked to the pentose sugar of the

nucleotide just like the phosphate

group.

The pentose sugars found in the

nucleotides are either ribose or

deoxyribose. These sugars determine

whether the nucleotide is a

ribonucleotide or deoxyribonucleotide.

Nucleotides function primarily as

structural components of nucleic acids.

Some of them are energy carriers in the

cells and examples of these are the

adenosine triphosphate (ATP) and

adenosine diphosphate (ADP) ATP is the


immediate source of energy in living

systems. ATP is readily broken down

into ADP and PO4 and in the process

releasing energy.

Chains of nucleotides form nucleic

acids. The pentose sugar of one nucleic

acid binds with the phosphate of

another. This bonding between the

phosphate and pentose sugar in

nucleoties in the form of sugar-

phosphate backbone of the nucleic

acids. Nucleic acids are the chemical

components for the chromosomes that

Nitrogenous bases Nucleotides


carry the information of life, the

nucleolus and ribosomes that synthesize

proteins in the cell.

Deoxyribose nucleic acid (DNA) is

a double helix structure with the

pentose deoxyribose and the bases

adenine, guanine, cytosine and thymine.

It is found in the nucleus of the cell,

specifically in the chromosomes, in the

mitochondria and chloroplasts. It is

used as a template in protein

synthesis.

Ribose nucleic acid (RNA) is a

single strand compound that has pentose

sugar ribose and the bases adenine,

guanine, uracil and cytosine. There

are three kinds of RNA, the linear

messenger RNA, the clover shaped

transfer RNA (tRNA) and the spherical

ribosomal RNA (rRNA). RNA is involved

in the process of protein synthesis and

is found in the nucleolus, ribosomes

and cytoplasm


Differences of DNA and RNA

Criteria DNA RNA

Pentose

sugar

Deoxyribose Ribose

Nitrogenous

bases

Adenine –

Thymine

Guanine-

Cytosine

Adenine,

Uracil

Guanine

Cytosine

Shape Double helix Single

strand

Locations Nucleus,

Chloroplast

Mitochondrio

n

Nucleus,

Cytoplasm

Ribosomes

Review Questions

1. Draw a diagram of a nucleotide, DNA and RNA

using different shapes as symbols for the pentose

sugar, phosphate and nitrogenous bases

2. What are the functions of DNA and RNA.


Summary table of major organic

compounds, their examples and functions CLASSES EXAMPLES FUNCTIONS

CARBOHYDRATES

MONOSACCHARIDE

glucose

energy source

DISACCHARIDE sucrose food component

POLYSACCHARIDE glycogen energy storage

LIPIDS

FATY ACID oleic acid energy source

TRIGLYCERIDE body fat energy storage

STEROL cholesterol steroid hormone

PHOSPHOLIPID lecithin membrane

structure

PROTEINS

CONTRACTILE myosin muscle

contraction

GAS CARRIER hemoglobin carry oxygen

CONNECTIVE collage cohesiveness

ENZME trypsin catalyst

NUCLEIC ACIDS

NUCLEOTIDE ATP energy carrier

DNA DNA information

storage,

protein

synthesis

RNA MRNA protein

synthesis

ENZYMES

Metabolism in living systems is

characterized by the myriad of

simultaneously occurring reactions.

Nearly all of these chemical reactions


are catalyzed by proteins called

enzymes. Enzymes are called organic

catalysts. If enzymes were absent in

living systems, chemical reactions

would occur at very slow rate that life

activities could not be achieved.

Enzymes integrate reactions and provide

order in the metabolism without which

life would not be possible.

Enzymes hasten chemical reactions

by lowering the activation energy. This

means that the like possibility of

reacting materials to encounter and

react with each other is increased. The

association of enzymes and substrate

takes place in the active site of the

enzyme molecules. These active sites

are varied in configuration making

enzymes highly specific that particular

reactions and reactants require

specific enzymes. The theory explaining

this specificity is known as the Lock

and Key Theory. This states that

enzymes will react with substrates at

specific active sites and will only

react with particular substrates. The

reaction of the enzyme and substrate

results in the formation of the enzyme-

substrate complex which breaks and

releasing the product and the unaltered

enzymes. These organic catalysts are

not consumed in the reaction but are

reused in the next like reactions.

Enzyme activity is influence by

the temperature, pH, concentration of


substrates and enzymes. As the

temperature increases, the rate of

enzyme activity also increases because

of the increase in the kinetic energy

of the reacting molecule. However, this

trend is observed up to a certain

temperature after which the trend is

reversed because of the proteinaceous

enzymes are slowly denatured. The

effect o pH is similar where the

different enzymes have varying optimum

pH of the activity. To cite an example,

digestive enzymes in the stomach

function best at very acidic pH which

other enzymes would be denatured.

Increased in the concentration of

enzyme or substrate result in the

increase enzyme activity.

Since enzymes denature, loss of

configuration of their active sites

means loss of their capabilities of

catalyzing reactions. This is one of

the reasons why a stable environment of

physiological equilibrium (homeostasis)

is important in living systems.


Questions to Answer

1. What do enzymes do?

2. Explain the mechanism of action of enzymes?

3. Enumerate the factors that affect the

enzymatic activity and their effects?

What happens to enzyme activity if there is

homeostasis in the living system is not maintained?

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