UCMS FOUNDATION PROGRAMME

BIOLOGY SEMESTER 1

Chapter 5: Chemical composition of living organisms

A. Objectives:

After learning this topic, students should be able to:

• Differentiate organic from inorganic compounds.

• List and describe the properties of water.
• Explain how a buffer works.
• List the functions of vitamins and minerals, their sources and the effects of their
deficiencies to human.
• Describe the types of carbohydrates with some examples and state their characteristics.
• Describe the characteristics of lipids, proteins, vitamins.
• Explain how triglycerides, phospholipids, proteins are formed.
• Differentiate saturated from unsaturated fatty acids and give examples to each.
• Differentiate essential and non-essential fatty acids.
• List several functions of fatty acids and steroids.
• Draw the basic structure of a steroid, testosterone, DNA, RNA, glucose alpha and beta,
fructose, nucleotide.
• Lists other forms of lipids and their functions.
• Explain the levels of proteins structure and their characteristics.
• Name water and lipid soluble vitamins, list their functions and the effects of their
deficiencies.
• Describe the formation of nucleotides, polynucleotides.
• Differentiate RNA and DNA.
• Differentiate the types of RNA
• Define the terms related to the topic.

B. Terms to know:

organic inorganic compound Evaporation cohesion

compound
Buffer Macronutrients Micronutrients Isomers
glycosidic links Esterification Unsaturated fatty Saturated fatty
acid acid
Essential fatty Non-essential fatty hydrophilic Hydrophobic
acid acid
amphoteric Denaturation Condensation Anticodon
reaction
codon

C. Assignment:

1. Introduction to the chemical of life.

1.1. Chemical compounds are divided into __________________ and ____________________

compounds.
1.2. What is an organic compound? What is an inorganic compound?
1.3. What are the main organic and inorganic compounds found in the living organisms?

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2. Water

2.1. What are the properties of water?

2.2. Name a biological molecule which cannot dissolve in water. Why?
2.3. Molecules of water are held together by hydrogen bonding. Provide an illustration and
explain.
2.4. Explain how evaporation occurs? What happens to the hydrogen bonding?
2.5. Define surface tension of water. Give 2 examples of its importance to life.
2.6. Explain the changes in water molecules at the temperature < 0o C.
3. Acid, bases and pH.

3.1. A pH scale is used for ___________________________________. Neutral is at pH 7. What does

it mean? What is the lowest and highest point of the scale and what do they mean?
3.2. Define acid and base. What does weak acid mean and give an example of a weak acid?
What does strong acid mean and give an example of a strong acid?
3.3. What is a buffer? Explain the action of a buffer when:
- a strong base is added into water.
- a strong acid is added into water.

4. Inorganic compounds (mineral salts).

4.1. Define salts and give an example.

4.2. What are macronutrients and micronutrients? Give a few examples to each.

5. Organic compounds.

5.1. Define an organic compound. What is a hydrocarbon?

5.2. How to construct an organic compound? The simplest organic compound is
_____________.
5.3. In general, describe carbohydrate, its functions and give a few examples of the
compound.
5.4. Differentiate monosaccharides, disaccharides and polysaccharides.
5.5. Define isomers and give an illustration using hexose sugar.
5.6. Describe the formation of disaccharide from monosaccharides using their structural
formula. Give several examples of disaccharides and state where they can be found.
5.7. Describe the characteristics of these polysaccharides:
- starch
- glycogen
- cellulose
5.8. What is an amino sugar? Give an example and draw its structural formula.

6. Lipids.

1.4. Describe the characteristics of lipids.

1.5. Name 3 main groups of lipids.
1.6. Describe the formation of triglycerides and provide an illustration to your answer.
1.7. What is the general formula of fatty acids?
1.8. What is esterification?
1.9. Differentiate saturated from unsaturated fat, give an example for each and state where
they can be found.
1.10. List the functions of fats.
1.11. Differentiate essential from non-essential fatty acids. Name 3 examples of essential
fatty acids.
1.12. Explain the formation of phospholipids.

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 1.13. Explain what happens when lecithin is poured into water. Provide a diagram to your
answer.
1.14. Name several steroids in our body and list their functions.
1.15. Draw the basic structure steroid and testosterone.
1.16. Name and explain 2 negative effects of steroids to human.
1.17. The use of anabolic steroids is banned in sports. What are the advantages of anabolic
steroids to the athletes?
1.18. List other forms of lipids and their functions.

7. Proteins.

7.1. Briefly describe the characteristics of proteins.

7.2. Draw the basic structure of amino acids. What does amphoteric mean?
7.3. Name the 20 essential and non-essential naturally occurring amino acids.
7.4. Briefly give the characteristics and a few examples of amino acids with:
i. non-polar –R group.
ii. polar –R group.
iii. acidic (negatively charged) –R group.
iv. basic (positively charged) –R group.
7.5. Amino acids solutions can act as buffer. Why?
7.6. Describe the primary, secondary, tertiary and quaternary structures of protein. List their
properties.

8. Vitamins.

8.1. What are vitamins?

8.2. Name water soluble vitamins and fat soluble vitamins. List their functions and the
effects of their deficiencies.

9. Nucleic acids.
9.1. Differentiate nucleic acids and nucleotides. Describe how nucleotides are formed.
9.2. What gives the acid property to nucleic acid?
9.3. Draw the structure of the pentose sugar in RNA and DNA. What is the difference?
9.4. Describe about the nitrogenous base in a nucleotide.
9.5. Explain the formation of polynucleotide.
9.6. Describe the characteristics of DNA molecule.
9.7. It is much easier to separate the 2 DNA strands longitudinally. Why? What will happen
when the 2 strands separate?
9.8. Describe the characteristics of RNA molecule.
9.9. Differentiate RNA and DNA.
9.10. Differentiate mRNA, rRNA and tRNA. Draw their structures and list their functions.

D. References:

• Robert, Reiss and Monger (2000). Advanced Biology. Nelson.

• Taggart (2004). Biology. Thompson.
• Lee and Liew (2005). Biology for STPM. Fajar Bakti.
• http://www.realtime.net/anr/vitamins.html

E. Chemical composition of the living organisms (summary)

1. Water: Properties of water

2. Acids and bases: pH
3. Minerals (Inorganic compounds): functions and sources
4. Organic compounds
a. CHO – monosaccharides, disaccharides: formation
i. Polysaccharides – Glycogen, Cellulose

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 b. Lipids
i. Triglycerides: Glycerol, Fatty acids, Functions of fats
ii. Phospholipids
iii. Steroids: Steroids in the human body, Negative effects
iv. Other forms of lipids
5. Proteins - Amino acids, Dipeptides, tripeptides and polypeptides
a. Protein structure
6. Vitamins: functions and sources
7. Nucleic acids: nucleotide, Polynucleotide
a. DNA, RNA, Differences

Notes:

Chemical compounds are divided into organic and inorganic compounds. Organic compounds
are compounds which contain atom carbon. Inorganic compounds are compounds which do not
contain atom C. The main organic compounds found in the living organisms are CHO, fat,
protein, nucleic acids and vitamins. The main inorganic compounds found in the living
organisms are minerals and water.

Properties of water
• Acts as a solvent
Water is an excellent solvent for ions or salts or polar or charged molecules such as sugar, NaCl,
amino acids. The dissolved substance is called the solute. Lipids cannot dissolve in water
because it is a non-polar molecule.

H2O + Na Cl O2 (negative) attracts Na (pos)

H (pos) attracts Cl (neg)

The bonds between the molecules of water are H bonds.

• Has temperature stabilizing effect

Water stabilizes the To in the living organisms. A large increase in energy only results in a small
rise in the To of water. During an infection, the body To increases but since the body comprised
of 60% of water, the To does not rise greatly.

Evaporation is when water change from liquid state to gaseous state. It happens when we heat
the water (give energy to it) the H bonds between the water molecules break.

• Surface tension or cohesion

It is the force that causes the surface of a liquid to contract so that it occupies the least possible
area. Good examples are mercury, water on coated windscreen, water on daun keladi.

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The surface tension of water enables the movement of water through small vessels (e.g. in
plants). It also support and provides habitat for aquatic organisms. E.g enables pond skater
skates on water.

• Freezing properties
Water solidifies at 0 oC and below. On solidification its density reduces. That is why ice floats in
water. Water is at the greatest density at 4 oC. On solidification, hydrogen bonds form a lattice-
like structure which resists breaking.

• Transparency
The importance:
Underwater plants can perform photosynthesis.
Underwater animals can see

Acids and bases

Acids are substances which donate proton or H+ when dissolved in water. Bases are substances
which accept proton or H+ when dissolved in water. Weak acids are substances which reluctant
to donate proton or H+ when dissolved in water. E.g. carbonic acid. Strong acids are substances
which readily donate proton or H+ when dissolved in water.

Buffer is a solution (weak acid or base) which resists change of pH upon addition of small
amounts of acid or base. Buffer will bind to the excess H+ or OH- in order to do that.

Buffer (weak acid/ H+ donor) will neutralize OH- from the base or
Buffer (weak base/ OH- donor) will accept H+ from the acid
Buffer does not make new H+ or OH-.

pH 7 is when [H+] = [OH-]. pH meter is a device for measuring [H+] in a solution. pH ranges
from 0 – 14. 0 to 6.9 is acidic. 7 is neutral. 7.1 to 14 is alkaline.

Minerals (inorganic compounds)

Salts are compounds that release ions other than h+ and OH-. E.g Na Cl. Macronutrients are
minerals that are needed in large amount by our body. E.g. Ca2+, Fe2+, Mg2+, K+, Na+, Cl-,
NO3-, PO4 2-, SO4 2-. Micronutrients are minerals that are needed in small amount. E.g.
Cobalt, Copper, Zn 2+.

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Type Benefits Sources
Calcium Calcium, the most abundant mineral in the human Milk and other dairy
body, has several important functions. More than 99% products —such as yogurt,
of total body calcium is stored in the bones and teeth cheese, and cottage cheese
where it functions to support their structure [1]. The — are good sources of
remaining 1% is found throughout the body in blood, calcium. Also in broccoli
muscle, and the fluid between cells. Calcium is and dark green, leafy
needed for muscle contraction, blood vessel vegetables.
contraction and expansion, the secretion of hormones
and enzymes, and sending messages through the
nervous system [2]. A constant level of calcium is
maintained in body fluid and tissues so that these
vital body processes function efficiently.
Iron Almost two-thirds of iron in the body is found in Iron-rich foods include red
hemoglobin, the protein in red blood cells that carries meat, pork, fish and
oxygen to tissues. Smaller amounts of iron are found shellfish, poultry, lentils,
in myoglobin, a protein that helps supply oxygen to beans and soy foods, green
muscle, and in enzymes that assist biochemical leafy vegetables, and
reactions. Symptoms of iron-deficiency anemia raisins. Some flours,
include weakness and fatigue, lightheadedness, and cereals, and grain products
shortness of breath. Iron deficiency develops are also fortified with iron.
gradually and usually begins with a negative iron
balance, when iron intake does not meet the daily
need for dietary iron. This negative balance initially
depletes the storage form of iron while the blood
hemoglobin level, a marker of iron status, remains
normal. Iron deficiency anemia is an advanced stage
of iron depletion. It occurs when storage sites of iron
are deficient and blood levels of iron cannot meet
daily needs. Blood hemoglobin levels are below
normal with iron deficiency anemia.

Iron deficiency anemia can be associated with low

dietary intake of iron, inadequate absorption of iron,
or excessive blood loss [1,16,35]. Women of
childbearing age, pregnant women, preterm and low
birth weight infants, older infants and toddlers, and
teenage girls are at greatest risk of developing iron
deficiency anemia because they have the greatest
need for iron [33]. Women with heavy menstrual
losses can lose a significant amount of iron and are at
considerable risk for iron deficiency [1,3].

Magnesium Approximately 50% of total body magnesium is foundYou get magnesium from
in bone. The other half is found predominantly inside
whole grains and whole-
cells of body tissues and organs. Only 1% of grain breads, nuts and
magnesium is found in blood. seeds, green leafy
vegetables, potatoes,
Magnesium is needed for more than 300 biochemical beans and peas, spinach.
reactions in the body. It helps maintain normal
muscle and nerve function, keeps heart rhythm
steady, supports a healthy immune system, and
keeps bones strong. Magnesium also helps regulate

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 blood sugar levels, promotes normal blood pressure,
and is known to be involved in energy metabolism
and protein synthesis [2-3]. Early signs of magnesium
deficiency include loss of appetite, nausea, vomiting,
fatigue, and weakness. As magnesium deficiency
worsens, numbness, tingling, muscle contractions and
cramps, seizures, personality changes, abnormal
heart rhythms, and coronary spasms can occur
Phosphorus Phosphorus helps form healthy bones and teeth. It Phosphorus is found in
also helps the body make energy. It is part of every most foods, but the best
cell membrane, and every cell in the body needs sources are dairy foods,
phosphorus to function normally. meat, and fish.
Potassium Potassium helps with muscle and nervous system Potassium is found in
function. It also helps the body maintain the balance broccoli, potatoes (with
of water in the blood and body tissues. skins), green leafy
vegetables, citrus fruits,
bananas, dried fruits, and
legumes such as peas and
lima beans.
Zinc Zinc is an essential mineral that is found in almost You'll find zinc in red meat,
every cell. It stimulates the activity of approximately poultry, oysters and other
100 enzymes, which are substances that promote seafood, nuts, dried beans,
biochemical reactions in your body (1,2). Zinc soy foods, milk and other
supports a healthy immune system (3,4), is needed dairy products, whole
for wound healing (5), helps maintain your sense of grains, and fortified
taste and smell (6), and is needed for DNA synthesis breakfast cereals.
(2). Zinc also supports normal growth and
development during pregnancy, childhood, and
adolescence.
iodine The only function of iodine involves the synthesis of Although most foods do not
thyroid hormone. Approximately 60% of the total contain iodine, one
body pool of iodine is stored in the thyroid gland. The teaspoon of iodized salt
remainder is found in the blood, ovary, and muscle. consumed daily is more
Thyroid hormone is necessary for regulation of human than sufficient to satisfy
growth and development. Signs of iodine deficiency physiological requirements
include hypothyroidism, lethargy, and weight gain. for this nutrient. Other
The clinical presentation of iodine deficiency is goiter. dietary sources of iodine
Cretinism is a condition which develops in the fetus include drinking water,
from iodine deficiency during pregnancy. This seafood (clams, lobster,
condition is characterized by mental retardation and oysters, sardines and ocean
dwarfism. fish) and dairy products
from food additives

Phosphorou Physiological Functions Good Dietary Sources of

s Phosphorous is a component of bone, teeth, nucleic phosphorous are typically
acids, phospholipids, ATP, and a number of enzymes also rich in protein. These
and coenzymes. Phosphorylation of glucose is a foods are mainly milk,
requirement for its metabolism. meat, nuts, legumes, and
Phosphorylation/dephosphorylation of cellular grains.
compounds is a mechanism for regulating enzyme
activity and for transport and storage of cell
compounds. Approximately 85% of the total body
phosphate pool is found in bone. The remaining

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 amount of phosphate is distributed in blood and soft
tissues.

Fluorine Fluorine has a recognized pharmacological benefit Fluoridated water is the

that include prevention of dental caries and best source of this mineral
protection of bone from osteoporosis-induced because it provides a more
fracture. Fluoridation of the water supply and addition bioavailable source of the
of fluoride to toothpaste have decreased the mineral than the protein-
incidence of dental caries by 50%. The antibacterial bound form found in foods.
properties of fluorine may contribute to this reduction For dental health, exposure
in dental caries and may also facilitate wound to fluorine through
healing. fluoridated water supplies
is more beneficial for
preventing dental caries
than use of topical fluoride
rinses.
Salt-water fish such as
salmon, halibut or orange
roughy are good animal
sources of fluorine.
Concentrated amounts of
fluorine are also found in
tea leaves.

Chlorine Chlorine is involved in maintenance of acid-base Processed or commercially

balance. Plasma chlorine contributes to plasma prepared foods containing
buffering capacity by diffusion into red blood cells salt (sodium chloride) are
which allows bicarbonate to exit without upsetting rich in chlorine. A small
electrical neutrality in these cells. Transmembrane amount of chlorine is
exchange of chlorine with sodium and potassium in all obtained from the water
cells maintains electrical neutrality and fluid balance supply.
needed for appropriate intracellular osmolality and
pH, and for normal muscle contraction and nerve
transmission. Chlorine also promotes renal retention
of potassium. Chlorine aids in protein digestion by
contributing to synthesis of gastric hydrochloric acid.

Sodium Sodium is the primary electrolyte that regulates the Common dietary sources of
extracellular fluid levels in the body. Sodium is sodium are often processed
essential for hydration (maintaining water balance) food to which salt is added
because this mineral pumps water into the cell. during preparation, such as
Hyponatremia is characterized by lethargy, confusion, cheeses, soups, pickles and
muscle twitching, seizures and coma. Hypoatremia pretzels. Additionally,
may also be due to excessive intake of fluid. processed, commercially
prepared or restaurant
foods are generally high in
sodium.

Organic compounds

Carbohydrate

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It contains C,H,O atoms. It is the most biomolecules. It is a source of energy in animals, plants
and human. It also provides structural function in plant. E.g. sugar, starch, cellulose, glycogen.

Monosaccharide (mono = one, saccharide = sugar, Greek word).

Taste sweet. Soluble in water. Forms crystals. General formula (CH2O)n 3 ≤ n ≤ 7
When n=3  triose, n=4 tetrose, n=5 pentose (e.g. ribose, deoxyribose in RNA or DNA),
n=6 hexose (e.g. glucose, fructose), n=7 heptose
Has at least 2 OH groups bonded to the carbon backbone plus an aldehyde or a ketone group.
Glucose is the main energy source for most organisms. It is also a building blocks for
polysaccharides. There are 2 isomers – alpha and beta-glucose.

Isomers are compounds which share the same formula but differ in their molecular structure.

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Disaccharides
They are double sugar. The general formula is C12 H22 O11. e.g. lactose (milk) = glu +
galactose
sucrose = glu + fructose (sugar beet, sugar cane, commersial sugar).
Plants convert larger CHO to sucrose which is easily transported through leaves, stems and
roots.
maltose (e.g. barley) = glu + glu
Taste sweet, soluble, forms crystals. Amino sugars are sugars that contain nitrogen e.g.
glucosamine

Polysaccharides
they are multisugar (a long links of monosaccharides). The general formula is (C6 H10 O5)n.
They are insoluble in water. Not sweet and cannot be crystallized. They can be stored and when
sugar is needed, they can be hydrolyzed to release free sugar.
e.g.
starch: glucose isomer = alpha glu
glycogen: = alpha glu
cellulose: = beta glu

They have different properties because of differences in covalent bonding patterns

between glucose units.
They can be straight or branch chains.

Starch
Consists of 20-30% amylose (unbranched, spiral shaped) and 70-80% amylopectin (branched).
OH groups onesided. Plants store sugar as starch. Enzymes can easily hydrolyse starch to
glucose units.

Glycogen

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It is a storage of CHO of animals and human. It is a long, branched chains, linked by 1-4 or 1-6
glycosidic links. It is more soluble than starch. It exists in cytoplasm as tiny granules. It is
abundant in liver and muscles.

Cellulose
It is found in plant's cell wall. It is a long, straight chains of beta glucose, linked by 1-4 glycosidic
links. It has a strong properties. Why? because it has both glycosidic and hydrogen bonds. OH
groups stick outwards from the chain in opposite direction. It is tough, insoluble, resistant to
mechanical stress.

* Draw beta glucose on a piece of paper. Flip upside down.

Lipids
They are organic compounds that contain C,H,O. ratio of O atom to H is much lower than the
ratio found in carbohydrates. e.g. triolein (fat in olive oil). Some lipid may contain P and N. They
are hydrophobic. Insoluble in water and only dissolve n organic solvent. e.g. acetone, ether,
chloroform, alcohol.

3 main groups of lipids

1. Triglycerides (fat/ oil)
2. phospholipids
3. steroids

Triglycerides
Formed through the process of esterification. They are esters that are formed from the
condensation (release water) of one molecule of glycerol (an alcohol, propane-1,2,3-triol) and 3
molecules of fatty acids. (FA). Esterification is a reaction involving alcohol and acids. OH group
of glycerol reacts with COOH group of FA. Ester bond is established between glycerol and FA.

Glycerol
Has 3 carbon atoms, each with hydroxyl group (OH). Also known as glycerine. There is only 1
type of glycerol.

Fatty acids

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General formula is as below

n = can be between 14 – 22.

FA can be of the same types or 2 or 3 different types (i.e. shows considerable structural
variation). The physical and chemical properties of a particular lipid depend on the FA which it
contains.
E.g. tristearin = a triglyceride formed form 1 molecule of glycerol and 3 stearic acids. The
compound is saturated because of the presence of stearic acid. Usually found in animal fats.

Stearic acid (saturated FA)

The hydrocarbon chain has the maximum no. of atoms H. all have single bond. C17 H35 COOH, a
straight molecule. Usually found in animal fats.

Oleic acid (unsaturated FA)

The hydrocarbon chain has one or more double bonds. Called unsaturated because atom C that
forms the double bond can still accept atom H. C17 H33 COOH, a bent molecule because of the
double bonds. The molecule cannot pack together closely enough to solidify at room T. so, it is
liquid. Usually found in vegetable oil.

Essential FAs– our body cannot synthesize them in sufficient quantities and must be obtain
from diet. E.g. linoleic acid, linolenic acid, arachidonic acid = ALL these are unsaturated.

Non-essential FAs – our body can synthesize during metabolic activities involving CHO and
proteins.

Functions of fats
1. Source of energy. Fats store more energy than the same mass of CHO or protein.
2. Good insulator. It conduct heat slowly. E.g. for polar bears, penguin. Fat is deposited as
adipose tissue.
3. Protect internal organs. Fats in abdomen provides mechanical protection to the visceral
organs.
4. Waterproof substance for hair, feathers, leaf cuticle.
5. Precursor of steroid hormones
6. For structural support. Fats are components of plasma and nuclear membrane, myelin
sheath.
7. Source of water for some desert animals. They obtain water from fat metabolism.

Phospholipids
Phosphoric acid reacts with one of the 3 OH groups of glycerol. This forms the polar head
(hydrophilic). The other 2 OH groups of glycerol react with FA chains. This forms the non-polar
tail (hydrophobic). The most common phospholipid is lecithin. When a phospholipid is put into
water the molecules spontaneously arranged themselves to form a double layer. Hydrophobic
tails face inside. Hydrophilic head face outside.

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Steroids
They are lipids with no FA. They consists of 4 carbon rings fused together. Attached to it is a
side chain. Different side chains give rise to different types of steroid. They are classified as
lipids because they are insoluble in water. E.g. cholesterol.

Steroids in the human body

1. Cholesterol – the component of cell membranes, nerve cells. Precursor of other steroid.
Human body contains it from diet (saturated fat from animal contains cholesterol). It can
also be synthesized by the liver. The cholesterol level in our body is regulated by the
liver. Excess cholesterol will be deposited as gallstone in the gallbladder. Saturated fats
contain more cholesterol than unsaturated fats. Unsaturated fats have less tendency to
stick to arterial wall and can inhibit the synthesis of cholesterol in the liver.
2. Bile acids – helps in emulsification and digestion of fat. E.g. glycocholate and
taurocholate
3. Cortisol and aldosterone – involved in stress response.
4. Oestrogen and progesterone – are female reproductive hormones.
5. Testosterone – is male reproductive hormone.
6. Calciferol (Vit. D2) – facilitates absorption of calcium and phosphate from the small
intestine.

Negative effects of steroids to human

1. Arteriosclerosis – hardening of the blood vessels
2. Gallstones – can block the bile passage to the small intestine.
3. The use of anabolic steroids can cause liver damage, sterility, musculinisation in
female. How steroid increase the muscle content in the body? – anabolic steroids are fat
soluble. So, they can access through the cell membrane freely and go to the nucleus.
Here, it hasten the gene transcription involved in the synthesis of actin and myosin. This
will increase the total muscle content in the body. Physical power will increase. Athletes
become more aggressive and feeling of tiredness is delayed.

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Other forms of lipids
1. Terpenes – are compounds smaller than steroids. E.g. turpentine.
2. Waxes – a long chain of FA linked to a long chain of alcohol or carbon rings. It protects
and lubricate skin, hair. Birds secrete waxes to waterproof feathers. Bees use beeswax to
construct honeycomb which is water repellent.
3. Cutin – plants cuticle contains waxes and cutin. Both are synthesized by the epidermis
and secreted onto the surface of plants. They restrict water loss from plants.

Proteins
Are complex macromolecules. They always contain N as well as C, H, O. sometimes they have S,
P and other elements. The MW is very high. They consist of one or more polypeptide chains.
Each polypeptide chain consists of many units of amino acids (aa). They are easily denatured by
extreme T, pH.

Amino acids
All share the same structure but differ in their side chains (-R). The simplest aa is glycine, where
R = H. see below.

Amino acid is amphoteric because each aa consists of acidic COOH group and basic amino (NH2)
group. They are >100 naturally occurring aa but only 20 are used in biosynthesis of protein. Aa
that have hydrocarbon as side chain (-R) are non-polar. Proteins with this type of aa are
insoluble and non-reactive. They usually form structural proteins. E.g. collagen. Aa that have
polar (-R) group produce partial charges but they do not receive or donate electrons. This type
of protein has increased solubility and enables H bonding between the polypep chain. Basic or
acidic aa produce positively and negatively charged ions, respectively. The proteins are strongly
hydrophilic and are soluble in water. E.g. globular proteins.

Aa with non-polar R group = glycine, alanine, valine, leucine

Aa with polar R group = serine, asparagines, glutamine, tyrosine
Aa with acidic R group (-vely charged) = aspartic acid, glutamic acid
Aa with basic R group (+vely charged) = lysine, arginine, histidine.

Dipeptides, tripeptides and polypeptides

2 aa linked together through a peptide bond. Reaction occurs between the amino group of one
aa and COOH group of the other aa. When an aa is linked to a dipeptide, a tripeptide is formed.

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Polypeptides are long chains of aa. Although only 20 aa are used in the synthesis of proteins,
the number of ways in which thy can combine is infinite. Proteins may differ with each other in:
• The total no of aa. e.g. 200 aa, 1000 aa
• The sequence of aa. e.g. ….Ala-Val-Leu….. or …..Leu-Ala-Val…..
• The quantity of each type of aa. E.g. 20 polar aa or 30 non-polar aa.

Protein structure
There are 4 levels of protein structure.
1. Primary – is the linear sequence of aa in a polypep chain. The sequence of aa is
determined by the genetic code in DNA molecule. The sequence is unique for a particular
protein and is exactly the same for all molecules of that protein.

2. Secondary – refers to the way a particular polypep chain is coiled or fold upon itselt as a
results of the H bonds. The polypep chain folds to form either:
• Alpha helix looks like a wire of a telephone. The shape of alpha helix is maintained
by H bonds. Function of alpha helix is to maintain the shape of a molecule. It is
more stable than a straight polypep structure.

• Beta pleated sheet is formed when polypep chains are arranged parallel to each other
and folded longitudinally. It has a high resistance to stretching, strong and flexible. It
is mainly produced by insects, spiders.

3. Tertiary – refers to the way a polypep chain folds and coils to form a compact protein
molecule. The tertiary structure is held by H bonds, ionic bonds and disulphide bridges
(-S-S-). These are the strongest and contribute to the toughness of proteins. E.g. globular
proteins such as enzymes, hormones, antibodies, globulin, actin, tubulin.

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 4. Quarternary – is found in very large proteins or very complex proteins. It is formed
when a protein consists of 2 or more polypep chains and often have non-protein
additions such as lipids, carbohydrates, polynucleotides. E.g Hb in the red blood cells.

Denaturation is a process of which a protein molecule changes their structure and loss its
function because of the breaking of bonds. It can be cause by excessive T or pH, detergent,
heavy metal ions, Organic solvent. Everyday example of denaturation is coagulation of egg
white when cooked.

Vitamins
All natural vitamins are organic food substances found only in living things, that is, plants and
animals. With few exceptions the body cannot manufacture or synthesize vitamins. They must
be supplied in the diet or in dietary supplements. Vitamins are essential to the normal
functioning of our bodies. They are necessary for our growth, vitality, and general well-being.
Vitamins help regulate metabolism, help convert fat and carbohydrates into energy, and assist
in forming bone and tissue. They cannot be digested into simpler molecules. ADEK – water
soluble. Others insoluble in water.

VITAMIN A (Beta Carotene)

IMPORTANCE: Necessary for growth & repair of body tissues; helps maintain smooth, soft skin;
prevent night-blindness & weak eyesight
DEFICIENCY SYMPTOMS: May result in night blindness; rough, dry, scaly skin.

Vitamin B-1, otherwise known as thiamine, is necessary for most every cellular reaction in the
body as a participant in an enzyme system known as thiamin pyrophosphate. It is vital to normal
functioning of the nervous system and metabolism. It can be found in meat, whole grains, fish,
and nuts. Functions:
Maintains health of mucous membranes
Keeps normal workings of nervous system, heart, and muscles
Helps treat beriberi
Supports normal growth and development
Reduction of depression, fatigue, and motion sickness
Potential improvement in appetite and mental alertness

Vitamin B-9, otherwise known as folic acid, serves as a coenzyme during the creation of DNA.
This vitamin is also very important to the growth and reproduction of all body cells, including red
blood cells. Great food sources of vitamin B-9 include liver and dark green leafy vegetables.
Functions:
Formation of red blood cells
Creation of genetic material
Promotes a healthy pregnancy by regulating the nervous system development of the fetus
Helps treat anemic patients resulting from folic acid deficiency
This Vitamin is Found in Asparagus, Avocados, Bananas, Beans, Calf liver
Vitamin B-12, otherwise known as cyanocobalamin, performs as a coenzyme for the creation
of DNA material. It also promotes growth and cell development and is important to fat,
carbohydrate, and protein metabolism. Although vitamin B-12 is not found in plant foods, good
sources of this supplement include meats, fish, eggs, and dairy products. Functions:

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Growth and development of nerve, skin, hair, and blood cells
Produces genetic material
Metabolizes amino and fatty acids
Works to release food energy
Could improve immune system
May see increase in energy and memory

Vitamin C is essential for the manufacturing of collagen, necessary for tissue repair. It is
needed for metabolism of phenylalanine, tyrosine, folic acid, iron. Vitamin C is also vital for
healthy immune and nervous systems because it strengthens blood vessels, as it is an
antioxidant that participates in oxidation-reduction reactions. Also, it is required for utilizing
carbohydrates and synthesizing fats and proteins. Functions:
defense mechanism against disease and infection
promotes the production of red-blood-cell in bone marrow.
supports healthy capillaries, gums, teeth, and even helps heal wounds, burns, and broken
tissues.
preventing blood clots.
Another large benefit of this vitamin is the fact that it plays a large role in the production of
antibodies.
Tthe promotion of iron absorption and calcium absorption.
Reduces free-radical production
May reduce cholesterol
Potential protection against heart disease
This Vitamin is Found in Fruits, Grapefruit, Guava, Lemons, Mangoes.

Vitamin D, otherwise known as the sunshine vitamin, is significant in normal body growth and
development. In particularly, vitamin D is used to absorb calcium and phosphorus to create
bone. Great sources of this supplement include fortified milk, oily fish, liver, and eggs. Functions:
Absorbs calcium and phosphorus to aid in the development of bones and teeth
Promotes normal cell growth and maturation
Prevents rickets
Maintains a healthy nervous and immune system

Vitamin E, otherwise known as alpha-tocopherol, serves as a cofactor in several enzyme

systems. It keeps excessive oxidation from occurring that could cause harmful effects in the
body. Great sources of vitamin E may be found in wheat germ, nuts and seeds, whole grain
cereals, eggs, and leafy greens. Functions:
Protects fats, cell membranes, DNA, and enzymes against damage
Encourages normal growth and development
Acts as an antioxidant to protect against heart disease and cancer
Anti-blood clotting agent
Improves immune system

Vitamin K, otherwise known as phytonadione, promotes production factors critical to normal

blood clotting. When foods are processed or cooked, very little of vitamin K contained in foods is
lost. Great sources of this vitamin include dark leafy greens, oils from green plants, and some
dairy products. In our body it Regulates normal blood clotting, Promotes normal growth and
development and it is Essential for kidney functioning. This Vitamin is Found in Alfalfa,
Asparagus, Broccoli, Spinach, Cabbage.

Nucleic acids – a complex molecule containing C, H, O, P, N atoms.

The 2 major nucleic acids are DNA and RNA.
Each nucleic acid molecule consists of 1 or 2 polynucleotide chains.
The building blocks of nucleic acids are nucleotides which are linked together forming a
polynucleotide.

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Nucleotide
Each nucleotide consists of 3 parts – phosphoric acid (phosphate, H3PO4)
- pentose sugar: ribose, C5 H10 O5, found in RNA
: deoxyribose, C5 H10 O4, found in DNA

- nitrogenous base (consists of carbon-nitrogen compound): purine (double

rings) – adenine, guanine
: pyrimidines (single ring) – cytosine, thymine, uracil

The 3 parts are linked together through a condensation reaction – 2 water molecules are
removed during the process. The phosphate group gives the acidic property to nucleic acid.

Polynucleotide - 2 nucleotides are joined forming a dinucleotide. This process is a

condensation reaction. One molecule of water is released.
- Phosphodiester bond (covalent bond) is formed between the pentose sugar from the 1st
nucleotide (at position 3) and the phosphate group from the next molecule.
- the backbone is sugar-phosphate- sugar.
- The bases point to one side.
- sugar and phosphate groups are identical along the polynucleotide chain but the sequence of
bases vary. It is in this sequence of bases that the nucleic acid carries information controlling
the organism’s development.

DNA
• each molecule consists of 2 polynucleotide strands.
• The 2 strands are in the opposite directions (anti-parallel). Then the 2 strands coiled
together to form a double helix. This structure is held together by hydrogen bonds
formed between the purine bases on 1 strand and the pyrimidine bases on the other
strand.

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 • The purine and pyrimidine bases pair up: A  T; G  C. This is called complementary
base pair. Between A-T there are 2 hydrogen bonds. Between G-C there are 3
hydrogen bonds.
• It is much easier to separate the 2 DNA strands longitudinally than transversely
because the hydrogen bond is weaker than the phosphodiester bond.
• The separation of the 2 strands would result in each strand attracting its
complementary nucleotide to itself.

RNA
• each molecule consists of a single polynucleotide chain (which is shorter than DNA).
• There are 3 types of RNA: ribosomal RNA (rRNA), messenger RNA (mRNA), transfer
RNA (tRNA). All types involved in protein synthesis.
• The nitrogenous bases are A, G, C, U only. The purine and pyrimidine bases pair up: A
 U; G  C.

Differences between RNA and DNA

RNA DNA
Single strand - Always Double
helix, anti-parallel, coiled
Sugar unit is Sugar unit is
ribose deoxyribose
3 types One type only
- Short molecule, Longer and
smaller molecular mass larger molecular mass
Found in any - Found in
place within the cell chromosomes in the nucleus.
Also found in small amount in
mitochondria and chloroplasts
Nitrogenous - Nitrogenous
bases are A,C,G, U bases are A,C,G, T

Ratio of A-U and - Ratio of A-T and

C-G varies C-G is one
Chemically less - Chemically more
stable stable
Exists for short - It is permanent
period only

rRNA – large molecule, found in the cytoplasm

- its base sequence is similar in all organisms
- comprises more than ½ of the mass of ribosomes
- manufactured by nuclear DNA.
- function: the main component of ribosome.

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tRNA – is a small molecule (80 nucleotides)
consists of a single strand.
Manufactured by nuclear DNA
Makes up 10-15% of the cell’s RNA
Forms a clover leaf shape
- The end of chain ending in a CCA sequence (at 3’). At this point amino
acid attaches itself.
There are at least 20 types of tRNA, each carrying a different amino
acid.
Its 3-dimensional shape is maintained by H bonds
- In loop 2 there is a sequence of 3 bases called the anticodon which
lines up alongside the appropriate codon on the mRNA during protein synthesis.
- Function: carries amino acid to ribosomes

mRNA – a long, single stranded molecule which is formed into a helix.

manufactured in the nucleus through a process called transcription.
It is a mirror copy of part of one strand of the DNA helix.
Makes up <5% of the total cellular RNA
Easily broken down, a transient molecule.
- Function: carrying genetic information from the chromosomal DNA in
the nucleus to the ribosomes in the cytoplasm. It associates with the ribosomes and
acts as a template for protein synthesis.

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