Chapter 1: Molecules of Life

Edited by : NJ.NS.MMAP.WSWO June 2015

1. Structure of water molecules
1. A water molecule consists of 2 hydrogen atoms & 1
2 2 oxygen atom share electrons in covalent bonds.
Hydrogen bond
(dotted lines) 2. Covalent bond is a bond within water molecules.
Covalent
bond 3. Form triangle shape, hydrogen atoms are 104.5o from
each other.

2 4. Hydrogen bond is a bond between water molecules.

5. Hydrogen bonds are weaker than covalent bonds

but strong enough to holds water molecules.
2 104.5˚
2
6. 1 water molecules form hydrogen bonds with
another 4 water molecules.

7. Hydrogen bond account for unique properties of

water.

2. Properties of water
Polar Molecules High surface tension
Polarity: Surface tension?
Unequal distribution of electrical charge in a molecule. Measure of strength of the water’s surface film

Why water are polar? Importance?

1. Large oxygen atoms pulls electrons in covalent  Permits water to hold up substances heavier and
bonds closer giving it net negative charge while denser than itself.
net positive charge on the hydrogen atoms Example :
- Steel needle place on the surface of water in a
2. The charge of H atom in water represents by glass will float
+
partially positive (δ ) while for O atom - Aquatic insects (water strider) able to walk on
represents by 2 partially negative (2δ-). water
Cohesive and Adhesive Forces
What is the effect of water polarity?
Cohesion and adhesion of water molecules. Water is
Hydrogen bonds; positively charge hydrogen atoms sticky and elastic and tend to clump together in drops
attracted to negatively charged oxygen atoms of rather than spread out in thin film.
neighbouring water molecules.
1. Capillary action: water can move up a narrow tube
Importance? due to cohesion and adhesion
1. Act as universal solvent. Able to dissolve many 2. Cohesion : Attraction between water molecules
ionic substances with positive and negative 3. Adhesion : Attraction between water molecules and
charged / medium for chemical reaction. other molecules
2. Hydrophilic substances; able to mix well and Example :
dissolve in water such as salt (NaCl), sugars, acid, - Water move water up the xylem vessels
alkali, O2 & CO2. (transport water and dissolve minerals)
3. Hydrophobic substances; do not mix well such as - Blood moves in capillaries
fats & oil.

How do water act as a solvent?

1. Water surrounds charged particles forming
hydration/solvation shell & pulling them into
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solution.
2. Negative oxygen ends surround cations / positive
hydrogen ends surround anions / negative

Why oils insoluble in water?

 Non net electrical charges across oil molecules

High specific heat capacity Low viscosity

Specific heat capacity? Viscosity?
Quantity of heat that must be absorbed or lost for 1g of measure of a fluid inability to flow/ fluid internal
substance to increase temperature by 1oC resistance

Why do water has high specific heat capacity? Importance of water having low viscosity/ high fluidity
Extensive hydrogen bonding between its molecules 1. Ease cellular motion (movement of organelles).
2. Facilitate endocytosis & exocytosis
Importance? 3. Aid circulatory system (95% of blood plasma is
1. Water can absorbed large amount of heat energy water); blood can flow through the narrow
before increase in temperature. capillaries
2. Buffer earth’s temperature fluctuation 4. Lubricant; to reduce friction
3. Help organism maintain body temperature Example; synovial fluid (thick & stringy) found in
4. Can be used as a coolant for radiator in car or cavities of synovial joints to reduce friction/ cushion
industries because water can also lose heat. between cartilage and tissue joints.
High latent heat of vaporisation Maximum density at 4oC
Latent heat of vaporization? Water become less dense upon freezing (increase in
 Quantity of heat must be absorbed for 1g of liquid volume/ same mass)
to be converted to gas.
Importance?
Importance?  Ice float on water which insulates temperature in the
 Evaporation (sweating) and transpiration cools water beneath of around 4oC (organisms able to
organisms because lots of body heat absorbed to survive)
break hydrogen bonds between water molecules to How to water density decrease upon freezing?
change the water molecules from liquid to solid.  Hydrogen bonds becomes more stable to form the
ice crystalline structure compare to semi ordered
molecular structure in liquid form where hydrogen
bonds constantly break and reform.

3. Describe the various form and classes of carbohydrates

Classification: Class of monosaccharides:
 Number of carbon atoms : 6 carbons (pentose)  Linear or ring form.
 Position of functional group  Simple carbohydrate.
- carbonyl group; aldose/ ketose  Cannot be hydrolyzed into simpler form.
- hydroxyl group; α-glucose (below)/ β-glucose  Characteristics;
(above) - Colourless
- Water soluble
- Crystalline solids
- Sweet taste
 Example: glucose, fructose & galactose
 Importance;
- Building blocks of disaccharides and
polysaccharides
- To synthesis other monomers (amino acids &
α-glucose β-glucose fatty acids)
- Produce ATP (cellular respiration)
-
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Disaccharide : Polysaccharide :
 Condensation of 2 monosaccharides by forming  Thousands of monosaccharides join by
glycosidic bonds. glycosidic bonds
 Glycosidic bonds can be broken by hydrolysis.  Variable in length, branched/ unbranched, folded,
 Characteristics; straight / coiled
- Water soluble  Characteristics :
- Sweet taste - Insoluble in water
- Can be crystallised - Cannot be crystallised
 Examples;  Example : starch / glycogen / cellulose
- Maltose: glucose + glucose (α-1,4 glycosidic bonds)  Importance;
- Lactose: glucose + galactose - As energy storage.
- Sucrose: glucose + fructose - Building materials for cell wall/ whole
organisms.
Why is starch and glycogen used as energy storage?
 Large molecules
 Insoluble in water (stored in large amount without affecting water potential)
 Easily hydrolysed

Describe characteristics of energy storage molecules:

Similarities:
- Made of α-glucose
- Form granules in cell
- Helical structures
Starch Glycogen
 Starch is made form 2 substances : amylose +  Found in liver and muscle cells where there are
amylopectin high rate of metabolism.
Amylose  Linear chain of α-glucose
 Found in plants organelle amyloplast  More extensively branched compare to
 Linear unbranched amylopectin
 α-1,4 glycosidic bonds  Linear chain: α-1,4glycosidic bonds
Amylopectin  Branches occur every 30 units by α-1,6
 Found in plants organelle amyloplast glycosidic bonds
 Long branched
 Linear chain : α-1,4 glycosidic bonds
 Branches occur every 30 units by α-1,6 glycosidic
bonds
Cellulose
Describe the role of cellulose as major building materials for plant cell walls:
 Macromolecules
 Long-unbranched chain of β-glucose held together by β-1,4 glycosidic bonds
 Adjacent chains linked by hydrogen bonds
 Insoluble in water
 High strength / strong

4. State the type of lipid

What is lipid? Importance?
 Water insoluble organic molecules that contain C, H  Energy storage
& O atoms.  Components of cell membrane
 Soluble in organic solvent (alcohol, ether &  Heat insulator (animal fat)
chloroform)  Transport fat soluble vitamins
 Deliver information (hormone)
 Buoyancy
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Health problems associated with lipid:

 Obesity
 Coronary heart disease
Triglyceride
 3 fatty acids & 1 glycerol hold together by ester
linkage.
 Ester linkage form by condensation & broken by
hydrolysis
 Example : fat & oil Condensation/
esterification
+ H2O
Fatty acids:

 Carboxyl group attached to long hydrocarbon chain

(16-18 carbon skeleton) which is hydrophobic Fatty
acid
Saturated fatty acids:
 Hydrocarbon chain lack/no double bonds Triglyceride Water
 Example : stearic acid Formation of triglyceride:
- Condensation reaction
Unsaturated fatty acids: - OH from carboxyl end of fatty acid and H from
 1 or more double bonds in hydrocarbons (kink/bend hydroxyl group of glycerol removed.
in the chain) - Ester linkage formed
 Example : oleic acid
R1
Glycerols: R1
 3 carbons chain + hydrogen atoms + OH group Hydrolysis
R2
R2
+
R3 R3

+ H2O
OH

Breakdown of triglyceride:
- Hydrolysis reaction
- OH react with carboxyl end of fatty acid and H
react with hydroxyl group of glycerol
- Carboxyl group of each fatty acid is formed
- Hydroxyl group of glycerol is formed

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Phospholipid
 2 fatty acids + 1 glycerol +1 phosphate group
 Additional functional group may attached to the
phosphate

Importance?

 Components of plasma membrane

 Example : lecithin

Phospholipid bilayer?

 Hydrophilic head (Glycerol + phosphate group) in

contact with aqueous solution while hydrophobic tails
(2 fatty acids) face one another forming hydrophobic
region.
 Act as semipermeable barrier between cytoplasm and
extracellular environment.
 Permeable to water (small size) but impermeable to
polar molecules/ ions

*single layer of phospholipid self-assemble into micelle

(a ball of lipid with hydrophilic head pointing outside &
hydrophobic tail form hydrophobic region inside)

Steroid
 4 ring hydrocarbon structure which soluble in lipid
 Example : cholesterol
 Precursor of steroid hormone (testosterone &
oestrogen

Importance?
 To maintain fluidity of cell membrane (low fluidity at
high temperature & high fluidity at low temperature)

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5. Describe the basic structure and of amino acids
R-group define amino acids into 4 chemical classes :
Amino group/(basic) Carboxyl group/ (acidic)  Non-polar (-CH2/ -CH3)
- E.g : Gly, Ala, Val, Leu, Ile, Met, Trp, Phe, Pro

 Polar (Oxygen/ Hydrogen)

- E.g : Ser, Thr, CYs,Tyr, Asn, Gln

 Acidic
- E.g : Asp, Glu
R-group / side group (varies in different amino acids
: total 20 amino acids)  Basic
- E.g : Lys, Arg, His

*amino acids can be group into polar, non-polar, acidic &

basic

6. Draw a diagram illustrating formation and breakdown of dipeptide. Name the process involved

Hydrolysis

+ H20

Condensation

7. What is protein? Describe the level of protein organization (structure)

Protein is a polymer of protein formed from amino Primary structure:
acids joined by peptide bond via condensation  The amino acid sequence of a protein
reaction.  Peptide bond only
Level of protein structure (structure) :  Slight change in the amino acid sequence affect protein’s
 Primary conformation and ability to function (sickle cell anaemia;
 Secondary valine instead of glutamic acid)
 Tertiary
 Quaternary
Secondary structure: Tertiary structure:
 Hydrogen bonds between peptide bonds along  Interaction between R-groups and polypeptide backbone
polypeptide backbone (ionic bonds, hydrogen bonds, disulphide bridges,
 α-helix (coiling caused by hydrogen bonds) hydrophobic interaction & van der Waals)
 β-pleated sheet (folding between amino acids
in a polypeptide caused by hydrogen bonds).
 Example : silk

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Quaternary structure:
 Aggregation of two or more polypeptide
chain.
 Collagen (connective tissue) : fibrous protein of
3 polypeptide super coiled
 Haemoglobin; globular protein of 4
polypeptides (2α & 2β)

Fibrous : Eg : Collagen Globular : E.g Haemoglobin

8. How do pH and temperature affect protein structure

Protein structures are sensitive to physical and
chemical changes in the environment.
Changes in protein’s conformation structure (2nd,
3rd & quaternary) that affect function known as
denaturation.

Denaturation is reversible.
 Extreme pH (ionic)& temperature
disrupt/break ionic bonds, hydrogen
bonds, disulphide bridges, hydrophobic
interactions and van der Waals.
 Protein will be denatured.

9. Name the 3 classes of protein based on their structure and states the functions of protein
3 Classes Of Proteins Function of protein:
Conjugated protein: (i) Nutrition
o Protein with non-protein components. Amylase and lipase involved in food digestion.
o E.g : haemoglobin (ii) Transport of respiratory gases
Haemoglobin transport oxygen.
Fibrous protein:
o Little or no tertiary structure. (iii)Immunity
o Long parallel polypeptide chains. Antibodies recognize the antigen and defense the body
o Cross linkages at intervals forming long fibres against diseases
or sheets.
o Usually insoluble. (iv) Co-ordination
o Many have structural roles. Hormones act as chemical messengers.
o Static molecules Insulin and glucagon:
o E.g. keratin in hair and the outer layer of skin,  Regulates blood sugar level
collagen (3 polypeptides chain).  Controls blood pressure

Globular protein: (v) Growth

o Have complex tertiary and sometimes Hormones (thyroxin and growth hormone) controls
quaternary structures. growth and metabolism.
o Folded into spherical (globular) shapes.
o Generally water soluble as hydrophobic side (vi) Support and movement
chains in centre of structure.  Keratin in the hair, surface layer of skin, collagen in
o Roles in metabolic reactions. tendon, ligaments and arteries provides support and
o Non-static (move around) strength.
E.g. enzymes, haemoglobin in blood,  Contractile proteins (actin and myosin) in muscles
Immunoglobulin, Insulin & Glucagon. involved in muscle contraction.

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10. Describe the structure of nucleotide :

What is nucleic acid? Describe the different structure of a nucleotide in DNA
Organic molecules that store genetic Hereditary and RNA (monomer).
Information in the cell

DeoxyriboNucleic Acid (DNA);

Information for cell activities (cell division)

RiboNucleic Acid (RNA);

Transfer information for protein synthesis
 mRNA is transcribed from the DNA
 rRNA involved in translation of mRNA into
protein.
 tRNA delivers amino acids to the ribosomes
(rRNA) during translation

Components of nucleotide:
 Pentose : ribose (RNA) / deoxyribose
(DNA)
 Nitrogenous base : purine (A,G) pyrimidine
(C,U,T)
 Phosphate group Drawing of
RNA nucleotide
Phosphate group
State the difference in the following components of
This bent is referring to
nucleotide; carbon number 5
i) Ribose vs. deoxyribose P Nitrogenous base :
Lack of 1 oxygen atom at Carbon number O A, C, G, U
2 in deoxyribose
ii) 2 types of nitrogenous base : Purine and
pyrimidine :
Purine has double rings while compared to
pyrimidine has single ring. O atom at carbon number 2
Ribose sugar

5’ end
OH
P
O

OH

P
O

OH

Drawing of RNA single strand

P
O

OH

P
O

3’ end
OH

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Chapter 1: Molecules of Life
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Describe the formation of phosphodiester bond in
a polynucleotide sequences.

 Formation of phosphodiester bond is via

condensation reaction (water is removed) to
bridge adjacent nucleotides (also known as
phosphate-sugar backbone).
 Polynucleotides contain a 5' end
(phosphate group attach to carbon
number 5) and 3' end (hydroxyl group).
 The common representation of
polynucleotides is as an arrow with the 5'
end at the left and the 3' end at the right.

11. Structure on DNA based on Watson and Crick model

Describe the structure of DNA molecules;
 Double stranded called Double Helix
5’ end 3’ end  2 strand of polynucleotide in opposite
direction (antiparallel); 5’------> 3’ & 3’---
>5’
 Held together by hydrogen bonds between
DNA nitrogenous basses of opposite strands.
double (G-C : 3 hydrogen bonds, A-T : 2
helix hydrogen bonds)
 Nucleotide basses in DNA:

Hydrogen bond

3’ end
5’ end Phosphodiester bond

Drawing of DNA double strand

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12. Compare the differences between DNA & RNA
DNA RNA
Basic unit of DNA is Deoxyribonucleotide Basic unit of RNA is Ribonucleotide
Pentose sugar is Deoxyribose Pentose sugar is Ribose
Nitrogenous bases are Nitrogenous bases are
Adenine, Guanine, Cytosine and Thymine Adenine, Guanine, Cytosine and Uracil
Double helix consisting of two strands of polynucleotides Single strand of polynucleotides
coiled around each other
Large in size/ longer chain Relatively small in size/ shorter chain
Can be found in the nucleus Can be found In the nucleus and cytoplasm
One type only Three types of RNA: mRNA, tRNA and rRNA.

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