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Ch 2 Molecular Organization
2.1 INORGANIC IONS
Water is the most important
molecules in life.
Dissolved in water within living
organisms are numerous
inorganic ions: macronutrients &
micronutrients.
Macronutrients (main elements):
Nitrate/Ammonium (NO3 - / NH4+)
- component of amino acids, proteins, vitamins,
co-enzymes, chlorophyll, etc.
- Deficiency: chlorosis & stunted growth
in plants
Phosphate/Orthophosphate (PO43- / H2PO4-)
- component of nucleotides, ATP & proteins,
- for phosphorylation of sugars (respiration)
- constituent of bones & teeth;
component of cell membranes
Sulphate (SO42-)
- component of proteins & co-enzymes
- forms bridges between polypeptide chains
- Deficiency: chlorosis & poor root development
Potassium (K+)
- maintains electrical balance & active transport
across cell membranes
- necessary for protein synthesis;
cofactor in photosynthesis & respiration
- important for transmission of nerve impulses
- Deficiency: yellow-edged leaves
& premature death
Calcium (Ca2+) Source: milk & cheese
- forms middle lamella of cell walls
- main constituent of bones, teeth & shell
- needed for blood clotting & muscle contraction
Sodium (Na+)
- maintains electrical balance
& active transport across cell membranes
- Deficiency in mammals: muscle cramps
Chlorine (Cl-)
- maintains electrical balance across
cell membranes
- forms HCl in stomach/gastric juice;
assists in CO2 transport by blood
Magnesium (Mg2+)
- constituent of chlorophyll;
- deficiency: chlorosis in plants
Iron (Fe2+ or Fe3+) source: liver, red meat, spinach
- constituent of electron carriers in respiration
& photosynthesis; constituent of some enzymes
- for synthesis of chlorophyll
- forms the haem group in haemoglobin & myoglobin
Micronutrients
Manganese: activator of enzymes
Copper: constituent of enzymes,
component of haemocyanin
Iodine: component of thyroxine, (from sea food, salt)
Cobalt: component of vitamin B
Zinc: activator of enzymes
Fluorine: component of bones & teeth
2.2 CARBOHYDRATES
- group of organic compounds containing
C, H & O
- divided into 3 groups:
monosaccharides,
disaccharides,
polysaccharides
- main functions:
storage and energy release
2.3 MONOSACCHARIDES
- group of sweet, soluble crystalline molecules
- either aldoses (-CHO) or ketoses (C=O)
2.3 MONOSACCHARIDES
- group of sweet, soluble crystalline molecules
- either aldoses (-CHO) or ketoses (C=O)
2.3 MONOSACCHARIDES
- group of sweet,
soluble crystalline molecules
- either aldoses (-CHO) or
ketoses (C=O)
- general formula: (CH2O)
- triose sugar: (CH2O)3
pentose sugar: (CH2O)5
hexose sugar: (CH2O)6 , C6H12O6
2.3.1
Structure of monosaccharides C6H12O6
Glucose:
a straight chain of 6 carbon atoms but
easily forms stable 6-sided (pyranose)
ring structure
Glucose:
6-sided
pyranose
ring
2.3.1
Structure of monosaccharides C6H12O6
Fructose:
forms 5-sided (furanose) ring structure
Fructose:
5 sided
furanose
ring
2.3.1
Structure of monosaccharides C6H12O6
Glucose:
a straight chain of 6 carbon atoms but
easily forms stable 6-sided (pyranose)
ring structure
Fructose:
forms 5-sided (furanose) ring structure
Isomers:
1. structural isomers - glucose and fructose
2. sterioisomers - same atoms or groups are joined
together but are arranged differently in space
(with an asymmetric carbon):
a) optical isomers - isomers which can rotate the
plane of polarized light (D or + towards right)
- most sugars (L or - towards left)
b) geometric isomers - due to double bonds in the
molecule, OR
-glucose (H pointing up) and
-glucose (H pointing down)
optical
isomers
geometric
isomers
OH
group
2.4 DISACCHARIDES
Condensation reaction:
glucose + glucose 
glucose + fructose 
glucose + galactose 
2.4 DISACCHARIDES
Condensation reaction:
glucose + glucose  Maltose + water
glucose + fructose  Sucrose + water
glucose + galactose  Lactose + water
(The reverse is hydrolysis)
+
Reducing groups
+
(no reducing power)
2.4 DISACCHARIDES
Condensation reaction:
glucose + glucose  Maltose + water
glucose + fructose  Sucrose + water
glucose + galactose  Lactose + water
(The reverse is hydrolysis)
- sweet, soluble and crystalline
- reducing sugars: with reducing power
Reacts with Benedict’s to give a red precipitate
non-reducing sugars: with no reducing power
-ve results
2.5 POLYSACCHARIDES
- condensation reaction of many monosaccharides
- number of monosaccharides is variable;
chains can be branched or unbranched
- ideal for storage because chains are folded
& insoluble, e.g.
- hydrolysis back to monosaccharides
- structural polysaccharide: cellulose in cell walls
2.5.1 Starch
- found in most plants
2.5.1 Starch
- found in most plants
- a mixture of
two substances
amylose
amylopectin
2.5.2 Glycogen
- major storage material in animals & fungi
- stored mainly in ______________
and
liver
_______________
muscles
- made up of -glucose molecules
- similar to amylopectin but has
shorter chains & is more highly branched
2.5.3 Cellulose
- makes up 50% of a plant cell wall
- a long unbranched polymer of ß-glucose with
cross linkages between parallel chains:
a very stable structural material
- synthetic products: cotton, rayon, cellophane
& paper
Cellulose
2.5.4 Other polysaccharides
Chitin - component of exoskeleton of
insects
Inulin - a polymer of fructose,
therefore a storage carbohydrate
2.5.5 Reducing and non-reducing sugars
- use Benedict's or Fehling's solutions for
testing reducing sugars
-sucrose: test for reducing activity after
hydrolysis with enzyme/dilute HCl
starch: Iodine solution test
2. Distinguish between
Cellulose & Starch (5 marks) (82-I-7)
Cellulose
Starch
1 Long chains of -glucose molecules 1 Long chains of -glucose molecules
2 Straight chains
2 Molecules with branched chains
3 Building material for plant cell walls 3 Storage material for plant cells
4 Not stained dark blue with 4 Stained dark blue with
iodine
iodine solution solution
5 Not digested by man
5 Can be digested by man
6 Provides raw materials for
6 As food for animals
textile, wood, cotton, plastics, etc.
7 Forms H bonds as linkages
7 No such property
to form microfibrils (larger units)
(any 5 for 5M)
2.6 LIPIDS
- contain C, H & O atoms;
proportion of O is much less
- insoluble in water but readily dissolves in
organic solvents likes alcohol, acetone
- Two types:
solids at room temperatures - fats
liquid at room temperatures - oils
Chemistry of lipids:
2.6.1 Fatty acids
- type of fatty acids determine the
characteristic of a particular fat
- unsaturated fatty acid: with double bonds
saturated fatty acid: no double bonds
- a long hydrocarbon chain (tail) which is
hydrophobic or water repelling
2.6.2 Phospholipids
- lipids with one of the fatty acid groups replaced
by phosphoric acid
- phosphoric acid is hydrophilic or water attracting
- form molecules/structure of the cell membrane
2.6.3 Waxes
- glycerol replaced by complex alcohol
groups, therefore more complex structure
- form waterproofing structures
2.6.4 Functions of Lipids
1 An energy source
2 Storage
3 Insulation
4 Protection
5 Waterproofing
6 Cell membranes
7 Other functions: plant scents, bees wax
2.6.5 Steroids
- fat-related compounds like
cholesterol for making hormones,
vitamin D and bile acids
2.7 PROTEINS
- proteins have large organic mass
(several thousand to several million)
- forms colloidal suspensions
- contain C, H, O S, N & P
- number of proteins is limitless,
thus determines characteristics of
a species by forming various cell /
body structures
2.7.1 Amino acids
- about 20 amino acids commonly occur
in proteins
- basic groups:Amino group (NH2-) Carboxyl group
(-COOH)
basic amino acids: more amino groups
acidic amino acids: more alkaline groups
dipolar/zwitterions:
an ion having
+ve & -ve
poles (charges)
dipolar/zwitterions: an ion having
positive & negative poles (charges)
amphoteric: having both acidic
& alkaline properties
buffer solutions: a solution which can
resist any changes in pH when small
amounts of acid or alkali are added
2.7.2 Formation of polypeptides
- condensation reactions:
two or more amino acids joined together
2.7.2 Formation of polypeptides
- condensation reactions:
two or more amino acids joined together
dipeptide: with two amino acids
joined together
polypeptide: more than two amino acids
joined together
1. 81-I-2
(a) Name two amino acids.
(b) Account for the amphoteric nature of amino
acids.
(c) How does one amino acid become chemically
linked to another?
(5 marks)
(a) glycine, lysine, tyrosine
(any 2 for 1M)
(b) Carboxyl group contributes to its acidic nature,
while the amino group contributes to its alkaline
nature.
2M
(c) Carboxyl group of an amino acid combines with the
amino group of another amino acid to form a peptide
bond which links two amino acids together.
2M
2.7.3 Structure of polypeptides
The three dimensional shape of a protein is
formed by 4 types of bondings:
1. disulphide bond
2. ionic bond
3. hydrogen bond
4. hydrophobic interactions:
between non-polar R groups, causing
folding of the chain to repel from water
2.7.4 Fibrous proteins
- have a primary structure of regular
repetitive sequences; forming long chains
which run parallel to one another, being
linked by cross bridges
- form very stable molecules for structures
within organisms, e.g. collagen in tendon
a) The primary structure of a protein is the
sequence of amino acids found in its
polypeptide chain. This sequence
determines its properties and shape.
2.7.4 Fibrous proteins
- have a primary structure of regular
repetitive sequences;
- forming long chains which run parallel to
one another, being linked by cross bridges
- form very stable molecules for structures
within organisms, e.g. collagen in tendon
2.7.5 Globular proteins
- have irregular sequences of
amino acids in their polypeptide
chains
- chain/chains fold into a 'ball'
- less stable molecules with metabolic
roles in organisms, e.g. all enzymes
Comparison of fibrous &
globular proteins
Fibrous proteins
Globular proteins
Repetitive regular
sequences of a. a.
Actual sequences
vary slight same
protein
Irregular amino acid
sequences
Sequences highly
specific
Forms long
parallel strands
Folds into
spherical shapes
COMPARISON OF FIBROUS
& FLOBULAR PROTEINS
Fibrous proteins
Globular proteins
Length of chains
Length always identical
vary in same protein in same protein
Stable structure
Unstable structure
Insoluble
Soluble
Support & metabolic Metabolic functions
functions
e.g. keratin & collagen e.g. enzymes, hormones
2.7.6 Conjugated proteins
- proteins joined with other chemicals
(prosthetic group) which have vital roles in
functioning of the protein
- examples: haemoglobin in blood
(haem which contains Fe)
mucin in saliva ( carbohydrate )
casein in milk ( phosphoric acid
)
2.7.7 Denaturation of proteins
Three-dimensional structure of proteins is due to
fairly weak ionic and hydrogen bonds.
Denaturation: breaking of these bonds change
globular proteins into a more fibrous forms with
actual sequence of amino acids unchanged
Any shape/structural changes cause lost of its
normal function
Factors affecting protein denaturation
1. Heat -
Vibrate more vigorously, breaking hydrogen
and ionic bonds, e.g.
coagulation of albumen (egg-white)
Factors affecting protein denaturation
1. Heat 2. Acids -
Breaks ionic bonds (COO-) to form COOH, e.g.
souring of milk to coagulate casein to insoluble
form (curds)
Factors affecting protein denaturation
1. Heat 2. Acids 3. Alkalis -
NH3+ changed to NH2, ionic bonds are broken
e.g. souring of milk
Factors affecting protein denaturation
1. Heat 2. Acids 3. Alkalis 4. Inorganic chemicals Ag+ and Hg+ combine with COO- while CN- with NH3+
e.g. respiratory enzymes are denatured by cyanides
Factors affecting protein denaturation
1. Heat 2. Acids 3. Alkalis 4. Inorganic chemicals 5. Organic chemicals Alter hydrogen bonding within a protein, e.g.
Alcohol denatures bacterial proteins (sterilization)
Factors affecting protein denaturation
1. Heat 2. Acids 3. Alkalis 4. Inorganic chemicals 5. Organic chemicals 6. Mechanical force Breaks hydrogen bonds, e.g. in hair styling (P 29 of text)
2.7.8 Functions of proteins
Proteins perform a wide variety of
functions in living organisms:
1. Nutrition
2. Respiration & transport
3. Growth
4. Excretion
5. Support & movement
6. Sensitivity & co-ordination
7. Reproduction
3. Describe the functions of lipids, and proteins in living
organisms. Illustrate your answer with examples and
provide explanations where appropriate. (14 marks)
(96-11-4)
Lipids (max. 7 marks)
Functions
(a) Energy source (½)
- has a higher energy value/yield double the amount of
energy compared to carbohydrates (½) when used as a
respiratory substrate.
- when body is short of carbohydrates as energy source,
lipids will be mobilized to supply energy (½)
(b) Important form of storage compound (½)
- in the form of fatty tissue/fat in animals, oil in plants (½)
- stores more energy per unit mass therefore efficient in
minimizing space in the bodies of both plants and animals.
(1)
- when stored beneath the skin of mammals/sub-cutaneous
fat, can serve as insulation against heat loss (1), due to the
low heat conductivity of fat (½)
- when stored around the essential organs, serves to cushion
against shock/protection of these organs.(1)
(c) Structural component (½)
- phospholipids are basic components of the unit
membrane (1), contribute to the differential
permeability of the membrane (½) and helps to
maintain ceIl/organelle integrity (½)
- waxy layer in exoskeleton of insects/cuticle of
plants as a moisture barrier (1)
- high lipid content in myelin sheath of nerve fibre
facilitates the transmission of nerve impulse (1)
and insulates against cross-talks (½).
Proteins (7 marks) Functions
(a) Structural component (½)
- raw material for growth (½), repair (½)/make up protoplasm of cells
(½)
- component of the unit membrane (½)
(b) Functional molecules
- three-dimensional conformation of proteins (1) and their binding
sites (1) and essential for these functions.
- enzyme : regulates cellular chemical reactions (1)
- hormone : regulates physiological process (1)
- transportation, haemoglobin - transports oxygen; (1)
- movement, actin, myosin provide movement through muscle
contraction(1)
- defence/immunity, antibodies (1) / immunoglobulins
- as carrier molecule for transport across membrane (½), active
transport (½), channel protein (½), membrane-bound enzyme (½),
receptor molecule (½), electron carriers (½).
Discuss the roles played by protein molecules in living
organisms. (6 marks) 99-II-5