HKAL Biology – Cell, Metabolism and Functioning of the Organisms 9789622791948

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HKAL Biology – Cell, Metabolism and Functioning of the Organisms
 9789622791948

Table of contents :
Preface
Contents
1. The Chemical Constituents of Cells
2. Cell Structure
3. Histology
4. Membrane Permeability
5. Enzymes
6. Autotrophic Nutrition
7. Heterotrophic Nutrition
8. Cell Respiration
9. Circulatory System in Mammals
10. Transport in Angiosperm
11. Support and Movement
12. The Detection of Environmental Conditions and Response to the Environment
13. Co-ordination
14. Homeostasis
15. Perpetuation of Species
16. Growth and Development
Index

Citation preview

HKAL BIOLOGY

Y.K.To

GREENWOOD PRESS P. 0. Box 50450, Sai Ying Pun Post Office, Hong Kong. Tel: 254 7 7041

© Greenwood Press 1999 All rights reserved. No part of this publication may be reproduced, stored in a retrieval system, or transmitted in any form or by any means electronic, mechanical, photocopying, or otherwise - without the prior permission of the copyright owner.

First published 1999 Reprinted 2002, 2009

ISBN: 978-962-279-194-8

PRINTED IN HONG KONG

Preface

Due to the small local market, books published for the Advanced Level Biology in Hong Kong are quite limited. Apart from my book "Genetics Evolution and Ecology for 'A' Level ", virtually no textbook has been published for the Hong Kong Advanced Level Biology syllabus. It has long been my wish to write a textbook to cover the remaining parts of the Advanced Level Biology syllabus for students in Hong Kong. From my 25 years' experience in teaching AL Biology in Hong Kong, I have grasped the right depth of treatment for each topic to meet the requirements of the syllabus and the demands of the Exam Board. This book covers the most important part of the Advanced Level Biology syllabus in Hong Kong - Section II : The Cell and Section III : The Functioning of Living Organisms. The other two sections: Section IV: Genetics and Evolution and Section V: Interrelationship of Organisms with Each Other and with Their Environment are covered in the book "Genetics Evolution and Ecology for 'A' Level " published by Greenwood Press. This book has the following features: 1. It is written in simple English that enables the student to follow the content easily. 2. The topics are arranged close to the order listed in the Hong Kong Advanced Level Biology syllabus. This saves the student lots of time as they do not have to browse among several reference books to get the required materials. 3. The content is presented in Note Form that eliminates unnecessary detail. The systematic arrangement of points enhances the logical deduction of the biological principles and promotes the understanding of biological concepts.

4. Key words or phrases are printed in bold type and italics to enable the students to have a concise, precise and rapid revision before the examination. 5. Further information is marked with a solid vertical line at the left-hand side of the paragraph concerned. This additional information aims to stimulate the students to think more critically and to grasp the concepts more clearly.

6. There are many diagrams and photographs that help to clarify the point and facilitate understanding and memorizing the biological principles. Y.K.TO B.Sc.(Hons). Dip.Ed.

Content~

1. The Chemical Constituents of Cells ..............................................................................

1

2. Cell Structure ...............................................................................................................

35

3. Histology ......................................................................................................................

59

4. Membrane Permeability .........................................................................................

_...... 71

5. Enzymes .......................................................................................................................

89

6. Autotrophic Nutrition ................................................................................................

100

7. Heterotrophic Nutrition .............................................................................................

132

8. Cell Respiration .........................................................................................................

170

9. Circulatory System in Mammals ...............................................................................

203

10. Transport in Angiosperm ...........................................................................................

240

11. Support and Movement ..............................................................................................

266

12. The Detection of Environmental Conditions and Response to the Environment ...... 323 13. Co-ordination .............................................................................................................

348

14. Homeostasis ...............................................................................................................

403

15. Perpetuation of Species ..............................................................................................

450

16. Growth and Development ..........................................................................................

514

Index ..........................................................................................................................

537

l. The Chemical Con~tituenh ofCell~ The chemical constituents of cells include carbohydrates, lipids, proteins, nucleotides, ions and water.

CARBOHYDRATES

Carbohydrates are made up of the elements carbon, hydrogen and oxygen. The ratio of hydrogen to oxygen atoms is usually 2: 1 as in water. The basic unit of carbohydrates is the single sugar called saccharide. 1.1

MONOSACCHARIDE (SIMPLE SUGAR) (CH2 0)

They are called simple sugars because they cannot be hydrolyzed (broken down) into any simpler carbohydrates. They are the building units for the more complex carbohydrates. Its number of carbon atoms varies from 3 to 8.

A. Trioses (3-carbon sugars) (CH 2 O\; C3H6 O3 (Fig. 1. 1) I. (a) Glyceraldehyde contains an aldehyde (-CHO) group and is called an ALDOSE (aldo-sugars ).

(b) Dihydroxyacetone contains a ketone (C=O) group and is called a KETOSE (keto-sugars). Because of the presence of the aldehyde group and the ketone group, they can reduce the alkaline Benedict's solution to insoluble red cuprous oxide. Thus these sugars are called reducing sugars.

glyceraldehyde

dihydroxyacetone

Fig 1. 1

H I

2Cu (OH\ + R-C=O cupric hydroxide

sugar

cuprous oxide

water

sugar acid

Trioses

2. Functions (a) They are the important intermediates in the glycolysis (respiration) of sugars. From them hydrogen will be transferred by NAD (nicotinamide adenine dinucleotide) to the mitochondria to release energy. (b) They are also the intermediates in the Calvin Cycle (photosynthesis) of the green plants. The PGAL (phospho-glyceraldehyde; glyceraldehyde-3-phosphate; triose phosphate) can either be synthesized into hexose or be re-generated into ribulose bisphosphate (starting reagent in the Calvin Cycle). B. Pentoses (5-carbon sugars) (CH 20) 5 ; C5H 100 5 (Fig. 1.2)

1. They are the intermediates in metabolic pathway e.g. ribulose bisphosphate starts the Calvin cycle (photosynthesis). 2. They are part of the more complex molecules such as nucleic acids (DNA, RNA-see Section 1.7A) and co-enzyme (flavin adenine dinucleotide, FAD). Deoxyribose differs from ribose by lacking an oxygen atom at carbon-2.

5 CH2 0H

H

l~o~;

4

C

1

/\H

Ribose

H/\

\I

H

C

1/

OH

3C--2C

I

I

oH

loHI

sCH2 0H

f/

0

C

~/

C

/\H H/\ I I 4

1

H

Deoxyribose

OH

3 C--

2C

!H ~ Fig. 1.2 Ribose and deoxyribose

C. Hexoses (6-carbon sugars) (CH 20) 6 ; C6H 120 6 1. Types (a) The hexoses glucose,fructose

and galactose are commonly found in most plants.

(b) Fructose differs from glucose in that it is a ketose and the other is an aldose. 2

(c) The specific relationship between the carbon atoms and side group determines the nature and properties of the sugars.

2. Ring structure Glucose, in common with other hexoses and pentoses, normally exists in a stable ring or cyclic form rather than in straight chain form. (Fig. 1.3)

(A) a-glucose (pyranose form) (six-sided)

(B) Fructose (pyranose form) (six-sided)

(C) Fructose (furanose form) (five-sided)

Fig. 1.3

The ring forms of fructose

(a) In the case of glucose, carbon atom number 1 may combine with the oxygen atom on carbon atom 5 . .This forms a six-sided structure known as a PYRANOSE ring. (Fig. 1.3(A)) (b) In the case of fructose, it is carbon atom number 2 which links with the oxygen on carbon atom 5. This forms afive-sided structure called a FURANOSE ring. (Fig. 1.3(C)) Both glucose and fructose can exist in both pyranose and furanose forms. 3. Isomers Compounds that have the same chemical formula but which differ in the arrangement of the atoms are known as isomers. (a) Structural isomers

(i)

They have the same molecular formula, but their atoms are linked together in different sequences. e.g. glucose and fructose.

(ii) Another kind of isomerism in the ring form of glucose, is interchanging the positions of 3

the-Hand -OH on carbon atom 1. This gives rise to two different structures, the a- and ~-glucose. (Fig. 1.4) Though a- and~- glucoses appear very similar in structure, they are quite different in their physical, chemical and biological properties. 1. a - glucose builds up starch as a common storage substance. 2. ~ - glucose builds up cellulose of the cell wall.

a Glucose

~

Glucose

Fig. 1.4 Structural isomers of glucose

(b) Optical isomers (Fig. 1.5) (i)

Optical isomers are identical in every way except that they are mirror images of each other. Glyceraldehyde has two forins that have identical chemical properties, but in solution they rotate the plane of polarized light in opposite directions; they are said to be optically active. These two forms of glyceraldehyde are optical isomers.

( ii) The optical isomer that rotates the plane of polarization to the right (clockwise) is said to be dextro-rotatory (+); the optical isomer that rotates the plane of polarization to the left (anti-clockwise) is laevo-rotatory (-). Angles of rotation are measured in a polarimeter.

4

OHC

I

/1\

HO D- glyceraldehyde

Fig. 1.5

H

CH2 0H

L- glyceraldehyde

The optical isomers of carbohydrates

D. Properties of monosaccharides 1. They are soluble, sweet and form crystals. 2. Because of its terminal aldehyde group, it is a reducing sugar which can reduce the Benedict's solution to an insoluble red cuprous oxide.

E. Functions of monosaccharides 1. Glucose produced in photosynthesis can be converted to starch for temporary siorage. It can also be converted to sucrose for transport. 2. Glucose is the chief building unit for the structural material of plants: cellulose, hemicellulose and pectin. 3. It can be oxidized to release energy.

1.2

DISACCHARIDES (COMPLEX SUGARS; DOUBLE SUGARS) (C12 H22 O 11 )

A. Formation Disaccharides are formed by two monosaccharide units combining together with the elimination of a molecule of water, a process called condensation. The two monosaccharides are joined by a covalent bond, the glycosidic bond. (Fig. 1.6)

B. Types and functions of disaccharides

1. Maltose It results from the union of two glucose. Large concentration of maltose is found in some germinating seeds e.g. barley. Maltose is used in brewing andfood manufacturing. 2. Sucrose It results from the union of glucose and fructose. It is the main form in which carbohydrate is transported in plants. It is particularly abundant in the stems of sugar cane and the roots of sugar beet, which are the sources of commercial sugar. 3. Lactose It results from the union of glucose and galactose. Lactose is the sugar found in milk.

5

C. Properties of disaccharides They resemble simple sugars and are reducing except sucrose. In sucrose the aldehyde group of glucose and the ketone group of fructose are linked together by the glycosidic bond so that both sugars units lose their reducing property.

Maltose is a reducing sugar

H~~{)H +

OH

~

OH a-1, 4-glycosidic

Hydrolysis

+

::,~,

Condensation

linkage

Maltose

Glucose

Glucose

Sucrose is a non-reducing sugar

Hydrolysis Condensation

Fig. 1.6

1.3

p Fructose

a Glucose

Sucrose

The hydrolysis and condensation

of disaccharides

POLYSACCHARIDES (MULTI-SUGARS; NON-SUGARS) (C6 H10 O5 )n

A. Formation Monosaccharides may link up through glycosidic bonds to form a polysaccharide by condensation reactions. B. Properties They are insoluble in water, do not taste sweet and cannot be crystallized.

C. Functions 1. The compact insoluble structure makes it ideal as a storage carbohydrate not diffuse out of the cell nor exert an osmotic effect within the cell.

because they will

2. In case of demand, the polysaccharide can be hydrolyzed to release free sugars. These sugars can be oxidized to release energy or are synthesized to new compounds. 6

D. Types 1. Starch (a) Structure (Fig. 1.l(A))

Starch consists of long chain of a-glucose molecules and may have branches at places. There may be 300 to 1000 glucose molecules combined in a starch. Starch consists of 2030% amylose and 70-80% amylopectin. 0)

Amylose is an unbranched chain of 200-1500 glucose residues linked by a-1,4glycosidic bonds. The molecule takes the form of a helix.

( ii) Amylopectin contains from 1300 to 1500 glucose units. It is a branched molecule with both the a-1,4 glycosidic and a-1,6 glycosidic bonds. ( b) Properties

( i)

The chain is coiled into a helix forming a cylinder in which most of the hydroxyl group, OH, capable of forming cross linkage projecting INTO the interior. Because no crosslinkage can be formed BETWEEN starch molecules, it lacks structural properties.

l 00°0°0°0°····· ····· a-1, 4-glycosidic

CH,OH

bond

CH,OH

OH

CH,OH

OH

CH,OH

OH

OH

Amylase

•0-5-0 l~~ -~I OH

O

~

a-1, 6-glycosidic

bond

I

····•00-0000-000•·· OH

OH

OH

OH

Amylopectin

Fig. 1.7(A)

The structure of starch 7

( ii) Since the starch chains are folded by the hydrogen bonds projected inwards,they are packed together in spherical plastids to form starch grains for storage function in plants. (Fig. 1.7(8))

Wheat

Potato

Fig. 1.7(8)

Maize

The shape of different starch grains in different species

2. Glycogen It is the storage carbohydrate

of animals.

(a) It consists of long, profusely branched chains of a-glucose molecules linked by 1-4 or 1-6 a-glycosidic bonds. (b) Glycogen is more soluble than starch and exists in the cytoplasm as tiny granules. It is particularly abundant in liver and muscles.

(Each of us has approximately 500 g of glycogen in our bodies that can only provide energy for 90 minutes exercise.)

3. Cellulose (Fig. 1.8)

Simplified representation

of the arrangement

of glucose chains Hydrogen bonds forming cross bridqes ~-glucose molecules

t

Fig. 1.8 8

The structure of cellulose

Cellulose is a polysaccharide consisting of long chains of p-glucose molecules linked by 1-4 glycosidic bonds. The orientation of the molecule causes the OH-groups to stick OUTWARD from the chain in all directions. These chains form hydrogen bonds with neighbouring chains thereby establishing a 3-dimensional lattice. These help to give cellulose its considerable stability which makes it a valuable structural material. The stability makes it difficult to digest.

1.4

CELL WALL

A. Structure of cell wall (Fig. 1.9(A)) 1. A single cellulose chain may contain as many as 10 000 sugar units with a total length of 5 um (1 um= micro-metre= 10 -6 m). The crosslinks between adjacent chains make it tough. 2. In the cell wall, groups of about 60 or 70 cellulose chains are massed together to form ribbonlike microfibrils each about 10 nm (1 nm = nano-metre = 10-9 m) in diameter. 3. These microfibrils are arranged in larger bundles to form macrofibrils (50 nm in diameter) or fibres. These macrofibrils are laid down in parallel layers which are interwoven to form a very tough structure. 4. In the cell wall the cellulose microfibrils are embedded in a gel-like organic matrix containing hemicellulose and pectin (Fig. 1.9(8)).

(i) Hemicelluloses are short polysaccharides that bi11dtightly to the surface of the cellulose microfibrils and to each other, thus holding the microfibrils in a complex three diniensional network. (ii) Pectins are another group of polysaccharides with acidic, negatively charged residues that bind calcium ions (Ca++)forming calcium pectate. Calcium pectate is particularly abundant in the middle lamella that serves to cement together the cellulose walls of adjacent cells.

Macrofibril

(50 nm diameter) Microfibril

( 10 nm diameter) (60-70 cellulose chains)

Cellulose molecule

(10,000 sugar units)

Fig. 1.9(A)

Structural

organization

of cell wall 9

Ca 2 + bridges between Pectin molecules

Hemicellulose molecule

Fig. 1.9(8)

Microfibrils

embedded in matrix

The cell wall of a plant resembles reinforced concrete: the matrix of hemicellulose and pectin is equivalent to the concrete, the cellulose microfibrils to the metal framework within the concrete.

B. Properties of cell wall Despite its strength, the plant cell wall is fully permeable to water and solutes. This is because the niatrix is full of water-filled channels. (Moreover, the molecules of the matrix are strongly hydrophilic (water-loving) with the result that in normal circumstances the cell wall is saturated with water like a sponge.)

C. Lignification of cell wall Cells become lignified when the space between the cellulose molecules is filled with lignin, a complex polymer of various derivatives of alcohol. (a) It makes the cell wall very rigid to provide mechanical support. (b) It also renders the cell wall impermeable so that the protoplasm dies due to dehydration.

The resulting hollow tube-like structure facilitates the transport of water and mineral salts.

1.5

LIPIDS

The lipids are organic substances which contain carbon, oxygen and hydrogen. A lipid molecule contains a much smaller proportion of oxygen than a molecule of carbohydrate.

10

A. Building up of a lipid (Fig. 1. 10) Lipids are esters of fatty acids and an alcohol, of which glycerol is by far the most abundant. Glycerol has three hydroxyl (-OH) groups and each hydroxyl group (-OH) combines with the carboxyl group (-COOH) of a fatty acid, forming a TRIGLYCERIDE. In this condensation reaction three water molecules are removed and three oxygen bonds (ester bonds) are established between the glycerol and the three fatty acids, forming a TRIGLYCERIDE (Triacylglycerol).

0

..

. I ,

RCOIOH + HlO-C-H

+ HIO-C-H

·························I

R'CO!OH

R"COIOH + H!O-C-H ,............................ 3 molecules of fatty acid

+

glycerol

II

R-C-O-CH

R'-

?

C-0-CH 0

II

2

R"-C-O-CH

HOH

2

I

+ HOH

I

A triacylglycerol (fat)

HOH

2

+

3 molecules of water

Fig. 1. 10 Structure of a lipid

B. Kinds of fatty acids (Fig. 1.11) As most naturally occurring lipids contain the same alcohol, namely glycerol, it is the FATTY ACIDS which determine the characteristics of any particular lipid. 1. All fatty acids contain a carboxyl group (-COOH) which is partially ionized and can form ionic bonds. The carboxyl group is therefore polar and is hydrophilic i.e. they attract water. 2. The remainder of the molecule is a hydrocarbon chain of varying length. (a) This chain may possess one or more double bonds in which case it is said to be

UNSATURATED. T4ey have low melting point. They are OILS or soft fats at room temperature. Oils occur mainly in plants.

(b) If, however, it possesses no double bonds, it is said to be SATURATED. They have higher melting points and are solid at room temperature. They are FATS which are characteristic of animals. e.g. palmitic and stearic acids (M.P. is at 63.1 °C and 69.6°C). 3. The hydrocarbon chains may be very long. Within the fat they form long 'tails' which extend from the glycerol molecule. These 'tails' are non-polar and are hydrophobic i.e. they repel water.

11

Unsaturated fatty acids.

e.g. oleic acid C17H33COOH

H H H H H H H H H H H H H H H H

I I I I I I

I I I I

I I I I I

I

I I I I I I

H3C-C-C-C-C-C-C-C-C=C-C-C-C-C-C-C-C-C H H H H H H H

Saturated fatty acids.

I I I I I I

H H H H H H H

~o --0-H

e.g. palmitic acid C15H31COOH

H H H H H H H H H H H H H H

I I I I I I

I I

I I I I I I I I

I I I I I I

H3C-C-C-C-C-C-C-C-C-C-C-C-C-C-C-C

I I I I I I

I I

H H H H H H H H H H H H H H

~o

~

--o-H

Fig. 1. 11 Different kinds of fatty acids

C. Properties of lipids 1. They are insoluble in water. They are less dense than water. 2. They dissolve readily in organic solvents such as acetone and alcohols.

D. Types of lipids

1. Fats and oils There is no basic difference between these two: fats are simply solid at room temperature (20°C) whereas oils are liquid. The higher the proportion of unsaturated fatty acids, the lower their melting points.

2. Phospholipids (Fig. 1. 12) (a) Phospholipids are lipids in which one of the fatty acid groups is replaced by phosphoric acid (H 3PO 4 ). (b) The phosphoric acid is hydrophilic (attracts water) in contrast to the remainder of the molecule which is hydrophobic (repels water). Having one end of the phospholipid attracting water while the other end repelling it affects its role in the cell membrane. 12

H2 C-

I I

HC-

COO

~ }

/"-.. /'../"-..

COO ,, ...,.,, 'V'

,r.... ,,,,..._ ,,,..__ .,, ......,,, ......,,, .......,,,, .......,,,,

Non-polar hydrocarbon

tails of two fatty acids condensed with glycerol

o1

H2 C-0-P-o-

g~ Phosphate group from

phosphoric acid which has condensed with the third-OH of glycerol

Phosphoric acid OH

I II

HO-P-OH 0

Fig. 1. 12 Structure of phospholipid

3. Waxes Waxes are formed by combination with an alcohol other than glycerol. This alcohol is much larger than glycerol and therefore waxes have a more complex chemical structure.

(a) They are fairly tough and tend to have a high melting point. Their main role is used as a water-proofing material in plants and animals e.g. the waxy cuticle of flowering plants and insects and sebum of mammals. ( b) They form storage compounds in a few organisms e.g. castor plant, fish.

4. Steroids (Fig. 1. 13) (a) Cholesterol is the best known steroid.

(b) Steroid is important in the synthesis of steroid hormones, such as oestrogen and cortisone. ( c) Other important steroids include vitamin D and Bile acids.

Hydrophilic pa1/

of molecule (

Fig. 1. 13 Structure of a steroid

13

E. Functions of lipids 1. As energy source Upon oxidation they yield 38 kJg- 1 of energy. It has a higher energy value which is almost double the amount of energy released by carbohydrates. When the body is short of carbohydrates as energy source, lipids will be mobilized to supply energy. 2. Storage (a) On account of their high energy yield upon breakdown, they make excellent energy stores. They are stored in the form of fatty tissues in animals, or oil in plants. (b) They store more energy per unit mass therefore it is efficient in minimizing space in the bodies of plants and animals. (i) This makes them especially useful for animals where locomotion requires mass to be kept to the minimum. (ii) In plants they are useful in seeds where dispersal by wind or insects makes small mass necessary. (This explains the abundance of oils extracted from seeds and fruits e.g. olive, castor, linseeds, peanut, coconut and sunflower.) The insoluble property is an advantage in storage because they are not easily dissolved out of cells. 3. Water-proofing Terrestrial plants and animals have a need to conserve water. (a) The oily secretion (sebum) produced from the sebaceous glands of mammals provides a water-proof layer for the body. (b) Oils also coat the fur of mammals, helping to repel water which would otherwise wet it and reduce its insulatory function. Birds spread oil over their feathers from a special gland near the cloaca for the same purpose. (c) Insects have a waxy cuticle to reduce water lost by evaporation. Plants also have cuticle to reduce transpiration. 4. Insulation

(a) In endothermic animals, such as mammals, fat is stored beneath the skin (subcutaneous fat) where it helps to retain body heat because of its low heat conductivity. (b) In aquatic mammals, such as whales, seals and manatees, hair is ineffective as an insulator because it cannot trap water in the same way as it can in air. These mammals have extremely thick subcutaneous fat, called blubber, which forms an effective insulator. 5. Protection When stored around the essential organs, fat serves to cushion against shock and protect these organs. Fat surrounding the kidneys, for instance, helps protect them from physical damage.

14

6. Cell membranes

Phospholipids are major components of the cell membrane. They contribute to the differential permeability of the membrane and help to maintain cell and organelle integrity. 7. Other functions

(a) Plant scents are fatty acids (or their derivatives) to attract insects for pollination. (b) Bee wax is used to construct honeycombs. (c) The high lipid content in myelin sheath of nerve fibre facilitates the transmission of nerve impulse and insulates against cross-talks.

1.6

PROTEINS

Proteins contain carbon, hydrogen and oxygen. They always contain nitrogen, usually sulphur and sometimes phosphorus. A. Amino acid (Fig. 1.14) Proteins are macro-molecules which consist of a large number of amino acids. All amino acids contain both a basic amino group (-NHz) and an acidic carboxyl group (-COOH). R may be one of a variety of organic chains or rings.

R

I C H Carboxyl group

Amino group

COOH

H

H

Amino acid

Fig. 1.14

Amino acid

Different ways to represent the structure of an amino acid

15

B. Amphoteric property 1. Zwitterion (Fig. 1. 15) Amino acids are soluble in water to form ions. (a) These ions are formed by the loss of a hydrogen ion from the carboxyl group, making it negatively charged (-Coo-). (b) This hydrogen (-NH/)

ion associates with the amino group, making it positively

charged

The ion is therefore dipolar. An ion which has both positively charged and negative charged fegions is called ZWITTERION. Amino acids are amphoteric because they have both acidic and basic properties.

The amino group (-NH can pick up an W from the surroundings

The carboxyl group (-COOH) can lose an W to the surroundings

2)

l

Fig. 1. 15

Structure of a zwitterion

Some amino acids containing additional amino groups are basic amino acids e.g. histidine. Some amino acids containing additional carboxyl groups are acidic amino acids e.g. aspartic acid, glutamic acid. 2. Buffer (Fig. 1. 16) (a) Being amphoteric amino acids can act as BUFFER SOLUTIONS. A buffer solution is one

which resists the tendency to change its pH even when small amounts of acids or alkali are added to it. Such a property is essential in biological systems where any sudden change in pH could adversely affect the function of enzymes. (i)

16

In an acidic solution (low pH) the amino group picks up H+ and becomes positively charged.

(ii) In an alkaline solution (high pH) the amino acid donates its H+ ions to the medium and becomes negatively charged. The pH at which the amino acid is electrically neutral is celled the isoelectric point.

In alkaline solutions, hydrogen ions (H+) are released from the amino group, thus increasing the acidity of the solutions.

In acidic solutions, hydrogen ions (H+) are taken up by the carboxyl group of the amino acid, thus decreasing the acidity of the solutions.

Net charge zero zwitterion forms at isoelectric point

R

R

H"--

N-C-C

H/

I I

~o

""-o-

H

W ion is donated by the amino acid which becomes negatively charged. It will migrate to the positive electrode (anode) if placed in an electric field.

Fig. 1. 16

H"-.. HH/

N+-c-c

I

~o

I

"---oH

H

W ion is accepted by the amino acid which becomes positively charged. It will migrate to the negative electrode (cathode) if placed in an electric field.

The buffering effect of an amino acid

(b) The presence of amino (basic) and carboxyl (acidic) groups at the free ends of the polypeptide chain makes it possible for the protein to combine with basic or acidic substances. It is a very important feature that enables it to form the building materials of the body. C. Occurrence Although there are over 100 naturally occurring amino acids, only 20 are used in the synthesis of proteins. (Fig. 1. 17)

(a) 8 are essential amino acids because they cannot be synthesized in our body and therefore have to be taken in our diet.

17

( b) The remaining 12 amino acids are called non-essential

Names of the twenty amino acids

amino acids because they can be synthesized in our body and therefore not essential in the human diet.

Fig. 1. 17 Table to show the m:,mes of the twenty amino acids

Non-essential

Essential

Alanine Arginine* Asparagine Aspartic acid Cysteine Glutamic acid Glutamine Glycine Histidine * Praline Serine Tyrosine

lsoleucine Leucine Lysine Methionine Phenylalanine Threonine Tryptophan Valine

D. Peptide linkage to form polypeptide (Fig. 1. 18)

Dipeptide I

Condensation (water removed)

H-N

I HeO 1I II C

Amino acid

Fig. 1. 18

18

1i

I Hydrolysis (water added)

Heo I N

I

~

II

C-OH

Amino acid

Peptide linkage to form polypeptide

"Essential in children

1. Protein is formed by having amino adds linked together by a chemical bond called a PEPTIDE BOND or peptide linkage. This bond is formed by the amino group of one amino acid attaching to the carboxyl group of another amino acid. This union is usually the removal of a molecule of water (condensation) from the molecules that unite. The resulting molecule formed by the union of two amino acids is called a DIPEPTIDE. 2. Further condensation reactions lead to the addition of further amino acids to form a long chain called POLYPEPTIDE. Polypeptides may contain up to around 400 amino acids.

E. Types of bonds in a polypeptide The shape is important in the functioning of proteins (polypeptides), especially enzymes. The shape of a polypeptide is due to three types of bonding which occur between various amino acids in the chain.

1. Disulphide bond (Fig. 1. 19) It arises between sulphur-containing groups on any two cysteine molecules. These bonds may arise between cysteine molecules in the same amino acid chain (intrachain) or between molecules in different chains (interchain).

Strong covalent bonds formed by the oxidation of- SH of two cysteine side-chains. Disulphide

~ ,ed"ction

g_CH,-:r:-CH,j e ~

Fig. 1. 19 Disulphide bond

2. Ionic bond (Fig. 1.20) (a) In the case of acidic amino acids, however, there are additional-COOH groups which may ionize to give coo- groups. (b) In the same way, basic amino acids may still retain NH/ groups even when combined into the structure of a polypeptide. (c) In addition NH 3+ and coo- can occur at the ends of a polypeptide chain. Any of these available NH 3 + and coo- groups may form ionic bonds which help to give a polypeptide molecule its particular shape. These ionic bonds are .weak electrostatic bonds that may be broken by alteration in the pH of the medium around the polypepti~e. 19

Weak electrostatic interaction between oppositely charged ions: at a suitable pH,the bond may be broken by changing the pH.

IAcidic amino acid I IBasic amino acid I

Fig. 1.20

Ionic bond

3. Hydrogen bonds (Fig. 1.21) This occurs between certain hydrogen atoms and certain oxygen atoms within the polypeptide molecule. (a) The hydrogen atoms have a small positive charge on them (electro-positive) and the oxygen atoms have a small negative charge (electro-negative). These two charged atoms are attracted together to form a hydrogen bond. (b) Though each bond is very weak, the sheer number of bonds plays a considerable role in the shape and stability of a polypeptide,chain.

Ionic bond (weak link)

Electropositive hydrogen

Electronegative atom

Disulphide bond (strong link)

Fig. 1.21

20

Hydrogen bond

Fig. 1.22

Hydrogen bond (very weak link)

Types of bond in a polypeptide chain

F. Structural organization of proteins Individual protein is determined by the sequence of amino acids comprising its polypeptide chain, together with the pattern of folding and cross-linkage.

1. Primary structure (Fig. 1.23(A)) The PRIMARY STRUCTURE of a protein is its sequence of amino acids found in its polypeptide chain. This sequence determines its properties and shape. Many proteins contain more than one polypeptide chain, a connection between them is held by a disulphide bond (S-S) on the amino acid cysteine. e.g. insulin 2. Secondary structure (Fig. 1.23(81)) The polypeptide chains may become folded or twisted in various ways as a result of hydrogen bonds. The most common ways are to coil to form a spiral (a-helix) or to fold into sheets (~ sheets). These forms are referred to as the SECONDARY STRUCTURES of the protein. There are about 3.6 amino acid residues per turn of the a-helix. e.g. Collagen forms a triple helical structure. The three polypeptide chains twisted together achieve stability from the hydrogen bonds formed between the NH groups in one chain and the CO groups in an adjacent chain. (Fig. 1.23(82)) 3. Tertiary structure (Fig. 1.23(C)) The TERTIARY STRUCTURE is due to the bending and twisting of the polypeptide helix into a complex molecular shape. The shape is held by different types of bonding (disulphide, ionic and hydrogen) between adjacent parts of the chain. e.g. myoglobin 4. Quaternary structure (Fig. 1.23(0)) The QUATERNARY STRUCTURE arises from the combination of a number of different polypeptide chains that are held together by various forms of binding into a large compact molecule. e.g. Haemoglobin consists of 4 polypeptide chains -2 a-chains and 2 {3-chains.

21

0I

CH 2

(A)

Primary Structure

Determined by amino acid number, type and order, forming a polypeptide.

Hydrogen bond

(81)

Secondary Structure

The polypeptide can form a beta sheet or a coiling alpha helix. Hydrogen bonds form between carboxyl and amino groups.

(82) Beta sheet

( C)

The triple helical structure of collagen

Tertiary Structure

Occurs when the helix (or sheet) becomes folded in highly specific ways. It is characteristic of globular proteins. haemoglobin (contains no beta-pleated sheet) Alpha chain Alpha chain

(D)

Haem group

Quaternary Structure Folded protein chains may be joined to form a single protein made up of several subunits. Haemoglobin, the oxygencarrying protein of blood, has two alpha chains and two beta chains.

Beta chain

Fig. 1.23

22

The structured

organization

of protein

G. Comparison of globular and fibrous proteins

Fibrous proteins

Globular proteins

1. Repetitive regular sequences of amino acids

Irregular amino acid sequences

2. Actual sequences may vary slightly between two examples of the same protein

Sequence highly specific and never varies between two examples of the same protein

3. Polypeptide chains form long parallel strands

Polypeptide chain folded into a spherical shape

4. Length of chain may vary in two examples of the same protein

Length always identical in two examples of the same protein

5. Stable structure

Relatively unstable structure

6. Insoluble

Soluble to form colloidal suspensions

7. Support and structural functions

Metabolic functions

8. Examples include collagen (Fig. 1.23(82)) and keratin

Examples include all enzymes, some hormones (e.g. insulin) and haemoglobin (Fig. 1.23(D))

H. Conjugated proteins Many proteins incorporate other chemicals within their structure. These proteins are called conjugated proteins and the non-protein part is referred to as the prosthetic group. The prosthetic group plays a vital role in the functioning of the protein. Examples of conjugated proteins Name of protein

Location

Prosthetic group

1.

Haemoglobin

Blood

Haem (contains iron)

2.

Cytochrome oxidase

Electron carrier system of cells

Copper

Ribosomes

Nucleic acid

3. Nui:leoprotein

23

I. Factors causing protein denaturation Explanation

Example

Increases the kinetic energy of the protein molecules. Their atoms vibrate so vigorously that this may eventually break the hydrogen and ionic bonds

Coagulation of albumen (boiling eggs makes the white more fibrous and less soluble)

Additional H+ ions in acids or the reduced number of H+ ions in alkalis break the ionic bonds.

The souring of milk by acid (e.g. bacteria produce lactic acid, lowering pH and causing it to denature casein, making it insoluble and thus forming

Factor 1. Heat

Acids or Alkalis

2.

curds) Inorganic chemicals

3.

The ions of heavy metals such as mercury and silver are highly electropositive. They combine with coogroups and disrupt ionic bonds. Similarly, highly electronegative ions, e.g. cyanide (CN-), combine with NH 3+ groups and disrupt ionic bonds.

Many enzymes are inhibited by being denatured in the presence of certain ions, e.g. cytochrome oxidase (respiratory enzyme) is inhibited by

cyanide.

J. Functions of proteins in living organisms 1. Structural components (a) They are the raw material m_aking up protoplasm for growth and repair. (b) They are the main structural component of the unit membrane and have an important role to control the permeability of the ,nembrane. (c) The collagen gives strength with flexibility in tendons and cartilage for support and movement. The keratin of skin makes it tough enough to protect the delicate tissues. 2. Functional molecules ( a) Binding sites

The three-dimensional conformation of proteins provides the active sites for enzymes and the binding sites for various functions. ( b)

Catalysis Enzymes catalyze cellular chemical reactions e.g. hydrolysis of proteins to polypeptides, starch to maltose and fats to fatty acids and glycerol.

( c) Chemical messenger

Hormone regulates physiological processes e.g insulin and glucagon control the blood glucose level

24

(d) Transport

The haemoglobin in red blood cells increases the oxygen-carrying capacity to transport oxygen to the tissues. (e) Movement

The actin and myosin molecules of the myofilaments provide movement through muscle contraction (f) Defence / immunity

The antibodies (immunoglobulin) produced by the lymphocytes defend the body against bacterial invasion. The fibrinogen and thrombin take an important part in blood clotting to prevent the entry of germs into the body. (g) Carrier molecules

They control the active transport across membrane and they can act as the channel proteins that control the selective permeability of membrane. Some act as the membrane-bound enzymes that carry electrons to trap or release energy. Some act as receptor molecules to recognize the signal arriving at the cell (h) Sensitivity

Rhodopsin or opsin are visual pigments in the retina that are sensitive to light for vision. The phytochromes are plant pigments that control flowering and germination in the right environmental conditions. ( i) Homeostasis

The soluble plasma proteins and haemoglobin act as buffers that maintain a constant pH in the body fluid. (j) Storage

Casein in milk and aleurone protein in seeds provide the nutrients to support growth and development of the young organisms. 1.7

NUCLEOTIDES

A. Components of nucleotides (Fig. 1.24) A nucleotide has three components, a pentose sugar (5-carbon sugar), an organic base and a phosphoric acid. 1. Pentose sugar (5-carbon sugar)

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

(a) Those containing ribose are called ribonucleic acids (RNA) and (b) those containing deoxyribose (ribose with an oxygen atom removed from carbon atom 2) are called deoxyribonucleic acids (DNA). 2. Organic bases (Nitrogenous bases) Each nucleic acid contains four different bases, two derived from purine and two from pyrimidine. The nitrogen in the rings gives the molecules their basic nature.

25

(A)

(CJ Phosphoric acid

5C sugar (pentose)

OH

Join to phosphate

@CH2O

Join to base

O=

I

P-OH

I

OH Join to base 2 / Ribose

OH

/

This oxygen removed in deoxyribose

OH

(BJ Nitrogenous

bases

Purine (two rings)

Pyrimidine (one ring)

(X)

0 N

H

0

0

:.XN HN5:JCH,HN~ N:xN~ H,)~N ) 0

OAN

O~N

O~N

i* Cytosine

~

HN

HN

~N

N

*

*

Uracil

i*

i*

i

i

Adenine

Guanine

Thymine

Fig. 1.24

The components

of a nucleotide

(a) PURINES have two rings (one hexagonal ring and one pentagonal ring). They consist of adenine (A) and guanine (G) (b) PYRIMIDINES have one ring. They consist of cytosine (C) and thymine (T) in DNA or uracil (U) in RN A The bases are commonly represented by their initial letters A, G, C, T and U. RNA contains uracil (U) in place of thymine (T) in DNA. Thymine is chemically very similar to uracil (it is 5-methyl uracil). 26

3. Phosphoric acid This gives nucleic acids their acid character.

B. Condensation reactions form nucleotides (Fig. 1.25) of a pentose sugar (at CJ) with a base forms a compound called a NUCLEOSIDE. This occurs with the elimination of water and is a condensation reaction.

1. The combination

2. A NUCLEOTIDE is formed by further condensation between the nucleoside (at CS) and phosphoric acid forming a phosphoester link.

Phosphoric acid

Phosphoester link -H 2 0 condensation

+H 2 0 hydrolysis

Nucleotide of DNA

Deoxyribose

Fig. 1.25

Formation of a nucleotide

C. Structure of dinucleotides and polynucleotides (Fig. 1.26) 1. Two nucleotides join to form a dinucleotide by condensation between the phosphate group of one nucleotide (at CS) with the pentose sugar of the other nucleotide (at CJ) to form a phosphodiester bridge. 2. The process is repeated up to several million times to make a polynucleotide. An unbranched sugar-phosphate backbone is formed by phosphodiester bridges between the 3' and 5' carbon atoms of the sugars. 3. Phosphodiester linkages are formed from strong covalent bonds and these confer strength and stability on the polynucleotide chain. This is an important point in preventing breakage of the chain during DNA replication.

27

IB) Formation of a polynucleotide

(A) Structure of a dinucleotide

OH

I I

O=

Sugar-phosphate backbone

p-OH 5' end

C:=J} One nucleotide

0

Base

Phosphodiester bridge formed by condensation to join 2 nucleotides together

0

Base

OH

O

H

0

Phosphate

Fig. 1.26

5C sugar (pentosel

Formation of a dinucleotide

C:=J

Base

and a polynucleotide

D. DNA (Fig. 1.27 and 1.28) A DNA molecule is made up of two parallel polynucleotide chains running in opposite direction and twisted to form a double helix. It is known as the Watson-Crick Model of DNA. 1. The X-ray analysis of the DNA helix reveals that the diameter of the DNA is about 2 nm. There are 10 base pairs in one complete turn and each base pair is about 0.34 nm apart. 2. The two chains are held together by the weak hydrogen bonds which link the purine (a base) of one chain in complementary relationship with the pyrimidine (a base) of the other chain. An adenine (a purine) must pair with a thymine (a pyrimidine) by two hydrogen bonds between them. A guanine (a purine) must pair with a cytosine (a pyrimidine) by three hydrogen bonds between them. (A= T; G = C).

28

3.4 nm (One complete turn contains ten base pairs)

Two polynucleotide chains--'---~~----.::::_,.,,.c.........,,/ run in opposite directions

2 nm

Fig. 1.27

The double helix of DNA

5' Pentose sugar Phosphate group

Key:

Phosphate

e

Deoxyribose (pentose sugar)

PURINES:

LX]

Adenine

[TI

Guanine

PYRIMIDINES:

[D

Thymine Cytosine

5'

Fig. 1.28

The complementary

relationship between two polynucleotides

in DNA

29

E. RNA Differences between RNA and DNA:

1. RNA is a single stranded molecule while DNA is a double one. 2. The pentose sugar of RNA is ribose while that of DNA is deoxyribose. 3. In RNA uracil replaces thymine in DNA. F. Functions of DNA 1. The sequence of bases in DNA provides the genetic code to give information that controls the cell activities and is specific to each species.

2. The complementary relationship of the bases in the DNA molecule enables the DNA to replicate (make an exact copy) so that the same genetic information can be passed to the offspring. It also controls protein synthesis. G. The replication of DNA 1. In time of replication the two poly nucleotide chains of the DNA unwind and separate by breaking the hydrogen bonds between them.

2. The bases of each chain then pair with the bases of the free nucleotides in a complementary pattern: adenine (A) pairs with thymine (T) and guanine (G) pairs with cytosine (C). 3. The newly lined up nucleotide:s are joined together by sugar-to-phosphate bonds (phosphoester bond), thereby forming a new chain complementary to the old one. Now two new DNA molecules are formed, each identical to the parent one. It is a semi-conservative mechanism of replication. (Fig. 1.29)

H. Mononucleotide Adenosine triphosphate (ATP) is an energy rich compound. It consists of an adenine linked to a pentose sugar which in tum is linked to three phosphate groups. When the third phosphate group breaks away from the second phosphate group by hydrolyzing the energy rich bond, a large amount of energy, about 30.6 kJ mol- 1 is released.

I. Nicotinamide adenine dinucleotide (NAD) is a co-enzyme which assists the enzyme dehydrogenase to catalyze the reaction called dehydrogenation in respiration. This coenzyme accepts the hydrogen atoms from the substrate molecule. NADP (Nicotinamide adenine dinucleotide phosphate) is the co-enzyme used in photosynthesis. 1.8

WATER

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

30

Old DNA Two old complementary "Backbones" composed of phosphate and sugar

chains separate

/\..._

Key:

PURINES: ._____

A _ _,_< Adenine

....__-=-G--l.(

Guanine

PYRIMIDINES:

[=r=)

Thymine

~

Cytosine

l~=~=~=~=t=~=D-----1

Fig. 1.29

The semi-conservative

mechanism of the replication of DNA

A. Chemical properties of water

I. Water is the REAGENT participating in many metabolic activities of protoplasm. (a) It provides reducing hydrogen which is in form of NADPH in photosynthesis of green plants.

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

2. Water is the PRINCIPAL SOLVENT for many substances. (a) Only dissolved substances can take part in metabolic activities. (b) Only materials in aqueous solution can pass through living cells by the process of diffusion. (c) The transport of nutrients, excretory products, dissolved gases, inorganic ions and honnones can only take place in aqueous solution within organisms.

3. The HIGH DIELECTRIC CONSTANT of water allows the dissociation of substances dissolved in it. Hence affects their chemical and/or electrical activities that in turn affect the functioning of the organisms e.g. osmotic concentration of ionized solution. B. Physical properties of water 1. The HIGH SPECIFIC HEAT CAPACITY of water enables organisms to have a relatively stable thermal environment. 31

(a) The organisms will not be subject to extremely rapid fluctuations in temperature of the surrounding which would affect the rate of biochemical changes. (b) This property also enables the organism to absorb large amount of heat produced from chemical reactions inside its body to avoid the body temperature rising too high to denature enzymes.

2. The HIGH THERMAL CONDUCTIVITY of water allows good transfer of heat throughout the body that will avoid the occurrence of destructive local 'hot spots'. 3. The GREATEST DENSITY of water at 4°C enables ice to float on water. This saves the lives of many aquatic organisms which have a viable habitat in cold winter. The irihabitants of aquatic environment are not subject to the sudden freezing of the water throughout its bulk.

4. The LOW VISCOSITY of water allows its rapid movement into and through cells. Moreover it makes water a useful lubricant to reduce friction in places with constant movement. (a) Mucus in the alimentary canal (b) Synovial fluid in the synovial joints (c) Pleural fluid in the pleural cavity of the lungs (d) Pericardia[ fluid in the pericardia/ cavity of the heart

5. The HIGH LATENT HEAT OF VAPORIZATION of water makes it a good evaporative coolant to remove the excess heat from many terrestrial organisms

(a) Sweating in humans (b) Panting in dogs (c) Transpiration in flowering plants 6. The strong COHESIVE FORCE between water molecules takes a very important role in the transport of water in plants.

(a) It accounts for its capillarity in soil and the capillarity in the narrow xylem. All these help the plants absorb water from soil.

(b) It accounts for the transpiration pull on the continuous water column in the xylem of the plants.

7. The INCOMPRESSIBILITY of water is a useful mean of support. It forms the hydrostatic skeleton of many organisms to achieve support in

(a) the aqueous and vitreous humour of the eyeball. (b) the coelom of the earthworm. (c) the erection of penis.

32

(d) the ventricles of the brain and the central canal of the spinal cord.

Water also acts as a cushion for protection e.g amniotic fluid protects the embryo. 8. The HIGH DENSITY of water provides the buoyancy support of aquatic organisms which do not need a bulky skeletal system. 9. The FLUID MEDIUM of water enables the male gametes swimming to achieve fertilization. It also aids the dispersal perpetuation of species.

of spores and seeds. Thus water takes an important role in the

10. The HIGH SURFACE TENSION of water allows surface dwelling organisms attaching to the water surface to breathe. e.g. mosquito larvae hanging on the water surface. It also permits movement on the water surface e.g water boatman and water skater.

1.9

IMPORTANCE OF CARBOHYDRATES TO LIVING ORGANISMS

A. Trapping, transferring

and release of energy

1. Ribulose (Pentose, SC-sugar) Ribulose bisphosphate photosynthesis.

(RuBP) is the important C0

2

acceptor in the Calvin Cycle of

2. Phospho-glycer-aldehyde (PGAL) and phospho-glyceric acid (PGA) (Triose, 3C-sugars) They are important intermediates in photosynthesis and respiration. Without them, the light energy trapped in organic compounds cannot be converted to sugar for future use. Eventually the energy stored in sugar can be progressively broken down in respiration to release energy for supporting life.

3. Glucose (Hexose, 6C-sugar) It is the immediate form of carbohydrates that can easily be oxidized to release energy to support metabolic activities.

B. Transport 1. Glucose (monosaccharide) It is the common form of carbohydrate for transport throughout the body of animals. 2. Sucrose (disaccharide) It is the usual form of carbohydrate for transport in plants from the site of production (leaves) to the organs that need them e.g. growing points and storage organs. It ensures even distribution of nutrients throughout the plant.

C. Nutrient reserves for development

1. Lactose (disaccharide) It is an important energy reserve in milk, which is a balanced diet for growing mammals. It

33

partially accounts for the success of mammals which can receive such a high degree of parental care.

2. Maltose (disaccharide) It is an important energy reserve in seeds of flowering plants particularly the monocotyledons. It provides nutrients for the growth of embryo in the seed.

D. Support 1. Chitin (polysaccharide) It is the constituent of the exoskeleton of insects and crustaceans.

2. Cellulose (polysaccharide) It is the constituent of cell wall of plant cells. K Control Ribose (Pentose, SC-sugar) 1. Nicotinamide adenine dinucleotide (NAD) It is a co-enzyme which assists the enzyme dehydrogenase to catalyse the reaction called dehydrogenation. This co-enzyme accepts the hydrogen atoms from the substrate molecule. 2. Ribose nucleic acid (RNA) The messenger-RNA and transfer-RNA take an important role in the synthesis of protein. Thus they control the synthesis of enzymes which in turn control the biochemical metabolic activities of the bodies.

reactions in the

F. Reproduction Fructose (Hexose, 6C-sugar) It is the constituent of nectar to attract insects for pollination. It sweetens fruits to assist the dispersal of seeds.

G. Storage 1. Starch (polysaccharide)

It is the most importantfood reserve in plants to meet the future needs. lt is present in great abundance in seeds which have to pass through a long period of dormancy under adverse conditions.

2. Glycogen (polysaccharide) It is the storage form in animals to meet the need of nutrients supply at times other than feeding.

H. Heredity Ribose and deoxyribose (Pentose, SC-sugar) They are the important constituent of nucleic acids (RNA, DNA). Without them, the backbone of nucleic acids cannot be formed. The genetic information cannot be systematically built up. They are very important in heredity. 34

1. Cell ~tructure

All living organisms are made of CELLS. A typical cell is about 10 um (1 um= micrometre= 10-6m) in diameter. It is made of living material called protoplasm. Protoplasm consists of a central nucleus which is surrounded by a colloidal mass called cytoplasm. The cytoplasm is bounded by a thin layer of cell membrane and it contains many sub-cellular organelles. (Fig. 2. 1 and 2.2)

Cell membrane (controls transport in and out of the cell)

Centriole (controls spindle formation in nuclear division)

Cytoplasm (metabolic activities take place)

Nucleolus (formation of ribosomes) Chromatin (fine threads of genetic material)

Mitochondrion ----,---,, (releases energy by aerobic respiration) ---1--,,,r------+-----

Golgi apparatus-----+-----~~(controls secretion)

Nuclear membrane (has nuclear pores)

" ~

;._:--..L-~==------Diameter: about 20 µm

Nucleus

Secretary granules or food granules

Fig. 2. 1 The structure of a typical animal cell seen under the light microscope

35

Microvillus (increases surface area for absorption or secretion)

Exocytosis (release of secretary prdducts)

Vesicle formed by pinocytosis (cell drinking) Secretary vesicle (contains secretion)

Smooth endoplasmic reticulum (synthesis and transport of lipids)

~r----lHr----

__L.---1111\----

Microtubules (intra-cellular transport and support)

Golgi apparatus (controls secretion)

Two centrioles (spindle formation in nuclear division)

-~-~--------+---

Free ribosomes---+--,(protein synthesis)

Nuclear envelope (controls transport in and out of the nucleus)

Rough endoplasmic---+----#-, reticulum with ribosomes (synthesis and transport of proteins)

11.,,,, ____

Nuclear pore (passage of m-RNA)

Nucleus

Chromatin (fine threads of genetic material) Mitochondrion (releases energy by aerobic respiration)

2.1

-+--

Nucleolus (formation of ribosomes)

Cell membrane (controls transport in and out of the cell)

Fig. 2.2

Lysosome (intracellular digestion)

The ultrastructure microscope

Cytoplasm (metabolic activities take place)

of a generalized animal cell seen under the electron

CELL MEMBRANE (Plasma lemma; plasma membrane)

A. Occurrence Membrane occurs not only at the surface of cell but also around the nucleu~· and the subcellular organelles such as endoplasmic reticulum (ER), Golgi bodies, lysosomes, mitochondria and chloroplast.

B. Structures Under light microscope (LM) the membrane appears as a single line. 1. Trilaminar (three-layered) structure (Davson-Danielli in 1930s) (Fig. 2.3)

Under the high magnification of the electron microscope (EM) the membrane appears as a threelayered (trilaminar) structure of about 7.5 nm (lnm=nanometre = 10-9 m) thick.

36

(a) (i) It consists of a bimolecular layer of phospholipid which is about 3.5 nm. thick. The hydrophobic (water-repelling) tails facing each others at the centre of the membrane, while the hydrophilic (water-loving) ends extending towards the surface. (ii) Organic solvents such as alcohol, ether and chloroform penetrate membrane more rapidly than water. This suggests that membranes have non-polar portions, the phospholipids. (b) It is sandwiched between two layers of proteins, each of the protein layer is about 2 nm thick.

Protein molecules (2nm) {

Phospholipid layer (3.5nm) {

crrn 'llli JI\\\

I

l

l////i1:////Ji///

1//P--H(water-repelling) ydrophobic tails (non-polar)

Protein molecules (2nm) {

Fig. 2.3

The trilaminar structure of the cell membrane

2. Fluid mosaic model (Singer and Nicolson in 1935) (Fig. 2.4) Recent researches find that the protein does not form a continuous layer covering both sides of the membrane. Instead the membrane consists of a mosaic of protein floating in a fluid layer of phospholipid. ( a) Mosaic pattern of proteins

Protein is in form of globules scattered here and there in mosaic pattern on the phospholipid layer. Some protein penetrates only part of the way into the lipid layer, some penetrate all the way through the lipid layer of the membrane. ( i)

Hydrophilic channels or pores sometimes occur within a protein, or between adjacent protein molecules. These pores span through the membrane, allowing the passage of the polar molecules. According to the trilaminar model these polar molecules cannot pass through the lipid section.

(ii) Some proteins act as carrier molecules for transporting specific substances through the membrane. These carrier molecules control the selective permeability and the active transport of the membrane. (iii) Some are glycoprotein and glycolipid molecules projecting OUT of the membrane surface. They act as the recognition sites for recognizing antigens and hormones. (iv) Some membrane proteins act as enzymes, electron carriers and the energy transducers in photosynthesis and respiration to trap or release energy. 37

(b) Fluid pattern

The bimolecular layer of phospholipids has the polar (hydrophilic; water-loving) part at the surface of the membrane and the non-polar (hydrophobic; water-repelling) portion in the middle of the membrane.

Hydrophilic channel

Globular protein molecules

Glycoprotein

Glycolipid

or porl

7Lnn nn nnnnnnn~ aT

~~

t~ ~ ~ o~ ~8~ ~

Hyd:p:ili:

Hydrophobic tail

(water-loving)

(water-repelling)

Fig. 2.4

The fluid mosaic model of the cell membrane

C. Functions of cell membrane 1. They form the boundary to separate the contents of the cells from their surroundings. The protein and phospholipid contribute the membrane integrity to restrict the passage of certain ions and molecules. (Compartmentalization). 2. Their selective permeability membrane.

controls the exchange of materials between the two sides of

(a) The bimolecular layer of phospholipid is only permeable to fat-soluble substances. (b) The channel proteins or pores bounded by adjacent protein molecules facilitate the passage of polar rnolecules and small particles. (c) The carrier proteins facilitate the passage of specific solutes and are responsible for the active transport of certain substances against concentration gradient into the cell.

3. They provide sites for binding certain specific proteins. (a) At the cristae of mitochondria the respiratory enzymes (electron transport system) are arranged in specific order to transport the electrons for energy release. (b) At the thylakoids of chloroplast carrier molecules are located at specific sites for transporting electrons to convert the light energy into che,nical energy.

38

4. They can act as receptor/ recognition sites at the outer swface of the cell membrane to recognize the stimuli of hormones and other chemicals. The glycoproteins and glycolipids act as the recognition sites for antigens.

5. Endocytosis The membrane is often thrown into numerous folds to increase area to facilitate the exchange of materials with environment. (a) Microvilli of intestinal epithelial cells promote the absorption of digested products. ( b) Membranous folds and vesicles are associated with pinocytosis (cell drinking).

e.g. Basal folds (infoldings) of the tubular cells of the nephron increase the area to facilitate the reabsorption of useful substances.

2.2

CYTOPLASM

A. The cytoplasm is a viscous substance composed of many molecules in forms of soluble proteins, carbohydrates, oil droplets, glycogen granules and vacuoles of secretion. These fluid substances of the cytoplasmic matrix form the cytosol. B. Suspended in the cytoplasm are numerous membranous structures called the endoplasmic reticulum and many organelles specialized for performing particular functions inside the cell. C. A network of fine strands of globular proteins, known as microtubules and microfilaments, are collectively referred to as the cytoskeleton.

2.3

ENDOPLASMIC RETICULUM (ER)

A. Structures (Fig. 2.5)

The endoplasmic reticulum (ER) is a double membranous structure and the space between the two membranes range from 15 nm to over 100 nm ( 1 nm= l(r 9 m). It is in form of a complex system of membrane bound tubes and.flattened sacs called cisternae. It originates from the outer membrane of the nucleus. 1. Most endoplasmic reticulum has its outer surface attached with granules called ribosomes.

This membranous system is called rough endoplasmic reticulum (RER). It is concerned with the synthesis and transport of proteins. 2. Some ER is not covered with ribosomes and is called smooth endoplasmic reticulum (SER). It is concerned with lipid metabolism.

B. Functions of endoplasmic reticulum 1. The endoplasmic reticulum is connected with the cell membrane and the nuclear membrane.

Therefore it provides a kind of intra-cellular transport system that facilitates the movements of materials from one part of the cell to another. 2. (a) The proteins synthesized by the ribosomes on the surface of the rough endoplasmic reticulum are transported through the cisternae. These proteins are usually modified inside the 39

Sheet form of ER

Double membranes of ER Smooth endoplasmic reticulum

Rough (granular) endoplasmic reticulum

Fig. 2.5

endoplasmic

The three-dimensional

model of the endoplasmic

reticulum e.g. it may be phosphorylated

reticulum

or converted into a glycoprotein.

(Fig. 2.6)

(b) These proteins are packaged up in the membranous vesicles, and then moved to the Golgi apparatus. They can be secreted from the cell or passed to other organelles in the same cell, such as storage bodies or lysosomes. 3. It provides large area to attach enzymes in specific order that facilitates the biochemical reactions to proceed in a regular pattern inside the cell.

It provides a structural skeleton to maintain cell shape e.g. the smooth endoplasmic reticulum of a rod cell in the retina of eyeball.

Messenger RNA

---------

Rough endoplasmic reticulum (ER)

Growing polypeptide chain --------~·}

Fig. 2.6

40

Channel through ER membrane for the polypeptide chain to enter the ER

Space inside endoplasmic reticulum Width of endoplasmic reticulum membrane

The entry of the newly synthesized protein from the ribosome endoplasmic reticulum

into the

5. The smooth endoplasmic reticulum are thought to be concerned with the synthesis and transport of lipids and steroids. It is most abundant in those cells producing lipid related secretion e.g. the sebaceous glands of mammalian skin.

2.4

GOLGI APPARATUS (Golgi complex; dictyosome) (Fig.2. 7)

A. Structure 1. It consists of a stack of flattened membranous sacs (cisternae) together with a system of associated vesicles. It is formed by the fusion of vesicles which are pinched off from the

endoplasmic reticulum. A cisterna is about 1 to 3 µm (1 µm = 10--0m) in diameter and 14 to 20 nm (1 nm= 10 -9 m) thick. 2. At their outer edges the cisternae pinch off numerous vesicles which contain secretory granules.

B. Functions of Golgi apparatus 1. They act as sites to concentrate and chemically modify the materials contained within them. (a) Proteins newly synthesized in the rough endoplasmic reticulum are transported in the vesicles to the Golgi apparatus where carbohydrates are added to form glycoproteins. fb) These glycoproteins are packed in vesicles which are pinched off the Golgi apparatus. They move to the cell membrane where the glycoproteins are discharged out of the cell i.e. secretion occurs.

C--C--10

0t

~

0/

Golgi apparatusstack of flattened cisternae with vesicles

c=)~ Vesicles pinched off rough ER fuse to

~ form flattened membranous sacs

vnn--

Rough endoplasmic reticulum

Fig. 2. 7

The formation

and functions of the Golgi apparatus 41

( i)

Golgi apparatus is particularly numerous in the actively secreting cells e.g. liver cells. cells.

(ii)

Mucin (a glycoprotein) is secreted by the goblet cells of the respiratory and intestinal epithelial cells for protection and lubrication.

(iii) The root cap cells of plants contain Golgi apparatus which secretes a mucous polysaccharide, helping to lubricate the tip of root as it penetrates through soil.

(c) Some vesicles containing hydrolytic enzymes will fuse with the lysosomes. 2. They are also involved in the secretion of carbohydrates such as the synthesis of cell wall. They aggregate in large number in the region of cell plate formation during cell division.

2.5 A. Structure I. Ribosomes are produced in the nucleolus. They are 20 nm (1 nm = 10-9 m) in diameter, each consisting of two sub-units. (Fig. 2.8(A)) 2. A ribosome particle is composed of ribosomal RNA and proteins in roughly equal amount.

B. Occurrence I. Ribosomes are present in large number lyingfree in the cytoplasm. These ribosomes synthesize proteins that are retained within the cell. 2. Ribosomes bound to endoplasmic reticulum produce proteins that are subsequently secreted outside the cell. 3. They are also found in chloroplast and mitochondria. 4. A number of ribosomes (4 to 20) may be linked together by a piece of messenger RNA (mRNA) to form POLYSOME (poly-ribosomes) (Fig. 2.8(8)).

Ribosomes

Ribosomal subunits

SSS~-+-

----t----1-c§-r---t+c§

Fig. 2.8(A)

42

A ribosome

Fig. 2.8(8)

A polysome

m-RNA

C. Functions of ribosomes They are the sites of protein synthesis. During protein synthesis, the ribosomes move along the thread-like m-RNA molecule that controls the sequence of amino acids in the protein formed. (In polysome a number of ribosomes move simultaneously along the mRNA so that the process is carried more efficiently.)

LVSOSOME

A. Structure (Fig. 2.9) 1. It is a small spherical vesicle which is about 0.2 µm to 0.5 µm ( I µm = 10-0 m) in diameter. 2. It is bounded by a single membrane and contains hydrolytic enzymes such as proteases, lipases and nucleases in acidic solution. The membrane isolates the enzy,nes from the remains of the cell. 3. They are present in most eukaryotic cells, but are particularly abundant in animal cells exhibiting phagocytic activity e.g. neutrophils and macrophages (white blood cells).

B. Formation The enzymes synthesized in the rough endoplasmic reticulum are transported via the Golgi apparatus in form of vesicles to the lysosomes.

C. Functions of lysosomes 1. Lysosomes move towards large engulfed particles such as food vacuoles of Amoeba or bacteria engulfed by white blood cells (e.g. neutrophils and macrophages). They fuse with the vacuoles or vesicles formed by endocytosis to discharge their hydrolytic enzymes to break down the content i.e. intra-cellular digestion.

Discharge of debris

Digestive vacuole

Phagocytosis

.. . .

(the taking in of solid material at the cell membrane)

··1· • ~!·. ;:, •

Fig. 2.9

.

.

The formation and functions of /ysosomes 43

2. Unwanted organelles (e.g. mitochondria) are enclosed in a ,nembrane and broken down by lysosomes in a similar manner. 3. When their membranes burst, enzymes are released out to digest the cell content to kill it. This process is known as autolysis. They are important in the re-organization of cells involved in

wound healing. 2.7

MITOCHONDRION

A. Structure (Fig. 2. 10) 1. It is a rod-shaped structure with a diameter of 1.0 µm (1 µm = 10-6 m) and a length of 3-10 µm. 2. It is a hollow structure bounded by a double membrane. (a) The outer membrane is a sniooth and continuous boundary. (b) The inner membrane is folded inwards to form many tubular processes called cristae. These cristae greatly increase the area for attachment of more respiratory enzymes (electron transport system; cytochrome system). Its inner surface is densely covered with particles (FlP), the ATPase, which are very important in the oxidative phosphorylation i.e. production ofATP.

3. (a) The central cavity is filled with a matrix which contains the enzymes for Krebs' cycle and beta oxidation of fatty acids. (b) It contains ribosomes for protein synthesis.

Granule

inner membrane

t1f

Outer membrane

Outer chamber

Outer membrane

Outer chamber

Ribosome

Fig. 2. 10

44

The structure of a mitochondrion

B. Function of mitochondrion The enzymes (electron transport system) in the mitochondrial cristae and the enzymes of the Krebs' Cycle in the matrix are responsible for the oxidative breakdown of food to release energy. Thus mitochondria are present in great number in the cells that require a lot of energy. They are often packed close together in the part of the cell where energy is required. e.g. 1. In the middle piece of spermatozoan for swimming. 2. Alongside the myofibrils of the muscle fibre for muscle contraction. 3. In the base of the tubular cells of nephron for active transport in reabsorption.

2.8

CILIUM

A. Structure (Fig. 2. 11) Cilia and flagella possess identical internal structures. Cilia are shorter (5-10 µm) and ,nore numerous. Flagella are longer (150µm) andfewer.

Ciliary membrane continuous with plasma membrane t.LU-11---r==--

Two central filaments

One of nine peripheral filaments

{'9 + 2' array)

Cilium

Plasma membrane

____._____

Basal body

~"" G 9

I!

l"\I"-

.1:::!

:::::..aa---

(.)

0

©

>

substrate is limited the graph levels off

C

0

·;; (.) ro

C

0

·;; (.) ro

(I)

-

+-'

+-'

0:

0:

-

~

~

Many active sites are still vacant

0

0

(I)

ro

ro

Enzyme concentration

Fig. 5.5

The effect of enzyme concentration on the rate of enzyme reaction

Substrate concentration

Fig. 5.6

The effect of substrate concentration on the rate of enzyme reaction

B. Substrate concentration (Fig. 5.6) 1. For a given amount of enzyme, the rate of an enzyme reaction increases with an increase in substrate concentration up to a point. 2. (a) At low substrate concentration, the active sites of the enzyme molecules are notfully used and many active sites are left vacant. As the substrate concentration is increased, more and more sites are occupied by the substrate molecules so that the rate increases.

(b) Eventually when all active sites are used, increasing the substrate concentration cannot increase the rate of reaction, as the amount of enzyme is the limiting factor. Thus the curve

flattens off. 93

C. Temperature 1. Increase in temperature affects the rate of an enzyme reaction in two ways:

(a) As the temperature increases, the kinetic energy of the substrate and enzyme molecules increases. As these molecules move faster, there will be more chance of collision. This leads to orL>r1u 1r rate of reaction. (b) As the temperature increa'Ses, the more the atoms which make up the enzyme molecule vibrate. This breaks the hydrogen bonds and the three-dimensional shape of the enzyme molecule is altered to such an extent that their active sites no longer fit the substrate. The enzyme is denatured. 2. The overall effects of temperature on the movement of reactants and the enzyme denaturation.

(a) From 4°C to 40°C, the rate increases smoothly. For most reactions the rate roughly doubles for every 10 °Crise. The temperature coefficient [Q 10] is 2.

rate of reaction at (x + 10) °C rate of reaction at x° C

=

(b) For many enzymes the optimum temperature is 40°C.

• Many arctic and alpine plants have enzymes which function efficiently at around l0°C. • Whereas those algae inhabiting some hot-spring can function at around 80°C.

(c) Above 40°C the rate begins to fall off and then declines rapidly. It ceases at about 60°C because enzymes are proteins which are denatured at high temperatures. @

-- -

----......

CD-----

CD

·'

....,

I

''

',

C: 0 ',i:i

iI

'A'\

Rate at which reaction increases due to increased kinetic energy of substrate and enzyme molecules.

@ ------

Rate at which reaction decreases due to denaturation of enzyme molecules.

@ ---

Actual rate of reaction as a result of the combined effect of these two influences.

I

I

()

Optimum temperature

co

iE .... 0 Q)

+-'

co

a:

0

10

20

30

Temperature

Fig. 5. 7 94

40

50

60

(°C)

The effect of temperature

on the rate of an enzyme reaction

D. pH (Fig. 5.8) 1. Any extreme change in pH may break the hydrogen bonds that may alter the shape of the enzyme molecule and denature them. 2. Each enzyme has its own range of pH (optimum pH) in which it functions most efficiently.

(a) Most intracellular enzymes function best at or around neutral (pH = 7). Excessive acidity (lower pH) or alkalinity (higher pH) renders them inactive. (b) Pepsin and rennin secreted by the mammalian stomach work best in an acidic medium of

pH 1.2 to 2.5. (c) Trypsin only functions in an alkaline medium of pH 8.5 in the duodenum.

Pepsin

Salivary amylase

Trypsin

7

8.5

Rate of reaction i.e. Velocity [VJ

pH

Fig. 5.8

The effect of pH on the rate of reaction of three different enzymes

E. Inhibitors The rate of enzyme reactions may be decreased by the presence of inhibitors. There are two types of inhibitors: reversible inhibitors and non-reversible inhibitors.

1. Reversible inhibitors The effect of this type of inhibitor is temporary and causes no permanent damage to the enzyme. Removal of the inhibitor therefore restores the activity of the enzyme to normal. There are two types: (a) Competitive inhibitors

They compete with the substrate for the active site of the enzyme molecule. 95

(i)

The inhibitor (e.g. malonic acid) may have a structure similar to that of the substrate (e.g. succinic acid) so that it can combine with the active site of the enzyme (e.g. succinic dehydrogenase ). While it remains bound to the active site, it prevents substrate molecule (succinic acid) occupying them and so reduces the rate of the reaction.

(ii) The same quantity of product is formed because the substrate continues to use any enzyme molecules which are unaffected by the inhibitors. However it takes longer time to make the products. (iii) If the concentration of the substrate is increased, less inhibition occurs. This is because, as the substrate and inhibitor are in direct competition, the greater the proportion of substrate molecules the greater their chance of finding the active sites, leaving fewer to be occupied by the inhibitor.

Application: Sulphonamide drugs and antibiotics such as penicillin are competitive inhibitors. They are used to destroy or prevent the growth of pathogenic bacteria. They exert their action by combining with enzyme essential for the metabolism of the bacteria. Substrate molecule (succinic acid)

Inhibitor molecule (malonic acid) occupying the active site of the enzyme

Active site--~

Enzyme molecule (succinic dehydrogenase)

(A) Active site occupied by substrate molecule

Fig. 5.9

The effect of competitive

(BJ Active site occupied by inhibitor so that it is not available for the substrate molecule

inhibitor

on the active site of enzyme

(b) Non-competitive inhibitors (Fig. 5.10) (i)

96

They do not attach themselves to the active sites of the enzyme, but elsewhere on the enzyme molecule. They change the shape of the enzyme molecule in such a way that the active site can no longer properly fit the substrate.

(ii) As the substrate and inhibitor molecules attach to different parts of the enzyme molecule, they are not competing for the same sites. An increase in substrate concentration will not therefore reduce the effect of the inhibitors.

Cyanide is a non-competitive inhibitor. It attaches itself to the iron prosthetic group of cytochrome oxidase thereby inhibiting respiration.

Shape of active site changed

Substrate molecule occupies the active site

Substrate molecule cannot fit into the changed active site

(A) Functional enzyme

Fig. 5. 10

(BJ Inactivated enzyme

The effect of non-competitive

inhibitor

2. Non-reversible inhibitors (a) Heavy metals ions

The mercury (Hg 2+) and silver (Ag+) ions break the disulphide bonds. These bonds help to 1naintain the shape of the enzyme molecule. Once broken the structure of the enzyme molecule becomes irreversibly altered with permanent loss of its catalytic properties. (b) Applications of enzyme inhibitors

(i)

They give us important information about the shape and properties of the active sites of enzymes.

(ii) They can be used to block particular

reaction, thereby enabling biochemists

to

reconstruct metabolic pathways. (iii) They have important medical and agricultural uses. e.g. drugs and pesticides.

97

5.5

ENZYME COFACTORS

A cofactor is a non-protein substance which is essential for some enzymes to function efficiently. There are three types of cofactors: activators, coenzymes and prosthetic groups. 1 . Activators • Activators are metal ions (inorganic ions) which are necessary for the jimcNoning of certain enzymes. They assist infonning the enzyme-substrate complex by moulding either the enzyme or substrate molecules into a suitable shape. Thus it increases the chance of reaction between reactant and enzyme. • The salivary amylase requires the presence of chloride (Cl-) ions before it will efficiently change starch into maltose. 2. Co-enzymes

• Coenzymes are complex non-protein organic substances which are essential to the efficient functioning of some enzymes, but are not themselves bound to the enzymes. Coenzymes function as carriers for transferring chemical groups or atoms from one enzyme to another. Many coenzymes are derived from vitamins .. • Nicotinamide adenine dinucleotide hydrogen acceptor.

(NAD) acts as a coenzyme to dehydrogenase by acting as a

3. Prosthetic groups • Like coenzymes, prosthetic groups are organic molecules. But unlike coenzymes they are bound tightly to the enzynie itself and form an integral part of it.

• Haem is a prosthetic group. It is a ring-shaped organic molecule with iron at its centre. Haem is the prosthetic group of the electron carrier cytochrome and of the enzyme catalase. 5.6

CONTROL OF METABOLIC PATHWAYS

A. Cell organelles 1. Certain cell organelles have enzymes bound to their inner membranes in a precise order. This increases the chances of them coming into contact with their appropriate substrates and leads to ordered metabolic pathway. 2. The organelles may also have varying conditions to suit the specific enzymes they contain. By controlling these conditions and the enzymes available the cell can control the metabolic pathways within it.

B. End product inhibition (negative feedback) (Fig. 5. 11) The end product of a pathway may inhibit the enzyme at the start. enzyme El

A

98

enzyme E2

B

enzyme E3 C

p

1. The product Pacts as an inhibitor to enzyme El. If the level of product P falls, this inhibition is reduced, and so more A is converted to B, and subsequently more P is produced. 2. If the level of Prises above normal, inhibition of enzyme El increases and so the level of P is reduced. In this way the homeostatic control of P is achieved. The mechanism is termed negative feedback because the information from the end of the pathway which is fed back to the start has a negative effect i.e. a high concentration of P reduces its own production rate.

Negative feedback Allosteric site

Active site

Fig. 5. 11 End-product

inhibition

on the control of the metabolic pathway

99

6.1

MODE

NUTRITION

Nutrition is the process by which an organism makes or obtains food substances

from the

surroundings to support its life.

A. Autotrophic nutrition The organisms carrying out autotrophic nutrition are called autotrophs. They can make complex organic foodfr01n simple inorganic substances.

1. Photosynthetic (photoautotrophic;

phototrophic) nutrition

Green plants absorb light energy by chlorophyll to form biological energy (ATP) and chemical energy (NADPH) to change carbon dioxide to carbohydrates. This process is called photosynthesis. It is also called holophytic nutrition because it is found in ,nost plants.

2. Chemosynthetic (chemoautotrophic; chemotrophic) nutrition Certain bacteria (e.g. iron bacteria I sulphur bacteria I nitrifying bacteria) use the chemical energy obtained by oxidation of inorganic substances such as ammonium compound I nitrite /iron (II) compound I sulphur to synthesize the complex organic food from carbon dioxide.

B. Heterotrophic (chemoheterotrophic)

nutrition

The organisms carrying out heterotrophic nutrition are called heterotrophs. They cannot synthesize organic food from simple inorganic substances. They acquire energy from the ready-made organic food obtained by them.

1. Holozoic nutrition Most animals obtain solid organic food by eating other organisms and digesting them internally.

100

(a) Herbivores-They

feed on plants. e.g. rabbit, sheep, horse

(b) Carnivores-They

feed on animals. e.g. frog, dog, tiger

(c) Omnivores-They

feed on both plants and animals. e.g. cockroach, man and pig.

2. Saprophytic nutdtion (saprotrophism)

In saprophytic nutrition the organisms feed on dead or non-living organic matter and obtain the nutrients by external digestion. e.g. saprophytic bacteria and fungi. 3. Parasitic nutrition (parasitism)

In parasitic nutrition the organisms (parasites) live in or on the body of another living organisms (hosts) and directly absorb simple food from them. The parasites may give harm to the hosts. e.g. parasitic bacteria, fungi and protozoans, tapeworm and dodder.

6.2

PHOTOSYNTHESIS

Photosynthesis is the use of light energy to split water and to transfer the hydrogen to carbon dioxide. Through oxidation-reduction reactions, sugar is produced. Energy stored in carbohydrate molecule is equivalent to 470 kJ per carbon dioxide fixed. The JC sugar (triose) can be converted to hexose, sucrose or starch. Photosynthesis involves two stages: the light and dark reactions. Evidences for their existence are as follows: A. Flashing light experiments

1. Photosynthesis continues for a short time after a flash of light. Thus photosynthesis includes a stage which can take place in the absence of light (dark reactions) (Fig. 6. 1(A)) photosynthesis

light

Fig. 6. 1(A)

proceeds

dark

Photosynthesis proceeds even in the absence of light for a short period

2. (a) A plant is exposed to alternative light and dark periods. The amount of carbohydrates formed is x mg. (Fig. 6. 1(8)) (b) A similar plant is exposed to continuous light period for the same amount of light as that in the previous experiment. The amount of carbohydrates formed is y mg. Light

Dark

Light

Dark

Light

xmg

1 hr

1hr

1hr

Light

ymg

3 hrs

Fig. 6. 1(8)

Different light treatments of the plants

101

(c) It is found that x is greater than y. It is suggested that the light stage results in a product which is then fed into the dark stage. A

B

(light stage)

(dark stage)

C

It is supposed that B built up during the light reactions cannot be used by the dark reactions as quickly as it is formed. Intermittent light ensures the complete conversion of B into C, and prevents B from accumulating in the light reactions that may retard the formation of B from A.

B. Summary of the two stages in photosynthesis (Fig. 6.2) light

+ chlorophyll

1. The first stage requires light to split water into hydrogen and oxygen. The LIGHT REACTIONS occur on the thylakoid membranes of the chloroplast. The light energy is converted to ATP (adenosine triphosphate) and NADPH 2 (reduced nicotinamide adenine dinucleotide phosphate). Oxygen is released as a waste product. 2. In the second stage, the ATP and NADPH 2 are used to reduce carbon dioxide to carbohydrate. This stage does not require light and is called the DARK REACTIONS. It occurs in the stroma of the chloroplost. Raw materials

2Hp 2NADP

light

light reactions

Dark reactions

in the thylakoids

in the stroma

chloroplast

2ADP + 2 Pi

Products

Fig. 6.2

6.3

Summary of the light reactions and dark reactions

LIGHT STAGE-THE

PHOTOCHEMCIAL REACTIONS

This stage takes place in the thylakoids of the chloroplast.

A. The formation of NADPH 2 When light activates chlorophyll a (in photosystem I), the high energy electrons will be boosted to electron acceptors X. Electrons are passed 'downhill' via a chain of electron carriers that are at different energy levels. At each stage energy is released (some of the trapped energy is lost as heat energy) and at the final stage energy and electrons are used to form NADPH 2 • 102

B. The formation of ATP When light activates another chlorophyll a (in photosystem II), the high energy electrons will be boosted to electron acceptors Y. Electrons are passed 'downhill' via a chain of electron carriers. As the electrons move from one carrier to another, alternatively oxidizing and reducing the carriers, the change in potential energy can be coupled in one or more instance to the formation of ATP. This is known as photosynthetic phosphorylation (PHOTO-PHOSPHORYLATION). Electron transfer is responsible for the production of ATP and NADPH 2

x

High-energy electrons pass from X ', 'downhill' via a chain of electron , carriers; to change NADP to NADPH 2

·.'

''

''

High-energy electrons pass 'downhill' via a chain of carriers; at each stage energy is lost as heat energy and at one stage the energy is used to synthesize ATP

'

' '-.4e-'-

''

"- "-

2NADP

(photophosphorylation)

Light/

Photosystem I

'(2NADPH I

(chlorophyll molecules)

~h!s:I1,o-:::// e- -+---

(chlorophyll molecules)

Fig. 6.3

I

I 4

2

4

Light

I

4H +.

H'

__.

The formation of NADPH 2 and ATP in the photo-chemical

reactions

C. Photolysis of water 1. In losing an electron the chlorophyll molecule becomes positively charged and unstable. Neutrality and stability is restored when the electron is returned. 2. The electron lost is replaced by an electron donated from the hydroxyl ion (OH-) that is derived from the spontaneous dissociation of water molecule by light (at photosystem II). This process is called PHOTOLYSIS of water.

103

(a) After the hydroxyl ion has lost the electron, the hydroxyl radical rearranges to form water and molecular OXYGEN which is released out.

40H-

+ 40H

4 electrons

40H

----

2H 2 0

+ 02

(b) The proton (H+) eventually combines with the electron to reduce NADP to NADPH 2 which will participate in the reduction of carbon dioxide.

Further evidence came from the use of a heavy isotope of oxygen (180} incorporated into water as H/ 80. When this was used, the oxygen released from the plant during photosynthesis was shown corning from water. 180 2 is detected by a mass spectrometer. D. Non-cyclic photo-phosphorylation The non-cyclic passage of electrons from water to reduce NADP via the electron carriers also leads to the synthesis of ATP. This process is called non-cyclic photo-phosphorylation.

E. Cyclic photo-phosphorylation 1. Under ce11ainconditions chlorophyll can function as both donor and ultimate acceptor of electron.

Light strikes the chlorophyll to boost the excited electron to pass through a. series of electron carriers that eventually leads to the synthesis of ATP. 2. The electron will eventually return back to neutralize the charged chlorophyll molecule. Such cyclic flow of electrons that leads to the production of ATP is called cyclic photophosphorylation. NO oxygen is evolved. F. Comparison

of cyclic and non-cyclic photo-phosphorylation Non-cyclic

1. 2. 3. 4.

Pathway of electrons First electron donor Last electron acceptor Products

5, Photosystems

(PS) involved

Cyclic

photo-phosphorylation

photo-phosphorylation

Non-cyclic Water NADP ATP, NADPH 2 , 0 2 I and II ,

Cyclic Chlorophyll molecule Chlorophyll molecule ATP only I only

G. Hill Reaction

In 1938 Robert Hill at Cambridge found that isolated chloroplasts from spinach leaves could, when illuminated, reduce various artificial electron acceptors such as iron (Ill) oxalate (or DCPIP, dichlorophenol idophenol) and at the same time produce oxygen. 2Hp

104

iron (III) oxalate DCPIP (oxidized)

4 Fe 2 + + 4H+ + 0 2 iron (II) oxalate oxygen DCPIP (reduced)

(blue)

(colourless)

+ 4 Fe 3+

The above reaction is called Hill Reaction. This discovery has the following significance: 1. It showed that OXYGEN could be produced without the reduction of carbon dioxide. It supported the presence of light and dark reactions and the splitting of water. 2. It showed that chloroplast could carry out the REDUCTION of an electron acceptor in the presence of light. Eventually it led to the discovery of the naturally occurring electron acceptor in chloroplast. They are the oxidized forms ofNAD and NADP (nicotinamide adenine dinucleotide phosphate). 3. It gave evidence that the light reaction of photosynthesis was taking place completely in the chloroplast. 6.4

DARK STAGE (CARBON FIXATION)

This stage takes place in the stroma of chloroplast. This involves the REDUCTION of carbon dioxide by NADPH 2 to form carbohydrates. This endergonic reaction requires energy which is further provided by ATP. Both the reducing power (NADPH) and ATP are produced in the light stage. A. Calvin Cycle (Fig. 6.4) 1. Carbon dioxide combines with a 5-carbon organic compound called ribulose bisphosphate (RuBP). This acts as a carbon dioxide acceptor and fixes the carbon dioxide. 2. This combination gives an unstable 6-carbon compound which splits immediately into two . molecules of 3-C compound, phosphoglyceric acid (PGA) [glycerate-3-phosphate (GP)] 3. The phospho-glyceric acid (PGA) is reduced by NADPH 2 to triose phosphate, TP [phosphoglycer-aldehyde (PGAL); glyceraldehyde -3-phosphate]. NADPH 2 supplies most of the energy, the rest coming from ATP. Carbon dioxide

Light stage

Dark stage (in stroma of chloroplast)

(in thylakoids of chloroplast) NADP~f---+----------NADP

u

ATP ADP+ P1

NADPH 2

NAO~ 2 Phospho-

---fix~~-ti~on /

~ ~-gl-yc_e_ri_c____. _acid (PGA) (3C)

r-

Ribulose bisphosphate

(5 C)

CALVIN

CYCLE

Triose phosphate (TP); PGAL

ADP+ P,

Hexose phosphate (6C sugar phosphate)

ADP+ P,-------; ATP-+---

\ Ribulose ---------. phosphate

sucrose starch cellulose

Regeneration of acceptor

Fig. 6.4

Calvin cycle 105

4. (a) Triose phosphate (TP) [Phospho-glycer-aldehyde (PGAL)J combines to form hexose phosphate [6-C sugar phosphate]. The energy is provided by the ATP formed in the light reaction. This hexose phosphate [6-C sugar phosphate] can be converted to sucrose for export, or starch for storage or cellulose for building. (b) The majority (516) of triose phosphate (TP) [PGAL] enters a series of reactions which use ATP and result in the re-generation of ribulose bisphosphate. This is very important because only by ensuring a supply of ribulose bisphosphate can the continued fixation of carbon dioxide take place.

B. Synthesis of other macro-molecules in photosynthesis (Fig. 6.5) 1. Formation of lipids (a) PGA (phospho-glyceric acid) [glycerate-3-phosphate] enters into the Glycolytic pathway of respiration. This is eventually converted to an acetyl group which is added to coenzyme A to form acetyl coenzyme A. By the reverse process of beta oxidation this is converted to fatty acids in both cytoplasm and chloroplasts. (b) Triose phosphate (TP) [PGALJ is changed to glycerol. Fatty acids and glycerol combine to form lipids. 2. Formation of proteins (a) PGA (phospho-glyceric

acid) [glycerate-3-phosphate] is first converted to one of the carboxylic adds of the Krebs' cycle via acetyl coenzyme A.

(b) Amino groups will be added to these carboxylic acids by amination or transamination to form amino acids. Nitrogen, sulphur and occasionally phosphorus are needed for protein

Ribulose bisphosphate

Photosynthesis

----.P

Phosphoglyceric acid (PGA)

Respiration ~lycolysis ~

Triose phosphate

Pyruvate

~

~ TP (PGAL)

Acetyl coenzyme

Hexose phosphate (6-carbon sugar phosphate)

I t ___________ 1 ~

\., Sucrose

Starch

ICarbohydrates I

../ Cellulose

Glycerol ~-------/

I

A ~

Oxalo~L

Fatty acids

Citric acid

~;!:'

a-~oglutaric

ac_1d~/ I ~ I

T

I Lipids I

Amino acids Polymerization

1

l

Proteins

Fig. 6.5

106

Synthesis of other macro-molecules

I I 1

t Transam1nation

in photosynthesis

acid

I

NH 3

~ NO 3

formation and are obtained from the soil water as inorganic salts. The aniino acids are polymerized to form proteins.

C. The experiments used to find out the pathway of CARBON in photosynthesis (Fig. 6.6) The work was done by Melvin Calvin at the University of California. He won the Nobel Prize for his work in 1961.

I. A suspension of algae (Chlorella) in nutrient solution was allowed to carry out photosynthesis under constant temperature and light intensity in a clear transparent reservoir. Carbon dioxide, labelled with the radioactive isotope of carbon, 14C, was passed into the culture at the start of the experiment. 2. After the algae had been exposed to the radioactive carbon at different lengths of time (from a few seconds to several minutes), samples of algae were collected and killed immediately by draining them into boiling ethanol. The boiling ethanol stopped all metabolic activities instantaneously.

14 C0 2 is injected at the start of the experiment

.

Air bubbled 1n

t

\\_)

Algae in nutrient solution

Spot arbitrary separated -m_e-ta_b_ol_it_es_~

Transparent reservoir

LIGHT

Hot ethanol (kills algae and extracts photosynthetic products)

x4

Tap (opened at regular interval to run out samples of algae)

X3

j)

Each sample is concentrated by evaporation and the extract is separated by 2 dimensional chromatography

Extract loaded here

Auto-radiography

X 4 X3 X2

Chromatogram

Drys and rotates the chromatogram through 90°

Developing solvent A

Developing solvent B

Relative amount of radio-activity measured by putting the Geiger counter over the spot

~1

I

I Radiation sensitive film placed over chromatogram to detect spots containing 14 C labelled compounds

Fig. 6.6

14 C-labelled compound developed as dark spot

Original position of extract

The experiment used to find out the pathway of carbon in photosynthesis

107

3. Each sample is concentrated by evaporation to obtain an extract. The radioactive compounds in the extract were separated by paper chromatography. 4. (a) The chromatograms were dried. The radioactive substances on the chromatogram were identified by auto-radiography. It was done by placing a photographic film sensitive to radiation from 14C over the chromatograms. The film and the chromatograms were left in contact in the dark for two weeks. The film became darkened where radioactive compounds were present.

(b) The relative amount of radioactivity in the various labelled metabolites with time was measured by using a Geiger counter. 5. When the time of exposure was 5 seconds or less, the first product of photosynthesis was identified as phosphoglyceric acid (PGA) [glycerate-3-phosphate]. He went on to find the sequence of compounds through which the fixed carbon passed and the various stages involved are summarized in Fig.6.7. They have since become known as the Calvin Cycle (Calvin-BensonBassham cycle).

Time of exposure

Main substances containing

14

C

5 sec

3-phosphoglyceric acid (PGA)

15 sec

PGA, hexose phosphate

1 min

PGA, hexose phosphate, sucrose, amino acids

6 min

PGA, hexose phosphate, sucrose, starch, amino acids, proteins, lipids

Unicellular algae are preferable to green leaves 1. Being unicellular, they are all immediately killed on contact with the ethanol. A leaf may continue to photosynthesize in sub-epidermal cells while the ethanol penetrates through epidermis.

70~GA: •

50

I

:

~ Sugar

Total activity/%

. /A A.1~~r • A Sugar

30

I

._~ 1

phosphates,

10

I

0

4

8 12 16

----"'phosphates .... ~ePGA

----------

Ma late

~ Alanine 2

I

Seconds

3

4

Minutes Time

Fig. 6. 7

108

Graph showing the radioactivity of the different labelled compounds plotted against time

2. In addition, the products of photosynthesis in algae are not translocated from one cell to another, as they may be in a leaf. 3. It is also easier to maintain controlled conditions in such a piece of apparatus with unicellular organisms than with an angiosperm. D. Identification of carbon dioxide acceptor 1. Evidence to show that Ribulose bisphosphate (RuBP) is the carbon dioxide acceptor (Fig. 6.8)

When the cells are illuminated, photosynthesis occurs and eventually it reaches a steady state. At this condition the ribulose bisphosphate (RuBP) and phospho-glyceric acid (PGA) are broken down and formed continually. However, then the light is TURNED OFF, there is a sharp decrease in RuBP and an increase in PGA. (a) It suggests that RuBP is used to form PGA. This leads to the decrease in RuBP. The formation of PGA is a step in the dark reaction, not requiring any of the co-factors (ATP, NADPH 2) which are produced in the light reactions of photosynthesis. (b) But the reaction by which PGA reduced to triose phosphate (TP)[PGAL] greatly depends on these co-factors, ATP and NADPH 2 • Thus PGA will not be used in darkness. Instead PGA will continue to be formed until the supply of carbon dioxide acceptor (RuBP) is used up. This leads to the increase in PGA.

It shows that RuBP is the carbon dioxide acceptor and PGA is the first stable product in the dark reactions. Light reactions

t

LIGHT

PGA

i

.c :§ u C: ro ::, Q)

0

-o- u

§

g /~~-~.--:: -~.,-;; ...-~:~.~ ....

OE~

1/./

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