Pra U STPM Biology Term1 CC039142a

Biology Term 1 STPM Chapter 2 Structure of Cells and Organelles 2 92 • There are no capillaries in the cells as the cell layers are too thin for capillaries to enter. • Mitosis can take place to replace dead or worn out cells of the skin epidermis. (iii) Their functions are as follows: • The epithelia help to protect tissues or organs below them. • They help to absorb substances and allow substances to cross them. • Some of the epithelial cells are modified to form special receptors for stimuli. (iv) They are classified based on their cell arrangement or the shape of the cells. • Based on the arrangement of cells, they are classified into three groups: Simple epithelium – The cells are arranged in one layer. Stratified epithelium – The cells are arranged in more than one layer. Pseudo-stratified epithelium – The cells seemed to be arranged in layers but each is attached to the basement membrane. • Based on their cell shapes, they are classified into four groups: Squamous epithelium – The cells are flattened like scales or tiles. Cuboidal epithelium – The cells are more or less shaped like cubes. Columnar epithelium – The cells look like pillars, their height is longer than their base width. Transitional epithelium – The cells can change shape when stretched. (v) There are eight types of covering epithelia and the examples are as follows: • Simple squamous epithelium. This is found in the outer layer of Bowman capsule, endothelium of blood vessels and alveolar walls. • Bowman capsule channels filtrate into proximal convoluted tubule. Endothelium allow exchange of gases and small molecule within the blood capillaries and body fluid. Alveolar walls allow gaseous exchange in the capillaries and the lungs. • Simple cuboidal epithelium. This epithelium is found in the collecting ducts and tubules of the nephron. Top view Vertical section Figure 2.37 Simple squamous epithelium

Biology Term 1 STPM Chapter 2 Structure of Cells and Organelles 2 93 • The proximal convoluted tubules allows absorption of filtrate molecules back into blood capillaries. The distal convoluted tubules and collecting ducts are affected by ADH to reabsorb back water in the kidneys. Cross section Basement membrane Longitudinal section Figure 2.38 Simple cuboidal epithelium • Simple columnar epithelium. This epithelium is found lining the innermost layer of the intestines and stomachs. • The epithelia in stomach and small intestine can be modified to form glands to produce mucus and digestive enzymes. • The epithelia in small intestine can absorb digested food molecules. In the large intestine, the epithelium can absorb water beside producing mucus. Vilus Crypt of Lieberkuhn Capillary Lacteal Venule Arteriole Lymph vessel Vertical section of a simple columnar epithelium Epithelial lining Figure 2.39 Simple columnar epithelium • Stratified squamous epitelium. This epithelium is found in the epidermis of skin, lining the innermost layer of the oesophagus. The epithelium top layer keeps worning off while the cells at the bottom divide and grow to replace the loss. It’s function therefore is more for protection. • Stratified cuboidal epithelium. This epithelium is found in the excretory ducts of sweat glands. Therefore, the ducts are to channel sweat out. Vertical section Figure 2.40 Stratified squamous epithelium

Biology Term 1 STPM Chapter 2 Structure of Cells and Organelles 2 94 Vertical section Figure 2.41 Stratified cuboidal epithelium • Stratified columnar epithelium. This is found in the secretory ducts of the mammary glands. • The duct is to channel the milkout. Vertical section Figure 2.42 Stratified columnar epithelium • Pseudo-stratified epithelium. This is found in the innermost layers of the trachea, bronchi and bronchioles. • The function of its cilia is to sweep the dust out. Vertical section Figure 2.43 Pseudo-stratified epithelium • Transitional epithelium. This is found in walls of urinary bladders. • The epithelium allows the bladder to stretch when filled with water. Wall relaxes Wall stretches Figure 2.44 Transitional epithelium (b) Glandular epithelia (i) Glandular epithelia are gland cells derived from epithelia and can secrete liquid containing mucus, hormones or enzymes. (ii) There are two types of glandular epithelia i.e. exocrine glands and endocrine glands. (iii) Exocrine glands • They have ducts that secrete substances. Epithelial tissues Covering epithelia 1. Simple squamous • for absorption in endothelium and alveoli 2. Simple cuboidal • for absorption in collecting duct of nephron 3. Simple columnar • for absorption in small intestine 4. Stratified squamous • for protection in skin 5. Stratified cuboidal • for transport in sweat ducts 6. Stratified columnar • for transport in milk ducts 7. Pseudo-stratified • for transport in airways of lungs 8. Transitional • for stretching in wall of urinary bladder Glandular epithelia 1. Exocrine glands • Formed by invagination with ducts for transport 2. Endocrine glands • Formed by detachment with no ducts and produce hormones-into capillaries Summary

Biology Term 1 STPM Chapter 2 Structure of Cells and Organelles 2 95 • There are little capillaries in them. • They produce liquid with proteins or enzymes. • They are formed by invagination of epithelia as shown in Figure 2.45. Duct Gland Figure 2.45 Formation of exocrine gland • Examples include tubular glands of the large intestine and the sweat glands. (iv) Endocrine glands • They do not have ducts, thus the secretion is directly emptied into the blood capillaries around them. • There are a lot of capillaries in them. • They produce hormones. • They are formed is by detachment from the epithelia as shown below in Figure 2.46. Detached from epithelium Gland with capillaries Figure 2.46 Formation of endocrine gland • Examples include the thyroid and the adrenal gland. Nervous tissue 1. Nervous tissue is a group of nerve cells or neurones together with neuroglia or supporting cells, which transmits electro-chemical messages called impulses along their membrane. 2. Neurone consists of two parts, the cell body and the nerve process. 3. The cell body has different shapes, depending on the types of neurone. It is surrounded by a plasma membrane and contains a nucleus like any normal cell. It has a lot of mitochondria, Golgi apparatus, endoplasmic reticulum, ribosomes (previously called Nissl’s granules) but no centriole. 4. The nerve process is the thin slender structure attached to the cell body. It includes the axon, dendron and dendrites. Dendron transmits impulse towards the cell body whereas axon transmits impulse away from the cell body. The length of dendron and axon varies. It can be very long, up to over a metre in our body. Both are protected by myelin sheath. The end of the axon or dendron is branched to form smaller dendrites. Axon dendrites end with little knobs called synaptic knobs. 2013 Exam Tips Remember the formation of endocrine and exocrine glands. Nervous tissues 1. Motor neurone • Short dendron, long axon for transmitting impulse from CNS to muscles 2. Sensory neurone • Long dendron, short axon for transmitting impulses from receptors to CNS 3. Interneurone • Dendron and axon same length for transmitting impulses from sensory to motor neurones Summary

Biology Term 1 STPM Chapter 2 Structure of Cells and Organelles 2 96 5. There are three types of neurones namely the motor, sensory and associative neurones. (a) Motor neurone Motor neurone transmits impulse from the central nervous system to the effector i.e. muscle or gland. Its structure is as shown in Figure 2.47. Effector Myelin sheath Cell body Node of Ranvier Nucleus of Schwann Dendron Axon Nerve impulse Figure 2.47 Structure of a motor neurone (b) Sensory neurone Sensory neurone transmits impulse from the receptor to the central nervous system. Receptor cell Axon Myelin sheath Synaptic knob Dendron Nerve impulse Cell body Nucleus Figure 2.48 Structure of a sensory neurone (c) Interneurone (associative / intermediate neurone) Interneurone receives impulse from the sensory neurone and transmits it to the motor neurone. It is found in the brain or spinal cord. Some can generate impulse and others transmit impulse from one to the other. It varies in shape, bipolar and multipolar with one or more dendrons or axons. Axon Dendrons Axon Nucleus Dendron Dendrits Cell body Bipolar Multi-polar Figure 2.49 Types of interneuron

Biology Term 1 STPM Chapter 2 Structure of Cells and Organelles 2 97 6. Neuroglia are supporting cells closely associated with neurones. They include the Schwann cell and the supporting cells in the brain and spinal cord. Schwann cell forms the myelin sheath that insulates the axon or dendron which enables impulse to travel faster. Other neuroglia supply nutrients to neurones, remove wastes from neurones, guide axon migration and provide immune functions. Muscle tissue 1. Muscle tissue is a group of cells or multinucleated syncytial tissue which can contract. 2. Muscles are divided into striated, cardiac and smooth muscles. (a) Striated muscle (i) Striated muscle also known as skeletal or voluntary muscle, consists of a bundle of muscle fibres attached to the bone by tendons at both ends. Contraction of striated muscle produces movement of the bone at the joints as well as certain parts of the body. Tendon Connective tissue One muscle fibre Bone Complete muscle Bundle of muscle fibres Figure 2.50 Striated muscle (ii) Each fibre is supplied with a motor nerve through a special neuro-muscular synapse called the end plate. Contraction is a result of impulse sent to the muscle fibre. It is under our conscious control. Each fibre consists of many myofibrils as shown in Figure 2.51. Nucleus Sarcomere A band I band Myofibril Figure 2.51 Part of a muscle fibre (iii) Within each myofibril, there is an alternating dark and light bands that produce striations seen under light microscope. Dark band (A band) consists of thick myosin Exam Tips Remember the general structure, including drawings of motor, sensory and associative neurones. Muscle tissue 1. Striated muscle • Multinucleated fibres for movement in bones 2. Cardiac muscle • Branched fibres for pumping in heart wall 3. Smooth muscle • Non-striated fibres for movement in intestinal wall Summary

Biology Term 1 STPM Chapter 2 Structure of Cells and Organelles 2 98 filaments supported at the centre by M membrane. Light band (I band) consists of thin actin filaments supported at the centre by Z membrane. The whole myofibril may be considered as containing many units called sarcomeres as shown in Figure 2.52. Sarcomere Z membrane A band I band H band Myosin filament (thick) Actin filament (thin) M membrane Figure 2.52 (b) Cardiac muscle Cardiac muscle is only found in the heart. It is also striated, consisting of fibres and myofibrils as in striated muscle but differs in many ways. (i) Cardiac muscle consists of individual cells and not syncytial tissue. (ii) Unlike striated muscles with straight fibres, cardiac muscle fibre is branched and is connected to the neighbouring fibres by bridges. (iii) Each of the individual cells is separated from its adjacent ones by intercalated discs so that excitation can be transmitted effectively across them from cell to cell. (iv) Cardiac fibre is not supplied with nerves from motor neurone as it does not require impulses from the brain before it can contract. (v) The muscle is myogenic. It has its own pacemaker to generate excitation that is transmitted across fibres before they contract. (vi) The structure of cardiac muscle is shown in Figure 2.53. Nucleus Intercalated disc Cross bridge Cell surface membrane Figure 2.53 Cardiac muscle

Biology Term 1 STPM Chapter 2 Structure of Cells and Organelles 2 99 (c) Smooth muscle (i) Smooth muscle is also known as involuntary muscle, as it is not under our conscious control but it is controlled by the autonomic nervous system. (ii) It is found in the alimentary canal, dermis, uterus, arteries and trachea. (iii) It is arranged in strands or layers. It is not branched or attached to the bone. (iv) It is made up of individual cells, each having its own nucleus and plasma membrane. (v) It has no striations, as its myofibrils do not align themselves with thick and thin filaments forming bands. (vi) It is supplied with nerves from the viseral motor neurone, a part of the autonomic nervous system. (vii) The muscle can contract rhythmically like peristalsis and produces waves of contraction as in intestines. Its structure is shown in Figure 2.54. Cytoplasm containing actin and myosin filaments Nucleus Cell surface membrane Figure 2.54 Smooth muscle Connective Tissues 1. Connective tissues are groups of cells together with their products that attach or are simply found between two different tissues. They originate from the mesoderm layer of the embryo, becoming mesenchyme and later form the bones, cartilages, blood cells and fibroblasts, which produce matrices. The matrices include the bone, cartilage, fine fibres produced by fibroblasts. Blood cells produce special proteins. 2. The compact bone has the following features: (a) Bone is formed from osteocytes that secrete the matrix of calcium phosphate and carbonate, together with proteins. (b) Compact bone consists of Haversian systems of cylindrical shape with a Haversian canal in the centre. (c) The Haversian canal is supplied with blood vessels that bring raw materials for bone construction or it can be reversed as in osteoporosis (a disorder of brittle bone). (d) The Haversian canals are linked by a Volkmann’s canal, forming an inter-connecting system for blood circulation. (e) The osteocytes are found in small spaces called lacunae with intricate tiny canaliculi for distributing the matrix during bone formation. Language Check Language Check • Canaliculus – singular Cannaliculi – plural • Lacuna – singular Lacunae – plural

Biology Term 1 STPM Chapter 2 Structure of Cells and Organelles 2 100 (f) The bone structure is shown in Figures 2.55 and 2.56. Lacuna with osteocyte Volkmann’s canal Lamellae Blood vessels and nerves Haversian system Figure 2.55 Compact bone (cross section) Haversian system Rod-like Haversian systems Bone marrow cavity Figure 2.56 Compact bone (longitudinal section) 3. Cartilage has the following features: (a) Cartilage is produced by chondrocytes which secrete the protein matrix with no calcium carbonate. (b) Cartilage differs from bone, as it is not as hard and it is flexible but of high tensile strength. (c) Chondrocytes are also found in lacunae but without canaliculus. They receive oxygen and nutrients through diffusion. (d) Cartilage is divided into three types: hyaline, elastic and fibrous, depending on the types of protein in the matrices. (e) One of the examples is the hyaline cartilage found in the rings of trachea. The u-shaped rings prevent the trachea from collapsing, and thus, allowing easy air passage. (f) Matrix of the hyaline cartilage consists of glycoprotein and collagen fibrils that make it translucent. Connective tissues 1. Compact bone • Produced by osteocytes in lacunae of Harversian system for body support and protection in the bone. 2. Cartilage • Produced by chondrocytes in lacunae of protein fibres in trachea for keeping it hollow. 3. Blood cells (a) Red blood cells • Biconcave filled with haemoglobin for O2 and CO2 transport (b) White blood cells (i) Granulocytes • With many lysosomes for phagocyting antigens and old cells (ii) Agranulocytes • Macrophages for phagocytosis • B-lymphocytes for producing antibodies • T-lymphocytes for helping B-lymphocytes Summary

Biology Term 1 STPM Chapter 2 Structure of Cells and Organelles 2 101 (g) The structure of hyaline cartilage is shown in Figure 2.57. Cartilage Matrix Lacuna Lacuna Lacuna Chondrocyte Cross section Longitudinal section Figure 2.57 The structure of hyaline cartilage in trachea Exam Tips Remember the definition, structures, functions and distributions of six types of epithelia, three types of neurones, three types of muscles, compact bone, hyaline cartilage, erythrocytes and leucocytes. 4. Blood cells Blood cells are divided into erythrocytes (red blood cells) and leucocytes (white blood cells). (a) Erythrocyte (i) Erythrocyte is formed in the bone marrow. The liver can form erythrocytes in foetuses too. (ii) Before it matures, an erythrocyte which has a nucleus is later digested to enable more haemoglobin to be filled for the carrying of oxygen. (iii) Its membrane is very thin, enabling easy gaseous exchange i.e. oxygen and carbon dioxide to move in or out. (iv) Its shape is biconcave so that its surface to volume ratio is increased for gaseous exchange. (v) The structure is shown in Figure 2.58. 8 μm 2 μm Figure 2.58 Structure of erythrocyte (b) Leucocytes Leucocytes are divided into granulocytes and agranulocytes. (i) Granulocytes • Granulocytes have granules in their cytoplasm. The granules are actually lysosomes. They are formed and mature in the bone marrow. • Granulocytes are divided into three types depending on the pH of the dye that can stain them. • The structure of the three types are shown below. Neutrophill Neutrophil Eosinophil Basophill Basophil Figure 2.59 Types of granulocytes

Biology Term 1 STPM Chapter 2 Structure of Cells and Organelles 2 102 (ii) Agranulocytes • Agranulocytes do not have granules in their cytoplasm. They are formed in the bone marrow and then get into the blood stream. • Agranulocytes are divided into monocytes and lymphocytes. Monocyte Lymphocyte Figure 2.60 Types of agranulocytes • Monocytes come out from the capillary into the tissue fluid becoming bigger to form macrophages. Macrophages engulf bacteria and dead tissue cells. • Lymphocytes are divided into T lymphocytes, which mature in the thymus gland and B lymphocytes, which mature in the bone marrow. B lymphocytes produces antibody and T lymphocytes help the B lymphocytes. Quick Check 5 1. Plants seem to have lesser types of cells but more types of tissues than animals. Explain. 2. How are organs organised in plants and animals? STPM PRACTICE 2 Objective Questions 1. Why bacteria is determined as prokaryotes? A It has a linear DNA B The DNA has no ends C The DNA forms a complex with histones D The DNA is surrounded by specific membrane 2. Which about a prokaryote is not correct? A Its genetic material is in the nucleoid. B Its DNA combines with histone. C It propagates via binary fission. D It has 70S ribosomes. 3. A student examined a cell under a microscope. He found that the cell has a cell wall. The cell does not contain membranebound organelles. What conclusion can be made by him from this observation? A It is a bacterial cell B It is a plant cell C It is an animal cell D It is either a plant or an animal cell 4. Prokaryotic cell can be differentiated from eukaryotic cell whether A the cell has ribosomes or not B the cell has a rigid cell wall or not

Biology Term 1 STPM Chapter 2 Structure of Cells and Organelles 2 103 C the cell carries out cellular metabolism or not D the cell is compartmentalised by internal membranes or not 5. Which of the following is the function of lipoprotein in cell membrane? A diffusion of water molecule and ions B selective permeability on molecules and ions C accumulation of monovalent ions inside cell D protein synthesis 6. Which of the following statements are true of plant membrane? I There are forces of electrostatic attraction between proteins and glycerol in the lipid layer II The membrane composes of hydrophillic and hydrophobic molecules III The fatty acids are unsaturated ones IV It allows phagocytosis and pinocytosis to occur V Transport of substances across it is by passive or active transport A I, II and III B III, IV and V C I, II, IV and V D I, II, III, IV and V 7. Which of the following organelle is only found in animal cells? A Large vacuole C Microtubule B Centrosome D Mitochondrion 8. Which of the following statements about chloroplast are not true? I It is not found in prokaryotic cell II It contains DNA III It is covered by a layer of membrane IV It has crista extensions A I and II B I and III C II and III D III and IV 9. Which of the following is true of the part of the chloroplast structure? Content Function A Quantasome for storage of starch B Pigment for trapping light C Granule for converting carbon dioxide to carbohydrates D Granum for carbon fixation 10. Which is the function of centrioles? A Holding together the sister chromatids of a chromosome B Organising of the microtubules to form spindle fibres C Helping in the pairing of homologous chromosomes D Breaking down of the nuclear membrane 11. What is the function of the Golgi body? A It detoxifies poison. B It synthesizes lipid C It assembles ribosomes. D It adds oligosaccharides to protein. 12. Which of the following can be abundantly found in a cell that primarily synthesises lipids? A Lysosomes B Ribosomes C Rough endoplasmic reticulum D Smooth endoplasmic reticulum 13. Human hair contains keratin that composes of high amino acid cysteine. Which bond is responsible for straightening or curling hair if treated? A Hydrophobic interaction B Disulphide bridge C Hydrogen bond D Ionic bond

Biology Term 1 STPM Chapter 2 Structure of Cells and Organelles 2 104 14. Which combination is of true of cells with extensively developed? I Liver II Pancreas III Salivary gland IV Adrenal cortex A I and II B I and IV C II and III D III and IV 15. Which combination is correct? Structure Function A Microtubule Movement of organelle B Nucleus Translation of mRNA C Rough endoplasmic reticulum Modification of lipid D Smooth endoplasmic reticulum Synthesis of protein 16. Which of the following cells has not undergone specialisation? A Sieve tube B Endodermis C Tracheid D Meristem 17. Which of the following statements about a sclerenchyma cell is true? A The mature cell exists in the region of the plant that has stopped growing in length. B The cell can retain the ability to divide and differentiate into other types of plant cells. C The cell can perform most of the metabolic functions, synthesise and store various organic products. D The mature cell has primary wall that is relatively thin and flexible, and most of the cells lack secondary cell wall. 18. Which of the following is true in xylem wall thickening? P With ring-like structure Q With spring-like structure R With step-like structure S With net-like structure T With abundant holes P Q R S T A Reticulate Annular Helical Pitted Scalariform B Helical Annular Pitted Reticulate Scalariform C Annular Helical Scalariform Reticulate Pitted D Pitted Reticulate Helical Scalariform Annular 19. Which of the following contains lignin and is stained red when treated with acidic phloroglucinol? I Collenchyma II Schlerenchyma III Sieve cell IV Tracheid A II and III B II and IV C III and IV D I, III and IV 20. A pear has a hard texture but juicy. Which cells give the characteristics? A Collenchyma and fibres B Fibres and sclereids C Parenchyma and collenchyma D Parenchyma and sclereids 21. What epithelium lines the intestinal innermost layer? A Stratified squamous B Simple squamous C Columnar D Cuboidal 22. The transitional epithelium found in the mammalian urinogenital system is for A secretion of mucus B glomerular filtration C reabsorption of water D elasticity for urinary bladder

Biology Term 1 STPM Chapter 2 Structure of Cells and Organelles 2 105 23. Which of the following is correct? Cardiac muscle Smooth muscle Striated muscle A Myogenic Syncitial control Autonomic B Syncitial Myogenic control Autonomic C Autonomic control Syncitial Myogenic D Myogenic control Autonomic Syncitial 24. Which of the following characteristics is not that of hyaline cartilage or compact bone? A To withstand compression B To bind with connective tissues C Their cells are chondroblas and osteoblas respectively D Their cells produce matrix substances 25. What is meant by resolution in microscopes? A The product of the magnifications of the eyepiece and the objective lenses B The shortest distance between two objects that can be seen separately C The size of the smallest object that can be seen D Twice the wavelength of the light used to illuminate the specimen 26. Which of the following statements is the advantage of using transmission electron microscope to study cell organelles? A It can be used to examine threedimentional structures of the organelles. B It requires a relatively simple preparation of the specimen. C It does not require a special technical skill to operate. D It has high resolution. 27. Which protein subunits are true of the cytoskeleton fibres? Microtubules Microfilaments Intermediate filaments A Fibrous Tubulin dimer Actin B Tubulin dimer Fibrous Actin C Tubulin dimer Actin Fibrous D Fibrous Actin Tubulin dimer 28. Which is not true of parenchyma cells? A Most parenchyma cells are undifferentiated and meristematic. B Photosynthesis occurs within the chloroplast of parenchyma cells of the leaf. C Parenchyma cells have thicker primary walls than those of collenchyma cells. D Most fleshy fruit tissue is composed mainly of parenchyma. 29. Which tissue function is correct? Tissue Function A Connective Lining of the body cavity B Epithelia Movement C Muscle Protection and support D Nerve Communication

Biology Term 1 STPM Chapter 2 Structure of Cells and Organelles 2 106 Structured Questions 1. The diagrams show interaction among endomembrane system in an animal cell. W Z X Y (a) Name the structures labelled W, X and Y. [3] (b) Name and state the importance of process Z. [2] (c) How does the membrane of X differ from the membrane of Y. [1] (d) What would happen if there is an excessive leakage due to a large number of structure Q in a cell? [1] 2. Three different types of plant cells X, Y and Z are shown in the diagram below. X Y Z (a) Name cell X, Y and Z. [3] (b) State one characteristic of cell Z. [1] (c) (i) Differentiate between cell X and cell Y. [2] (ii) What is the difference between the mechanical support of cell X and cell Y?[1] Essay Questions 1. Explain the structures and functions of the following: (a) cell wall, (b) cytoplasm. [15]

Biology Term 1 STPM Chapter 2 Structure of Cells and Organelles 107 2. (a) Distinguish the chromosome of a bacterium with that of a eukaryote. [4] (b) Describe the structure and functions of the Golgi apparatus with the help of a labelled diagram. [11] 3. (a) Two ultra-structures of xylem are important in transport and mechanical support. Explain. [6] (b) Describe the distribution and functions of three types of simple epithelia. [9] 4. Explain the meaning of meristem. Describe the structure, locations and functions of different types of meristem with reference to suitable examples. [15] 1 1. They are simpler and smaller cells. They contain fewer genes, unable to carry out complicated processes at the same time. They contain fewer organelles, not capable of carrying out reactions in compartments with little or no interference. They have no enveloped organelle like nucleus, mitochondria and chloroplast where specialised processes occur with high efficiency. Their cell wall is less rigid to support greater load. 2. They can be both autotrophs and heterotrophs. Autotrophs can be photoautotrophs which are capable of photosynthesis, and chemoautotrophs which are capable of chemosynthesis. Heterotrophs can be saprophytes which feed on ‘dead’ organic substances, or parasites that feed on ‘living’ organic substances. 2 1. (a) Both have cytoplasm. It is the cell body where all reactions of the cells occur. (b) Both have nucleus. It contains DNA and genes, which are required to control all cellular activities through the productions of proteins. (c) Both have plasma membrane. It is the structure that controls the exchange of substances between the cell and the environment. (d) Both have mitochondria. They are the power generators of the cell where they produce ATP as energy source for cellular activities. (e) Both have ribosomes. They are required to produce proteins especially enzymes to control cellular reactions. 3 1. Both contain DNA with genes and ribosomes, capable of independent survival like bacteria. They can divide like bacteria. Mitochondria require pyruvic and other organic acids, ADP, phosphate, NADH to produce ATP required by the cell. Chloroplasts require carbon dioxide and mineral ions to produce glucose and fatty acids for the cells. 2. Nucleus contains DNA that codes for the production of enzymes. It is the place where RNA and ribosomes are also produced. The mRNA from the nucleus is translated by the ribosomes on the rough ER to become proteins inside its cisternae. From here the proteins will be sent to the Golgi apparatus where they are packed in the form of vesicles for export out of the cell. However, if the proteins exported are hydrolases, they are required to be packed like lysosome so the hydrolases will not digest the membrane packing them. 4 1. Radioactive DNA contains 15N instead of the normal 14N. As a result, the radioactive DNA is heavier than the normal DNA. Such minor weight difference can be separated by ultra-centrifuge, which revolves 100,000 times gravitational force. ANSWERS

Biology Term 1 STPM Chapter 2 Structure of Cells and Organelles 2 108 2. There is a phase change in the light that passed through different refractive indices. Such phase difference can be neutralised or darkened by using suitable phase plate i.e. clear plastic of certain thickness and shape. 3. Electron beam has a wavelength shorter than 10 nm. The limit of resolution of a microscope is about half the wavelength of the radiation used to view the specimen. Two points shorter than 200 nm is beyond the resolution of the light microscope and therefore electron microscope is required to resolve them. 5 1. Plants have six major types of tissues i.e. meristem, parenchyma, collenchyma, sclerenchyma, xylem and phloem. Xylem is a complex tissue made up mainly of tracheid and vessel, so is phloem, made up of mainly sieve tubes and companion cells. Animals have four major types of tissues i.e. epithelial, muscular, nervous and connective tissues. Each of these four types is divided into many subtypes. 2. Plant organs consist of root, stem, leaf, flower and fruit. Each is organised from meristem like apical meristems that form the root and shoot. Special primordial outgrowths will organise to form more roots, branches, leaves, flowers and fruits. Animals have their organs formed during embryonic development and no new organ is formed thereafter. STPM Practice 2 Objective Questions 1. C 2. B 3. A 4. D 5. B 6. C 7. B 8. D 9. B 10. B 11. D 12. D 13. B 14. B 15. A 16. D 17. A 18. C 19. B 20. D 21. D 22. D 23. D 24. A 25. B 26. D 27. C 28. C 29. D Structured Questions 1. (a) W: Golgi apparatus X : Lysosome Y : Phagosome (b) (i) Autophagy (ii) To break down worn out organelle (c) The types of protein associated with the membrane. (d) Autolysis in which the whole cell will be broken down. 2. (a) X: Sclerenchyma Y: Collenchyma Z: Parenchyma (b) Thin cell wall (c) (i) Cell X is non-living whereas cell Y is living. Cell X with wall thicken evenly while cell Y with wall thickened at corners. (ii) Cell X provides mechanical support with lignified wall while cell Z provides support with non-lignified wall. Essay Questions 1. (a) • There are two types of cell wall, the primary cell wall and the secondary cell wall. • The primary cell wall is a thin layer, found on the outer layer of the secondary cell wall. • It consists of randomly arranged microfibrils of cellulose in an amorphous matrix as shown below. Microfibril Matrix • The primary cell wall is porous. It enables water to be transported apoplastically along it. • The secondary wall is made up of regularly arranged microfibrils or bigger macrofibrils. • The fibrils are arranged in layers of parallel rows, which are perpendicular to the upper or the lower layers as shown below. Macrofibrils • The matrix in the secondary wall is impregnated with lignin, forming a hard and impervious layer. • The cell wall protects the cell from physical injuries and haemolysis. • It supports the plant through cell turgidity or mechanical strength for tall woody trees. • It controls growth, limiting individual cell size and the shape of the cell through orientation of the fibrils in the wall. • It forms a system of transport pathways for water and mineral ions. Water can both be transported along the porous cell wall in

Biology Term 1 STPM Chapter 2 Structure of Cells and Organelles 2 109 apoblast or through the plasmodesmata of the symplast pathway. (b) • Cytoplasm is aqueous in nature, consisting of the ground substance and cell inclusions. • The ground substance or cytosol is the soluble part of the cytoplasm. It contains gases, mineral ions and organic substances. • The cell inclusions include the fine fibrils i.e. microtubules and microfilaments. • The microtubules are fine unbranched tubules with diameter of 25 nm, a wall of 5 nm thick and vary in length. • The microfilaments are fine filaments made of protein with a diameter of 7 nm and a length of several μm. • The cytoplasm stores vital chemicals including fats. • It is the site for certain metabolic pathways such as glycolysis, synthesis of fatty acids and amino acids. • It enables organelles to move about in it. These organelles include mitochondria, chloroplasts, ribosomes, lysosomes and vacuoles. • It forms the cytoskeleton that determines the shape of the cell. 2. (a) • The chromosome of a bacterium lies freely in the cytoplasm of the cell whereas that of eukaryote is found in the nucleus. • The chromosome of a bacterium consists of one circular DNA whereas the eukaryote consists of linear DNA. • The chromosome of the bacterium is naked, not bound to histone protein, but the eukaryote has histone bound to it. • The chromosome of a bacterium has no centromere and chromatids whereas the eukaryote has two chromatids attached at the centromere during cell division. • The chromosome of a bacterium has no more than 3500 genes whereas the larger chromosome of eukaryote has more than that number. (b) Network of tubules Inter–cisternal space Vesicle budding off and moving towards cell Cisterna Sac from ER added to the convex face • The Golgi apparatus (GA) is made up of a stack of at least three flattened sacs called cisternae. • The cisternae are kept in place by microfilaments with a thin layer of cytoplasm between one cisterna to another. • Each cisterna is covered with a layer of lipoprotein menbrane with a colloidal sol in it. • The colloidal sol within has enzymes and proteins like glycoprotein that are derived from the endoplasmic reticulum. • Besides protein, other substances such as lipids like steroid hormomes and carbohydrates such as cellulose may be found within the cisterna. • Each cisterna is formed with vesicles that keep pinching off from the endoplasmic reticulum at one side i.e. the cis side. • On the other side, i.e. the trans side, vesicles keep pinching off from the periphery of the cisterna. • Therefore, the outer trans cisterna will finally disappear completely to become vesicles. • The main function of the GA is to package secretion in the form of vesicles. • Thus, the GA packages proteins, especially enzymes, for internal transport or use within the cell. • The GA can form larger vesicles in the form of lysosomes with hydrolases. • The GA also packages secretions like digestive juice from digestive glandular cells of the stomach, pancreas and small intestine. • The GA also packages hormones, both steroid and peptide from cells of the endocrine glands e.g. Leydig cells. 3. (a) • One ultra-structure of mature xylem cells is no protoplasm but hollow lumen. • The mature vessels join end to end without cross walls to form long continuous vessels. • These hollow vessels offer no resistance to water flow from the roots into the leaves. • Another ultra-structure of the mature xylem cells is their thick lignified hard wall enabling them to support the plant. • These thick-walled vessels enable water to be transported upwards by high suction and would not collapse. • Such thick hard wall is made up of layers of cellulose fibres impregnated with lignin. (b) • Simple squamous epithelia are found in alveoli of lungs, endothelium of blood vessels and Bowman capsule of kidneys. • In the alveoli, the thin epithelia enable oxygen to diffuse into the blood capillaries and carbon dioxide to diffuse out.

Biology Term 1 STPM Chapter 2 Structure of Cells and Organelles 2 110 • Through the endothelium, oxygen and nutrients can diffuse out of the blood capillaries while carbon dioxide and urea can diffuse into them. • Simple cuboidal epithelia are found in the tubules of the nephron of kidneys. • In the proximal convoluted tubule, their plasma membrane facing the lumen is modified to form ultra-villi for reabsorption of molecules. • In the distal and collecting ducts, the epithelia form tubule to channel urine though can be affected by ADH for special water reabsorption. • Simple columnar epithelia are found in the outermost lining of the stomach and intestines. • These epithelia serve more of protection as their outer surfaces are covered with mucus. • In the small intestine, their plasma membranes have special transport proteins for absorption of digested food molecules. 4. • Meristem is a group of cells that are able to divide and continue to divide. • It consists of a group of initial cells that can divide very fast. The cell products will divide at a slower pace. • After cell division, one of the daughter cells will move away and become differentiated while the others are retained and continue to divide. • Therefore, meristem is a localised tissue and tends to move up for the bottom cells to grow as in the shoot apical meristem. • All the cells in the meristem are young and have not undergone differentiation. • The cells have isodiametric prismatic shapes. • The cell wall is thin, made up of only primary cell wall. • The nucleus is large, relative to the volume of the cell. • There is no intercellular space; the cells are compact. • The protoplasm is dense, with few organelles and the organelles are small. • Apical meristem is found at the shoot and root tips. • Its function is to produce primary tissues, such as tissues found in a herbaceous plant. • Vascular cambium is found mainly in woody stems and roots. • Its function is to produce secondary xylem (wood) and phloem. • Cork cambium (phellogen) is found on the outer layer of dicotyledonous woody stems and roots. • Its function is to produce cork cells (phellem) on the outside and secondary cortex (phelloderm) on the inside. • Intercalary cambium is only found in monocotyledons especially Gramineae. • It is a thin layer of cells above the node of the stem when it is young. Its function is to produce more cells for the internode and will later disappear.

CHAPTER MEMBRANE STRUCTURE 3 AND TRANSPORT Concept Map Membrane Structure and Transport Structure of membrane Role of each component Endocytosis Exocytosis Transport across membrane Passive transport Active transport Bulk transport Phospholipid Cholesterol Diffusion Facilitated diffusion Proteins Osmosis Carbohydrates Bilingual Keywords Facilitated – Berkemudahan Pinocytosis – Pinositosis Exocytosis – Eksositosis Diffusion – Resapan Endocytosis – Endositosis Phagocytosis – Fagositosis

112 The Structure of a Membrane Based on Singer-Nicolson Fluid Mosaic Model 1. The structure of the membrane based on Singer and Nicolson’s fluidmosaic model is shown below in Figure 3.1. Cell membrane Phospholipid bilayer Phospholipid (Phosphatidylcholine) Phospholipid bilayer Phospholipid molecule Filaments of cytoskeleton Hydrophilic head Hydrophobic tail Globular protein (integral protein) Integral membrane Cholesterol Protein chanel (Transport protein) Globular protein Glycolipid Glycoprotein Carbohydrate Cell Alpha-helix protein (Intergral protein) Hydrophilic heads Peripheral protein Figure 3.1 Fluid mosaic model of membrane 2013 3.1 Fluid Mosaic Model Students should be able to: (a) describe the structure of a membrane based on Singer-Nicolson fluid mosaic model; (b) explain the roles of each component of the membrane. Learning Outcomes VIDEO The Fluid Mosaic Model Biology Term 1 STPM Chapter 3 Membrane Structure and Transport 3

113 2. The basic structure of all membranes consists of a bimolecular phospholipid fluid layer with globular protein units embedded it forming a mosaic pattern. This is from the study of freeze drying of membrane that can be separated into two layers as shown in Figure 3.2 below. Knife Plasma membrane Cytoplasmic layer Extracellular layer Protein Figure 3.2 Lipid bimolecular layers 3. The heads of the phospholipid are hydrophilic pointing outwards into the aqueous medium on both sides of the membrane. The outside of plasma membrane is the interstitial fluid and the inside of a plasma membrane is the cytoplasm. 4. The tails of phospholipid are hydrophobic facing each other and forming a non-polar interior in the middle of the membrane. This is due to the tails having hydrophobic interactions. 5. The membrane structure is dynamic, each phospholipid molecule can move within its own monolayer by lateral movement. Therefore, both phospholipid and protein molecules can move. The lipid can flip too though less frequently. This will lead to the protein units floating around. Some protein units are immobilised by microfilament within the interior of the cell. More frequent Lateral movement Less frequent Flip-flop Figure 3.3 Movement of phospholipid molecules 6. Unsaturated fatty acids in the phospholipid tails increase the fluidity of the membrane. This is due to the trans nature of bending the tail as shown in Figure 3.4. Biology Term 1 STPM Chapter 3 Membrane Structure and Transport 3

114 Unsaturated fatty acid tails Can flow freely Fluid Saturated fatty acid tails More rigid Viscous Figure 3.4 Fluidity of membrane 7. The present and increase of the amount of cholesterol also increase the fluidity of the membrane. Cholesterol molecules with their hydrophilic heads and hydrophobic tails fit neatly within the phospholipid layer. Cholesterol controls mechanical stability, flexibility and permeability of membrane, particularly reduces leakage of small polar molecules. Cholesterol Figure 3.5 Cholesterol in animal membrane 8. Protein units are embedded in the phospholipid layer like mosaic and can move about. The protein unit can span half or the whole membrane. These are integral or intrinsic proteins, fitted neatly because of their hydrophilic and hydrophobic surfaces bind correspondingly with those of phospholipids. Different types of proteins are present. C-terminus N-terminus Extracellular side Cytoplasmic -Helix side Figure 3.6 Intrinsic or integral protein in membrane Structure of membrane based on Singer – Nicolson fluid mosaic model. 1. Phospholipid forms bilayer acting as fluid 2. Globular proteins embedded in bilayer form mosaic 3. Both phospholipid and protein molecules can move about laterally 4. Fluidity can be regulated with input of cholesterol or unsaturated fatty acid tails in phospholipid 5. Fibrous proteins on internal surface can restrict movement of membrane molecules 6. Carbohydrate molecules on external surface give stability to membrane structure Summary Biology Term 1 STPM Chapter 3 Membrane Structure and Transport 3

115 9. Extrinsic or peripheral proteins can bind to the membrane surfaces. These proteins may be in the form of globular or fibrous proteins found on both sides of the plasma membrane. 10. Carbohydrate and other molecules can also bind to the outer membrane surface. The carbohydrate molecules may be in the form of monosaccharides or oligosaccharide bonded to phospholipid or protein molecules. The Roles of Each Component of the Membrane 1. Phospholipid (a) Phospholipid layer acts as a barrier to most water-soluble substances. (b) The presence of the double bond in phospholipid tails prevents tight packing. (c) Phospholipid forms the basic bilayer for other components to bind. The molecule offers both hydrophilic head and hydrophobic tails for complementary molecular part to bind. 2018 2. Cholesterol (a) It maintains the fluidity of the membrane i.e. it prevents the membrane from becoming too rigid. (b) It stabilises the hydrophobic layer and strengthens the basic bilayer of phospholipid. (c) It prevents ions and hydrophilic molecules from passing through the membrane (i.e. ionic insulation). 2018 3. Protein (a) It acts as a carrier or channel protein for facilitated diffusion. (b) It acts as a carrier protein for active transport. 2018 (c) It is used for cell recognition or distinguishing self from nonself thus, it acts as antigen when it gets into the body of another person. (d) It acts as a receptor for hormones especially non-steroid hormones e.g. insulin. (e) It acts as a T-cell receptor for binding with antigen e.g. bacterium. This protein molecule is added to immature T-cells when the cell gets into the thymus gland. (f) It is used in cell to cell adhesion usually in the form of glycoprotein. (g) It can act as an enzyme attached to the cell membrane. An example is adenyl cyclase that catalyses the formation of cAMP from ATP. (h) It forms hydrogen bonds with water to stabilise membrane e.g. plasma membrane. (i) It can bind with cytoskeleton to maintain the shape of the cell. The roles of each component of the membrane 1. Phospholipid – barrier to watersoluble substance – double bond in its tails prevents tight packing 2. Cholesterol – maintains fluidity – strengthens membrane hydrophobic nature 3. Protein – transport water – soluble substances across membrane – receptor for binding of hormone or antibody – acts as enzyme at membrane 4. Carbohydrate – Adhesion with another cell – Stabilises membrane by forming hydrogen bonds with water Summary Biology Term 1 STPM Chapter 3 Membrane Structure and Transport 3

116 Enzyme Outside Plasma membrane Inside Receptor Outside Plasma membrane Inside Transport protein Outside Plasma membrane Inside Marker Outside Plasma membrane Inside Bind to cytoskeleton Outside Plasma membrane Inside Cell adhesion Outside Plasma membrane Inside Figure 3.7 Functions of plasma membrane proteins 4. Carbohydrate (as glycolipids or glycoprotein) (a) It acts as receptor molecules for hormones e.g. insulin or neurotransmitters e.g. acetylcholine. (b) It acts as antigens which allow cells to be recognised. (c) It is used in cell adhesion especially when cells gather to form tissue. (d) It stabilises the membrane by forming hydrogen bonds with water. 3.2 Movement of Substances across Membrane Passive Transport 1. It is a transport that does not require energy in the form of ATP. 2014 Students should be able to: (a) explain the processes of passive and active transports, endocytosis and exocytosis; (b) explain the concepts of water potential, solute potential and pressure potential; (c) calculate the water potential of a plant cell in a solution. Learning Outcomes Biology Term 1 STPM Chapter 3 Membrane Structure and Transport 3

117 2. It has the following characteristics: (a) It follows the concentration gradient i.e. from a region of high solute concentration to that of low solute concentration. (b) Net movement of solute stops when equilibrium is reached. The solute concentration on both sides of the membrane is equal. The amount of solute molecules moving in and out is the same. (c) It may or may not require a transport protein to transport solute across the membrane. (d) If a transport protein is required, it is very specific. It only transports a particular solute and no other molecule. 3. Examples are diffusion, facilitated diffusion and osmosis. Diffusion 1. Diffusion is the random movement of substances from a place of high concentration to a place of low concentration. 2. It is driven by kinetic energy and chance movement. This is because molecules are always in a state of movement according to the theory of kinetics. The chances of moving away from high concentration are greater than the opposite direction. 3. For example, glycerol will enter the cell if it has a higher concentration on the outside. The glycerol molecules are small and can easily slip through the phospholipid bilayer into the cell. 4. Another example is the diffusion of oxygen gas into the red blood cells from the alveoli in the lung while carbon dioxide diffuses the opposite way. 5. Factors affecting diffusion are: (a) The concentration gradient, the rate of diffusion is proportional to the concentration gradient. (b) The temperature, the rate of diffusion is proportional to the environmental temperature. (c) Surface area of membrane, the rate of diffusion is proportional to the surface area. Cells active in absorbing substances have microvilli to increase surface area. (d) Size of diffusing molecule, the rate of diffusion is inversely proportional to the size. The smaller the diffusion molecules, the faster the molecules can move. (e) Polarity of diffusing molecule, the rate of diffusion is inversely proportional to the degree of polarity. This refers to the diffusion of molecules across the phospholipid bilayer. The most nonpolar ones are easy to cross and vice versa. (f) Distance over which diffusion occurs, the rate of diffusion is inversely proportional to the distance travelled. The molecules need to diffuse a longer distance before reaching the membrane. Biology Term 1 STPM Chapter 3 Membrane Structure and Transport 3

118 SMALL HYDROPHOBIC MOLECULES Synthetic lipid bilayer O2 CO2 N2 benzene SMALL UNCHARGED POLAR MOLECULES H2O glycerol ethanol LARGER UNCHARGED POLAR MOLECULES amino acids glucose nucleotides IONS H+ , Na+ HCO3 – , K+ Ca2+, Cl– Mg2+ Figure 3.8 Examples of diffusion molecules Facilitated diffusion 1. Facilitated diffusion, also called carrier-mediated diffusion, is the movement of hydrophilic molecules or ions across the cell membrane via special transport proteins that are embedded within the cellular membrane. 2. The diffusing molecules must go through specific channels or bind with carrier proteins, before they are moved across the plasma membrane. 3. The molecules diffuse down concentration gradient, from high to low concentration across the membrane. 4. The direction of net movement is determined by which side of the membrane that has a higher concentration of the molecule involved. 5. The transport proteins can be saturated by molecules to be transported i.e. there is a maximum rate. If all the transport proteins involved are in use, increase in the concentration of the molecule does not increase in the rate of the molecule movement. 6. Finally, it will reach equilibrium when the concentration of molecules is the same on both sides of the membrane. Then, there is no net movement. 7. An example is the movement of sodium ions into the nerve cell or potassium ions out of the cell when there is no impulse. Exam Tips Remember the molecules that can pass directly through the plasma membrane. (STPM 2013) Biology Term 1 STPM Chapter 3 Membrane Structure and Transport 3

119 8. Another example is glucose diffusing into and out of the red blood cells. It requires channel proteins as glucose is hydrophilic, insoluble in lipids and too big to diffuse across the phospholipid layer. This facilitated diffusion enables the red blood cell to maintain its shape even if there are changes in glucose concentration in the plasma. 9. The mechanism involved is as shown in Figure 3.9. Protein channel Extracellular space Intracellular space Carrier protein Cell membrane Figure.3.9 Mechanism of facilitated transport Osmosis 1. Osmosis is the movement of water from a region of high water potential (ψ) to a region of low water potential through a partially permeable membrane. For example, when a cell is immersed in water; water will enter by osmosis. Pure water has a water potential equal to zero (ψ = 0) and sugar solution has water potential of negative value. 2. When a cell is immersed in a solution of low solute potential like concentrated sugar solution, osmosis will also take place. Water will move out of the cell causing the cell to shrink or plasmolyse in the case of plant cells. 3. Osmosis takes place due to the diffusion of water through the phospholipid layer and water channels called aquaporin of the partially permeable membrane. These aquaporin are found in most plant and animal plasma membranes. 4. The fine pores prevent the diffusion of larger sugar molecules; thus the membrane creates a concentration gradient for the water molecules to diffuse following the gradient. 5. As long as there is a concentration gradient, there will be a net flow of water. ψ Cell wall Sugar molecule Water ψp ψs0 ⇑ ⇓ ⇐ ⇒ Figure 3.10 Mechanism of osmosis Passive transport No ATP is required, follows concentration gradient, no net movement at equilibrium and affected by temperature. (a) Diffusion – for gases and lipid soluble substances (b) Facilitated diffusion – through protein channels for specific small water soluble substances (c) Osmosis – for water depending on water potential gradient Summary Biology Term 1 STPM Chapter 3 Membrane Structure and Transport 3

120 6. Osmosis will finally stop when equilibrium is reached, that is when the water potential on both sides of the membrane is the same. 7. In plant cells, as the water enters the cell, there is a turgor pressure exerted on the wall called pressure potential (ψp ) resisting the entry of water. 8. Finally, an equilibrium is reached when the water potential on the outside of the cell is the same as the inside of the cell. Active Transport 1. Active transport is the transport of substances across membranes against the concentration gradient which requires ATP. 2. A carrier protein is required in active transport. This is an intrinsic or integral protein spanning across the membrane. 3. Each type of carrier protein is specific for one type of substance. However, some carrier protein may transport more than one type of substance. 4. It goes against the concentration gradient i.e. although there are a lot of substances inside the cell, more can still be taken in. 5. The carrier protein has a receptor site and the substance binds to it from one side of the membrane. 6. A molecule of ATP is required to change the shape of the carrier protein and the substance is released on the other side of the membrane. 7. Factors that increase the production of ATP increase the rate of active transport. For examples, increase in temperature and oxygen concentration increases the transport rate. 8. Cells that have more mitochondria can carry out faster rates of transport as more ATP can be produced. 9. Cells with more surface area especially those cells with microvilli can have higher rates of active transport. 10. Any respiratory inhibitors like cyanide can stop the active transport as the production of ATP is stopped. 11. Examples of active transport are as follows: (a) Mineral ions are actively absorbed into the root hair cells or young epidermal cells of the root. (b) Digested food substances like glucose is actively taken into the epithelial cells of the small intestine. This is with the help of the proton pump. (c) Sodium-potassium pump maintains a potential difference between the inside and the outside of nerve cells. Biology Term 1 STPM Chapter 3 Membrane Structure and Transport 3

121 12. (a) A carrier protein that takes in mineral ions in the membrane of the root epidermis is as shown in Figure 3.11. (i) ATP binds to the carrier protein. (ii) The carrier protein is ‘energised’ with the binding of phosphate. This allows an ion to bind to the receptor site of the carrier protein. (iii) Then, the carrier protein changes its conformation. The ion is brought to the inner side of the membrane. (iv) The ion and phosphate are released with the carrier protein reverting to its original conformation. (v) Another ion is bound to the carrier protein and the process is repeated. (vi) The ion only moves in one direction and against concentration gradient. (b) The mechanism of sodium-potassium pump is as shown in Figure 3.12. Outside (low ion) Inside ATP ADP (i) ATP binds to carrier protein (ii) Carrier protein is phosphorylated. Ion binds to the protein. (v) The carrier protein reverts to original shape (iv) Ion and phosphate are realeased (iii) The carrier protein changes its shape Membrane P P P P P A Figure 3.11 Active transport using channel protein ATP Na+ ions Na+ ions are released (i) 3 Na+ ions bind to transport protein (ii) ATP binds to transport protein and phosphorylates it (iii) Transport protein changes shape (iv) 2 K+ (vi) K (v) Phosphate leaves transport protein ions bind from outside + ions are released inside Outside Inside Membrane P P P A ADP is released P P P A P P P K+ ions Figure 3.12 Special active transport–sodium–potassium pump Active transport 1. ATP is required to transport hydrophilic substances against concentration gradient 2. Carrier protein required for each type of substance 3. Factors increasing ATP production increases the rate e.g. O2 concentration 4. Inhibitors of respiration decreases the rate 5. ATP is required to change the shape of carrier for substance to cross Summary Biology Term 1 STPM Chapter 3 Membrane Structure and Transport 3

122 Endocytosis 1. Endocytosis is the uptake of substances by cell in mass or in bulk in the form of vesicles. 2. Endocytosis can be divided into two types i.e. phagocytosis and pinocytosis. Phagocytosis 1. Phagocytosis is what we call cell ‘eating’ in which solid particles such as bacteria are taken in by a cell like a white blood cell. Such white blood cells are called phagocytes. The process happens in amoeba to take in food as shown in Figure 3.13. Pseudopodia Entrapment Lysosomes containing digestive enzymes Engulfment Food Food vacuole Digestion Absorption Food is digested by hydrolase Lysosome fuse with food vacuole Food is absorbed Lysosome Figure 3.13 Phagocytosis (a) Folds of the plasma membrane extend outward and enclose the particle to be ingested and form a vacuole around it as shown in Figure 3.13. (b) The vacuole then frees itself from the membrane and moves into the cytoplasm, forming a food vacuole or phagosome. (c) Then, lysosome fuses with the vacuole or phagosome and releases hydrolases into it. (d) When the content is digested, the products are absorbed and the vacuole disappears. 2. Any undigested content in the vacuole will be egested through the reverse of the process. 3. Bacteria that are bound by antibodies are easily engulfed by phogocytes because the antibody molecules act as markers. The phagocytes have receptors corresponding to these markers, they bind to them and then engulf them. The process of marking by antibody is called opsonisation. Pinocytosis 1. Pinocytosis is what we refer to as cell ‘drinking’ in which liquid and dissolved substances are taken into the cell in the form of vesicles. The process is as shown in Figure 3.14. Biology Term 1 STPM Chapter 3 Membrane Structure and Transport 3

123 Outside cell Inside cell Figure 3.14 Pinocytosis 3. It is the same process as phagocytosis except that no solid particles are involved. 4. Tiny droplets of fluid are trapped by microvilli. They are then pinched off from the cytoplasm as vesicles with fluid containing oil droplets occuring in the epithelial cell of small intestine. 5. The vesicles may be digested and absorbed or moved across the cell to the opposite side where the content is released. 6. In the small intestine, it is known as micropinocytosis for the uptake of fat droplets. 7. Pinocytosis occurs in other cells which include the liver cells, the cells in the proximal convoluted tubule of nephron and the white blood cells. Exocytosis 1. Exocytosis is the reverse of endocytosis in which the cell egests or cell secretes substances. 2. Mechanism of exocytosis is shown in Figure 3.15. Exam Tips Remember the definitions of passive transport, diffusion, facilitated diffusion, osmosis, water potential, active transport, endocytosis including phagocytosis and pinocytosis, and exocytosis. Memorise the mechanisms or processes involved and the examples of the above. (STPM 2008 structured question on diffusion) Bulk transport Phagocytosis (solid in) Cell egestion (solid out) Pinocytosis (fluid in) Reverse pinocestosis (secretion out) Endocytosis (large/many substances in) Exocytosis (large/many substance out) Summary Outside cell Inside cell Figure 3.15 Exocytosis (a) A vacuole with waste products or a vesicle from Golgi complex moves towards plasma membrane, binds and fuses with it. (b) The vacuole or vesicle opens up and empties its content. Its membrane becomes part of the plasma membrane. The content is discharged out of the cell. Biology Term 1 STPM Chapter 3 Membrane Structure and Transport 3

124 3. Examples of exocytosis are as follows: (a) Cell egestion. This happens in the amoeba or the white blood cell in which undigested solids from phagocytosis is egested. (b) Cell secretion or reverse pinocytosis. This happens in the glandular cells such as cells in the thyroid glands that secrete hormones or cells in the tubular glands in large intestines that secrete mucus. Quick Check 3 1. What are the differences between the following pairs of processes? (a) Passive and active transports (b) Diffusion and osmosis (c) Facilitated diffusion and sodium-potassium pump (d) Exocytosis and endocytosis The Concepts of Water Potential, Solute Potential and Pressure Potential Water potential (ψ) 1. Water potential is a concept that helps to describe the tendency of water to move from one area to another, particularly into or out of cells. 2. It is the potential energy of water in a solution or a cell compared with pure water under the same conditions. Therefore, water potential of pure water is zero. 3. It is measured in units of pressure i.e. in kPa, MPa and bar. 4. Water potential determines the rate and direction of osmosis when a cell is immersed in a solution. Water moves from a higher (less negative) water potential to a lower (more negative) water potential. 5. The movement of water depends on the difference in water potential between two systems e.g. two adjacent cells, or a cell and the surrounding solution. This difference is called the water potential gradient. Water will always move down the water potential gradient. 6. A cell with a more negative water potential will draw in water but this depends on other factors as well such as solute potential (pressure in the cell e.g. solute molecules) and pressure potential (external pressure e.g. cell wall). 2015 Biology Term 1 STPM Chapter 3 Membrane Structure and Transport 3

125 7. For example, if red blood cells are dropped into solutions of different water potentials, water will move out of the cells in hypertonic solution; in and out in isotonic solution and into the cell in hypotonic solution as shown in Figure 3.16. Hypertonic Isotonic Hypotonic H2O H2O H2O H2O Hypertonic Isotonic Hypotonic H2O H2O H2O H2O Figure 3.16 Movement of water out or into cells Solute potential 1. Solute potential (ψs ) is the component of water potential due to solutes. Water potential becomes negative when solute is added to water. This is because, solute molecules reduce the movement to water molecules thus further reduce the energy of water molecules. 2. Solute (osmotic) potential (ψs )= –iCRT i = The number of particles the molecule will make in water; for sucrose or glucose, this number is 1; for NaCl this would be 2 C = Molar concentration R = Pressure constant = 0.0831 liter bar/mole K T = Temperature in degrees Kelvin (273 + °C) of solution 3. For example, the molar concentration of a sugar solution in an open beaker has been determined to be 0.3 M. The solute potential at 27°C degrees can be calculated. 4. Solute potential = -iCRT = -(1) (0.3 mole/1) (0.0831 liter bar/mole K) (300 K) = -7.48 bars 5. Therefore, water potential of the solution = -7.48 + 0 = -7.48 = -0.748 MPa 1 atmosphere (atm) = 0.101 MPa ; 1 MPa = 9.90 atm 1 bar = 0.1 MPa ; 1 MPa = 10 bars Concepts of 1. Water potential (ψ) – tendency of water to move in or out of cell due to solutes = zero for pure water 2. Solute potential (ψs ) – water potential due to solutes = negative when solutes added to water 3. Pressure potential (ψp) – pressure other than atmosphere exerted on water e.g. plant cell wall = positive when plant cell becomes turgid Summary 2015 Biology Term 1 STPM Chapter 3 Membrane Structure and Transport 3

126 Pressure potential (ψp ) 1. Pressure potential (ψp ) of a solution is the component of water potential due to pressure exerted on it other than the atmosphere. 2. Pressure increases the movement of the water molecules thus increases their energy and the water potential. Therefore, pressure potential can be positive or negative when a solution is subjected to increased pressure in a syringe or suction pressure respectively. 3. Changes in pressure potential will result in the change of water potential as shown in Figure 3.17. 0.2 M solution Pure water fiP = 0 fiS = –0.46 ––––––––– fi = –0.46 MPa fi = 0 MPa H2O Positive pressure fiP = 0.46 fiS = –0.46 ––––––––– fi = 0 MPa fi = 0 MPa Positive pressure H2O fiP = 0.50 fiS = –0.46 ––––––––– fi = 0.14 MPa fi = 0 MPa Negative pressure H2O fiP = –0.50 fiS = 0 ––––––––– fi = –0.50 MPa fiP = 0 fiS = –0.46 ––––––––– fi = –0.46 MPa Figure 3.17 Changes in pressure potential changes the water potential 4. Pressure potential of a plant cell is always positive as turgor pressure acts inwards to counteract the solute potential of the cell. This is so after the cell absorbs water by osmosis when immersed in water and becoming turgid. Water potential of a plant cell in a solution 1. Water potential of a plant cell depends on the amount of solutes, the water content and the wall pressure or turgor pressure when the cell is turgid. ψ = ψs + ψp 2. When the cell is not immersed in a solution, the pressure potential is zero. Therefore, water potential of the cell is same as the solute potential. ψ = ψs + ψp If ψp = 0, ψ = ψs 2013 Biology Term 1 STPM Chapter 3 Membrane Structure and Transport 3

127 3. If a cell of –3 units of water potential is put into distilled water, the water potential of the cell is equal to zero after some time as shown in Figure 3.18. Calculation of water potential of plant cell in solution 1. ψ = ψs + ψp 2. ψ of plant cells changes that of solution after some time of immersion 3. No net flow of water if immersed into solution of same ψ. 4. Gain of water and ψp if immersed in solution of higher ψ. 5. Loss of water + ψp if immersed in solution of lower ψ. Summary Distilled water Cell wall Cell wall Distilled water ψP = 0 +ψS = 0 ψ = 0 Plant cell immediately after being put into distilled water ψP = 0 +ψS = –3 ψ = –3 Plant cell after being in distilled water for some time ψP = +3 +ψS = –3 ψ = 0 Figure 3.18 Water potential of plant cell changed in water 4. If potato cell has –820 kPa of solute potential and pressure potential or turgor pressure of 500 kPa, then its water potential is ψ = –820 + 500 = –320 kPa. If the cell is put into distilled water, water will enter by osmosis and will finally have water potential of zero. The cell will have 320 kPa increase in wall pressure equal to +820 kPa. It is assumed that there is no exchange of solute molecule between the two sides of the membrane. 5. If it is put into a sugar solution with solute potential of –320 kPa same as that within the cell, osmosis will not take place. The cell is also known to be in insipient plasmolysis. Insipient plasmolysis can also mean when 50% of the cells in a tissue are plasmolysed. 6. If it is put into a sugar solution with solute potential of –150 kPa, the difference between the inside and outside of the cell is –820 – (–150) + 500 = –820 + 650 = –170 kPa. Water will move inside to generate a wall pressure of another 170 kPa to become 670 kPa. Finally, the water potential of the potato cells is equal to –150 kPa, the same as that on the outside. 7. If it is put into a sugar solution with solute potential of –1,000 kPa, the difference between the inside and outside of the cell is –820 – (–1000) + 500 = –820 + 1,000 + 500 = 680 kPa. Water will move outside and plasmolysis will occur i.e. 680 kPa of wall pressure is deducted from the cell. Finally, the water potential of the cell is –1000 kPa, the same as that on the outside. Biology Term 1 STPM Chapter 3 Membrane Structure and Transport 3

128 Objective Questions 1. Which can diffuse across the plasma membrane? I Lipid III Glucose II Water IV Hydrogen ions A I and II C II and IV B I and III D III and IV 2. What will happen to an animal cell if it is placed in distilled water? A The cell will undergo crenation B The cell will undergo plasmolysis C The cell will undergo lysis D The cell will remain unchanged 3. The diagram below shows the sequence of movement of a molecule across membrane. Outside Molecules Inside The movement of the molecules is called A diffusion B facilitated diffusion C pinocytosis D phagocytosis 4. Which characteristic determines why plasma membrane structure is referred as fluid mosaic model? I The phospholipids move freely within the plane. II The membrane proteins that are scattered in the phospholipid bilayer move laterally. III The presence of cholesterol within the membrane. IV The position of glycoproteins and glycolipids in the outer layer of plasma membrane. A I and III B I and IV C II and III D II and IV 5. The diagram shows a section of a plasma membrane. P Q R What is the correct function for each of the structures labelled? Regulates membrane fluidity Forms hydrogen bonds with water to stabilise membrane Transports ions and polar molecules A B C D P P Q R R Q R P Q R P Q 6. The diagram shows two kinds of molecules found in cell surface membranes. Which part affects the fluidity of the membrane? A D B C STPM PRACTICE 3 Biology Term 1 STPM Chapter 3 Membrane Structure and Transport 3

129 7. Which molecule prevents the cell surface membrane from becoming too fluid or too rigid? A Phospholipid C Glycoprotein B Glycolipid D Cholesterol 8. Which pair of factors is proportional to the rate of diffusion? A Concentration gradient and size of diffusing molecule B Distance over which diffusion occurs and surface area over which diffusion occurs C Size of diffusing molecule and distance over which diffusion occurs D Surface area over which diffusion occurs and concentration gradient 9. What are the features of facilitated diffusion? Uses protein channels in membrane Uses ATP Molecules move down a concentration gradient A ✗ ✓ ✗ B ✗ ✗ ✓ C ✓ ✗ ✓ D ✓ ✓ ✗ 10. Which statement is true of active transport? A Movement of large molecules through the cell surface membrane into the cytoplasm of a cell. B Movement of molecules or ions from where they are in a low concentration to a higher concentration. C Movement of molecules or ions from where they are in a high concentration to a lower concentration. D Net movement of water molecules across a partially permeable membrane from a region of higher water potential to one of lower water potential. 11. Which structures are present in large numbers at sites of active transport? A Golgi bodies B Lysosomes C Mitochondria D Rough endoplasmic reticulum 12. The osmotic potential of a plant cell sap is –1000 kPa, which direction of net movement of water in each of the X and Y cells below is correct? Cell X ψp = 400 kPa ψs = –300 kPa Cell Y ψp = 400 kPa ψs = –1 200 kPa Cell X Cell Y A At ψ = –300 kPa, water moves into the cell. At ψ = 600 kPa, water moves out of the cell. B At ψ = 100 kPa, water moves out of the cell. At ψ = –800 kPa, water moves out of the cell. C At ψ =–300 kPa, water moves out of the cell. At ψ = 600 kPa, water moves into the cell. D At ψ = 100 kPa, water moves into the cell. At ψ = –800 kPa, water moves into the cell. 13. Which process allows the movement of molecules that are too large to pass in through a plasma membrane? A Active transport B Facilitated diffusion C Endocytosis D Exocytosis 14. When cylinders of potato tissue were immersed in a 0.35 mol dm–3 sucrose solution, they showed no change in mass. What will happen when the cylinders are immersed in a 0.1 mol dm–3 sucrose solution? A The pressure potential of the cells will become more positive. B The solute potential of the cell will become more negative. C The water potential of the cells will become more negative. D The water potential of the solution will become less negative. Biology Term 1 STPM Chapter 3 Membrane Structure and Transport 3

130 15. A turgid plant tissue is placed in a solution which has the same solute potential as the contents of the cell. Which equation describes the value of the pressure potential for this cell? A Pressure potential = solute potential of the cell B Pressure potential = solute potential of the external solution C Pressure potential = water potential of the cell D Pressure potential = zero 16. Name the type of transporting molecules across membrane is against concentration gradient. A Facilitated diffusion B Passive transport C Active transport D Diffusion Structured Questions 1. The figure below shows a diagram of a plasma membrane. K L M N (a) State the thickness of the membrane. [1] (b) Outline the functions of K, L, M and N. [4] (c) Some substances may cross plasma membranes by simple diffusion. Glucose, however, does not. Explain why glucose cannot pass across membranes by simple diffusion. [2] (d) State three ways how active transport differs form facilitated diffusion. [3] 2. The following equation shows the relationship between water potential and solute potential and pressure potential in a plant cell. Water potential = Solute potential + Pressure potential The table below shows the data obtained in the study of direction of water movement in plant cells. Slices of potatoes are immersed for 50 minutes in sucrose solutions of different molarities at 25o C. Molarity of sucrose solution/ (dm3 ) Solute potential of sucrose solution/ (MPa) Pressure potential of sucrose solution/ (MPa) Percentage of change in mass of potatoe (%) 0.20 M –0.48 0 + 6.6 0.30 M –0.76 0 0 0.40 M –0.95 0 –3.8 Biology Term 1 STPM Chapter 3 Membrane Structure and Transport 3

131 (a) What is water potential? [1] (b) (i) Why is the pressure potential shown in the table for the sucrose solutions 0 MPa? [1] (c) (i) Explain the direction of water movement in potato cells which are immersed in 0.20 M sucrose solution. [2] (ii) Calculate the pressure potential of potato cells in 0.20 M sucrose solution if at equilibrium. [1] (iii) What conclusion could be made regarding the condition of the potato cells in (c)(ii)? [1] (d) State the condition of the potato cells when they are immersed for 50 minutes in the 0.50 M sucrose solution. [1] Essay Questions 1. (a) Describe how lipid components of the plasma membrane influence the membrane fluidity. [9] (b) Explain the categories of proteins with specific functions. [6] 2. (a) Discuss the importance of selective permeability in plasma membrane. [9] (b) The electron microscope and paper chromatography technique contribute greatly to the study of the structure of organelle and its contents. Explain. [6] 1 1. (a) No energy in the form of ATP is required for passive transport whereas ATP is required for active transport. Passive transport may or may not require transport protein whereas active transport requires the protein. Passive transport follows concentration gradient and later become equilibrium whereas active transport goes against concentration gradient and simply stops if there is nothing to transport. (b) Diffusion refers to any substance whereas osmosis refers to water, seldom other solvent. Diffusion needs not go through membrane whereas osmosis is the movement of water through a partially permeable membrane. (c) Facilitated diffusion is a passive transport involved any substance whereas sodiumpotassium pump is an active transport involved in pumping Na+ out and K+ in. Facilitated transport requires no ATP and follows concentration gradient whereas sodium-potassium pump requires ATP and goes against concentration gradient. (d) Exocytosis is egestion or secretion involves bulk export from cell whereas endocytosis is phagocytosis or pinocytosis involves bulk intake from outside the cell. One is the opposite of the other. STPM Practice 3 Objective Questions 1. A 2. C 3. B 4. D 5. C 6. B 7. D 8. D 9. C 10. B 11. C 12. C 13. C 14. A 15. D 16. C Structure Questions 1. (a) 7 – 8 nm (b) K permits movement of water soluble substances to cross / facilitated diffusion or active transport L is for cell recognition / cell adhesion / acts as receptor ANSWERS Biology Term 1 STPM Chapter 3 Membrane Structure and Transport 3

132 M acts as barrier to ions and water soluble substances N regulates fluidity (c) Glucose is a large molecule. Glucose is water soluble (d) Active transport requires ATP / energy, facilitated diffusion does not. Active transport is against concentration gradient, facilitated diffusion follows concentration gradient. Active transport rate is affected by oxygen concentration, facilitated diffusion is not. 2. (a) Water potential is the tendency of water to move from one area to another, particular into or out of cells. (b) (i) This is due to no pressure exerted on it. (ii) Water potential of potato cells = external molarity of sucrose solution when there is no change in mass of potatoes after immersed for 50 minutes = –0.48 MPa (c) (i) The net water movement is into the potato cell. This is due to water potential outside the cell (0.20 M) is more than the inside (0.30 M). (ii) Water potential = solute potential + pressure potential At equilibrium = water potential = 0 0 = –0.48 /MPa + Pressure potential Pressure potential = 0.48/ MPa + Pressure potential = 0.48 MPa (iii) The cells are turgid. (d) The cells are flaccid. Essay Questions 1. (a) • The main lipid component in the plasma membrane that determines the fluidity is the phospholipid. • The phospholipid consists mainly of lecithin or phosphatidylcholine, a derivative of phosphatidic acid. • Each lecithin molecule consists of a hydrophilic head and two hydrophobic tails of fatty acids with glycerol molecule as central support. • The phospholipid molecules are arranged in bilayers in the membrane with the tails of one layer facing the tails of the other layer. • Fluidity of the plasma membrane is determined by the length of the fatty acid usually of 18C and shorter would be more fluid. • The saturation of the fatty acid would cause the tail to be more compact so less fluidity. • The tails is more unsaturated which means the tails are bent or open giving more movement and fluidity. • Another lipid component that makes the membrane more fluid is cholesterol that is also amphipathic but with four hydrocarbon rings. • More cholesterol is found within the phospholipid layers. Hence, the lipid molecules is easier to move about giving rise to more fluidity. (b) • Transport proteins; for facilitated diffusion and active transport. • Enzyme; act as a catalyst. • Receptor; for binding with hormones especially non-steroid hormones. • Adhesion; for adhesion especially during the formation of tissues in the embryonic stages. • T-cell receptor; binding with antigen. This protein molecule is added to immature T-cells when the cell gets into the thymus gland. 2. (a) • This allows small, non-polar molecules especially gases such as O2 and CO2 to diffuse across the membrane. • CO2 and O2 will diffuse down the concentration gradient. • This enables aerobic respiration and waste gas such as CO2 to leave the cell. • The diffusion of water in and out depends on the osmotic gradient. • Ions are not allowed to diffuse across the membrane to interfere cellular activities. • Only when the membrane with specific channel or carrier proteins will allow specific ions to diffuse across the membrane. • Red blood cells with specific channel proteins for glucose intake allow glucose to diffuse across the membrane of red blood cells as well as maintaining their shape. • Neurones with specific transport proteins enable the polarisation of cells and impulses to be transmitted. • Kidney tubular cells with specific carrier protein enable substances to be transported against the concentration gradient. • Phagocytic white blood cells are able to carry out phagocytosis due to the selective permeable nature of the plasma membrane. (b) • Electron microscope contributes to the study of organelles such that single, double or no membrane can be detected. • It can detect the shape and the orientation of the membrane such as in the chloroplast. • Besides thin membrane, electron microscope also can detect the presence of small particles such as ribosomes or stalked particles in mitochondria. • Paper chromatography enables the detection of polar biochemical in the organelles. • An example is the detection of specific amino acids from different organelles. • Another example is to find out the different types and the concentrations of the photosynthetic pigments in the chloroplasts of different plants. Biology Term 1 STPM Chapter 3 Membrane Structure and Transport 3

CHAPTER ENZYMES 4 Concept Map Enzymes Catalysis and activation energy Mechanism of action and kinetics Enzyme structure Mode of action of enzymes Induced fit model (Koshland) Roles and importance Effects of competitive and noncompetitive inhibitors International Union of Biochemistry (IUB) Absorption, entrapment and covalent coupling Lock and key model (Fischer) Significance of KM and Vmax Time course of an enzyme – catalysed reaction Factors affecting the rate of reaction Cofactors Inhibitors Classification of enzymes Enzyme technology according to Bilingual Keywords Enzyme – Enzim Catalyst – Mangkin Allosteric – Alosterik Classification – Pengelasan Oxidoreductase – Oksidoreduktase Phosphorylase – Fosforilase Reversible – Berbalik Cofactor – Kofaktor Lock and key – Kunci dan mangga Concentration – Kepekatan Activator – Pengaktif Inhibitor – Perencat Competitive – Persaingan Immobilisation – Pentakmobilan

134 Structure of Enzyme 1. Enzymes are protein catalysts that speed up metabolic reactions. For most organisms, enzymes have an optimal temperature of 37°C to carry out reactions at maximum velocity. 2. Enzymes are globular proteins with precise three-dimensional shapes formed from primary, secondary and tertiary structures. Few enzymes even have quaternary structures. 3. All enzymes have hydrophilic side chains (R groups) on the outside of the molecules. So, they are all soluble in water. 4. Each enzyme molecule has an active site, which can bind with one or more substrate molecules. The active site is a cleft on the surface or located deeper within. 5. The active site is very specific for each type of enzyme. It can only be bound by a certain substrate. For example, amylase can only attach to a polysaccharide with α –1,4-glycosidic bond. 6. The active site has specific shape due to the side chains of amino acids. Only substrate molecules with complementary shapes can bind to it. This would interact with substrates to bring about their conversion to products. 7. The active site is formed from 3-12 side chains of the amino acids in their primary structure as shown in Figure 4.1. Primary structure: Side chains that form active site Active site Allosteric site Hydrophobic side chain inside Hydrophilic side chain outside Figure 4.1 A three-dimensional shape of enzyme with an active site and a ribbon model of lysozyme Remember the definition of enzymes. Exam Tips Structure of enzyme 1. Enzyme is a globular protein. 2. It is soluble in water. 3. Its surface is covered with hydrophilic side chains. 4. It has an active site for substrate to bind. 5. The active site is complementary to the shape of substrate. 6. The active site is determined by side chains of amino acids. 7. Some enzymes have allosteric or control site. Summary 4.1 Catalysis and Activation Students should be able to: Energy (a) explain that enzyme is a globular protein which catalyses a metabolic reaction; (b) explain the mode of action of enzymes at active sites involving enzyme-substrate complex and lowering of the activation energy and enzyme specificity. Learning Outcomes Biology Term 1 STPM Chapter 4 Enzymes 4

135 8. Some enzymes may also have allosteric sites. Such sites when attached with certain chemicals; either speed up the reaction or slow it down. 9. The allosteric site is similar to the active site, very specific, with shape that can only bind with certain chemicals. For example, phosphorylase (enzyme that breaks down glycogen) has allosteric site. It is activated by AMP but inhibited by ATP when bound to the allosteric site. Mode of Action of Enzyme 1. Enzymes like other inorganic catalysts lower the activation energy. Activation energy is the minimal energy required for a reactant or substrate to start a reaction. It is also true in the case when more than one substrate is involved. 2. Enzyme lowers the activation energy by having an active site with side chains that bind with the substrate to form an enzyme-substrate complex. 3. For example, catalase catalyses the breakdown of hydrogen peroxide to form water, oxygen and energy is also given out. The mechanism is as shown in the Figure 4.2. Progress of reaction Free energy Overall change in energy (the same in both cases) Catalysed reaction Ea of catalysed reaction (lower) Ea of uncatalysed reaction (higher) Uncatalysed reaction Initial state intermediate state final state (substrate) (enzyme-substrate complex) (product) H2 O2 H2 O + O2 + energy Hydrogen peroxide water oxygen Figure 4.2 Comparison of uncatalysed and catalysed reactions 4. Enzyme weakens the bonds within a substrate, causing it to rearrange or break up to form one or more substances called products. Literally, the enzyme may exert a force that helps to change the substrate to product. For example, a hydrophobic active site may force a change in a hydrophilic substrate or vice versa. 5. Enzyme brings two reacting molecules closer and starts a reaction. Two reacting molecules are bound in the active site of an enzyme and the enzyme breaks certain bonds of one molecule and rejoins them to form one product or two different products. This literally pulls two substrates together rather than waiting for them to collide. Exam Tips Remember the meaning of catalysis and how enzyme lowers the activation energy. (STPM 2010 structured question) Mode of action of enzyme. Enzyme lowers the activation energy of reaction by 1. Forming enzymesubstrate complex 2. Weakening bonds of substrate 3. Forming new bonds in substrate molecule 4. Bringing two substrate molecules close together 5. Orientating two substrate molecules to react 6. Providing correct environment for reaction to occur Summary 2015 Biology Term 1 STPM Chapter 4 Enzymes 4

136 6. Enzyme orientates substrates and helps in the progress of the reaction. Two reacting substrates are made to face each other in such a way that favours the reaction to start. 7. The active site of an enzyme provides a special microenvironment favouring a particular reaction. This is especially so in the case of certain side chains of amino acids that helps to donate or remove hydrogen ions. 8. Enzyme is very specific in action and only binds with certain substrates. This is due to the active site's three dimensional shape. The shape is complementary to the shape of the substrate molecule. Glucokinase is very specific only binds with glucose whereas hexosekinase can bind with any hexose. 4.2 Mechanism of Action and Kinetics Lock and Key Model (Fischer) and Induced Fit Model (Koshland) Lock and key model (Fischer 1890) 1. The ‘lock and key’ model assumes that the substrate is a smaller molecule and fits into the active site of the enzyme like a key fits into a padlock. This implies that the fitting is rigid. This also accounts why enzyme is specific; only certain substrate molecule with complementary shape can fit into the active site. 2. The model is as shown in Figure 4.3. + Enzyme Substrate Enzyme – substrate complex Enzyme Products + or + Enzyme Substrate Enzyme – substrate complex Enzyme Products + Enzyme – products complex Figure 4.3 An enzyme in action Students should be able to: (a) illustrate enzyme specificity using induced fit (Koshland) and lock and key (Fischer) models; (b) explain the time course of an enzyme catalysed reaction by measuring the rate of formation of product(s) or rate of disappearance of substrate(s) as the rate of reaction; (c) deduce the MichaelisMenten constant (KM) from the Michaelis-Menten and Lineweaver- Burk plots; (d) explain the significance of KM and Vmax; (e) explain the effects of temperature, pH, enzyme concentration and substrate concentration on the rate of an enzymecatalysed reaction. Learning Outcomes Biology Term 1 STPM Chapter 4 Enzymes 4

137 3. The substrate binds to the active site forming enzyme –substrate complex. The reaction is reversible. Then, the substrate within the active site is changed to form the product that no longer fits the active site. The product is released from the enzyme. Thus, the enzyme is free to bind with another substrate molecule. 4. The shape or the conformation of the enzyme determines the reaction rate. Any part of the enzyme if changed can distort the active site and it would not allow the substrate to fit into it anymore. This is because the active site is an integral part of the enzyme molecule. 5. Since enzyme is a globular protein, its mechanism of action and function are affected by environmental factors like temperature, pH and chemicals. This is because globular protein is denatured by heat, extreme pH, heavy metallic ions and organic solvents. The tertiary structure of the protein is affected including the active site. 6. The reaction does not destroy the enzyme. Continual use of the enzyme at optimum temperature for too long may affect its activity. This leads to the cell protein removal system to remove the enzyme. When there is no substrate in the vicinity, enzyme may be similarly removed. Induced fit model (Koshland 1959) 1. An alternative model suggested by Koshland (1959) is the induced fit model. In this model, the active site of the enzyme is larger, specific, not rigid but quite loose. 2. The substrate still binds to the active site complementarily. Only when the active site is bound with a substrate molecule then the enzyme molecule moulds around the substrate and causing it to stress. 3. Bonds especially hydrogen bonds are formed between the substrate and enzyme to form the product. Other bonds especially within the substrate molecules are broken caused by the enzyme. 4. Substrate is converted into product, the product no longer fits the active site and has to leave. The enzyme molecule can than be reused. 5. This model explains that the enzyme are more active by forming and breaking weak bonds of substrates to form product. Time Course of Enzyme-Catalysed Reaction 1. The rate of enzyme catalysed reaction is usually taken as the initial velocity. This is the velocity at the beginning of the reaction when a certain amount of enzyme is added to a fixed amount of substrate. 2. At the start of the reaction, the active sites of the enzyme are available for the substrate to bind to the enzyme molecule with the velocity depending on the affinity of the enzyme and concentration of both enzyme and substrate. Lock and key model (a) Substrate is smaller (b) Enzyme is bigger with rigid active site (c) Substrate fits into the active site complementarily (d) Enzyme – substrate complex is formed reversibly (e) Substrate is converted into product (f) The product cannot fit the active site and then is released Summary Induced fit model (a) Active site is larger but still specific (b) Substrate binds to active site complementarily (c) Binding of substrate causes enzyme to mould around it (d) Bonds especially hydrogen bonds are formed (e) Other bonds are broken, caused by the enzyme (f) The substrate is converted into product that leaves the active site Summary 2015 INFO The Lock and Key Mechanism Biology Term 1 STPM Chapter 4 Enzymes 4

138 3. This initial rate will gradually slow down depending on which concentration is limiting. This is due to the conversion of substrate molecules to product molecules. 4. Finally, the course of the reaction will end when all of the substrates are converted to product. 5. There are two ways to determine the rate or initial velocity of enzymecatalysed reactions. (a) Measuring the rate of formation of the product • An example is the rate of oxygen formation in the breakdown of hydrogen peroxide by catalase. • Catalase is added to 5% hydrogen peroxide solution. • Oxygen is collected every 15 s or the number of bubble per minute is recorded. • Amount of gas collected is plotted against time. • Rate of reaction = amount of oxygen (cm3 )/unit time (s). (b) Rate of disappearance of the substrate: • An example is the rate of amylase hydrolyses starch to form maltose. • Amount of starch in mol is added with amylase. • Samples are taken at timed intervals of every minute. • The sample is tested with iodine solution. • The end point is determined until no blue colour is formed. • Time taken to reach end point is recorded. • Rate of reaction = amount of starch in mol / time taken in min. Deduction of Michaelis-Menten constant (KM) From Michaelis-Menten plot 1. This is done by ploting the velocity of the reaction against the substrate concentration. The curve as shown in Figure 4.4 was obtained. Velocity (v) VM KM a b [Substrate] V1/2 Figure 4.4 Graph of velocity against substrate concentration Biology Term 1 STPM Chapter 4 Enzymes 4

139 2. From the graph, the reaction velocity is proportional to the concentration of the substrate when the substrate concentration is low. However, when the substrate concentration increases, the velocity turns maximum. This is because the enzyme molecules are saturated with substrate molecules. The maximum velocity of an enzyme is determined by the turn over number, which measures the number of substrate molecule converted to product molecule per enzyme molecule per minute. 3. From the graph, Michaelis-Menten constant (KM) can be determined. KM is the substrate concentration when the velocity of the reaction is half maximum. The constant is fixed for a particular enzyme under a certain condition of temperature and pH. 4. The velocity of the reaction is determined by Michaelis-Menten formula i.e. V = Vmax [S] KM + [S] where Vmax is equal to maximum velocity and [S] is the substrate concentration. 5. We can look at the reaction under three conditions. (a) When the [S] is much smaller than KM, as indicated in the region a of the graph, the formula can be approximated as follows: V ≈ Vmax [S] KM ≈ Vmax KM [S] ≈ K [S] Therefore, the velocity v is proportional to the substrate concentration [S]. When v is plotted against [S], a straight-line graph is obtained with the gradient of the line equals to K ≈ dv ds ≈ Vmax KM (b) When [S] is much larger than KM, as indicated in the region b of the curve, the formula can be approximated as follows: V ≈ Vmax [S] [S] ≈ Vmax Therefore, the velocity is maximum. (c) When [S] = KM, the Michelis-Menten formula can be simplified as follows: V ≈ Vmax [S] [S] + [S] ≈ Vmax [S] 2[S] = Vmax 2 Therefore, the velocity is half maximum. That is how we can get the KM from this graph. Deduction of KM from Michaelis-Menten plot (a) A graph of velocity is plotted against substrate concentration (b) The maximum rate is determined, then half the maximum rate is noted (c) KM is the substrate concentration at half maximum velocity (d) If KM = [s], r = Vmax [s] [s] + [s] = Vmax [s] 2[s] = Vmax 2 Summary Biology Term 1 STPM Chapter 4 Enzymes 4

140 From Lineweaver-Burke plot 1. We can determine KM from the reciprocal of Michaelis-Menten formula as follow: 1 v = KM + [S] Vmax [S] 1 v = KM Vmax × 1 [S] + [S] Vmax [S] 1 v = KM Vmax × 1 [S] + 1 Vmax (y = ax + c) 2. When 1 v is plotted against 1 [S] , a straight line is produced as in Figure 4.5. – ––1 KM ––– 1 Vmax –– 1 [S] –– 1 v VM KM Figure 4.5 A Lineweaver-Burke plot 3. To get the value of KM, assume 1 v = 0 (i.e. y = 0), 0 = KM Vmax x + 1 Vmax KM Vmax x = – 1 Vmax KM = – 1 x Therefore, the x intercept is equal to – 1 KM . So, KM can be determined. 4. To get Vmax , assume 1 [S] = 0 (i.e. x = 0) y = 1 Vmax Vmax = 1 y Therefore, the y intercept is equal to 1 Vmax . Deduction of KM from Lineweaver-Burke plot (a) A graph of 1 V is plotted against 1 [s] (b) A straight line graph is obtained (c) The y-intercept is = – 1 KM , so KM can be determined. (d) V = Vmax [s] KM + [s] 1 V = KM + [s] Vmax [s] 1 V = KM Vmax × 1 [s] + 1 Vmax if 1 V = 0, KM Vmax × 1 [s] = – 1 Vmax 1 [s] = – 1 KM Summary Biology Term 1 STPM Chapter 4 Enzymes 4

141 Significance of KM and Vmax 1. KM is the index to measure the affinity of enzyme towards the substrate. 2. KM is inversely proportional to affinity. Thus, enzyme with low KM has high affinity for the substrate. 3. The KM is an indication of the efficiency of the enzyme to attract the substrate and to convert the substrate to product under a fix set of conditions like temperature, pH and the presence of other chemicals. 4. Vmax is the maximum velocity when a fixed amount of enzyme is mixed with an unlimited amount of substrate under a fixed set of conditions too. 5. Vmax is directly proportional to the enzyme concentration when other factors are constant. 6. Vmax reveals the maximum turn over number, the number of substrate molecule that is converted to product per enzyme molecule per minute under fixed set of conditions. Effects of Environmental Factors on the Rate of An EnzymeCatalysed Reaction Effect of temperature 1. The increase in temperature will initially increase the rate of reaction until optimum but the rate will drop rapidly when the temperature is further increased as shown in Figure 4.6 below. Temperature/ °C Velocity Figure 4.6 The effect of increasing temperature 2. Increase in temperature causes an increase in kinetic energy of both enzyme and substrate molecules. 3. There is a greater chance of meeting each other forming enzymesubstrate complex. Thus, increase in temperature increases the chances of effective collision. 4. Enzyme molecules have better conformation at higher temperature. Exam Tips Remember how to obtain Vmax from a plot of velocity against substrate concentration and derive the enzyme concentration at that point. You should be able to write the MichaelisMenten formula and derive V = Vmax 2 when [S] = KM. Remember also how to get KM, Vmax, and the curves from competitive and noncompetitive inhibitions from Lineweaver-Burke plot (STPM 2007 essay question, together with ‘lock and key’ model). Significance of KM and Vmax (a) KM – KM is inversely proportional to affinity of enzyme to substrate – Smaller KM indicates higher enzyme efficiency and higher velocity can be achieved (b) Vmax – Vmax is the maximum velocity that enzyme reaction is possible to achieve – Higher Vmax indicates higher efficiency of enzyme Summary 2015 Biology Term 1 STPM Chapter 4 Enzymes 4