Pra U STPM Biology Term1 CC039142a

Biology Term 1 STPM Chapter 1 Biological Molecules 1 42 STPM PRACTICE 1 1. Which of the following makes water as a biological lubricant? A Water molecules exhibit polarity B Water is a liquid at room temperature C Water is inert D Water has a high surface tension 2. Which of the following properties of water are important for the temperature regulation of an exothermic animal? I High surface tension II Low viscosity III Highest density at 4°C IV High heat capacity A I and II B I and III C I and IV D II and IV 3. Mosquitoes can walk on the surface of water due to its property. What is that property? A Bipolar B Low viscosity C High adhesion D High cohesion (d) It is used in DNA sequencing. DNA is cut into short fragments added with a special dye that colours specific bases at one end. From the pattern formed, the sequence of DNA or gene can be deciphered. 6. Limitations of its uses are as follows: (a) Only small amounts of substance can be separated. (b) Substances which are of no charge or too similar in charges cannot be separated. Quick Check 6 1. Explain how chromatography can be used to identify the products of protein hydrolysis. 2. Explain how electrophoresis can be used to diagnose AIDS. H C C C C C O OH H OH OH H HO H H H C OH H 4. Under the hot sun, water in the pool is not so hot compared to that of the pavement. This is so because water has a A high heat capacity B high surface tension C high latent heat of fusion D high latent heat of vaporisation 5. The diagram below shows a type of sugar molecule, X. Which molecule is produce after two molecules of X undergo condensation process? A Mannose C Maltose B Cellulose D Sucrose

Biology Term 1 STPM Chapter 1 Biological Molecules 1 43 6. Which of the following is a monosaccharide? A Galactose B Lactose C Maltose D Sucrose 7. Which of the following sugar is not a reducing sugar? A Glucose B Sucrose C Fructose D Maltose 8. The diagram below shows a bond X which links two monosaccharide. O O O X OH OH OH OH HOCH2 CH2 What type of bond is represented by X? A α-1,4 glycosidic bond B α-1,6 glycosidic bond C b-1,4 glycosidic bond D αb-1,2 glycosidic bond 9. Which of the followings are the properties of amylopectin? I It is less soluble than starch. II It is composed of α-glucose molecules. III It is a long and branching polysaccharide. IV Its bonds between the glucose is helical in shape. V Its glucose molecules are linked with 1-4 or 1-6 glycosidic bonds. A I, III and V B II, III and IV C II, III and V D II, IV and V 10. Starch, glycogen and cellulose are complex carbohydrates with different properties due to their type of A bonding B repeating units of monosaccharide C side chains D functions 11. Which of the following is composed of or contains glucose molecule? A DNA B RNA C Fructose D Cellulose 12. What are the components of maltose? A Galactose and galactose B Glucose and galactose C Glucose and fructose D Glucose and glucose 13. Why oleic acid is insoluble in water? A Has low carbon to hydrogen ratio B Has double bonds C Does not contain polar group D Exist in linear form 14. Which of the following is true about fat? Soluble in water Provide energy Produce water when respired A False True True B True False True C True True False D False True False 15. Which of the properties of lecithin are

Biology Term 1 STPM Chapter 1 Biological Molecules 1 44 important in the formation of the structure of a cell membrane? I Lecithin can be hydrolysed. II The backbone of the molecule composes of three carbon atoms. III Two alcohol groups bind with one fatty acid respectively. IV The tip of two hydrocarbon chains is non-polar. V The tip of the molecule with the phosphate and nitrogen groups is polar. A I, II and IV B I, II, IV and V C II, III, IV and V D I, II, III, IV and V 16. The properties and functions of an amino acid are determined by the A amino group C peptide bond B carboxyl group D side group 17. Protein molecules and amino acids can be separated through electrophoresis which depends on the A temperature B concentration C net charge D conformation 18. Which of the followings are true of steroid drug abuse? I It is used to improve sexual power. II It is used to form feminine features. III It is used to improve athletic performance. IV It is used to cure pain, asthma and weak hearts. V It is injected into animals for faster growth. A I, II and IV B I, II, IV and V C II, III, IV and V D I, II, III, IV and V 19. Which of the following is true? A Serine has a hydroxyl group B Glycine is polar C Aspartic acid is non-polar D Lysine is acidic 20. The similarity of two protein molecules is determined by A the alkyl group of certain amino acids B the carboxyl group of certain amino acids C the amino group of certain amino acids D the amino acid sequence of the protein molecule 21. The helical structure in the diagram below shows a portion of a biopolymer that is caused by N H C O H N C O A peptide bonds B covalent bonds C hydrogen bonds D double bonds 22. Which protein conformation corresponds to its correct description? Protein’s conformation Description A Primary A repeated regular structure of a polypeptide chain. B Secondary The coiling and folding of a polypeptide chain involve hydrogen bonds only. C Tertiary The aggregation of two or more proteins subunits. D Quarternary The complex threedimensional structure of polypeptide chains.

Biology Term 1 STPM Chapter 1 Biological Molecules 1 45 23. Which protein is a globular protein? A Keratin B Fibrinogen C Collagen D Haemoglobin 24. The table shows four types of protein and their examples. Proteins Examples I Messenger protein II Storage protein III Structural protein IV Contractile protein W Actin X Casein Y Insulin Z Collagen Which combination is correct? I II III IV A W Y Z X B Y X Z W C Y Z W X D Z X Y W 25. State the non-polar amino acid. A Aspartate B Glycine C Lysine D Serine 26. Which of the following indicates the number of water molecules needed for every one of the substances hydrolysed? Number of water molecules needed during hydrolysis of Tripeptide Trisaccharide Triglyceride A One Three One B Two One Two C Three Three Two D Two Two Three 27. A nucleoside contains nitrogenous base, pentose and A three phosphate groups B two phosphate groups C one phosphate group D no phosphate group 28. The two strands of polynucleotides in a DNA molecule are held together by A peptide bonds B hydrogen bonds C glycosidic bonds D phosphodiester bonds 29. If the ratio of A + G / T + C in one strand of DNA is 0.8, what is the ratio of A + G / U + C in its transcribed mRNA? A 0.2 C 1.0 B 0.8 D 1.25 30. If a DNA molecule contains 20% G, what is the percentage of A in the DNA? A 20 B 30 C 40 D 50 31. In what aspect does the cat DNA and human DNA differ? A Their DNA have different types of nucleotide. B Their DNA have different type of pentose sugar. C Their DNA have different structures of DNA molecule. D Their DNA have different purine base and pyrimidine base ratio. 32. Which of the followings are true about RNA? I It consists of double strands of polynucleotide II The pentose within is ribose III It is not stable IV There is only one type of DNA A I and II B I and IV C II and III D III and IV

Biology Term 1 STPM Chapter 1 Biological Molecules 1 46 33. Four disaccharides were each hydrolysed with dilute acid. The purified products were separated by one-dimensional chromatography. The final chromatogram is shown in the digram below. x Lactose 1 2 3 x x x If the first column represents the products of hydrolysis of lactose, which of the following indicates the results obtained from the hydrolysis of sucrose and maltose? Sucrose Maltose A 1 2 B 1 3 C 3 2 D 3 1 Structured Questions 1. The diagram shows three types of amino acids. C C OH H O OH H2N CH2 C C OH H O H H2N C C OH H O H2N CH2(CH2)3 NH2 X Y Z (a) Name the amino acids X, Y and Z. [3 marks] (b) (i) What are the structures in the dotted lines boxes above known as? [1 mark] (ii) In which group do amino acids X and Z belong to? [2 marks] (c) Name the process P and Q in the reaction below: [2 marks] X + Y + Z P Q NH2 – X – Y – Z – COOH

Biology Term 1 STPM Chapter 1 Biological Molecules 1 47 2. The diagram shows a short fragment of DNA molecule. P P G (ii) S S S S S S S S T (iii) C (iv) A (i) 3ʹ OH P P P P P (a) Name the bases (i), (ii), (iii) and (iv). [3] (b) (i) Name the pyrimidine base. [1] (ii) If the bases in a DNA molecule consist of 26% guanine, calculate the percentage of adenine in the molecule. [2] (c) Distinguish between RNA and DNA molecules. [2] Essay Questions 1. (a) What is meant by polymerisation as referred in the formation of starch and cellulose? Explain how polymerisation of polysaccharides is different from that of polypeptides. [8] (b) What is esterification? Explain the similarities and differences between esterification and polymerisation. [7] 2. (a) (i) Make an annotated drawing of the molecular structure of cholesterol with its hydrophilic and hydrophobic ends. Describe its properties. [6] (ii) What are the roles of steroid in human body? [4] (b) DNA can be separated using gel electrophoresis, explain the principle. [5] 3. (a) Describe the interactions which contribute to the tertiary structure of a protein.[8] (b) (i) What is meant by protein denaturation? [1] (ii) Describe how the structure of haemoglobin molecules is related to its function. [6]

Biology Term 1 STPM Chapter 1 Biological Molecules 48 1 1. Its boiling point is 100 °C. Its freezing point is 0 °C. It is inert and transparent. 2 1. All monosaccharides have free functional groups but not true for all those of disaccharides. The functional groups in sucrose are involved in bonding, so sucrose is non-reducing. 2. They are stereoisomers or optical isomers, one is the mirror image of another in the arrangement of groups around a tetra-valent carbon atom. D-form rotates polarised monochromatic light to the right and L-form rotates to that of the left. 3. They are easily converted back to glucose and metabolised. They are compact, osmotic inactive and do not affect other metabolic processes of the cell. 4. The molecules form microfibril by cross-linking through hydrogen bonds. The microfibrils can similarly cross-link together to form macrofibrils in the formation of secondary wall. 3 1. Fat is solid whereas oil is liquid. Fat becomes oil at higher temperature and vice versa. Animal stores fat whereas plant stores oil. 2. They can be respired or metabolised to form other substances. They can form micelles in lacteal or blood and help in the transport of lipids. 3. The low level of cholesterol in the diet results in its low level in the blood. This helps to cut down the risk of its deposition in the arterial wall causing arteriosclerosis. This would lower the chance of cardiovascular diseases associated with it. Low cholesterol level can affect the synthesis of vitamin D, steroid hormones and plasma membrane. Thus, may result in deficiency diseases though extremely rare. 4 1. The side chain makes each amino acid different. Each of the 20 has different side chains. They can be divided into seven groups based on the physical and chemical natures of the side chain. They can be polar, acidic, basic, hydroxyl containing or sulphur containing and non-polar. 2. Globular proteins are soluble in water. They have to interact with water so that the hydrophilic amino acids are on the outside. The hydrophobic ones cannot be on the outside, Instead they are inside to form nonpolar bonding to maintain the globular shape. 3. Fibrous proteins consist of many α-helix coiled chains of polypeptides. The chains are cross-linked along the entire length with hydrogen and disulphide bonds. The chains form hard structures like horn and hoof. 4. Albumin is a globular protein and on boiling, the polypeptides uncoil. All the chains interact with each other and cross-link by hydrogen bonds forming precipitate and later cake, which does not absorb light. Thus, it becomes white. 5 1. Purines are bigger molecules consisting of two fused nitrogenous hydrocarbon rings whereas pyrimidines are smaller and consist of single nitrogenous hydrocarbon rings. 2. DNA dissolves in water and is inactivated by combining with protein called histone. Other parts are active producing RNA, which are used to form proteins. Before cell division, all the DNA replicates combine with histone to form chromosomes. During division, the DNA are distributed into the daughter cells. DNA then become hydrated, histones dissociate from them and certain parts become active producing RNA again. 3. (a) rRNA has the least types of about 40, tRNA 61 whereas mRNA has more than 10,000. (b) rRNA varies in size, some with more than 1,000 bases, tRNA are the smallest with about 80 bases whereas mRNA can be the biggest with more than 2,000 bases. (c) rRNA combine with protein forming ribosome whereas tRNA and mRNA exist freely in the protoplasm. (d) rRNA and mRNA have no fixed shape of their own whereas tRNA has clover leaf shape. (e) rRNA and tRNA have longer life span whereas mRNA have shorter life span of just few minutes. 6 1. The products of protein hydrolysis are 20 types of amino acids, which are too many for a single dimensional chromatography. Hence, the use of a twodimensional one. Two different solvents e.g. water and ethanol are used. To identify the amino acids produced, 20 different chromatographies are done similarly. Each one uses a known amino acid. The unknown is identified with a standard. ANSWERS

Biology Term 1 STPM Chapter 1 Biological Molecules 1 49 2. HIV antibody is extracted from an AIDS patient and electrophoresis is carried out. This is used as a standard to compare with an unknown individual‘s blood to see if he or she has the antibody by carrying out electrophoresis on the blood. STPM Practice 1 Objective Questions 1. B 2. D 3. B 4. A 5. C 6. A 7. B 8. B 9. C 10. A 11. D 12. D 13. C 14. A 15. C 16. D 17. C 18. D 19. A 20. D 21. C 22. B 23. D 24. B 25. B 26. D 27. D 28. B 29. D ( 10 8 =1.25) 30. B 31. D 32. C 33. A Structured questions 1. (a) X : Serine Y : Glycine Z : Lysine (b) (i) R group / side chain (ii) X : Polar class Z : Basic class (c) P : Condensation Q : Hydrolysis 2. (a) (i) T (ii) C (iii) A (iv) G (b) (i) Cytosine, thymine (ii) Guanine = cytosine = 26% G + C = 26 + 26 = 52% So, A + T = 100 – 52 = 48% Adenine = 48 ÷ 2 = 24% (c) • RNA is a single-stranded molecule whereas DNA is a double-stranded molecule. • RNA contains A, C, G, and U whereas DNA contains A, C, G and T. Essay questions 1. (a) • Polymerisation is the formation of long repeated units of monomers called biopolymer, by condensation. • In the formation of starch, the monomers are α-glucose linked by α–1,4 glycosidic bonds. • In the formation of cellulose, the monomers are β-glucose linked by β–1,4 glycosidic bonds. • Polymerisation involves ligase and energy in the form of ATP. • Polymerisation of polysaccharides does not involve ribosomes whereas that of polypeptide does. • Polymerisation of polysaccharides involves only one type of monomer e.g. glucose, whereas that of polypeptide involves 20 different amino acids. • Polymerisation of polysaccharides involves the formation of glycosidic bonds whereas that of polypeptide involves the formation of peptide bonds. • Polymerisation of polysaccharides is not dictated by gene whereas each polypeptide is formed with its sequence of amino acids determined by a gene. • Polymerisation of polysaccharides is not intervened by RNA whereas that of polypeptide requires mRNA and tRNA before the genetic information can be translated into sequence of amino acids. (b) • Esterification is the formation of an ester bond between a hydroxyl group and a carboxylic group. • Example of esterification is the formation of fat or triglyceride that involves one molecule of glycerol and three molecules of fatty acids. • It requires enzyme esterase and occurs in the chloroplast or cytoplasm. • Both involve condensation in which a molecule of water is removed each time a bond is formed. • Both require enzyme ligase and energy in the form of ATP. • Both can occur in the chloroplast or cytoplasm of cells. • Esterification involves formation of an ester bond between a hydroxyl group and a carboxyl group whereas polymerisation involves other groups like two hydroxyl groups in the case of polymerisation of starch. • Esterification produces large molecules such as triglyceride whereas polymerisation produces long biopolymers like starch with repeating glucose units. • Esterification involves an alcohol and an acid like glycerol and fatty acid whereas polymerisation may involve just one substance like glucose in the formation of starch. 2. (a) (i) Cholesterol HO Hydrophilic part of molecule Hydrophobic part of molecule Properties of cholesterol • Cholesterol is soluble in organic solvents • It is less dense than water

Biology Term 1 STPM Chapter 1 Biological Molecules 1 50 • It solidifies at low temperature (ii) • Steroid is required for the formation of membrane to maintain healthy skin or healthy nerve cells with myelin sheath. • It is required for the formation of the male sex hormone, testosterone, to maintain male primary and secondary sexual functions. • It is required for the formation of female sexual hormones which include oestrogen and progesterone that maintain female primary and secondary sexual functions. • It is required for the formation of corticoid hormones like aldosterone to maintain sodium level in the blood. • It is required in the formation of vitamin D in the skin for healthy calcium metabolism and to evade the body from rickets. • It is required in the formation of bile salts to emulsify fats for their easy absorption together with fat-soluble vitamins like vitamin A, D, E and K. • Over consumption or production of steroid results in greater chance of getting cardiovascular diseases including heart attack and stroke. • Steroid together with fats are not very soluble in blood and tend to accumulate in arteries including coronary and carotid arteries. It causes arteriosclerosis and blockade of coronary artery resulting in heart attack. • If branches of carotid artery is blocked or burst because of hypertension, it causes stroke resulting in death or paralysis. (b) Principles of DNA separation using gel electrophoresis: • It uses electric field to separate DNA fragments of different lengths. • Commercially prepared agarose gel is placed in a special tray or column. • Electrodes are placed at both ends which are connected to a battery and DNA fragments are placed near the cathode. • When the electricity is switched on, the DNA fragments will move at different rates to the anode. • Smaller fragments will move at faster rate than the longer fragments. 3. (a) • The primary structure is the ultimate control of the structure through peptide bonds that link specific sequence of amino acids. • The primary structure also determines the secondary structure consisting of -helix or -pleated sheet. • Usually parts of the primary structure is secondary coiled or folded. • This α-helix or α-pleated sheet is caused by regular hydrogen bonds between amine and carbonyl groups. • The tertiary structure determine the three dimensional shape with further coiling or folding of secondary structure. • These coiling or folding is caused by disulphide bond, ionic bond, hydrophobic interactions and hydrogen bonds. • The bonds are between side chains or R groups of the amino acids. • The globular shape of proteins is further caused by hydrophilic groups at the surface interacting with water. • These globular proteins soluble in water with the hydrophobic groups in the centre. (b) (i) • It is the change of shape of globular proteins with the breakdown of intramolecular bonds. (ii) • Haemoglobin molecules are globular proteins. Hence, they can dissolve in the plasma to carry oxygen. • Each molecule consists of four haem groups, so each molecule can carry four molecules of oxygen. • The molecules consist of quarternary structure of four subunits to ensure proper binding and release of oxygen. • The four subunits in each haemoglobin molecule work in cooperation in which first oxygen molecule binding is not facilitated but subsequent two are facilitated and the last does not facilitated to ensure unique binding and dissociation of oxygen. • Such intra-molecular cooperation ensures that oxygenated blood releases oxygen at right partial pressure of oxygen and prevents sudden lack of oxygen. • Beside carrying oxygen, the protein structure of haemoglobin within the red blood cell also buffer change of pH. • This haemoglobin protein also helps in the transport of carbon dioxide directly or indirectly.

CHAPTER STRUCTURE OF CELLS 2 AND ORGANELLES Concept Map Cells Cellular components Specialised cells comparison comparison Unspecialised cells Specialised plant cells Specialised animal cells Prokaryotic cells Bacterial cells Plant cells Animal cells Eukaryotic cells Structures and functions of organelles Structures, functions and distributions Principles of light and electron microscopes Typical plant and animal cell Differential centrifugation Bilingual Keywords Prokaryotic cell – Sel prokariot Eukaryotic cell – Sel eukariot Cyanobacteria – Sianobakteria Capsule – Kapsul Nitrogen fixing – Pengikatan nitrogen Chromosome – Kromosom Cell wall – Dinding sel Cytoplasm – Sitoplasma Fungi – Kulat Cilium – Silium Lysosome – Lisosom Secretion – Rembesan Fluid – Bendalir Sieve tube – Tiub tapis Spindle fibre – Gentian gelendung Centromere – Sentromer Digestion – Pencernaan Gland – Kelenjar Pith – Empulur Muscle – Otot Nerve – Saraf Cartilage – Rawan

Biology Term 1 STPM Chapter 2 Structure of Cells and Organelles 2 52 Cell Theory 1. A cell is the basic unit of the structure and function of all living organisms. This is according to the cell theory, the result of studies by Schleiden, a botanist, and Schwann, a zoologist. 2. According to Rudolp Virchow, all cells arise from pre-existing cells by cell division. 3. A cell is made up of protoplasm surrounded by a selectively permeable lipoprotein membrane. Within the cell, the basic chemistry of life exists. 4. Cells are divided into two types, the prokaryotic cells and the eukaryotic cells. VIDEO Cell Theory Comparison Between Structures of Prokaryotic and Eukaryotic Cells 1. Prokaryotic cells are primitive cells. They are not true cells. They do not have nucleus and are found in bacteria and cyanobacteria, which belong to the kingdom Prokaryotae. 2. A generalised prokaryotic cell is as shown in Figure 2.1. Bacterial flagellum Nucleoid (circular DNA) Pili Plasmid Ribosomes Cytoplasm Plasma membrane Cell wall Capsule Figure 2.1 Structure of a generalised prokaryotic cell Learning Outcomes Students should be able to: (a) state the cell theory; (b) compare the structures of prokaryotic and eukaryotic cells; (c) compare typical animal and plant cells as seen under electron microscopes; (d) describe the basic principles of light and electron microscopy. Cell theory 1. A cell is a basic unit of structure and function of all living things. 2. Cells arise from preexisting cells by cell division. Summary • Bacterium – singular Bacteria – plural • Flagellum – singular Flagella – plural Language Check Language Check 2013, 2015 2.1 Prokaryotic and Eukaryotic Cells VIDEO Prokaryotic and Eukaryotic Cell

Biology Term 1 STPM Chapter 2 Structure of Cells and Organelles 2 53 3. Eukaryotic cells are true cells with nucleus and are more advanced cells as found in plants, animals, fungi and protoctists (Figure 2.2). Plasma membrane Microtubule Ribosome Rough endoplasmic reticulum Lysosome Mitochondrion Cytoplasm Centriole Golgi body Nucleus Nuclear envelope Figure 2.2 Structure of a generalised eukaryotic cell 4. Table 2.1 summarises the comparison between the structures of prokaryotic and eukaryotic cells. Table 2.1 Comparison between prokaryotic and eukaryotic cells Characteristic Prokaryotic cell Eukaryotic cell 1 Cell size Usually small (diameter 0.5-5 µm) Usually bigger (as big as 40 µm) 2 Form Unicellular / filamentous Unicellular, filamentous / multicellular 3 Cell wall Peptidoglycan (murein), not of cellulose Cellulose, chitinised in fungi 4 Flagellum type Fine, simple and only consists of one microtubule Complex, with ‘9+2’ pattern of triplet microtubules 5 Capsule May be present, of glycoprotein Usually absent Remember the differences between the prokaryotic and the eukaryotic cells including their examples Exam Tips Comparison of prokaryotic and eukaryotic cells 1. Both have cytoplasm and plasma membrane. 2. Differences on cell surface structures, wall material, membraneous organelles, ribosomes and DNA. Summary • Nucleus – singular Nuclei – plural • Nucleolus – singular Nucleoli – plural • Mitochondrion – singular Mitochondria – plural Language Check Language Check

Biology Term 1 STPM Chapter 2 Structure of Cells and Organelles 2 54 Characteristic Prokaryotic cell Eukaryotic cell 6 Pillus May be present for attachment No such structure present 7 Nucleus Absent, with no nuclear membrane Present, with nuclear envelope 8 Nucleolus Absent, ribosome formed in cytoplasm Present, for ribosome synthesis 9 DNA/ Chromosomes Circular, ‘naked’ DNA with no histone (contained in the nucleiod region) Linear, combined with histone to form X or inverted V shapes 10 Organelles Few, none with envelope Many, three with envelopes 11 Ribosomes Smaller types, 70S (18 nm) Bigger types, 80S (22 nm) 12 Mesosome or mitochondria Mesosome or plasma membrane for respiration Mitochondria for respiration 13 Spindle No spindle during cell division Spindle present during mitosis and meiosis 14 Vesicles for photosynthesis Foldings of plasma membrane for photosynthesis Chloroplasts involved in photosynthesis 15 Vesicles for nitrogen fixation Vesicles or plasma membrane can fix nitrogen No structure is capable of such ability 16 Cytoplasm and plasma membrane Present Present Quick Check 1 1. Why are prokaryotic cells considered as primitive? 2. What are the different forms of prokaryotic organisms? 2010 2011

Biology Term 1 STPM Chapter 2 Structure of Cells and Organelles 2 55 Comparison Between Typical Animal and Plant Cells 1. The structure of a typical plant cell e.g. mesophyll cell is as shown in Figure 2.3. Smooth endoplasmic reticulum Nucleus Sap vacuole Plasmodesma Middle lamella Lipid globule Golgi body Ribosomes Rough endoplasmic reticulum Mitochondrion Chloroplast Cell wall Tonoplast Figure 2.3 A mesophyll cell 2. The structure of a typical animal cell e.g. intestinal epithelial cell is as shown in Figure 2.4. Smooth endoplasmic reticulum Nucleoplasm Golgi body Nucleus Rough endoplasmic reticulum Ribosome A intestinal epithelid cell Lipid globule Desmosome Microtubule Centriole Nucleolus Mitochondrion Lysosome Microfilament Glycogen granule Figure 2.4 A intestinal epithelial cell Table 2.2: Comparison between animal and plant cell Characteristic Animal cell Plant cell 1 Shape Not restricted, can be altered Restricted by cell wall 2 Cell wall and middle lamella Absent Surrounding the cell 3 Plasmodesmata No such pore Present Exam Tips Remember the generalised ultra structure of animal cell and plant cell including a function each of their organelles (STPM 2000 essay). Comparison between plant and animal cell 1. Both are eukaryotic with basic similarities in organelles. 2. Differences in cell surface structures, cell wall, chloroplast, food reserves and centrioles. Summary • Plasmodesma – singular Plasmodesmata – plural • Lamella – singular Lamellae – plural Language Check Language Check VIDEO Animal Cells and Plant Cells

Biology Term 1 STPM Chapter 2 Structure of Cells and Organelles 2 56 Characteristic Animal cell Plant cell 4 Microvillus, cilium and flagellum Present in certain specialised cells Absent except sperm of fern has flagellum 5 Sap vacuole and tonoplast Small vesicles may be found instead Big, centrally located 6 Cytoplasm Throughout cell At the periphery 7 Nucleus position Centrally located At one side 8 Lysosome Usually present Usually absent 9 Centriole Present, to organise spindle fibre formation Not found, still can form spindle fibre 10 Chloroplast and other plastids Absent Present for photosynthesis and storage 11 Carbohydrate food reserves Glycogen Starch 12 Intermediate filaments Present Usually absent 13 Mitosis In all cells In meristem only 14 Secretory vesicles May be present Usually absent 15 Plasma membrane, nucleus, mitochondria, endoplasma reticulum Present Present Quick Check 2 1. List the structural similarities between plant and animal cells. Briefly explain why each of the structures you have listed is essential. Light and Electron Microscopes Light microscope 1. Light microscopes are the ones that make use of light to form an image. 2. There are compound microscopes and phase contrast microscopes. (a) Compound microscopes (i) Compound microscopes contain two sets of lenses i.e. the objective lens to form an enlarge image and an ocular (eyepiece) lens to further enlarge the image. (ii) Compound microscopes in the laboratory normally have three magnification powers. • Low power: 10 × 4 = 40 times. • Medium power: 10 × 10 = 100 times. • High power: 10 × 40 = 400 times. VIDEO Light Microscope

Biology Term 1 STPM Chapter 2 Structure of Cells and Organelles 2 57 (iii) The uses of compound microscopes are as follows: • Compound microscopes can be used to observe objects smaller than 0.1 mm. • The invention of microscopes led to the formulation of the cell theory, which states that all organisms are made of cells. • Observation of microscopes also proves that microorganisms cause diseases. (iv) They have the following limitations: • Objects have to be sectioned into thin slices, fixed and stained before they can be observed. This makes the study of living cells difficult as they have to be killed. • The resolution limit of light microscope is 0.2 µm, meaning that any object smaller than that cannot be seen clearly. (b) Phase contrast microscopes (i) These are compound microscopes that can adjust the contrast of the object against the background, either darkened or lightened. Living cells can be observed without staining. (ii) These microscopes are fitted with an annular diaphragm to form a cone of light passing through the object. A phase plate is then used to change the phase of the object relative to the background before the final image is formed. By using a phase plate of suitable thickness, the background light can be darkened or lightened. This is due to the difference in refractive indices of the object and its surrounding that causes the light passing through them to differ in phases, which can then be enhanced (lightened) or cancelled (darkened). Annular diaphragm Phase plate Figure 2.5 An annular diaphragm and a phase plate of a phase contrast microscope (iii) Its advantage is that freshly prepared living cells can be studied without being killed by dye. Activities such as mitosis, meiosis, phagocytosis and movement especially that of zooplanktons can be observed. (iv) Its limitation is that the adjusting of phase plate requires experience. The microscopes have a resolution limit of 0.2 µm.

Biology Term 1 STPM Chapter 2 Structure of Cells and Organelles 2 58 Electron microscope 1. Electron microscope is a microscope that uses beams of electrons to form an image. 2. They are divided into transmission electron microscope and scanning electron microscope. (a) Transmission electron microscope (TEM) (i) It is a microscope that makes use of beams of electrons to pass through a very thin section of an object to form an image on a monitor screen. (ii) The principle involved is the same as the compound light microscope in which the light is replaced by beams of electrons; electromagnet is used instead of lens to focus the beams of electrons as shown in Figure 2.6. Light source Condenser lenses Specimen Objective lens Ocular lens Image Electron source Electromagnetic condenser lens Specimen Objective lens Ocular lens Image Light microscope Electron microscope Figure 2.6 Comparison of light and electron microscopes (iii) Its uses are as follows: • The limit of resolution is very small which is around 0.5 nm. Therefore, the structure of virus and ultrastructure of cell including organelles can be studied. • The final magnification produced in the form of micrograph can be more than 250,000 times. (iv) It has the following limitations: • Experience is required to produce electro-micrograph of cell structures. Exam Tips Remember the basic principles of phase-contrast microscope, transmission and scanning electron microscopes including examples of their uses. 2014

Biology Term 1 STPM Chapter 2 Structure of Cells and Organelles 2 59 • Object has to be fixed by chemicals to prevent deterioration, impregnated with heavy metallic ions to produce clearer image and hardened by plastic so that it can be cut to less than 1 µm thick. This procedure will add in artefacts. • The instrument is very sensitive to external interference such as magnetic and electric fields. Getting clear images may take time to learn. • It is not portable. It is expensive and costly to maintain. (b) Scanning electron microscope (SEM) (i) It makes use of a beam of electrons to irradiate the surface of an object and form a three dimensional image of the fine structure of the object surface. (ii) The beam of electrons being reflected by the surface of fine object is projected and magnified on a screen. (iii) It has the following uses: • The surface of fine structure such as that of insect antenna, inner surface of uterus and even cell surface can be observed in great detail. • The three dimensional structure such as the internal structure of organelles like granal system of chloroplasts, cristal system in mitochondria and the outer structure of virus can be photographed or shown on the monitor screen. • Living process as such as movement of cilia and other cell surface activities such as the budding of HIV from lymphocyte can also be observed. (iv) It has the following limitations: • Experience is essential, so time has to be devoted to learn in order to get the best picture. • Images are easily distorted. 2.2 Cellular Components Cellular Components of Typical Plant and Animal Cells Cell membrane 1. Cell membrane is a lipoprotein layer that surrounds the cell and organelles such as the nucleus, mitochondria, chloroplast, vacuole and lysosome. 2. The structure of the membrane based on Singer and Nicolson’s fluid-mosaic model is as shown in Figure 2.7. Basic principles of light and electron microscopes Light microscope Electron microscope Light wave Electron beam Glass lenses Electromagnetic lenses Lamp as light source Cathode tube as electron source Light needs to be condensed Electron beam needs to be condensed Whole specimen possible Very thin section used Live specimen Dead specimen Coloured image Black and white image Low resolution High resolution Low magnification High magnification Summary Students should be able to: (a) identify the cellular components of typical plant and animal cells; (b) describe the structures of organelles and state their functions; (c) explain the basic principles of differential centrifugation used to fractionate cellular components (g and S values). Learning Outcomes

Biology Term 1 STPM Chapter 2 Structure of Cells and Organelles 2 60 Phospholipid bilayer Phospholipid molecule Filaments of cytoskeleton Globular protein (integral protein) Peripherial protein Cholesterol Protein channel (Transport protein) Globular protein Glycolipid Glycoprotein Carbohydrate Alpha-Helix protein (Intergral protein) Hydrophilic heads Surface protein Figure 2.7 The fluid-mosaic model of the cell membrane Exam Tips Remember the structure, functions of membrane based on the fluid-mosaic model of Singer and Nicholson and the roles of component molecules. (STPM 2009 essay on the role of carbohydrate) 3. The basic membrane structure consists of a bimolecular phospholipid fluid layer with globular protein units floating in it, forming a mosaic pattern. 4. The heads of the phospholipids are hydrophilic, pointing outwards into the aqueous medium on both sides of the membrane. 5. The tails of phospholipids are hydrophobic, facing each other forming a non-polar interior in the middle of the membrane. 6. The structure is dynamic where each lipid molecule can move within its own monolayer and so is each of the protein unit. Some protein units however, are immobilised by microfilaments in the interior of the cell. 7. The fluidity of the membrane depends on the length of the fatty acid chains, their saturation and the amount of cholesterol in them. Fluidity affects permeability, membrane enzyme activities, reception to molecules and with which membranes it will fuse. 8. Cholesterol with its hydrophilic head and hydrophobic tail fits neatly within the phospholipid layer. It functions to control mechanical stability, flexibility and permeability of the membrane, especially in reducing leakage of small polar molecules. 9. The proteins are embedded in the phospholipid layer like mosaic, either in only one monolayer or span the bilayer. These are integral or intrinsic proteins, fitted neatly because of their corresponding non-polar properties of their surfaces. The peripheral or extrinsic ones are attached on the outer polar layers of phospholipid. 10. The proteins function as carriers or channels for polar molecules to cross the membrane, as structural components, enzymes, receptors and electron carriers for respiratory or photosynthetic phosphorylations.

Biology Term 1 STPM Chapter 2 Structure of Cells and Organelles 2 61 11. The carbohydrates exist as short branched chain of sugars attached to proteins (glycoproteins) or lipids (glycolipids) on the outer surface of the membrane. They function as receptors for chemicals like hormones, adhesion to neighbouring cells and for immune responses. 12. Functions of cell membrane: (a) The membrane protects the cell. Thus, any chemical or reaction happening outside the cell will not harm it. (b) It serves as a boundary between the cell and its environment. Therefore, ions outside the cell cannot easily enter the cell. (c) It regulates or controls the passage of substances in and out of the cells. This happens especially through the protein channels, which allow only specific polar molecules to move in or out. (d) It acts as receptor sites in recognising external stimuli such as hormone and antigen molecules. This also enables the cells to recognise other cells and so to behave in an organised manner during the formation of tissues in the embryo. (e) Within the cells, membranes allow compartmentalisation and division of labour especially within membrane-bound organelles like nucleus, mitochondrion and chloroplast. (f) Certain membranes can perform special functions such as light reaction in the internal membranes of chloroplast and oxidative phosphorylation in the inner membrane of mitochondria. (g) It helps in cell mobility such as in the white blood cells where the membrane can carry out amoeboid movement. Cell wall 1. The cell wall is a carbohydrate layer of cellulose found outside the plasma membrane of plant cells. 2. There are two types of cell wall, the primary cell wall and the secondary cell wall. (a) Primary cell wall The primary cell wall is found in young cells and cells that are not highly differentiated such as meristem, parenchyma and collenchyma. The primary cell wall has the following characteristics: (i) It is a thin layer, found just outside the plasma membrane of most plant cells. It is also found on the outer layer of cells with secondary cell wall. (ii) It consists of randomly arranged microfibrils of cellulose in an amorphous matrix as in Figure 2.8.

Biology Term 1 STPM Chapter 2 Structure of Cells and Organelles 2 62 Microfibril Matrix Figure 2.8 Microfibrils arranged in an amorphals matrix (iii) Each microfibril consists of about 100 chains of cellulose molecule of 5-20 µm and a diameter of 1-2 µm. (iv) The matrix is made up of complex polysaccharides such as pectins and hemicellulose with long and branched molecules. (v) On the outer layer of the wall, there is a middle lamella layer that consists of magnesium and calcium pectates for cementing adjacent cells. (vi) The primary cell wall is porous. It enables water to be transported apoplastically along it. (vii) It is elastic and strong. It enables parenchyma cells to become turgid and support the whole plant especially in herbaceous plants. (viii) The wall is usually perforated with plasmodesmata for the transport of substances between cells. (b) Secondary cell wall The secondary cell wall is a harder and usually thicker layer of cell wall, formed between the plasma membrane and the primary cell wall. It has the following characteristics: (i) The wall is made up of regularly arranged microfibrils or bigger macrofibrils. The fibrils are arranged in layers of parallel rows, which are perpendicular to those of upper or lower layers (Figure 2.9). Microfibrils Figure 2.9 Fibrils arranged in layers of parallel rows (ii) The matrix in the secondary wall is impregnated with lignin, forming a hard and impervious layer. (iii) The deposition of lignin in xylem vessels is not uniform but in patterns like rings, helices or networks.

Biology Term 1 STPM Chapter 2 Structure of Cells and Organelles 2 63 3. The functions of cell wall are as follows: (a) It protects the cell from physical injuries and haemolysis. (b) It supports the plant through cell turgidity or mechanical strength for tall woody trees. (c) It controls growth by limiting individual cell size and shape of the cell through orientation of the fibrils in the wall. (d) It forms a system of transport pathways for water and mineral ions. Water can both be transported along the porous cell wall in apoplast way and through the plasmodesmata of cells in symplast way. (e) It controls excessive loss of water from epidermal cells of the leaves and stems by having a waxy cuticle on the surface of the cell wall. Cork cells have suberised cell wall for the same purpose. (f) Cell wall of the xylem vessels forms empty tubes for water transport from the roots to the leaves. Tracheids form a water transport system with a lot of pits so that water can be laterally transported. Sieve tubes with a thinner wall but with sieve plates (a sieve-like lignified cross wall) will give extra strength for transport of organic compounds. (g) It provides food storage in the form of hemicellulose in some seeds. (h) It provides large surface area to volume ratio in root hair cells where absorption can take place. (i) It controls passage of water and dissolved mineral ions into the plant by having lignified Casparian strip or passage cells in the endodermis of the root. Cytoplasm 1. Cytoplasm is the protoplasmic part of the cell, which is outside the nucleus and is surrounded by the plasma membrane. It is the aqueous part of the cell, after all organelles are removed by centrifugation. 2. The cytoplasm of plant cell is usually referred to as protoplast, excluding the sap vacuole. 3. The pH of the cytoplasm is 6.8 ± 0.2. 4. It has a considerable high density with a variety of solutes. 5. Cytoplasm can be divided into cytosol (ground substance) and cytoskeleton (cell inclusion). Cytosol (ground substance) 1. Cytosol or the ground substance is the soluble part of the cytoplasm. 2. The solutes can be divided into three groups. (a) True solutes or crystalloids. These consist of: (i) Micromolecules such as gases (O2 , CO2 and N2 ), mineral ions which include Na+, K+, Cl– , Ca2+, Mg2+, Mn2+ and Fe2/3+.

Biology Term 1 STPM Chapter 2 Structure of Cells and Organelles 2 64 (ii) Mesomolecules such as monosaccharides which include glucose and fructose, disaccharides which include maltose, sucrose (plant cells), amino acids, organic acids, nucleotides and vitamins. (b) Colloids. These include macromolecules such as proteins (enzymes, hormones and structural proteins), glycogen in liver cells and muscle tissues. (c) Particles, droplets and vesicles. These include glycogen granules in liver cells and muscle tissues, starch granules in plant cells, fine fat droplets and minute vesicles, which contain liquid. 3. The functions of cytosol are as follows: (a) It stores vital chemicals including fats. (b) It is the site for certain metabolic pathways such as glycolysis, synthesis of fatty acids, amino acids and proteins. (c) It enables organelles to move about in it. These organelles include mitochondria, chloroplasts, ribosomes, lysosomes and vacuoles. Cytoskeleton 1. The cytoskeleton determines the three dimensional shape of the animal cells and give certain firmness in the plant cells. 2. The fine fibrils can be divided into three types i.e. microtubules, microfilaments and intermediate filaments. (a) Microtubules (i) The microtubules are fine, unbranched tubules with a diameter of 25 nm, a wall of 5 nm thick and vary in length. (ii) The wall is composed of 13 rows of globular protein subunits called tubulin, which are arranged helically. (iii) Tubulin can grow from a certain organisation centre, which is made of dense protein. Tubulin can be added at the base or at one end of microtubule causing it to increase in length or be removed, causing it to decrease in length. (iv) The microtubules in cells are usually stable. However, some may be unstable as they can change their length suddenly. (v) Other tubulin subunits are able to attach to the base of cilia and flagella, participating in their growth and movement. (vi) The spindle fibres during cell divisions are microtubules. In animal cells, they are organised by the centrioles. Their formation can be inhibited by colchicine, causing nondisjunctions (chromatids not separating) and mutation in the number of chromosomes. 2010

Biology Term 1 STPM Chapter 2 Structure of Cells and Organelles 2 65 Microtubule Microfilament Intermediate filament Arrangement of tubulin Cytoskeleton Figure 2.10 Cytoskeleton and arrangement of tubulin in microtubule (vii) The functions of microtubules are as follows: • They form the cytoskeleton that determines the shape of the cell. • They can divide the cytoplasm of the cell into compartments so that specialised enzymes can be isolated from others to function better. • They can contract, causing movement in the cilia and flagella. • They can pull chromosomes or chromatids during mitosis or meiosis. • They can cause the movement of organelles, including mitochondria, lysosomes and vesicles to move along like railway tracks. (b) Microfilaments (i) The microfilaments are fine filaments made of protein with a diameters of 7 nm and lengths of several µm. (ii) They are composed of one or two types of protein including actin and myosin. (iii) They are dynamic which means they can change their length very quickly depending on their locations and functions. (iv) Each type of protein forms subunits that are arranged helically. (v) The subunits can slide over one another causing the microfilaments to contract. (vi) Microfilaments exist in bundles and they are normally found in layers in the cytoplasm. Two strands of actin subunits Microfilament composed of two strands of protein subunits Intermediate filament with eight strands of protein subunits Figure 2.11 Microfilament and intermediate filament

Biology Term 1 STPM Chapter 2 Structure of Cells and Organelles 2 66 (vii) They cause membrane invagination and evagination during endocytosis and exocytosis. (viii)They cause the protrusion of pseudopodium during amoeboid movement in the white blood cells. (ix) They assist in the cleavage process during cytokinesis of animal cells after nuclear division. (c) Intermediate filaments (i) The intermediate filaments are filaments bigger than the microfilaments but smaller than the microtubules, with diameter between 8 to 12 nm and are only found in animal cells. (ii) The filaments are made up of 4 long strands of α-helix coiled fibrous proteins, each consisting of only secondary coiled polypeptide. (iii) There are several types of intermediate filaments with each composing of only one type of protein, including one with keratin. (iv) They are very stable and branched, forming a network of cytoskeleton in the cytoplasm and nucleus. (v) Each type of cell has its own arrangement and types of protein. For example, the cells in the skin epithelium or forming the nail, hair and horn have keratin filaments, which are different from those in the muscle and nerve cells. (vi) They maintain the shape of the cell including the nucleus. (vii) They distribute the organelles and support them in the cytoplasm. (viii)They help some specialised cells to perform their functions. Some examples include the nail-producing cells to form nails, and neurone to transmit impulses. Structure and Functions of Organelles Nucleus 1. The nucleus is the largest organelle in the eukaryotic cell and functions to control all activities of the cell. 2. It is found in all cells, except in the red blood cells of mammals and the sieve tubes of phloem in flowering plants. 3. The nucleus is normally found in the centre of the cell but in matured plant cells, it is pushed to one side of the protoplast by the big sap vacuole. 4. There is one nucleus per cell, however, in some exceptional cases, two are found in Paramecium and abnormal liver cells. 5. It is normally spherical or oval in shape, but it may be cylindrical or lobed in the white blood cells. The shape can later be changed. Exam Tips Remember: membrane, cell wall and cytoplasm are cell components, not organelles but microtubules and microfilaments are considered as organelles. Cellular components of typical plant and animal cell 1. Plasma membrane • Phospholipid • Cholesterol • Protein • Carbohydrate 2. Cell wall • Primary – celulose • Secondary + lignin 3. Cytoplasm • Cytosol – water, gases, ions, carbohydrates, amino acids, nucleotides, vitamins and proteins • Cytoskeleton – microfilament, microtubule and intermediate filament Summary

Biology Term 1 STPM Chapter 2 Structure of Cells and Organelles 2 67 6. Nucleus has a diameter of 10 – 20 μm and it occupies 75% of the cell volume in the meristem. 7. The nucleus can be divided into (a) Nuclear envelope (b) Nucleoplasm (c) Nucleolus (d) Chromosome (a) Nuclear envelope (i) Nuclear envelope is the double lipoprotein membrane that surrounds the nucleus. (ii) The outer membrane is smooth, may have ribosomes attached to it and is possibly continuous with the membrane of the endoplasmic reticulum. Sometimes, it may be continuous right to the plasma membrane. Nuclear pole Chromatin Nucleolus Ribosomes Smooth endoplasmic reticulum Exocytosis Golgi apparatus Rough endoplasmic reticulum Figure 2.12 Relationship of outer nuclear membrane with other membranes (iii) The inner membrane is smooth; no ribosome is attached to it and it is not folded. (iv) This nuclear envelope disappears at prophase of cell division and reappears at the end of telophase. Therefore, the components of the membrane can be hydrated and reorganised into its original state. (v) There are nuclear pores in the envelope. The pores are relatively big, 40 – 150 nm and cover a surface of 8% of the envelope. However, the passage of substances is very well controlled. The bigger pores are specifically for the transport of RNA and ribosome subunits from the nucleus to the cytoplasm. Steroid hormones may enter the nucleus through the phospholipid layers by diffusion. (vi) There is a perinuclear space of about 10 – 40 nm wide between the outer and inner membrane of the envelope.

Biology Term 1 STPM Chapter 2 Structure of Cells and Organelles 2 68 (vii)The functions of the nuclear envelope are as follows: • It protects the inner structure of the nucleus especially the chromatin. • It separates the nucleus from the cytoplasm so that reactions occur in the nucleus are not affected by those of the cytoplasm. • It controls the shape of the nucleus. This provides a three dimensional space for processes such as the synthesis of DNA and RNA. • It controls the passage of substances like ribosomes and RNA from the nucleus to the cytoplasm. (b) Nucleoplasm (nuclear sap / karyoplasm) (i) Nucleoplasm is the part of protoplasm inside the nucleus, separated by the nuclear envelope. (ii) Its composition is the same as that of the cytoplasm, consisting mainly of water with crystalloids and dissolved colloids. It has DNA, histone and pentoses that are not found in the cytoplasm. (iii) The crystalloids are monosaccharides including glucose, ribose and deoxyribose; amino acids, organic acids, nucleotides and mineral ions like phosphates and K+ ions. (iv) The colloids are DNA, RNA and proteins particularly histone that mix with DNA forming chromatin. (v) Chromatin is made of DNA and histone protein. Eight molecules of histone, wound by DNA strand, form a nucleosome unit. Chromatin is divided into two types, the euchromatin and the heterochromatin. (vi) Euchromatin composes of more DNA that is less wound on histone protein. It is more lightly stained. It contains more genes that are active and is found in the centre of the nucleus. (vii) Heterochromatin found in the periphery of the nucleus composes of DNA that is more wound with histone forming more nucleosomes. The genes in it are not active. (viii) The chromatin is easily stained with acidic eosin to form a purple colour. This makes nucleoplasm different from cytoplasm. (ix) It is common to find foreign structures that are not supposed to be there. Such structures include mitochondria and parts of the endoplasmic reticulum. (x) Nucleoplasm performs various functions. It contains various enzymes for metabolism including that for glycolysis, Krebs cycle, phosphorylation and the synthesis of NAD, replication and transcription of DNA. (c) Nucleolus (i) Nucleolus is a spherical structure that is the site for ribosome synthesis in the interphase of nucleus. (ii) Its location is not fixed, it is usually found in the centre or on one side of the nucleus.

Biology Term 1 STPM Chapter 2 Structure of Cells and Organelles 2 69 (iii) The shape of the nucleolus is usually spherical, but it can be oval and it can change its shape. (iv) There is usually one nucleolus per nucleus, but in rare cases, there can be two per nucleus. (v) The structure of nucleolus as interpreted from the electron micrograph is shown in Figure 2.13. Region with chromosome/DNA Region with fibrils Region with granules Figure 2.13 Schematic interpretation of the nucleolus structure (vi) It has a region with chromosome where one or two chromosomes or DNA are found. In fact, it is the genes (organisers) found in the DNA that will start the process of nucleolus formation. The genes code the rRNA and protein of the ribosome. The nucleolus is the structure that is involved in the process of making ribosomes. (vii) It has another region with fibrils where the transcription of genes forms rRNA. Some of the RNA act like mRNA, move out into the cytoplasm and are translated into proteins by ribosomes there. The others are rRNA and combined with the proteins moved in from cytoplasm to form coarser fibrils before they coil to form the ribosome subunits. (viii) It has a third region with granules where rRNA and protein interact, coil and fold to form two types of ribosome subunits. One type is larger than the other. The larger is the 60S type and the smaller is the 40S type. These granular ribosome subunits will move away from the nucleus through the nuclear pores into the cytoplasm. (ix) There is a cyclic change for the nucleolus like the nuclear membrane. It disappears during prophase of cell division and reappears later at telophase. This is because RNA and protein can be hydrated at prophase. The cells have to form ribosomes after cell division. (d) Chromosomes (and its organisation) (i) Chromosomes are structures that are formed from DNA and histone during metaphase of mitosis. The DNA of the nucleus at other times can also be called chromosomes. (ii) Chromosomes have no shape and they are not organised during interphase. They exist as chromatin, long DNA molecules with certain parts attached with histone. The part of DNA that is not coiled around histone contains active genes. The genes can later be transcribed to form proteins.

Biology Term 1 STPM Chapter 2 Structure of Cells and Organelles 2 70 (iii) The number of chromosomes per cell ranges from 8 – 100. The chromosomes in diploid organisms exist in pairs. For example, each human somatic (non-gametic) cell has 46 chromosomes, in 23 pairs. In gametes, the number is halved. (iv) Homologous chromosomes are identical in structure, though not necessarily in allelic constitution. (v) Maternal chromosomes are the set of chromosomes which originates from the mother through the ovum. Paternal chromosomes are the set that originates from the father through the spermatozoon. (vi) Sex chromosomes determine the sex of the organism. For example, females have a pair of homologous X chromosomes whereas the males have an X chromosome and a nonhomologous and much smaller Y chromosome. A gene called the t factor in the Y chromosome determines the formation of testes during the formation of the sex organ in the foetus. Otherwise, the foetus will be a female. (vii) Chromosomes other than the sex chromosomes are called autosomes. They are usually in larger numbers. For example, the human cells have 22 pairs of autosomes and one pair of sex chromosomes. (viii) The size of the chromosomes varies between species. The average size of the human chromosome is 6 µm. The largest human chromosome is labelled as chromosome 1 and the smallest as chromosome 22 and chromosome Y. Plants usually have larger chromosomes than animals. Birds and fungi are among the organisms with the smallest chromosomes. (ix) The chromosome shapes vary during the cell cycle. When we refer to the chromosome shapes, we refer to their shapes during metaphase of mitosis. Chromosomes consist of two strands of cylindrical chromatids, which are attached together by a structure called centromere. Therefore, the shapes of chromosomes are determined by the position of the centromere, which can be metacentric, telocentric or acrocentric, as shown below. Metacentric Telocentric Acrosentric Figure 2.14 Types of chromosomes

Biology Term 1 STPM Chapter 2 Structure of Cells and Organelles 2 71 The centromere is the primary constriction of the chromosome. Besides the centromere, there may be another constriction which is called secondary constriction. Some chromosomes may have secondary constriction. Other chromosomes may be of longer or shorter length. All these determine the shape of chromosomes. Chromosome with secondary constriction Chromosome with extra length Figure 2.15 Two types of abnormal chromosomes (x) The structural organisation of chromosome is as follows: • Each chromosome is made up of two sister chromatids which are identical. Each chromatid is made up of one molecule of DNA as a result of replication. Each of the molecules becomes a chromatid and they are attached together by the centromere. • During prophase, each DNA molecule winds around a group of 8 histone molecules, forming a complex unit called nucleosome. During interphase, a certain amount of DNA forms nucleosomes, and the genes are inactivated. • 6 such nucleosomes may coil regularly to form a secondary structure, which may be folded or coiled to become the compact chromatid. • Such regularity may not be present in all species of organisms especially in bees, whose chromosomes with DNA and nucleosomes are folded, rather than neatly coiled. • The centromere is a constricted portion of the chromatid where protein keeps the two chromatids together. At the end of mitotic metaphase, the centromere divides, chromatids separate and are pulled by spindle fibres to the opposite poles. DNA Histone Nucleosome Secondary coiled Tertiary coiled Coiling Chromatin fibre Figure 2.16 Organisation of chromosomal structure

Biology Term 1 STPM Chapter 2 Structure of Cells and Organelles 2 72 (xi) The chromosomes perform two major functions as follows: • Chromosomes that contain genes, control the production of RNA and proteins in cells. Through these proteins, especially the enzymes, chromosomes control all the activities of the cell and inheritable characters of an organism. • The compact chromosomes formed during metaphase enables mitosis and meiosis to take place. These chromosomes can move easily compared to the untidy long slender DNA. Hence, chromosomes enable genes to be passed down from one mother cell to daughter cells and thus, one generation to the next generation. Endoplasmic reticulum (ER) 1. ER is a network of flattened sacs and tubules that interconnect to form a complex structure in the cytoplasm for internal transport of substances. 2. Each flattened sac or tubule is called cisterna. These interconnecting cisternae form the basic units of function for ER. 3. The membrane of the ER is the typical lipoprotein type. The membrane is not folded and the proteins on both sides are of different types. 4. The content of the cisternae is a sol called matrix. The matrix varies in content between different cells and contains a mixture of proteins. 5. The outside of the cisternae form a complex network of intercisternal space. Its composition is the same as the cytoplasm but with microfilaments attached on its outer membrane to maintain the ER’s shape. 6. The membrane of ER may connect to the outer membrane of the nucleus, which may continue to expand to form more ER membrane. The ER itself will bud off to form the Golgi apparatus. Certain parts of the ER may connect to the plasma membrane through the tubules. 7. The size of ER depends on the type of cell. In glandular cells and liver cells, the ER is very big and complex. 8. ER can be divided into two types: the rough ER and the smooth ER. The smooth ER is formed from the rough type. (a) Rough ER (i) The rough ER is the type with a lot of ribosomes attached to its outer surface. It is found in glandular cells that produce a lot of protein for secretion, such as the glandular or goblet cells of the digestive system including pancreas, stomach and small intestine. (ii) These ribosomes produce proteins for export in the cytoplasm attach themselves on the surface of the ER. Such proteins have signal sequence to attach to the surface of ER. The protein formed then enters the matrix of cisterna through special pores. The protein is later moved to the Golgi apparatus, packed into vesicles and exported through exocytosis. Exam Tips Remember that organisation of chromosomes includes not only structural organisation but also that during interphase, their organisation into pairs and sex chromosomes.

Biology Term 1 STPM Chapter 2 Structure of Cells and Organelles 2 73 Polysome Cisterna Fenestration (perforation) in reticulum sheet Ribosomes Lamela of reticulum node made up of double membrane Rough endoplasmic reticulum Smooth endoplasmic reticulum with branching tubes Figure 2.17 Structure of rough and smooth endoplasmic reticulum (iii) The two major functions of the rough ER are as follows: • Rough ER produces proteins such as digestive enzymes found in the glandular cells of the pancreas, stomach, small intestine and liver. • Rough ER transports proteins to smooth ER or to the Golgi apparatus through sacs pinched off from its surface membrane. Protein like mucus has its carbohydrate component added in the smooth ER or the Golgi apparatus. (b) Smooth ER (i) Smooth ER is the type with little or no ribosome on its surface. Embedded on the inner surface of the membrane, there are a lot of enzymes catalysing the synthesis of carbohydarates and lipids. Vesicles and larger sacs bud off to fuse with the cisternae of the Golgi apparatus. (ii) The functions of the smooth ER are as follows: • In animal cells, the smooth ER produces and transports lipids, including oils and phospholipids, sex hormones such as in the testes and ovaries, and in the brain cells. • In the liver cells, smooth ER detoxifies drugs and toxins in our body, with the help of enzymes. • In the striated muscles, smooth ER, called sarcoplasmic reticulum is involved in the storage and transport of calcium ions. • In the meristem cells, smooth ER forms cellulose, hemicellulose and pectin. The smooth ER transports them to the central plate where they are used to form new cross walls after mitosis. • Smooth ER forms lysosomes which are vesicles that are used for internal transport and reactions. 2011

Biology Term 1 STPM Chapter 2 Structure of Cells and Organelles 2 74 Mitochondria 1. Mitochondria are the ‘power houses’ of the cell, where energy in the form of ATP is formed. The energy comes from cellular respiration where ATP is formed from the bonding of phosphate to ADP. 2. Mitochondria are found in every eukaryotic cell. Their location inside the cell is not fixed as they can move around. 3. Protozoa and yeasts have only one mitochondrion per cell. In the liver cells, there are between 500-1,400 mitochondria per cell whereas in the root cap cell of maize, they vary between 100-3,000 per cell. The number can be increased when a cell becomes more active and needs more energy. 4. Each mitochondrion can divide to form two mitochondria. This happens when the cells become active or just before cell division. However, such division cannot occur outside the cells, as it requires enzymes coded by the nucleus. 5. Usually they are spherical, oval or sausage-shaped. It can be like a rod or a spiral. The shape is changeable. 6. Mitochondria are considered medium size organelles in the cell. They can hardly be observed under light microscope. Their diameter is 0.25-1 µm and length 3.5-10 µm. 7. They have 65-75% protein, 25-35% lipid and about 0.5% of nucleic acids. 8. They have an envelope with liquid matrix within as shown below. Cristae Stalked granule Outer membrane Matrix Inner membrane Figure 2.18 A mitochondrion 9. Its envelope is made up of two layers of lipoprotein membranes with an inter-membrane space in between. 10. The outer membrane is smooth with no granule attached. It has a lot of pores with diameters between 2.5-3.0 nm. Such pores are part of the channel proteins or translocase for the passage of ADP or ATP and NAD+ or NADH. 11. The inner membrane is folded to form cristae that are tube-like in plant cells or folding in animal cells. The cristae will increase in number when the respiration rate inside the cell increases. There are a lot of stalked granules embedded on the inner membrane. • Mitochondrian – singular Mitochondria – plural Language Check 2015

Biology Term 1 STPM Chapter 2 Structure of Cells and Organelles 2 75 12. The size of these granules vary. These are the ATP synthase enzyme that performs oxidative phosphorylation to produce ATP from ADP and phosphate, in the presence of oxygen. 13. The colloidal interior of the mitochondria contains ribosomes, DNA, RNA and a lot of enzymes, which are involved in the Krebs cycle and the oxidation of fatty acids. 14. The functions of mitochondria are as follows: (a) Mitochondria carry out Krebs cycle, part of cellular respiration within their matrices. (b) They carry out oxidation and complete breakdown of fatty acids into carbon dioxide and water to produce ATP. (c) They carry out oxidation and complete breakdown of amino acids. (d) They carry out oxidative phosphorylation, which produces ATP from ADP and phosphate. (e) They produce their own proteins from DNA with the help of RNA. The proteins are those required for the oxidative process. Golgi apparatus (Dictyosome in plant cells) 1. Golgi apparatus is an organelle consisting of a stack of flattened sacs, which produce vesicles full of secretion for internal or external uses. 2. They are found in large numbers in glandular cells, neurones, muscle tissues, root cap cells and meristems of plants. Their locations within the cell are not fixed. They are formed from ER. 3. There is usually one of them per cell. However, there are many in glandular cells and their number can increase as the secretory activities increase. Meristem has more of them per cell. 4. Each consists of a stack of flattened sacs called cisternae, which are rough and circular with a network of tubules around their periphery as shown in Figure 2.19. Vesicle budding off and moving towards cell membrane Cisterna Inter–cisternal space Sac from ER added to the convex face Network of tubules Figure 2.19 Golgi apparatus 2014 2018

Biology Term 1 STPM Chapter 2 Structure of Cells and Organelles 2 76 5. Each of the cisternae is of different sizes of 1-3 µm in diameter and 0.05 µm in thickness. There are channels connecting one cisterna to another. Usually the whole stack is curved with its convex cis face facing the nucleus. Sacs are added onto the convex surface from ER for the transport of protein, lipid or carbohydrate. 6. Vesicles can bud off carrying secretion of protein, glycoprotein or lipid. The whole cisterna of the outermost trans face can be completely budded off as vesicles. 7. The membrane is of lipoprotein type. The membrane can be added on to form new cisterna at one side and budded off completely on the other side. 8. There are microfilaments that bind the cisternae to keep them in a stack. 9. The functions of Golgi apparatus are as follows: (a) It forms lysosomes through the budding of larger vesicles or fusion of several smaller ones. (b) It processes proteins transported from ER to form glycoprotein before it is packaged into vesicles to be exported from the cell. (c) It packs digestive enzymes and export them as in the pancreatic glandular cells. (d) It produces cell wall materials in vesicles, which are directed to the cell plate where new cell wall is formed after mitosis in meristem. (e) It can process lipids to form glycolipids, package them, transport and store them within the cell. (f) It exerts some forms of control over internal transport of vesicles from one part of the cytoplasm to another part. (g) It also exerts control over the turn over of the plasma membrane as each time exocytosis takes place, a certain amount of plasma membrane is added. Lysosomes 1. Lysosomes are spherical vesicles that contain digestive hydrolases. 2. They are found in cells that carry out endocytosis such as phagocytes and protozoa. They are found in most animal cells as well as cells of metamorphorsising insects and tadpoles. Usually they are absent in plant cells except in immature xylem cells and sieve tubes. 3. There may be only one lysosome per cell. A lot of them are usually present in the phagocytes and cells of the tadpole tail. 4. It is spherical in shape, bound by a layer of lipoprotein membrane. 5. The size varies from 0.1 to 0.5 µm. 6. Its membrane is the usual single layer of lipoprotein but the enzymes it carry do not digest it. Exam Tips Remember the process of lysosome action, which includes its membrane fusing with the membrane of organelle or plasma membrane to release its content of hydrolases. The hydrolases will hydrolyse complex biochemicals to their simple and absorbable products. Remember that nucleus, ribosomes, ER, the Golgi apparatus and lysosome are inter-related.

Biology Term 1 STPM Chapter 2 Structure of Cells and Organelles 2 77 7. Their content is acidic, homogenous in nature and contain many types of hydrolases. They include proteinase, lipase, carbohydratase, acid nuclease (DNase and RNase) and acid phosphatase. 8. The functions of lysosomes are as follows: (a) It can digest foreign substances or cells that are endocytosised. (b) It clips certain bond such as that of thyroglobulin. Thyroglobulin is formed within the follicle of the thyroid gland. When it passes through cells lining the follicle, thyroxin is released from the globulin and emptied into the capillary. (c) It can carry out autophagy i.e. old or worn out organelles are digested by their digestive enzymes. Red blood cells have their nuclei digested during their course of development in bone marrows. (d) It exports their enzymes by exocytosis such as in the cartilage by osteoclasts during its development to form bones. (e) It can carry out autolysis in which the whole cells are digested for rebuilding of new tissue during metamorphorsis. This happens in the tail of the tadpole where the digestion products are used for building lungs and adult skin. Ribosomes 1. Ribosomes are small granules where synthesis of proteins occurs. 2. They are found in all cells particularly cells that produce a lot of proteins such as the glandular cells of pancreas and liver. Ribosomes are found in the nucleus, free in cytoplasm or in cytoplasm attached to ER, mitochondria and chloroplasts. 3. Their number is not fixed. It is found in large numbers in the glandular cell that produces a lot of proteins and its numbers can increase. 4. They are spheroid in shape, consisting of two subunits in which one is larger than the other such as shown in Figure 2.20. Head Wing Cleft Platform Small subunit Large subunit 20 nm Stalk Central ridge Front view Side view Small subunit Large subunit Figure 2.20 Ribosome structure

Biology Term 1 STPM Chapter 2 Structure of Cells and Organelles 2 78 5. They are very small, about 22 nm in diameter for the eukaryotic 80S types and 18 nm diameter for the prokaryotic 70S types which are found in prokaryotic cells as well as mitochondria and chloroplasts. 6. The subunits can be attached to form bigger functional units in the presence of magnesium ion. For eukaryote: 60S + 40S  80S For prokaryote: 50S + 30S  70S 7. They are made of RNA and protein synthesised in the nucleolus. As for the 80S types, the 60S subunits contain about 3 types of RNA and equal number of types of proteins. The 40S smaller subunits contain 1 type of RNA and protein. 8. As for the 70S types, the larger 50S subunits contain 3 types each of different RNA and proteins. The smaller 30S subunits contain only a single type each of RNA and protein. 9. The function of ribosomes is to provide the site for the formation of peptide bonds in which amino acids are joined to form polypeptide or protein. The subunits can form a complex with mRNA. Two sites are found on the surface where two tRNAs will each bring an amino acid to the corresponding site, matching the codons of mRNA to that of the anti-codon of the tRNA. Therefore, ribosomes can ‘read’ the codons on the mRNA and join specific sequence of amino acids to form specific protein. Chloroplasts 1. Chloroplasts are plastids, organelles that contain chlorophyll and carry out photosynthesis. 2. Chloroplasts are found in the part of the plant that is green in colour, especially in the mesophyll cells of leaves, parenchyma of young stems, fruits, sepals and even aerial green roots. 3. Their locations in cells are not fixed, they can move and orientate themselves with their larger surface towards the sunlight. This is to enable them to obtain the maximum amount of sunlight. 4. There are about 100 of them in a palisade mesophyll cell of flowering plants. The number can be increased when light intensity increases, or decrease if the light intensity decreases. 5. They have biconvex circular shapes like that of lenses. 6. They are reasonably big to be observed under a light microscope. They are about 3-10 µm in diameter and 2-3 µm thick. 7. The envelope consists of two layers of lipoprotein membranes that are smooth, with no foldings or granules. 8. There is an internal membrane system inside the chloroplast called the thylakoid system within a liquid called stroma. The internal structure is shown in Figure 2.21.

Biology Term 1 STPM Chapter 2 Structure of Cells and Organelles 2 79 Chloroplast envelope Stroma Chloroplast DNA Ribosomes Oil droplet Thylakoid Granum Starch grain Intergranal lamella (a) Intergranal lamellae Thylakoid (b) Figure 2.21 Structure of chloroplasts 9. The thylakoid membrane forms circular discs that are stacked like shillings called granum. 10. Each granum is made up of 10-100 thylakoids stacked together. There are 40-60 grana per chloroplast. 11. There are channels called inter-granal lamella connecting one thylakoid of a granum to another granum. These inter-granal lamellae form a network between the grana. The membrane of the tylakoids and lamellae is lipoprotein in nature, but there are photosynthetic pigments forming photosystems that are studded in the membrane of both the lamellae and grana. Each photosystem consists about a mixture of 300 various chlorophyll, carotenoid and protein molecules to form a complex. 12. Stroma contains a colloidal sol where enzymatic reactions that require no light to take place. It contains the followings: (a) Enzymes, especially those involved in the Calvin cycle where reactions forming carbohydrates and other organic compounds take place. (b) End products of photosynthesis such as sucrose, starch and fat droplets, which are usually attached to the lamellae. (c) Intermediate compounds, such as organic acids, phosphorylated monosaccharides and their acids. (d) Ribosomes of the 70S types. (e) A circular ring of DNA and RNA. • granum – singular grana – plural • lamella – singular lamellae – plural Language Check Language Check Exam Tips Remember the structure, functions and distribution of chloroplast of flowering plants. Remember that three organelles i.e. nucleus, mitochondria and chloroplasts are surrounded by envelope of double lipoprotein membrane and they have several similarities.

Biology Term 1 STPM Chapter 2 Structure of Cells and Organelles 2 80 13. The functions of chloroplasts are as follows: (a) The major function of chloroplast is to carry out photosynthesis producing organic compounds especially carbohydrates. (b) Chloroplasts carry out their functions by using the membranes of thylakoids and lamellae to trap lights and convert them to chemical energy mainly in the form of ATP. They carry out photoactivation and photophosphorylation through Calvin cycle. (c) The ATP is then used to perform the fixation of carbon dioxide to become organic compounds in the stroma. (d) The DNA and the protein synthetic system in the chloroplasts produces some of the specific proteins used in photosynthesis. The chloroplasts still depend on the nucleus to obtain most proteins within. (e) The chloroplast can divide especially in their premature protoplastid stage in the meristem. Mature chloroplasts do divide. Centrioles (Centrosome) 1. Centrioles are organelles that assemble spindle fibres in animal cells but are not found in plant cells. 2. They are found in all animal cells except the nerve cells. They are also found in fungal and algal cells. 3. One pair of centrioles is usually located beside the nucleus. 4. The two centrioles are cylindrical in shape, arranged perpendicular to one another as shown in Figure 2.22. Figure 2.22 The structure of centrioles 5. They are small and can be observed as a dot under a light microscope. Their length is about 0.3-0.4 µm with a diameter of about 0.2 µm. 6. Each is made up of 9 triplets of microtubules, which are attached lengthwise together as shown as a cross-section in Figure 2.23. Centriole cylinder consisting of 9 sets of microtubules. Each set has 3 microtubules 1 set (3 microtubules) Third microtubule Second microtubule First microtubule Figure 2.23 9 triplets of microtubules

Biology Term 1 STPM Chapter 2 Structure of Cells and Organelles 2 81 7. Centrioles divide during prophase of mitosis and each pair can move to opposite poles as shown in Figure 2.24. Figure 2.24 Division of centrioles and formation of spindle fibres 8. The functions of centrioles are as follows: (a) Centrioles organise the formation of spindle fibres, which are attached to the centromeres of chromosomes during metaphase. During anaphase, the chromosomes or the chromatids will separate and are pulled by the fibres to opposite poles in meiosis or mitosis respectively. (b) Centrioles organise the formation of cilia and flagella, which also have a “9 + 2” pattern. Vacuoles 1. Vacuoles are sacs with lipoprotein membrane, which are usually spherical in shape. 2. There are three types of vacuoles: (a) Sap or central vacuole (b) Food vacuole (c) Contractile vacuole 3. Sap or central vacuole (a) Sap vacuole is found in plant cells. (b) Sap vacuole is small and numerous in young plant cells but is big and can occupy 90% of the volume of matured plant cells. It contains water, sucrose, amino acids and some mineral ions especially those in excess or wastes such as silicates. (c) Sap vacuole stores water and mineral ions. It can balance water potential when required and acts as a store for waste products. (d) Sap vacuoles in mesophyll cells of leaves push the chloroplasts to the edges so that the chloroplasts can receive maximum amount of light. 4. Food vacuole (a) Food vacuole is found in cells that perform endocytosis such as phagocytic white blood cells and protozoans. Structures and functions of organelles 1. Nucleus (nuclear envelope, nucleolus, nucleoplasm and chromosomes) – to control all activities of cell through the genes. 2. Endoplasmic reticulum: RER (with ribosomes) – to produce proteins for export out of cell SER (with no ribosome) – to produce lipids – to detoxify toxins 3. Mitochondrion (double membranes with matrix) – to carry out respiration and production of ATP 4. Golgi apparatus (stack of flattened sacs) – to package substance for export out of cell 5. Lysosome (vesicles of hydrolases) – to digest internal substances and external substances 6. Ribosome (2 combined units of protein and RNA) – to produce protein 7. Chloroplast (double membranes + thylakoid system) – to carry out photosynthesis 8. Centrioles (2 short cylinders of microtubules) – to organise formation of spindle fibres in animal cell 9. Vacuoles (spherical sacs): Sap vacuole – stores water Food vacuole – digests food Contractile vacuole – to expel excess water Summary VIDEO Cell Structures

Biology Term 1 STPM Chapter 2 Structure of Cells and Organelles 2 82 (b) Food vacuoles or phagosomes in phagocytes are small. They contain bacteria, organic particles and dissolved proteins. (c) Food vacuole is a place for food digestion. Any undigested food is egested through the plasma membrane. 5. Contractile vacuole (a) Contractile vacuole is found in freshwater protozoans. (b) Contractile vacuole is spherical in shape, able to absorb water and contract, forcing water out through the membrane. Those found in Euglena and Paramecium have feeding smaller sacs or tubules to empty water into the main vacuole. (c) Contractile vacuole acts as an osmoregulatory mechanism to get rid of excess water in freshwater protozoans. If not, the cell may burst due to excessive water absorbed through osmosis. Quick Check 3 1. Mitochondria and chloroplasts seem to have evolved from endosymbiosis of prokaryotic cells. Suggest reasons for this. 2. Export of substances from cells requires concerted actions of nucleus, ER, the Golgi apparatus and lysosomes. Why? Differential Centrifugation 1. Differential centrifugation is a technique of separating cell components, including macromolecules using a centrifuge. Centrifuge uses centrifuging force equivalent to many times that of gravitational force (g) to spin down cell components of different S values (sedimentation units) step by step. 2017 2. The procedure to fractionate cellular components is as follows: (a) Tissue is first homogenated with a homogeniser, which can be very sophisticated using ultrasound to break up cells to the level required. (b) Normally the tissue has to be chilled and added with buffer to keep the enzymes functional and added with isotonic solution to prevent the organelles from breaking. (c) The homogenate is centrifuged at 600 times gravity for 10 minutes for animal tissues. Nuclei and unbroken cells are spun down. (d) Then, the supernatant is centrifuged at 10,000 times gravity for 20 minutes. Mitochondria, cisternae of endoplasmic reticulum and Golgi apparatus are spun down. (e) Further centrifuge at 100,000 times gravity for 60 minutes will spin down ribosomes, microtubules and microfilaments. The supernatant will then contain macromolecules such as nucleic acids and proteins.

Biology Term 1 STPM Chapter 2 Structure of Cells and Organelles 2 83 Animal tissues Homogenate Homogenisation Centrifugation at 600 g for 10 minutes Centrifugation at 10,000 g for 20 minutes Centrifugation at 100,000 g for 60 minutes Nuclei and unbroken cells Mitochondria, ER and Golgi bodies Ribosomes, microtubules and microfilaments Supernatant Supernatant Nucleic acids and proteins Figure 2.25 Step by step cell fractionation 3. Further differential centrifuge is ultra-centrifugation using force with more than 100,000 times gravity. 4. This technique is to separate mixture of macromolecules of different molecular weights or S values. S value is a scale of sedimentation units for molecule to move down in gel used in ultra-centrifugation. Higher S values are heavier and more stream-lined. For examples, DNA can be separated from RNA, nucleic acids can be separated from proteins and radioactive DNA can be separated from normal ones. 5. The method and precautions are as follows: (a) The space within the ultracentrifuge should be vacuumed to avoid any friction between the tubes and the air. (b) The temperature has to be lowered. (c) Gel is added to stop the molecule at certain levels in the tube. (d) Dye is added to the mixture to detect separation. Exam Tips Remember the basic principles of centrifugation. Remember the examples of uses in the isolation of cellular components. Quick Check 4 1. How can radioactive DNA and normal DNA be separated by ultra centrifugation? 2. How can the background of different refractive indexes with the object be lightened or darkened? 3. Why can electron beam and not light beam be used to resolve smaller objects? Differential centrifugation 1. Fractionation by homogenisation 2. Centrifuge 600 g for 10 min to obtain nuclei 3. Centrifuge 10, 000 g for 20 min to obtain mitochondria and chloroplasts 4. Centrifuge 100,000 g for 60 min to obtain ribosomes 5. Ultra-centrifuge with gel in vacuum to separate component of ribosome proteins, RNA and DNA of different S values Summary 80S ribosomes can be separated into 60s and 40s sub-units. Why 60s + 40s not equal to 100s? This is due to 80S ribosomes with one big and one small units are not so stream-lined. So, they have lower s units. Info Bio

Biology Term 1 STPM Chapter 2 Structure of Cells and Organelles 2 84 2.3 Specialised Cells 1. Specialised cells are cells that have undergone specialisation or differentiation in the course of embryonic development. All cells of a multicellular organism develop from a single zygotic cell after fertilisation. Since then, mitosis increases the cell number and ensures exact genetic makeup in all the cells formed later. However, in the course of development, cells acquire different structures and functions. 2. Specialisation is a result of genes being ‘switched on’ or ‘switched off’ during development, even though the cells have the same genetic content for a particular individual. 3. Red blood cells have their haemoglobin genes ‘switched on’ when they were developed in the bone marrow, but their melanin genes are ‘switched off’. Conversely, skin cells have their haemoglobin genes ‘switched off’ whereas their melanin genes ‘switched on’ in the course of development. Unspecialised Cells Found in Plants Meristematic cells 1. Meristematic cells are cells found in the meristem, a localised tissue that can divide by mitosis. 2. The structures of meristematic cells are as follows: (a) All the cells are young and have not undergone differentiation. They look the same and have the same size. (b) Apical meristematic cells have isodiametric prismatic shapes. They are all regular in shape and almost look spherical. Cambium cells are brick-like and some are very thin. (c) The cell wall is thin, only made up of primary cell wall. The cells can be easily damaged and nutrients can easily diffuse into them. (d) The nucleus is large, relative to the volume of the cell. All the nuclei are ready to start mitosis. (e) There is no intercellular space; the cells are compact and are close together. (f) The cytoplasm is dense, with few organelles which are small. All the organelles are young. Chloroplasts if present, are in the proto-plastid stage. 3. The distributions and functions of meristem are as follows: (a) Apical meristem. It is found in the shoot and root tips. Its function is to produce primary tissues, such as tissues found in a herbaceous plant. (b) Vascular cambium. It is found mainly in woody stems and Exam Tips Remember the eight basic plant tissues. Unspecialised cells in plants (meristematic cells) Thin wall, little cytoplasm and compact 1. Apical meristem – found at tips of shoot and root to form primary tissues 2. Vascular cambium – found in vascular bundle woody plants to form secondary xylem and phloem 3. Cork cambium – found beneath epidermis of woody dicots to produce cork 4. Intercalary cambium – found in grasses to produce cells above nodes Summary Students should be able to: (a) outline the structures, functions and distributions of unspecialised cells found in plants (meristematic cells); (b) describe the structures, functions and distributions of specialised plant cells found in epidermal, ground and vascular tissue; (c) describe the structures, functions and distributions of specialised animal cells found in connective, nervous, muscular and epithelial tissues, including the formation of endocrine and exocrine glands. Learning Outcomes

Biology Term 1 STPM Chapter 2 Structure of Cells and Organelles 2 85 roots. Its function is to produce secondary xylem (wood) and phloem. (c) Cork cambium (phellogen). It is found on the outer layer of dicotyledonous woody stem and root. Its function is to produce cork cells (phellem) on the outside and secondary cortex (phelloderm) on the inside. (d) Intercalary cambium. It is only found in monocotyledonous plants, 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 later, it disappears. Specialised Plant Cells Parenchyma 1. Parenchyma is a tissue with the least differentiation, with a thin wall and contains living protoplast and nucleus. 2017 2. It has the following structural features. (a) The cells are spherical, isodiametric and may be oval in shape. (b) The cells are the least differentiated i.e. with very few specialities. (c) The cells are alive, with protoplast and nucleus. All the enzymes within are active. (d) Their cell walls are thin, which are made up of only primary cell walls. (e) The sap vacuole is big and centrally located. It stores water and soluble mineral ions. (f) Their protoplast may store starch and they have chloroplasts. Some parenchyma are full of starch grains especially is storage organs. (g) The cells usually have large amounts of intercellular space. The air spaces allow easy exchange of gases especially for photosynthesis. (h) The cells can divide if stimulated by hormone such as auxin. 3. Its distributions are shown in all the eight basic organs (Figures 2.26 – 2.33). (a) In the cortices (singular cortex, layer beneath epidermis) of stems and roots. (b) In the pith (centre of root or stem) of dicotyledenous stem and monocotyledenous root. (c) In the mesophyll of leaves. (d) In the medullary rays of the secondary xylem and phloem. (e) Around vascular bundles in stems and leaf stalk. (f) In the epidermis with thickened wall and cuticle.

Biology Term 1 STPM Chapter 2 Structure of Cells and Organelles 2 86 Epidermis Collenchyma Sclerenchyma Phloem Cambium Pith Xylem Vascular bundle Figure 2.26 Dicot herbaceous stem Epidermis Secondary cortex Cortex Cambium Cork cambium Phloem Xylem Pith Figure 2.27 Dicot stem with secondary thickening Epidermis Sclerenchyma Vascular bundle Xylem Phloem Figure 2.28 Monocot stem Piliferous layer (epidermis) Cortex Xylem Phloem Endodermis Figure 2.29 Dicot herbaceous root Cork Cork cambium Secondary cortex Phloem Cambium Xylem Figure 2.30 Dicot root with secondary thickening Epidermis Sclerenchyma Cortex Endodermis Phloem Pith Xylem Figure 2.31 Monocot root Xylem Sclerenchyma Phloem Collenchyma Palisade mesophyll Spongy mesophyll Parenchyma Xylem Phloem Collenchyma Upper epidermis Lower epidermis Mesophyll cells Figure 2.32 Dicot leaf Figure 2.33 Monocot leaf (Zea mays)

Biology Term 1 STPM Chapter 2 Structure of Cells and Organelles 2 87 4. The functions of parenchyma are as follows: (a) It functions as a photosynthetic tissue as in the mesophyll of the leaves or in young stems. (b) It functions as a storage tissue as in the cortices or the pith of stems and roots. Some fruits and seeds have parenchyma cells as storage tissue. (c) It functions as packing tissue around the vascular bundles of stems and leaf stalks. (d) As epidermis, it protects the cells beneath physically and from desiccation. Collenchyma 1. Collenchyma is a tissue where the cells have thickened non-uniform primary cell walls. 2. The structure of collenchyma are as follows: (a) The cells are alive with protoplast and nucleus. (b) The shape of the cells is isodiametric or like an elongated prism. (c) The cell wall is not uniformly thickened. The collenchyma is divided into two types: angular (thickened at corners) and lamella (thickened at tangential wall) types. Figure 2.34 Collenchyma (d) The cell wall is of primary type and not lignified. (e) The cells are compact with no intercellular space. 3. Its distributions are shown in Figures 2.26 and 2.32. (a) It is found below the epidermis of dicotyledonous stems. (b) It is found beneath the epidermis of the main vein of dicotyledonous leaves. 4. The functions of collenchyma are listed as follows: (a) It functions to support the stem or the leaves of dicotyledonous plants. (b) It becomes meristematic and produces cork cambium in the dicotyledonous stem that undergoes secondary thickening.

Biology Term 1 STPM Chapter 2 Structure of Cells and Organelles 2 88 Sclerenchyma 1. Sclerenchyma is a simple tissue consisting of fibre cells or stone cells (sclereids), which have thick walls impregnated with lignin. 2. The structural features are listed as follows: (a) When sclerenchyma cells mature, the cells are dead and have no protoplast. (b) They have thick secondary walls impregnated with lignin. Lignin is a branched polymer which makes the wall very hard and impervious to water. The walls have many pits. (c) Their lumens are very small and empty. (d) The shapes of the cells depend on the types as shown in Figure 2.35. A single fibre A stone cell Thick wall Small lumen Thick wall Small lumen Pits Figure 2.35 Two types of sclerenchyma (i) Fibres They are like fibres i.e. long and thin with two sharp ends. They exist in bundles or layers. (ii) Stone cells They have a stone shape, usually exist as layers or scattered stone cells. 3. Their distributions are as follows: (a) Fibres are found beneath the epidermis and in the bundle sheaths of monocotyledonous stems or leaves as shown in Figure 2.28 and Figure 2.33. (b) Fibres are also found on the outside (Figure 2.26) or inside (Figure 2.27) the phloem of dicotyledonous stems. (c) Stone cells are found in fresh pears and ciku fruits, which give them their gritty texture. They are found as hard protective layers of plums, olive seeds and coconut shells. 4. Their functions are as follows: (a) Fibres support and protect the plants especially in stems and leaves. (b) Stone cells protect seeds and prevent germination so that the seeds can be dispersed further. Xylem 1. Xylem is a complex vascular tissue, which is used to transport water and support plants. 2. Xylem is divided into primary and secondary types. Primary xylem is formed from procambium at the shoot or root tips. Secondary xylem is formed from vascular cambium during secondary thickening or wood formation in the stem or root.

Biology Term 1 STPM Chapter 2 Structure of Cells and Organelles 2 89 3. Xylem consists of four types of cells, namely vessels, tracheids, parenchyma and sclerenchyma. (a) Vessels (i) These are the largest cells and are shaped like vessels. (ii) Their ends slant, open and connect to one another to form long pipes. (iii) They are dead cells with hollow lumen and no cross walls when mature. (iv) They have secondary wall impregnated with lignin. (v) The wall is specially thickened with patterns depending on their age or location as shown in Figure 2.36. Annular Spiral Scalariform Reticulate Pitted Figure 2.36 Different types of lignin deposition in xylem vessels (b) Tracheids (i) They are long, thin cells with polygonal cross sections. (ii) Their lumens are small and hollow when mature. (iii) Both ends are tapering, fitting those on the top and bottom like tiny tubes. (iv) Their walls are thick, lignified, and covered with a lot of pits. (c) Parenchyma (i) They are just like other parenchyma, only slightly smaller. (ii) They are young undifferentiated xylem, newly formed from meristems. They also form medullary rays in wood. (iii) Their walls are usually not thickened or lignified. (iv) They store starch in the form of granules. (d) Sclerenchyma (i) They originate from old tracheids. (ii) They look more or less like tracheids. 4. Their functions are as follows: (a) Vessels and tracheids (i) They transport water and mineral ions. (ii) They support the plants especially tall woody plants in which the wood of the plants consist of xylem. 2015

Biology Term 1 STPM Chapter 2 Structure of Cells and Organelles 2 90 (b) Parenchyma (i) They differentiate to form vessels and tracheids. (ii) They store food in the form of starch. (c) Sclerenchyma Their functions are mainly for support. 5. Xylem is found (a) in the stem, towards the inside of the vascular bundles, as in Figures 2.26, 2.27 and 2.28. (b) in the roots, towards the inside of the vascular tissue, as in Figures 2.29, 2.30 and 2.31. (c) in the leaves, on the upper part of the vascular bundles, as in Figures 2.32 and 2.33. Phloem 1. Phloem is a complex vascular tissue that translocates organic food especially sucrose and amino acid formed after photosynthesis. 2. Like xylem, phloem is divided into primary and secondary types. 3. Phloem consists of sieve elements, companion cells, parenchyma and sclerenchyma. (a) Sieve elements (i) Sieve elements consist of sieve cells and sieve tubes. (ii) Sieve cells are young cells with nuclei but with no defined sieve plates. (iii) Sieve tubes are mature cells, thin walled with no nucleus but with protoplast and sap vacuoles. (iv) Sieve tubes are long and slender cells connecting end to end to form tubes for translocation. (v) Their cross sections may be rectangular, round or polygonal. (vi) The cross walls of sieve tubes form lignified sieve plates with holes, allowing protoplast to flow from one tube to another. These plates have supporting functions as they prevent breakage of these thin-walled tubes under pressure. (b) Companion cells (i) They are small slender cells fitting neatly end to end, at least one beside a sieve tube. (ii) Their walls are thin and usually square in cross sections. (iii) They have nuclei, compact protoplast with high organic content, no sap vacuole but with a lot of mitochondria. (iv) Their cytoplasm is connected by many plasmodesmata to the sieve tubes. Sucrose and amino acid can diffuse to and fro between companion cells and sieve tube. (c) Parenchyma (i) They exist as undifferentiated phloem or medullary rays extended from xylem. (ii) Their structures are the same as ordinary parenchyma but smaller in size.

Biology Term 1 STPM Chapter 2 Structure of Cells and Organelles 2 91 (iii) They have thin primary wall. (iv) They are usually elongated prisms. (v) They are living cells with protoplasts and nuclei. They store starch. (d) Sclerenchyma (i) It is found in dicotyledonous stems, either on the outside or inside of the phloem. (ii) The structure is the same as an ordinary one. 4. The functions are as follows: (a) Sieve elements They translocate organic food substances especially sucrose, amino acids, organic acids and proteins. (b) Companion cells They provide energy in the form of ATP and their membranes have proton pumping-system for the loading of sucrose into the sieve tubes from neighbouring mesophyll cells. (c) Parenchyma They differentiate to form phloem cells and some remain as storage cells. (d) Sclerenchyma They protect and support the thin-walled phloem cells. 5. They are found in stems, roots and leaves as shown in Figures 2.26 – 2.33. Specialised Animal Cells 1. Animal cells are classified into four types, based on four fundamental tissues i.e. epithelial, nervous, muscle and connective tissues. Epithelial tissues 1. Epithelial tissues are covering or glandular cells. 2. They are divided into covering epithelia and glandular epithelia. (a) Covering epithelia (i) Covering epithelia are layers of cells that line the external or internal surfaces of organs. (ii) Their structural features are as follows: • The cells are arranged in a single layer called simple epithelium or in more than one layer called stratified epithelium. • The shape of the cells depends on the types; scale-like called squamous epithelium, cube-like called cuboidal epithelium and column-like called columnar epithelium. • The cells are attached to a thin layer of fine connective tissues at the bottom called basement membrane. This helps to attach it to other tissues. • At the top, the cells are exposed to air such as in the skin, or liquid such as those of the stomach. Specialised plant cells 1. Parenchyma (thin wall, living with intercellular spaces) found in epidermis, mesophyll, cortices, pith and ground tissue – for packing, storage of food and photosynthesis 2. Collenchyma (nonuniformly thickened wall, living and compact) found beneath dicot stem and leaf epidermis – for strengthening and support 3. Sclerenchyma (lignified thick wall fibres or stone cells) found in phloem of dicot stem, beneath epidermis in bundle sheath of monocot and in husk or stone of seeds – for protection and support 4. Xylem (mainly vessel element and tracheid of thick lignified wall) – for transport of water and soluble mineral ions 5. Phloem (mainly sieve tubes and companion cells of thin wall) – for transport of sucrose and amino acids. Summary