1. 9744 1.1 Lecture Notes (Student) 2023.pdf

CATHOLIC JUNIOR COLLEGE 9744 H2 Biology CORE IDEA: 1] THE CELL AND BIOMOLECULES OF LIFE 1.1 ORGANELLES AND CELLULAR STRUCTURES Narrative: Cellular structures provide the means to drive cellular processes Knowing how cellular structures facilitate specific cellular processes is fundamental to expla...

CATHOLIC JUNIOR COLLEGE 9744 H2 Biology CORE IDEA: 1] THE CELL AND BIOMOLECULES OF LIFE 1.1 ORGANELLES AND CELLULAR STRUCTURES Narrative: Cellular structures provide the means to drive cellular processes Knowing how cellular structures facilitate specific cellular processes is fundamental to explaining how life ‘works’. The cell theory states that the cell is the smallest and most basic unit of life and that cells grow only from existing cells. Understanding the role of cellular organelles (such as nucleus, ribosome, chloroplast and mitochondrion) and cellular structures (for example, the cytoskeleton) is crucial to understanding how organisms and life at large work. One key concept often explored in this chapter is “how are the structures of the organelles adapted for their functions?” There are significant differences between cells of prokaryotes and eukaryotes. Using bacteria as a model, the nucleoid is not enclosed by any membrane. Plasmid may be present as extra-chromosomal DNA. Membrane-bound organelles, such as mitochondria and endoplasmic reticulum, are absent. Prokaryotic ribosomes are different from eukaryotic ribosomes. Some bacterial cells have cell walls that comprise peptidoglycan rather than cellulose. Within the eukarya domain, the cell model of plants is also different from that of animals. Unlike unicellular organisms which merely undergo cellular division, cells of multicellular organisms undergo both division and differentiation to allow them to carry out their specific functions. Guiding Questions: Why is a cell the basic unit of life and how does it promote continuity of life? How is the basic unit crucial in understanding what constitutes life? What are the differences between cells of prokaryotes and eukaryotes, between cells of plants and animals, and between cells of unicellular and multicellular organisms? In what ways do viruses not fit the cell model? LEARNING OUTCOMES Candidates should be able to: Subtopic Learning Outcomes Pg. Cell Theory (a) Outline the cell theory with the understanding that cells are the smallest unit 3 of life, all cells come from pre-existing cells; and living organisms are composed of cells. Eukaryotes (b) Interpret and recognise drawings, photomicrographs and 3-22 electronmicrographs of the following membrane systems and organelles: rough and smooth endoplasmic reticulum, Golgi body, mitochondria, ribosomes, lysosomes, chloroplasts, cell surface membrane, nuclear envelope, centrioles, nucleus and nucleolus. (c) Outline the functions of the membrane systems and organelles listed in (b). Prokaryotes (d) Describe the structure of a typical bacterial cell (small and unicellular, 23-27 (Bacteria) peptidoglycan cell wall, circular DNA, 70S ribosomes and lack of membrane- bound organelles). Viruses (e) Describe the structural components of viruses, including enveloped viruses 28-32 and bacteriophages, and interpret drawings and photographs of them. (f) Discuss how viruses challenge the cell theory and concepts of what is 33 considered living. [not in student lecture notes, but discussed in tutorials] REFERENCES 1. Campbell, Neil A and Reece, J B (2015) Biology: A Global Approach (10 Th edition) (Pearson global edition) 2. Campbell, Neil A and Reece, J B (2011) Biology (Ninth edition) (Addison Wesley-Benjamin Cummings, www.aw-bc.com) 3. Campbell, Neil A and Reece, J B (2005) Biology: Concepts and Connections (Fourth edition) (Benjamin Cummings) 4. Taylor, D J, Green, N P O, Stout, G W and Soper R (1997) Biological Science 1 (Third edition) ( CUP, www.cambridge.org) ISBN 0521561787 5. Longman A-Level Course in Biology (Core Syllabus) by Hoh Y. K. 6. Biology of Microorganisms (Seventh Edition) by Brock Madigan Martinko Parker 1 CONTENT PAGE CONTENT Pg. 1 Cell Theory 3 2 Eukaryotes 3-22 Introduction to Eukaryotes 3 Concept Map for Organelles 7 2.1] Cell Surface Membrane 8 Non-membrane bound organelles 2.2] Ribosomes 9 2.3] Centrioles 10 Single membrane bound organelles 2.4] Endoplasmic Reticulum 11 2.4.1] Rough Endoplasmic Reticulum 2.4.2] Smooth Endoplasmic Reticulum 2.5] Golgi Body 13 2.6] Lysosomes 14 Double membrane bound organelles 2.7] Nucleus 15 2.8] Mitochondrion 18 2.9] Chloroplast 19 2.10] Endomembrane system 20 3 Prokaryotes (Bacteria) 23-26 Introduction to Prokaryotes 23 3.1] Cell Wall 24 3.2] Genome 25 3.3] Ribosome 26 4 Comparison between Eukaryotes and Prokaryotes 26-27 Concept Map of Eukaryotes and Prokaryotes 26 Table of Comparison 27 5 Viruses 28-36 5.1] Structural Components of Viruses 28 5.2] Examples of Viruses 29 5.3] Structure of Bacteriophages 30 5.3.1] T4 Phage 5.3.2] Lambda Phage 5.4] Structure of Animal Viruses 5.4.1] Structure of Influenza Virus 31 5.4.2] Structure of Human Immunodeficiency Virus (HIV) 32 5.5] Viruses challenge the cell theory 33 6 Experimental Skills and Miscellaneous 34-38 6.1] Units of Measurement 34 6.2] Microscopy 35 6.3] Calculating Magnification 36 6.4] Cell Fractionation 37 6.5] Endosymbiotic Theory 38 2 1] CELL THEORY Cell Theory LO (a) Outline the cell theory with the understanding that cells are the smallest unit of life, all cells come from pre-existing cells; and living organisms are composed of cells. Cell Theory arose in the mid-nineteenth century as a result of work by three German biologists, Schleiden, Schwann and later, Virchow. The Cell Theory states that: i) The cell is the smallest, most basic unit of life. ii) All living organisms are composed of cells. iii) All cells arise from pre-existing cells by cell division. 2] EUKARYOTES EUKARYOTES are organisms made of cells that have a true, membrane bound nucleus. They also possess membrane bound organelles. Examples of eukaryotic organisms are animals (Fig. 3), plants (Fig. 4), fungi and protoctists. A typical eukaryotic cell consists of the following: (a) Cell surface membrane This defines the boundary of a cell and retains its contents. (b) Nucleus This contains the genetic material that directs cellular activities. (c) Cytoplasm This consists of the following: o Cytosol This is the aqueous solution of ions and organic compounds (e.g. sugars, amino acids and proteins). o Organelles These include the organic cellular structures, usually enveloped by a membrane, such as the ribosome, endoplasmic reticulum, Golgi body, lysosome, mitochondrion, vacuole and centriole. o Cytoskeleton This consists of a network of microtubules, intermediate filaments and microfilaments made of protein. 3  FIG. 3: ANIMAL CELL Fig.3b An illustration of an Animal Cell as seen under a Light Microscope Fig. 3a 3-dimensional model of an Animal Cell Fig. 3c An illustration of a generalised animal cell as seen with the Electron Microscope 4  FIG. 4: PLANT CELL Fig.4b An illustration of a plant cell as seen Fig. 4a 3-dimensional model of a Plant cell under a Light Microscope Fig. 4c An illustration of a generalised plant cell as seen with the Electron Microscope 5 COMPARISON BETWEEN PLANT CELL AND ANIMAL CELL: Basis of Comparison Plant cell Animal cell (Features) Cell wall Tough, slightly elastic cellulose cell wall Cell wall absent – only a membrane present (in addition to the cell surrounds the cell membrane) Pits and Pits and plasmodesmata present in the No cell wall and therefore no pits or plasmodesmata cell wall plasmodesmata Middle lamella Middle lamella join cell walls of Middle lamella absent – cells are joined adjacent cells by intercellular cement Plastids Plastids, e.g. chloroplasts and Plastids absent leucoplasts, present in large numbers Vacuoles Mature cells normally have a large Vacuoles, e.g. contractile vacuoles, if single, central vacuole filled with cell present, are small and scattered sap throughout the cell Tonoplast Tonoplast present around vacuole Tonoplast absent Cytoplasm Cytoplasm normally confined to a thin Cytoplasm present throughout the cell layer at the edge of the cell Nucleus Nucleus at edge of the cell Nucleus anywhere in the cell but often central Lysosomes Lysosomes are not present (vacuoles Lysosomes almost always present carry out similar function) Cilia and flagella Cilia and flagella absent in higher Cilia or flagella often present plants Storage Starch grains used for storage Glycogen granules used for storage Cell division Only some cells are capable of division Almost all cells are capable of division Secretions Few secretions are produced A wide variety of secretions are produced Centrioles Centrioles absent in higher plants Centrioles present 6 2] EUKARYOTES Eukaryotes LO (b) Interpret and recognise drawings, photomicrographs and electronmicrographs of the following membrane systems and organelles: rough and smooth endoplasmic reticulum, Golgi body, mitochondria, ribosomes, lysosomes, chloroplasts, cell surface membrane, nuclear envelope, centrioles, nucleus and nucleolus. LO (c) Outline the functions of the membrane systems and organelles listed in LO (b). CONCEPT MAP FOR ORGANELLES Organelles Non-membrane Membrane bound bound Single Double ribosome membrane membrane centrioles Rough Endoplasmic Reticulum (RER) Nucleus (plural: nuclei) Smooth Endoplasmic Reticulum (SER) Chloroplast Golgi body Mitochondrion (plural: mitochondria) Lysosome 7 2.1] CELL SURFACE MEMBRANE (Fig. 6) A. STRUCTURE The cell surface membrane is a single membrane found at the periphery of the cell; it is named cell surface membrane to differentiate from other cell membranes found inside the cell. The cell surface membrane is made of biomolecules such as phospholipids, cholesterol, glycolipids, proteins and glycoproteins. The cell surface membrane comprises of two layers of phospholipids called the phospholipid bilayer. The hydrophobic “tails” facing away from the aqueous medium (“facing inwards”) and the hydrophilic “heads” facing towards the aqueous medium (“facing outwards”). B. FUNCTION The cell surface membrane regulates the movement of molecules into and out of the cell, a trait called selective permeability. Fig.6 Structure of cell surface membrane Fig.5 Structure of phospholipid 8 NON-MEMBRANE BOUND ORGANELLES: 2.2] RIBOSOMES (Fig. 7) A. STRUCTURE Ribosomes are organelles made of ribosomal RNA and protein. They are about 20-30 nm in diameter. Each ribosome consists of one small subunit made of one molecule of rRNA with 21 molecules of proteins and one large subunit made of two molecules of rRNA with 34 molecules of proteins. There are two types of ribosomes: 70S, which are found in prokaryotes, chloroplasts and mitochondria; and 80S, which are found in eukaryotes as free ribosomes in the cytoplasm and attached to the rough endoplasmic reticulum. (S = Svedberg unit or Sedimentation coefficient) - Prokaryotes - 70S ribosome is made up of a 30S small ribosomal subunit and a 50S large ribosomal subunit. - Eukaryotes - 80S ribosome is made up of 40S small ribosomal subunit and a 60S large ribosomal subunit. Each ribosome has three binding sites for tRNA (transfer RNA): i A site (aminoacyl-tRNA site): holds the tRNA carrying the next amino acid to be added to the chain. ii P site (peptidyl-tRNA site): holds the tRNA carrying the growing polypeptide chain. iii E site (exit site): discharged tRNAs leave the ribosome from the E site. B. FUNCTION 1. The main function of ribosomes is to serve as site of protein synthesis. 2. Ribosomes bound to endoplasmic reticulum generally make proteins that are destined either for inclusion into membranes, for packaging within certain organelles such as lysosomes or for export from the cell. 3. Ribosomes lying free in cytoplasm are sites of synthesis of proteins retained within the cell, i.e. function within cytosol, enzymes that catalyses metabolic processes localized within cytosol. Fig.7a Structure of Free and Bound Ribosomes 9  Fig. 7b Ribosome subunits with its corresponding binding sites 2.3] CENTRIOLES (Fig. 8) A. STRUCTURE They measure around 0.2 m in diameter and 0.3 to 0.5 nm in length From the transverse section of the centriole as seen under the TEM (Transmission Electron Microscope), 9 triplets of microtubules are fused together to give a rod-like structure. Each centriole is positioned at 90° to each other and are situated next to nucleus Only found in animal cells B. FUNCTION 1. Organise spindle fibres during cell division. 2. Anchorage for cilia and flagella. (a) (b) (c) Fig. 8 Structure of Centriole, (a) single (b) a pair (c) two pairs 10 SINGLE MEMBRANE BOUND ORGANELLES: 2.4] ENDOPLASMIC RETICULUM (ER) (Fig. 9 and Fig. 10) It consists of complex membrane-bound sacs called cisternae (plural; singular: cisterna). There are 2 types of ER of which each has a different role in synthesis and packaging. They are namely, the rough endoplasmic reticulum (rER) and the smooth endoplasmic reticulum (sER). Fig.9 Structure of Endoplasmic reticulum: Rough ER and Smooth ER Fig.10 Electron micrograph of Rough ER and smooth ER 11 2.4.1] ROUGH ENDOPLASMIC RETICULUM (rER) A. STRUCTURE Cisternae are flattened and interconnected with each other (Fig. 14) and are continuous with the outer membrane of the nuclear envelope. Ribosomes are found on the surface, which are sites of protein synthesis; these many ribosomes give the rough / granular appearance on the rER (Fig. 10) It can be broken into small pieces and resealed into vesicles known as microsomes during the homogenization procedure. B. FUNCTION Ribosomes are associated with the rough ER for protein synthesis. Enzymes built into the ER membrane attaches carbohydrates to proteins, forming glycoproteins. Rough ER increases surface area of the intra-cellular membranes for biochemical reactions. Rough ER forms a separate compartment allowing metabolic reactions to be localized. Rough ER stores secretions, e.g. hormones. Rough ER serves as an intracellular transport network between various parts of the cytoplasm and between cytoplasm and nucleus. For example, rough endoplasmic reticulum transports proteins to other parts of the cell by transport vesicles which are pinched off from the membrane of the endoplasmic reticulum. 2.4.2] SMOOTH ENDOPLASMIC RETICULUM (SER) A. STRUCTURE The smooth E.R. lacks ribosomes. It consists of tubular cisternae (Fig 11). It has a different set of membrane-bound proteins from the rough endoplasmic reticulum. B. FUNCTION 1. Lipid and steroid synthesis and transport. (e.g. phospholipids and steroid hormones) 2. Detoxification of drugs and poisons, e.g. detoxification of carcinogens in the liver. 3. Secretion of chloride ions (Cl-) in the stomach. 4. Storage and release of calcium ions (Ca2+) especially in the sarcoplasmic reticulum of muscles. Fig.11 Flattened cisternae of RER and Tubular cisternae of SER 12 2.5] GOLGI BODY / APPARATUS (Fig. 12) A. STRUCTURE It consists of flattened saucer-like membrane-bound stacks called cisternae and a system of associated vesicles called Golgi vesicles. This is seen as a single large stack in animal cells and in separate stacks in plant cells. It consists of a cis face and a trans face (Fig. 12). At the cis face or the outer convex face, new cisternae are constantly formed by the fusion of transport vesicles which budded from the rough ER and smooth ER. At the trans face or the inner concave face, the Golgi body breaks up to form vesicles such as lysosomes or transport vesicles. B. FUNCTION 1. Chemical modification of proteins and lipids Enzymes of the Golgi body attach short carbohydrate chains to proteins and lipids to form glycoproteins and glycolipids respectively. 2. Further Chemical modification of existing glycoproteins and glycolipids Note: Carbohydrates are first added to proteins in the rough ER usually during the process of polypeptide synthesis. The carbohydrate on the resulting glycoprotein is then further modified as it passes through the ER and the Golgi body. Enzymes of the Golgi body may also perform further modification, such as cleaving / trimming the carbohydrate chains or modifying the sugar on the carbohydrate chain. 3. Sorting and Packaging The various molecules in the Golgi body are then sorted and packaged into vesicles before distributed to other parts of the cell or secreted out of the cell. a. Hydrolytic enzymes of the lysosome will be sorted and packaged together to eventually form the membrane-bound digestive vesicle. b. Secretory proteins will be sorted and packaged into secretory vesicles, to be secreted out of the cell. c. Membrane proteins will be sorted and embedded into the membrane of the secretory vesicle which will be transported and fused with the cell surface membrane. d. Proteins meant for the other organelles are sorted and packaged into vesicles, to be transported to the target organelles. 4. In plant cells, non-cellulose polysaccharide of the cell wall (i.e. pectin) are also synthesised. 13  cis face trans face Fig. 12 Structure of Golgi body 2.6] LYSOSOMES A. STRUCTURE Spherical sacs of 0.2 - 0.5 µm in diameter. It contains hydrolytic enzymes such as proteases and lipases. It serves as a storage vesicle to keep the degradative enzymes apart from the rest of the cell, hence preventing them from destroying the cell. Its contents are acidic. There are 2 types of lysosomes: primary lysosome and secondary lysosome: i. Primary Lysosomes o Processed enzymes are contained in the Golgi vesicles which later bud off. o These enzymes are first synthesized on the rough ER and later transported to Golgi body. ii. Secondary Lysosomes o Primary lysosomes become secondary lysosomes after fusion with certain vacuoles. B. FUNCTION 1. Digestion of materials (Fig.13a). Enables the cell to breakdown the particles taken via phagocytosis. o Primary lysosomes fuse with the endocytotic vesicles so that the digestive enzymes could break down the contents. o The useful products are passed into the cytosol while the residue is discharged by exocytosis. 2. Autolysis Self destruction of the cell by the release of the lysosomal contents within the cell. 3. Autophagy (Fig.13b) Destruction of worn out organelles by fusing the organelles with primary lysosome to form secondary lysosome. 14 DOUBLE MEMBRANE BOUND ORGANELLES 2.7] NUCLEUS (singular; plural: nuclei) A. STRUCTURE OF NUCLEUS It is found in all eukaryotic cells except in mature red blood cells in mammals and in sieve tubes in plants. It is usually spherical or ovoid (Fig. 14) and averages about 2-10 µm in diameter. It is the largest and most conspicuous organelle within eukaryotic cells and can be easily observed under a light microscope. It has a double membrane, called the nuclear envelope. i. Note: Each of the membranes of the double membrane is a bilayer. ii. The double membrane is two bilayers with a gap in between them. Fig. 14 Structure of a nucleus and its associated structures and membranes B. FUNCTION 1. It contains DNA, which is the genetic material of the cell and controls all cellular activities including cell division and protein synthesis. 2.7a] DNA in the nucleus: The nucleus contains most of a eukaryotic cell’s DNA and is organized along with proteins, known as histones into long threads called chromatin. Two different levels of packing of DNA molecules: Heterochromatin (more condensed, appears darker) and Euchromatin (less condensed, usually not stained; see Fig. 15). Chromatin do not stain intensely and are too dispersed or thin to be observed under a light microscope. During nuclear division, chromatin condenses into a more tightly coiled thicker threads called chromosomes and hence stain more intensely. 15  Euchromatin Heterochromatin Nucleolus Fig. 15 Structure of a nucleus 2.7b] NUCLEOLUS (plural: Nucleoli) A. STRUCTURE OF NUCLEOLUS It is a large and dense region inside the nucleus. It is not an organelle but simply a region in the nucleus. [Note: Do not confuse with heterochromatin!] It consists of a fibrous part and a granular part. The fibrous part contains large loops of DNA from several chromosomes containing genes from which rRNA (ribosomal RNA) is transcribed to become part of ribosomes. (Fig. 16) The granular part contains transcribed rRNA fragments and synthesized ribosome subunits which then migrate to the cytoplasm to assemble into ribosomes. Most nuclei have two nucleoli, however in most diagrams only one is illustrated. B. FUNCTION OF NUCLEOLUS The function of nucleolus is to direct protein synthesis by synthesizing and controlling the synthesis of ribosomes. Fig.16 Relationship between nucleolus and rRNA 16 2.7c] NUCLEAR ENVELOPE A. STRUCTURE OF NUCLEAR ENVELOPE It is a double membrane including an outer membrane which is continuous with the rough endoplasmic reticulum. The double membrane is perforated by nuclear pores (about 50 nm in diameter). Each pore consists of eight pore proteins and a ‘plug’ protein (Fig.17). B. FUNCTION OF NUCLEAR ENVELOPE The nuclear pores provides a channel through which molecules (e.g. mRNA) can move between the nucleus and the cytoplasm. The exchange of materials through each pore is a carefully controlled and highly selective process. Hence nuclear envelope helps to maintain a chemical environment within the nucleus different from that in the surrounding cytoplasm. It disintegrates during nuclear division; i.e. mitosis and meiosis. Fig.17 Structure of a nuclear pore 2.7d] Nucleoplasm Similar to how the cytoplasm which fills up the cell outside the nucleus, this is a semi-fluid matrix that fills up the nucleus. Note: A matrix refers to a fluid-filled space in which structures are embedded in. 17 2.8] MITOCHONDRION (plural: Mitochondria) A. STRUCTURE The mitochondrion is an organelle that is responsible for the synthesis of energy (ATP) through the metabolism of glucose and other metabolites. (Fig. 18) It is 1.5 – 10 µm in length and 0.25 - 1.00 µm in width. It has a double membrane bound structure with an outer membrane that is smooth, and an inner membrane that is folded into finger-like projections called cristae (plural; singular: crista). The inner membrane is folded to increase the surface area for proteins and enzymes involved in the Electron transport chain (ETC) and oxidative phosphorylation processes in cellular respiration. E.g. Stalk particles are present on the inner membrane. Each particle contains a head piece, stalk and base. The head piece contains ATP (Adenosine triphosphate) synthase for ATP synthesis. The mitochondrial matrix contains circular mitochondrial DNA, ribosomes (70S), RNA and enzymes involved in the Krebs cycle of respiration. B. FUNCTION 1. Site for catabolic respiratory activity within the cell, where ATP is synthesized. Energy in the form of ATP is made available for cellular functions. This is the primary function of the mitochondria. 2. Lipid metabolism for cellular respiration. Fatty acids are broken down to acetyl CoA in the matrix and on the inner membrane of the mitochondrion. 3. A site for lipid synthesis. Fig. 18 Structure of mitochondrion 18 2.9] CHLOROPLAST This organelle is found in photosynthetic organisms like algae and plants. A. STRUCTURE Two membranes enclose the intermembrane space. Inside the chloroplast is a system of flattened sacs known as the thylakoid membrane (Fig.19). This membranous system forms stacks called granum (plural: grana), with intergranal lamellae between the grana. (Fig. 19) The fluid surrounding the thylakoid membrane is the stroma, which contains the DNA of the chloroplast, 70S ribosomes, enzymes and starch grains. A. FUNCTION 1. Chloroplasts are the sites of photosynthesis. 2. The light-dependent reactions of photosynthesis occur at the thylakoid membrane while the light- independent reactions occur in the stroma. Fig. 19 Structure of a chloroplast 19 2.10] ENDOMEMBRANE SYSTEM The endomembrane system is a series of closed membranes within eukaryotic cells that are either continuous with each other or communicate with one another via vesicles which are formed at one surface and move to a second where they are incorporated. A. STRUCTURE Organelles that are part of the endomembrane system include: nuclear envelope, endoplasmic reticulum (both smooth and rough endoplasmic reticulum), Golgi body, vesicles, lysosomes, various kinds of vesicles and vacuoles and cell surface membrane. Note: Mitochondria and chloroplast are NOT part of the endomembrane system. B. FUNCTION 2 main functions of the Endomembrane System are as follows: a) SYNTHESIS AND TRANSPORT OF SECRETORY PROTEINS b) FORMATION OF LYSOSOME Please refer to the 2 diagrams on the next 2 pages 20 a) SYNTHESIS AND TRANSPORT OF SECRETORY PROTEINS Smooth ER Golgi apparatus Transport vesicles Secretory vesicles Nucleus cis trans Nucleolus trans cis Ribosomes Cell surface membrane Rough ER ORGANELLE IN NUCLEUS ROUGH ENDOPLASMIC TRANSPORT GOLGI APPARATUS SECRETORY CELL SURFACE ENDOMEMBRANE RETICULUM (RER) VESICLE VESICLE MEMBRANE SYSTEM SYNTHESIS AND 1. Gene coding for 3. Ribosomes found on the 6. The folded 8. Transport vesicle fuses with the 11. The protein is 12. The secretory TRANSPORT OF protein is being RER translates mRNA polypeptide cis face of the Golgi apparatus. then being vesicle then moves SECRETORY transcribed into to form a polypeptide chain is then packaged into a to the cell surface PROTEINS mRNA in the chain. packaged into 9. Polypeptide is then being secretory membrane through nucleus. a transport transported from the cis to the vesicle, and it the help of the 4. Polypeptide chain is vesicle and it trans face of the Golgi buds out from cytoskeleton. 2. mRNA from the being passed from the buds out from apparatus, through a series of the trans face of passes through ribosome directly into the RER. transport vesicles. the Golgi 13. Secretory vesicle the pores of the the lumen of the RER. apparatus. fuses with the cell nuclear 7. The transport 10. Within the cisternae of the Golgi surface membrane envelope to the 5. Polypeptide chain vesicle moves apparatus, the polypeptide chain of the cell and ribosomes found undergoes folding in from the RER to undergoes sorting, packaging releases the on the Rough the cisternae into its 3D the Golgi and chemical protein out of the Endoplasmic shape and may undergo apparatus. modification/post- cell through Reticulum (RER). chemical translational modification by exocytosis. modification/post- adding/deleting and/or translational substituting sugar residues on modification. the polypeptide chain. 21 b) FORMATION OF LYSOSOME Smooth ER Golgi apparatus Transport vesicles Nucleus cis trans Lysosome Nucleolus Phagocytic vesicle Ribosomes Cell surface membrane Rough ER ORGANELLE IN NUCLEUS ROUGH ENDOPLASMIC TRANSPORT GOLGI APPARATUS LYSOSOME ENDOMEMBRANE RETICULUM (RER) VESICLE SYSTEM HOW A PROTEIN 1. Genes coding for 3. Ribosomes found on the 6. The folded 8. Transport vesicle fuses with the 11. The enzyme protein is then being MAY BE PASSED enzymes in RER translates mRNA to polypeptide cis face of the Golgi apparatus. packaged into a lysosome, and it OUT OF A CELL lysosome are form polypeptide chains. chains are then buds out from the trans face of being transcribed packaged into a 9. Polypeptides are then being the Golgi apparatus. into mRNA in the 4. Polypeptide chains are transport transported from the cis to the nucleus. being passed from the vesicle and it trans face of the Golgi apparatus, 12. The lysosome then fuses with the ribosome directly into buds out from through a series of transport phagocytic vesicle and the enzymes 2. mRNA pass the lumen of the RER. the RER. vesicles. from the lysosome hydrolyses the through the pores contents of the phagocytic vesicle. of the nuclear 5. Polypeptide chains 7. The transport 10. Within the cisternae of the Golgi envelope to the undergo folding in the vesicle moves apparatus, the polypeptide chain 13. The products of hydrolysis are ribosomes found cisternae into its 3D from the RER to undergoes sorting, packaging released into the cytoplasm. on the Rough shape and may undergo the Golgi and chemical Endoplasmic chemical apparatus. modification/post-translational Reticulum (RER). modification/post- modification by adding/deleting translational and/or substituting sugar modification. residues on the polypeptide chain. 22 3] PROKARYOTES (BACTERIA) Prokaryotes LO (d) Describe the structure of a typical bacterial cell (small and unicellular, peptidoglycan cell wall, (Bacteria) circular DNA, 70S ribosomes and lack of membrane-bound organelles). PROKARYOTES are unicellular organisms (as opposed to multicellular organisms) which are small and well organized, capable of achieving all of an organism’s life functions within a single cell. The most common example of prokaryotic organisms is the bacteria, which is used as the model organism to study prokaryotes. Most prokaryotes are unicellular, although the cells of some species remain attached to each other after cell division. Prokaryotic cells typically have diameters of 0.5 - 5 µm, much smaller than the 10 - 100 µm diameter of many eukaryotic cells. Prokaryotic cells have a variety of shapes (Fig. 20). (a) Cocci (singular, coccus) are spherical prokaryotes. They occur singly, in pairs (diplococci), in chains of many cells (streptococci), and in clusters resembling bunches of grapes (staphylococci). (b) Bacilli (singular, bacillus) are rod-shaped prokaryotes. They are usually solitary, but in some forms the rods are arranged in chains (streptobacilli). (c) Spiral prokaryotes include spirilla, which range from comma-like shapes to loose coils, and spirochetes, which are corkscrew-shaped. Fig. 20: The most common shapes of prokaryotes Prokaryotes are made of cells that lacks a true nucleus. The genetic material of a prokaryotic cell is a circular DNA molecule, which is not enclosed within a membrane but lies freely in the cytoplasm, in a region called the nucleoid. They also lack membrane bound organelles. Nearly all prokaryotes contain a cell wall made of peptidoglycan, which is surrounded by the capsule (Fig. 20a and 20b). 23  Fig.20a: Drawing of a Prokaryotic cell – Bacteria Fig.20b: Electron Micrograph of bacterium Bacillus coagulans 3.1] PROKARYOTIC STRUCTURE – CELL WALL A. STRUCTURE Most bacterial cell walls contain peptidoglycan, a polymer composed of modified sugars cross- linked by short polypeptides (Fig. 21). Note: This is in contrast to that found in eukaryotes that have cell walls, such as plants and fungi, where the walls are usually made of cellulose or chitin. B. FUNCTION The prokaryotic cell wall provides structural support and help prevents prokaryotes from bursting in an aquatic (hypotonic) environment, where water enters the cell, much like the cell walls of plants. Fig. 21 Peptidoglycan cell wall of Gram Positive Bacteria 24 3.2] PROKARYOTES (BACTERIA) – GENOME: NUCLEOID & PLASMIDS A. STRUCTURE Unlike eukaryotes, prokaryotes lack a membrane-bounded nucleus; their chromosome is located in the nucleoid, a region of cytoplasm that appears lighter than the surrounding cytoplasm in electron micrographs (Fig. 20). In majority of prokaryotes, this nucleoid region contains a single circular chromosome with fewer proteins as compared to the linear chromosomes of eukaryotes (Fig. 23). In addition to its single chromosome, the genome of a typical prokaryotic cell may also have rings of plasmids (Fig. 22) that are much smaller in size, mostly carrying only a few genes. These plasmids can replicate independently of the circular chromosome. B. FUNCTION The genome of prokaryotes functions similarly to that of eukaryotes, containing the DNA that holds the genetic information for the prokaryotes. Fig. 22 A prokaryotic chromosome and plasmid 25 3.3] PROKARYOTES (BACTERIA) – 70S RIBOSOME Unlike eukaryotes, prokaryotes contain the 70S ribosome is made up of a 30S small ribosomal subunit and a 50S large ribosomal subunit. The 70S ribosome in prokaryotes is slightly smaller than that in eukaryotes. This functions similarly to the ribosomes of eukaryotes. 4] COMPARISON BETWEEN PROKARYOTES AND EUKARYOTES CONCEPT MAP FOR PROKARYOTES AND EUKARYOTES Organisms made up of Cells which POSESSES LACKS True, True, membrane- membrane- bound nucleus bound nucleus and and LACKS Membrane Membrane bound bound organelles organelles are called are called EUKARYOTES PROKARYOTES For example For example Bacteria Animal Plant Fungi Protoctist 26 TABLE OF COMPARISON BETWEEN PROKARYOTES AND EUKARYOTES FEATURES PROKARYOTIC CELLS EUKARYOTIC CELLS ▪ Smaller, with diameter ranging ▪ Larger, with diameter ranging from Cell Size from 0.5 µm to 10 µm. 10 µm to 100 µm. ▪ Plant cell wall is made of ▪ Cell wall is made of Cell wall cellulose while fungal cell wall is peptidoglycan. made of chitin. ▪ Membrane-bound organelles are present (e.g. nucleus, Organelles ▪ No membrane-bound organelles. mitochondrion, endoplasmic reticulum and Golgi body). ▪ No nucleus, only has a nucleoid region. ▪ Nucleus is present. ▪ Circular DNA molecule lying free ▪ DNA molecule is linear. Genetic in the cytoplasm in nucleoid material ▪ DNA molecule is associated with region. proteins (histones) to form ▪ DNA associated with non-histone chromosome. proteins. ▪ Smaller, with sedimentation ▪ Larger, with sedimentation Ribosomes coefficient of 70S. coefficient of 80S. ▪ Mesosome present for ▪ Mitochondria present for Respiration respiration. respiration. ▪ Photosynthetic membranes ▪ Chloroplast present for Photosynthesis present for photosynthesis. photosynthesis. ▪ Complex, with “9+2” arrangement ▪ Simple, lacking microtubules and of microtubules and intracellular extracellular (i.e. not enclosed by Flagellum (i.e. surrounded by cell surface a cell surface membrane). membrane). ▪ Diameter of 20nm. ▪ Diameter of 200nm. 27  5] VIRUSES Viruses LO (e) Describe the structural components of viruses, including enveloped viruses and bacteriophages, and interpret drawings and photographs of them. 5.1] STRUCTURAL COMPONENTS OF VIRUSES Viruses range in size from about 20 nm – 300 nm. They cannot be seen with the light microscope and can pass through filters which retain bacteria. A virus is basically made up of a genome (made up of DNA or RNA) enclosed within a protective coat (made up of proteins). Viruses have a simple structure consisting of: core (i.e. viral genome), capsid (made up of capsomeres), collectively forming the nucleocapsid and (sometimes) envelope. Viruses that consists only nucleocapsid are called naked viruses and viruses that have an envelope surrounding their nucleocapsid are known as enveloped viruses. Fig. 23 Examples of enveloped and naked viruses i. Main structural components of viruses i. Core – the genetic material, either DNA or RNA. The DNA or RNA may be single-stranded or double-stranded. Usually a single linear or circular molecule of nucleic acid. Some viruses may have genomes with multiple molecules of nucleic acid. ii. Capsid – a protective coat of protein surrounding the core, i.e. viral genome. Capsids can come in many forms, some are helical (tobacco mosaic virus), some are icosahedral (adenoviruses) and others are complex (bacteriophage T4). iii. Capsomeres – capsids are often built up through self-assembly of identical repeating subunits called capsomeres. Capsomeres are coded by the viral genome. iv. Nucleocapsid – the combined structure formed by the core and capsid. v. Envelope – viruses, such as the HIV and influenza viruses, have an additional lipoprotein layer around the capsid derived from the cell surface membrane of the host cell. Viral envelopes are derived from cellular membranes and are acquired when nucleocapsids leave a cell by budding (not exocytosis) ii. A full assembled and complete virus is known as a virion. 28 5.2] EXAMPLES OF VIRUSES Fig. 24 (a) TMV (b) Adenoviruses (c) Influenza (d) Bacteriophage (e) Lambda phage lambda (λ) tobacco Feature T4 phage Influenza virus HIV phage mosaic virus Core dsDNA dsDNA ssRNA ssRNA ssRNA Complex Complex (Icosahedral (Icosahedral Capsid Helical Conical Helical head and tail head and tail apparatus) apparatus) Envelope Absent Absent Present Present Absent * ds – double stranded; ss – single-stranded 29 5.3] STRUCTURE OF BACTERIOPHAGES 5.3.1] T4 PHAGE (Fig. 25) Structural T4 phage Special Features components Core Double stranded DNA Capsid Complex (Icosahedral Tail portion of the capsid that is involved in attachment to head and tail the host cell comprises of: apparatus) - a contractile sheath - a base plate with attached tail pins - several tail fibres Envelope Absent Fig. 25a Components of T4 phage Fig. 25b Electronmicrograph of T4 phage 5.3.2] LAMBDA PHAGE (Fig. 26) Structural Lambda phage Special Features components Core Double stranded DNA Capsid Complex (Icosahedral Tail portion of the capsid that is involved in attachment to head and tail apparatus) the host cell comprises of: - a contractile sheath - a base plate with attached tail pins - one short tail fiber Envelope Absent Fig. 26a Structure of phage lambda (λ) Fig. 26b Electronmicrograph of phage lambda (λ) 30 5.4] STRUCTURE OF ANIMAL VIRUSES (ENVELOPED VIRUSES) 5.4.1] STRUCTURE OF INFLUENZA VIRUS Structural Influenza Virus Structure components Core 8 Single stranded RNA segments Capsid Helical Envelope Contain viral glycoproteins protrude from the outer surface of this envelope and bind to specific receptor molecules on the surface of a host cell. Additional RNA-dependent structures RNA Polymerase Fig. 27 Structure of Influenza virus 31 5.4.2] STRUCTURE OF HUMAN IMMUNODEFICIENCY VIRUS (HIV) Structural HIV Structure components Core Single stranded RNA Viral DNA (2 identical viral RNA strands) Capsid Conical Envelope Consist of viral glycoproteins protrude from the outer surface of this envelope and bind to specific receptor molecules on the Fig 28a Structure of HIV Fig 28b Electron Micrograph of HIV surface of specific types of white blood cells. Additional Reverse structures transcriptase HIV Protease Integrase Reverse Transcriptase Capsid protein Fig. 28a Structure of HIV 32 5.5] VIRUSES CHALLENGE THE CELL THEORY Cell Theory LO (f) Discuss how viruses challenge the cell theory and concepts of what is considered living. IN YOUR TUTORIAL GROUPS, PREPARE THIS QUESTION AS PART OF ESSAY QUESTION BEFORE YOUR TUTORIAL LESSON. The cell theory of life: A scientific theory is an explanation of an aspect of the natural world that can be repeatedly tested and verified in accordance with the scientific method, using accepted protocols of observation, measurement, and evaluation of results. Where possible, theories are tested under controlled conditions in an experiment. Here, the cell theory attempts to explain what constitutes a living organism. The cell theory of life can be summarised by three main principles: 1. The cell is the smallest, most basic unit of life. 2. All living organisms are composed of cells. 3. All cells arise from pre-existing cells by cell division. Therefore, according to the cell theory, all life must comprise cells and anything that is less than a cell (e.g. a nucleus, a mitochondrion, a chloroplast) is not considered a living thing. As viruses can replicate within host cells and cause many biological effects on living hosts, much like parasites, they are often considered in the grey area at the boundary of what is living and non-living (biochemical molecules). Thus, viruses are often used as the main example that challenges the cell theory of life. [For tutorial] Discuss how viruses challenge the cell theory and concepts of what is considered alive. Guiding points: Refer back to 3 fundamental principles of cell theory and how if viruses are considered living things, it challenges this theory. 33 6] EXPERIMENTAL SKILLS & MISCELLANEOUS 6.1] UNITS OF MEASUREMENT UNITS OF MEASUREMENT of length in cell studies are as follows: 1 millimetre (mm) = 10-3 metre (m) 1 micrometre (μm) = 10-3 mm = 10-6 metre (m) 1 nanometre (nm) = 10-3 μm = 10-9 metre (m) TRY THIS OUT! Q1. Convert 500 μm into metres. Q2. Convert 788 nm into millimetres. The approximate diameters of cells and their components are listed in Table 1. Table 1: Approximate diameters of cells and their components Cells and their components Diameter Plant cell 40 μm Animal cell 20 μm Nucleus 10 μm to 20 μm Bacterium 1 μm Mitochondrion 0.5 μm to 1.5 μm Lysosome 0.2 μm to 0.5 μm Ribosome 20 nm DNA molecule 2 nm 34 6.2] MICROSCOPY Cells are extremely small, and can only be seen with a microscope (Fig.1). There are two types of microscopes, the light microscope and the electron microscope. LIGHT MICROSCOPE is a type of microscope which uses visible light and a system of lenses to magnify images of small samples. Specimens can be magnified up to 1,000 times the actual size of the specimen. The resolution of the light microscope, however, is too low to show details on some of the cell’s smaller structures (i.e. the ultrastructures). ELECTRON MICROSCOPE [EM] is a type of microscope that uses an electron beam to illuminate a specimen and produce a magnified image. Electron microscopes have a higher resolution than light microscopes, and can resolve biological structures as small as 2 nanometres and can magnify up to 100,000 times. The fine structure of cells, known as ultrastructure, was largely discovered using the technique of electron microscopy. Two EM microscopes are routinely used. One is the transmission electron microscope (TEM), which is used to study internal cell structure, and the other is the scanning electron microscope (SEM), which is used to study the architecture of cell surfaces. Fig.2: Light Microscope Fig.1: The sizes of cells and related objects Fig.3: Electron Microscope 35 6.3] CALCULATING MAGNIFICATION Candidates may be presented with a magnified image as seen under a light microscope or an electron microscope and be required to calculate the actual size of the image. MAGNIFICATION is the ratio of an object’s image size to its real size. MAGNIFICATION = IMAGE SIZE OF OBJECT/ ACTUAL SIZE OF OBJECT [A-LEVEL 2006/P1/Q4] The diagram shows part of a plant cell as seen under an electron micrope, and a scale bar showing 3 x 10-3 mm. What is the approximate length of the nucleolus, S, in μm? 36 6.4] CELL FRACTIONATION CELL FRACTIONATION is used to isolate (fractionate) cell components based on size and density. TECHNIQUE OF CELL FRACTIONATION (Fig. 4) The instrument used to fractionate cell components is called a centrifuge. A CENTRIFUGE spins test tubes holding mixtures of disrupted cells at a series of increasing speeds. At each speed, the resulting force causes a fraction of the cell components to settle to the bottom of the tube, forming a pellet. The higher the speed of centrifugation, the higher the force at which the cell components are isolated. The smaller the cell components, the larger the force required to isolate them; hence a higher speed is used to isolate smaller cell components. At lower speeds, the pellet consists of larger components, and higher speeds yield a pellet with smaller components. APPLICATION OF CELL FRACTIONATION Cell fractionation enables researchers to prepare specific cell components in bulk and identify their functions, a task not usually possible with intact cells. Fig.4: Cell Fractionation 37 6.5] ENDOSYMBIOTIC THEORY Symbiosis occurs when two different species benefit from living and working together. When one organism actually lives inside the other it is called endosymbiosis. There is evidence that mitochondria and chloroplasts were once primitive bacterial cells. Over millions of years of evolution, mitochondria and chloroplasts have become more specialized and today they reside within the eukaryotic cells Hence, the endosymbiotic theory explains that the mitochondria of eukaryotes and the chloroplasts of green plants originated as free-living prokaryotes that invaded primitive eukaryotic cells and become established as permanent symbionts in their cytoplasm. (Fig.23) Fig.23: The Endosymbiotic Theory Think: What evidence would support this theory that these organelles were once prokaryotes? Evidence supporting this theory: i. Both mitochondria & chloroplasts contain their own DNA and ribosomes. DNA of these organelles resembles those of prokaryotes: both are circular, not wound on proteins & not enclosed by nuclear envelope. ii. Ribosomes of mitochondria & chloroplasts are smaller (70S) & more similar to prokaryotes than ribosomes (80S) of eukaryotes. iii. Mitochondria & chloroplasts divide by binary fission like bacteria. 38