1.1 Biological Field and Career Meaning of Biology ‘Bios’ is life & ‘logos’ is study. Biology is the study of living organisms, their life processes, and their interaction with the environment. Examples of biological research areas: Fields Explanations Botany Study plant life Physiology Study of the function and mechanisms in organisms. Genetics Study of inheritance and genetic variation. Microbiology Study of microorganisms. Study of interactions between organisms and their environment. Ecology The contribution of biology to everyday life: Medical: In vitro fertilization, family planning, plastic surgery, and gene therapy. Pharmaceutical: Production of synthetic vitamins, vaccines, insulin, and synthetic enzymes. Food production: Use of microorganisms in the production of cheese, soy sauce, tapas, and Tempe. Agriculture: Transgenic crops and animals, hydroponic and aeroponic technology. Careers related to biology: Ecologist Bio-technologist Pharmacist Nurses Doctors Optician Dentist Dietitian Physiotherapist Biochemist Veterinarian 1.2 Safety and Rules in Biological Laboratory Self-protection equipment: Self-protection equipment Descriptions and functions Gloves Lab coat and lab shoes Goggle and face mask Handwash Eye washer Fume hood Emergency shower station Laminar flow cabinet Biosafety cabinet Made from latex/rubber/plastics. Protects the hands from heat and dangerous chemical substances; strong acids and strong alkalis. Lab coat: aids to protect the skin and clothes from chemical spillage. Lab shoes: protect the legs from chemical spillage and broken glass. Protects the face and eyes from chemicals splashing and protecting from inhaling chemicals that can interrupt the respiratory system. Washing both hands before leaving the lab is a must. Contains salt solution used to wash the eyes if chemical substances/foreign particles get into the eyes. Station for work that involved fumes or toxic gas; chlorine, bromine, and nitrogen dioxide. Station used to wash the hand and body when someone is exposed to dangerous chemicals. Station for work involved with plant tissue culture, medium preparation that provides a sterile environment to the workplace. Station for work involved with bacteria, fungi, and virus cultures helps to prevent the cultures from contaminating the environment. Substances that cannot be thrown in the sink: 1. Chemical substances, glass, metals, plastics, woods, or any solid substances. 2. 3. 4. 5. 6. Grease, oil, and oil paint. Toxic substances; benzene, chloroform, hydrogen cyanide, Argentum. Heavy metals; mercury, lead, cadmium. Radioactive wastes. Unstable reactive substances: sodium metal, ether, hydrogen peroxide. Substances that can be thrown in the sink: 1. Any liquid/solution that has low concentrated waste are not dangerous and is biodegradable. Methods of handling biological wastes: Waste category Example Methods of handling Sharp waste A syringe with needle, needle, glass, and scalpel Throw it in the sharp bin waste Non-sharp Gloves, tissue paper, Petri waste dish, agar, culture waste Throw it in the biohazard bag, sterilize it, and throw it in the biohazard bin Animal carcass Organs, animal tissue waste, carcass Wrap it with tissue paper, put it in the biohazard bag, and freeze it Liquid Broth culture, liquid media, blood, and blood product Decontaminate the waste through the autoclave before throwing it in the biohazard bin Accidents in the laboratory: Steps to handle general chemical spills 1. 2. 3. 4. 5. Inform your teacher Declare the spill area as a restricted zone. Prevent the chemical spill from spreading using sand. Scoop up the chemical spill using the appropriate equipment. Dispose of it safely. Steps to handle mercury spills 1. 2. 3. 4. Inform your teacher Declare the spill area as a restricted zone. Sprinkle sulphur to cover the mercury spills Call the fire and rescue department. Practices in a biological laboratory: Practices Clothing ethics Explanations Use a lab cosafe gloves, safety shoes, and goggles when appropriate. Do not work alone in the laboratory without supervision. Wash your hand after experimenting. Do not bring irrelevant items into the laboratory. Clean your workstation using a disinfectant. Dispose of wastes according to the set procedures. Do not eat and drink in the laboratory. Identify all safety symbols on substances and equipment before use. Laboratory safety rules Safety measures for fires Handling glass and chemicals Handling live specimens Emergency help Stop work immediately and switch off all nearby power sources. Unplug appliances Exit the laboratory according to the emergency exit plan. Call the fire and rescue department. Do not panic and stay calm. Do not turn back to collect your belongings. Assemble at the assembly point. Be cautious when handling hot glassware. Report any damaged equipment or glassware to teachers immediately. Keep flammable chemicals away from fire sources. Do not touch, taste or smell chemicals directly. Use appropriate gloves when handling biological specimens. Speciements that are not harmful and have been dissected should be buried or frozen. Wash hands with antiseptic detergents before and after the experiment. All surfaces and workstations should be cleaned with disinfectant before leaving the lab. Inform your teacher Call the fire and rescue emergency number. Remove the victim from the scene. Give emergency treatment. Make the place of an accident a restricted area. 1.3 Communication in Biology Plane 1. The plane refers to a flat surface of a shadow passing through the body Consists of: 1. sagittal plane (divides the body into right and left parts) 2. frontal plane (divides the body into frontal and rear parts) 3. horizontal plane (divides the body into upper and lower parts) Section The cross-section divides the structure into upper and lower portions horizontally while the longitudinal section divides the structure into left and right portions Direction Direction consists of anterior, ventral, posterior, dorsal, superior, inferior, and lateral 1. 2. 3. 4. 5. 6. 7. Anterior: towards the front of the body Ventral: towards the lower part of the body Posterior: towards the back part of the body Dorsal: towards the upper part of the body Superior: the part that is above all other parts or towards the head Inferior: situated below other parts or towards the feet Lateral: far from the midline or at the side of the body 1.4 Scientific Investigation in Biology Scientific method – A series of steps to finding an answer to explain a certain phenomenon. Identify the problem ↓↓ Forming hypothesis ↓↓ Planning an experiment ↓↓ Identify & control variable ↓↓ Conducting the experiment ↓↓ 2.1 Cell Structure and Cell Function Cell organelles Plasma membrane Functions Regulates the movement of substances across the cell Separates the contents of the cell from the external environment Cell wall Maintains the shape of plant cells Protects the plant cells from burst Provides strength and support to the plant cell Cytoplasm Acts as a medium for biochemical reactions of most living processes in the cell Nucleus Carries genetic information in the form of DNA Vacuole Stores nutrients, wastes, and metabolic by-products Ribosome Synthesizes proteins Synthesises ATP Mitochondrion Site of cellular respiration Rough endoplasmic reticulum Transports proteins made by the ribosomes throughout the cell Smooth endoplasmic reticulum Synthesizes lipids and carries detoxification of drugs Golgi apparatus Lysosome Modifies, transports, sort, and package the proteins and carbohydrates Digests old and worn organelles Breakdown of complex organic molecules Centriole Form spindle fibres during cell division Chloroplast Site of photosynthesis Similarities between plant cells and animal cells: Both cells contain a nucleus, cytoplasm, plasma membrane, Golgi apparatus, mitochondrion, endoplasmic reticulum, and ribosomes. Differences between plant cells and animal cells: Plant Cells Animal Cells Has a fixed shape Does not have a fixed shape Has a cell wall Does not have a cell wall Has chloroplasts Does not have a chloroplasts Has a large vacuole No vacuole Stores carbohydrates in the form of starch Stores carbohydrates in the form of glycogen Does not have a centriole 2.2 Has centrioles Living Processes in Unicellular Organisms Unicellular organisms are made up of only one cell. For example Ameoba sp. and Paramecium sp. Differences in living process between Ameoba sp. and Paramecium sp.: Amoeba sp. Habitat: Freshwater and damp soil Structural characteristics: Can change shape Has one nucleus Has contractile vacuole and food vacuole Respiration: Simple diffusion Feeding: Phagocytosis Movement: Extend its pseudopodium Reproduction: Binary fission (favourable condition) Spore formation (unfavourable condition) Excretion: Osmoregulation through contractile vacuole Paramecium sp. Habitat: Freshwater Structural characteristics: Slipper-shape Has cilia Has two nuclei; macronucleus and micronucleus Has contractile vacuole and food vacuole Respiration: Simple diffusion Feeding: Oral groove Movement: Beats the cilia Reproduction: Binary fission (favourable condition) Conjugation (unfavourable condition) Excretion: Osmoregulation through contractile vacuole 2.3 Living Processes of Multicellular Organisms Specialised cells in animals and humans: Epithelium cell Structural adaptation: Thin cells; arranged closely Function: Provide protection Aid in gaseous exchange Helps in nutrients absorption, secretes mucus Muscles cell Structural adaptation: Contains many fibres; aid in movement Have many mitochondria; provide energy for muscle contraction Function: Contracts to produce movement Nerves cell Structural adaptation: Have long dendrites and axon Axons covered with myelin sheath; faster transmission Function: Transmits nerve impulses from one part to another part of the body Red blood cell Structural adaption: Contains haemoglobin; transport oxygen Elastic and flexible; allow the blood to squeeze through thin blood capillaries Has a biconcave disc shape; increases the ratio of surface area per volume; increase the diffusion of respiratory gases Function: Transports respiratory gases White blood cell Structural adaption: Can change shape; easily squeeze through the tiny blood vessels to the interstitial space to hunt the pathogens Function: Protects the body from pathogens Sperm cell Structural adaption: Has a long tail; helps the sperm to move Contains mitochondrion; provides energy for the sperm to swim Contains enzymes; helps the sperm to penetrate the ovum Function: Fertilises the ovum Specialised cells in plants: Spongy palisade mesophyll cell Structural adaptation: Packed loosely; efficient gaseous exchange Function: Facilitate gas permeation Xylem Structural adaptation: Consists of porous long tubes; to transport substances efficiently Strengthen by lignin; to prevent the xylem from collapse Function: Transport water and mineral salts from the roots to a whole plant Sieve tubes Structural adaptation: Matured sieve tubes have no nucleus; provide more space for transportation Have sieve plates No lignin Function: Transport organic substances; sucrose, amino acids and hormones from the shoots to other parts of the plant Root hair cell Structural adaptation: Have many mitochondria; provide energy to absorb more mineral salts through active transport The root hairs increase the surface area; maximising the absorption Function: Absorb water and dissolved mineral salts in the ground Guard cell Structural adaptation: Have chloroplasts; produce glucose Have a large vacuole; control the osmotic pressure of the cell; aid in controlling the opening and closing of the stoma Function: Control the opening and closing of the stoma Cell Organisation in animals: Types Characteristics and functions Epithelium Consists of one or more layers of cells Some epithelium tissues form glands (exocrine and endocrine glands) Epithelial tissues carry out functions associated with protection, secretion and absorption Muscles Musculoskeletal: involves involuntary movements; contracts and relaxes to move the bones Smooth: contracts and relaxes that allows involuntary movements; peristalsis in intestines Cardiac: found in the heart walls; contracts and relaxes that allows pumping the blood Nerve Consists of neurons or nerve cells Functions to transmit nerve impulses, control and coordinates the activities in the body Connective Consists of several types of cells and fibres that are distributed across the body that has many functions Connective Tissue: Types Loose tissues Characteristics and functions connective Places between the organs Functions to anchor the epithelium tissues to other tissues and places the organs in one place Fibrous connective Consists of fibrous collagens that are arranged close to one another tissues Found in tendon and ligament Strong and flexible Cartilage Supports the nose, and ears and covers the end of the bones, which functions to absorb pressure and shock Bone Consists of cells in one matrix of mineral salts and fibrous collagen The collagen matrix is hardened by the deposition of minerals such as calcium phosphate Blood tissues Functions to protect the organs and provides support to the body Consists of blood cells; red blood cells, white blood cells and platelets Adipose tissues Blood functions to protect, transport and regulate Functions to store fats protect the organs and insulate heat Found in the skin dermis and the surroundings of the organs Tissue organisation in plants: Meristematic tissue A group of undifferentiated cells; active in cell division Two types; apical and lateral meristems Function: Apical meristem: primary growth; vertical growth Lateral meristem: secondary growth; horizontal growth Parenchyma tissue Thin-walled cells; loosely arranged with spaces between them Function: Provides support and shapes Stores food Conducts photosynthesis Collenchyma tissue Elongated, polygonal cells with unevenly thickened cell walls The cell walls are thickened by cellulose and pectin Function: Provides support to: Herbaceous plants Young stems Leaf stalks Petioles Sclerenchyma tissue The cells are rigid Have cell walls; thickened by lignin Most of the cells are dead at maturity Function: Provide support and protection to the plant Epidermis The outermost layer that covers the whole plants The wall of epidermal cells is normally covered by cuticle Function: The cuticle on the epidermal tissue helps to: Prevent water loss Protects the plants from mechanical injury Prevent the invasion by disease-causing microorganisms In roots, some of the epidermal cells have long projections called root hairs; which increase the surface area for the absorption of water and minerals In leaves, the lower epidermis contains specialised cells, called guard cells; which control the opening and closing of stomata Xylem Consists of tracheids and xylem vessels; long tubes joined together end to end The cell walls of the xylem are thickened with lignin; provide support to plants Xylem tissues die upon reaching maturity; form hollow tubes Function: Xylem carries water and minerals from the roots to the leaves Xylem provides support and mechanical strength to the plant Phloem Phloem tissue consists of parenchyma cells, sclereids, sieve tubes and companion cells The sieve tubes have pores at both ends; called sieve plates Sieve tubes obtain nutrients and energy from the adjacent companion cells Function: Phloem transports carbohydrates, amino acids, and hormones from the leaves to storage organs and the growing parts of plants The density of certain cell components and specialised cell functions: Mitochondria Muscle cell; Provide energy for muscle contraction Sperm cell; Provide energy for the tail of sperm during swimming to fertilise the ovum Meristem cell; Provide energy for cell division and cell growth Kidney cell; Provide energy for active transport to transport substances across the plasma membrane Chloroplast Palisade mesophyll and spongy mesophyll; To conduct photosynthesis Rough endoplasmic reticulum and Golgi apparatus Goblet cell and pancreatic cell; Produces mucus, synthesises and secretes digestive enzymes Smooth endoplasmic reticulum and Golgi apparatus 2.4 Liver cell; Conduct carbohydrate metabolism and detoxification of drugs and poisons Levels of Organisation Cell → Tissue → Organ → System → Organism Main organ systems in the human body: Systems Endocrine system Functions and Organs involved The endocrine gland secretes hormones Main function: Coordinates body activities with the nervous system Respiratory system Trachea, nose, lungs and diaphragm Main function: Exchange of oxygen and carbon dioxide gases between the body and the external environment Muscular system Skeletal muscles, smooth muscles and cardiac muscles Main function: Contracts and relaxes to produce movements in different parts of the body Male reproductive system Testes, prostate gland and penis Main function: Produces sperm and male sex hormones Female reproductive system Ovary, uterus, Fallopian tube, vagina and cervix Main function: Produces ovum and female sex hormones Lymphatic system Spleen, lymph nodes and lymph vessels. Main function: Maintains balance of bodily fluids and prevents infectious diseases Nervous system Brain, spinal cord and peripheral nerves Main function: Detects and sends information in the body, as well as coordinates body activities Blood circulatory system Heart, artery, vein and blood capillary Main function: Transports nutrients, respiratory gases and waste products Digestive system Mouth, oesophagus, stomach, liver, pancreas, small intestine and large intestine Main function: Digests food into a simpler form for easy absorption Urinary system Kidney, ureter, urethra and bladder Main function: Eliminates waste products such as urea and uric acid from the body Skeletal system Bone, cartilage, ligament and tendon Main function: Supports the body, protects the internal organs and provides a base for muscle adhesion Integumentary system Skin Main function: Protects the body from physical injury, infection and dehydration Main systems in plants: The plant system is divided into the shoot system and the root system. The shoot system consists of stems, leaves, shoots, flowers and fruits. Stems and twigs are support systems that support the leaves at the vertical position to allow maximum absorption of sunlight during photosynthesis Flowers are involved in the pollination process The root system consists of all roots in a plant that function in absorbing water and mineral salts as well as providing support for plants 3.1 Structure of Plasma Membrane We will learn about the structure of the plasma membrane, the movement across the plasma membrane, passive and active transport in the plasma membrane. The necessity of movement of substances across a plasma membrane: Allow some substances to move into and out of the cells to maintain the living processes. Regulates the movement of substances across the plasma membrane The structure of plasma membrane: Types of molecules Description Cholesterol Carrier protein Strengthened the plasma membrane Makes the plasma membrane to be more flexible but less permeable to water-soluble molecules Transport large molecules such as glucose, amino acids, and vitamin C across the plasma membrane Pore protein Glycolipid Glycoprotein Allow small and water-soluble molecules such as ions to pass across the plasma membrane through passive transport A combination of lipids and polysaccharides helps the cell-cell recognition A combination of proteins and polysaccharides helps the cell-cell recognition The permeability of plasma membrane: The plasma membrane is semi-permeable because it only allows certain molecules or ions to pass through it by simple diffusion 3.2 Concept of Movement of Substances Across a Membrane Plasma The characteristics of substances that are able to move across a plasma membrane: There are three common factors that determine whether a molecule can pass through a plasma membrane, which are molecule size, polar molecule, and ionic charge. Characteristics of substances across the plasma membrane Lipid-soluble substances Non-polar molecules: Lipid insoluble substances Small molecules and ions Polar molecules; water Vitamin A, D, E, K Non-polar molecules; oxygen, carbon Steroid dioxide, and ion: K+, Na+, Ca2+, Mg2+ compounds Fatty acids and glycerol Large molecules Glucose and amino acids Passive transport: This process does not require energy Examples of passive transport are simple diffusion,osmosis and facilitated diffusion. Simple diffusion: A process where the substances pass through the plasma membrane follows the concentration gradient. The substances move from a high concentration region to a low concentration region. The moving molecules are said to move down the concentration gradient until a dynamic equilibrium is achieved. This may occur with or without the presence of a plasma membrane. Lipid soluble molecules (fatty acids and glycerol), oxygen, and carbon dioxide diffuse through the phospholipid bilayer through simple diffusion. Osmosis: Osmosis is a passive transport process that is similar to diffusion but it involves only water molecules. Osmosis refers to the net movement of water molecules from a higher water potential to a low water potential. Osmosis occurs through the phospholipid bilayer. Facilitated diffusion: Lipid-insoluble molecules such as ions, large molecules such as amino acids, and glucose are unable to pass through the phospholipid bilayer. These substances move across the membrane with the aid of transport proteins (carrier or pore proteins). Facilitated diffusion does not require energy because the transport proteins transport molecules down a concentration gradient. The process continues until a dynamic equilibrium is achieved when the concentration of molecules is the same at both sides of membranes. Active transport: The movement of a molecule or ion substances across a plasma membrane occurs against a concentration gradient. It requires energy from ATP (adenosine triphosphate) molecules generated during cellular respiration. It requires specific carrier proteins with specific active sites to bind with certain molecules or ions. Carrier proteins also possess receptors to bind with ATP molecules. Carrier proteins change shape when a phosphate group attaches to it. As a result, molecules or ions move across a membrane. The simillarities between passive and active transport: Occurs through a selectively permeable membrane Moving substance across a membrane The differences between passive and active transport: Passive Transport Active Transport Energy does not required Requires energy Occurs following the concentration of the gradient. Occurs againts the concentration of the gradient. Occurs untill a dynamic equillibrium is achieved. There are accumulation and disposal of molecule or ions. 3.4 Movement of Substances Across a Plasma Membrane in Living Organisms Active and passive transport in living organisms: Passive transport Active transport gaseous exchange between an alveolus and a blood capillary through simple diffusion. reabsorption of water occurs by osmosis through the renal tubule in the kidney. absorption of water by a plant root hair cell by osmosis. absorption of fructose molecule in the villus by facilitated diffusion. absorption of glucose and amino acids in the villus. reabsorption of glucose through the renal tubule in the kidney. transport of sucrose from a leaf to a phloem tissue. absorption of mineral ions by a plant root hair cell. Hypertonic,hypotonic and isotonic solutions: Solution Description Hypertonic A solution that has high concentration of solute Hypotonic A solution that has low concentration of solute Isotonic A solution that has the same concentration of solute with the water potential The effects of hypotonic, hypertonic and isotonic solutions on animal cells and plant cells: Animal cell Condition Plant cell Hypotonic Hemolysis A solution that has low concentration of solute than water in a cell; causing the water to diffuse in Hypertonic Crenation A solution that has high concentration of solute than water in a cell; causing the water to diffuse out Turgid Plasmolysis and flaccid Isotonic Maintain its A solution that has the same concentration of solute with shape the water potential in a cell; not net movement of substance 3.4 Maintain its shape Movement of Substances Across a Plasma Membrane and Its Application in Daily Life Phenomena of plant wilting: Excessive use of fertilisers may cause wilting in plants. Dissolved fertilisers will cause soil water to be hypertonic to the sap cell of roots. Consequently, water will diffuse by osmosis from the roots’ cell sap to the soil, and cells will become plasmolysed. Cells in plants will recover once they are watered. However, if the period of plasmolysis is prolonged, wilted plants will eventually die. Application in daily life: Rehydration drinks such as oral rehydration salts help to recover loss of water and electrolytes in individuals with diarrhea. Isotonic drinks help athletes to recover loss of water and electrolytes such as potassium and sodium through perspiration. Saline solutions, normally used in medicine, are isotonic solution to the blood plasma. It contains 0.85–0.90 g sodium chloride per 100 ml. Liposomes are vesicles that contain aqueous solution surrounded by a phospholipid bilayer membrane. Liposomes are used to protect drugs or active substances taken orally from being destroyed by gastric juices. This way, drugs can reach the target cells. Reverse osmosis is a technology commonly used to extract fresh water from seawater using the desalination process. In reverse osmosis equipment, pressure is applied to push the seawater through a semi-permeable membrane. The membrane allows water molecules to pass through it but not foreign particles, salt, and microorganisms. As a result, only pure fresh water is released. 4.1 Water 1. Consists of elements such as hydrogen and oxygen. 2. Polar molecule. Properties of water and its importance in a cell: Properties Descriptions and its importance Polarity of water Cohesive force and adhesive force of water Inorganic compound consisting of the hydrogen(H) and oxygen(O) elements. Polar molecules: shared electrons between oxygen (more electronegative). Produces hydrogen bonds and allows water to act as a universal solvent. Water molecules are attached to each other through a cohesive force. Water molecules attached to other surfaces through adhesive force. Both forces produce a the capillary action which allows water to enter and move along narrow spaces.Ex: xylem tube. Water has a high specific heat capacity of 4.2 kJ kg-1 °C-1 . 4.2 kJ of heat energy is required to raise the temperature of one kilogram of water by 1°C. Water absorbs a lot of heat energy with a small rise of temperature. Maintain body temperature of organisms. Specific heat capacity 4.2 Carbohydrates 1. Consists of elements such as carbon, hydrogen and oxygen. 2. Several types of carbohydrates such as monosaccharides, disaccharides and polysaccharides. Monosaccharides The monomer of carbohydrates. Example: glucose, fructose and galactose. Disaccharides Consists of two monosaccharides linked together through condensation. Disaccharide molecule can be broken down into monosaccharide through hydrolysis. Disaccharide Monomer Maltose Glucose + glucose Sucrose Glucose + fructose Lactose Glucose + galactose Polysaccharides The polymer of carbohydrates. Linked through condensation reactions of monomers to form a long chain of molecules. Example: starch, glycogen and cellulose. 4.3 1. 2. 3. 4. Proteins Consists of elements: carbon, hydrogen, oxygen and nitrogen. Some contain phosphorus. The monomer of proteins is an amino acid. Two molecules of amino acids are linked through condensation, by forming a peptide bond, which known as a dipeptide. 5. The polymer of proteins is a polypeptide. 6. The polypeptide can be broken down into amino acids through hydrolysis. 7. Have several levels; primary (linear), secondary (pleated, helix), tertiary (3D-shaped) and quarternary (having two or more tertiary structures). 4.4 Lipids 1. Consists of elements: carbon, hydrogen and oxygen. 2. The ratio of element hydrogen is much higher compared to carbohydrates. Fats and oils Triglycerides (3 fatty acids and 1 glycerol). Each molecule of the fatty acid consists of a long hydrocarbon chain. Fatty acids can be either saturated (single bond carbon atoms) or unsaturated (one or more double bond between carbon atoms). Example of saturated fats: red meat, animal fats and butter. Example of unsaturated fats: vegetable oils, olive oil and soybean oil. Waxes Long-chained molecules. Waterproof. Found on the cuticle of leaves and in the sebum. Phospholipids Main components of the plasma membrane. Controls the permeability of the plasma membrane. Consists of a hydrophilic head and hydrophobic tails. Steroids Raw material to synthesis vitamin, cholesterol and sex hormones. 4.5 1. 2. 3. 4. Nucleic Acids Found in DNA and RNA. A genetic material. Basic unit: nucleotide. Each nucleotide consists of a phosphate group, a pentose sugar and a nitrogenous base. 5. Nitrogenous base in DNA: adenine, guanine, cytosine and thymine. 6. Nitrogenous base in RNA: adenine, guanine, cytosine and uracil. 5.1 Metabolism Metabolism refers to all chemical reactions that occur in a living organism. There are two types of metabolism in a cell which are catabolism and anabolism. Catabolism Anabolism 5.2 The process of breaking down complex substances into simple substances. Releases energy. Example: The breakdown of glucose during cellular respiration to generate energy. The process of synthesising complex molecules from simple molecules. Uses or absorbs energy. Example: The formation of glucose during photosynthesis. Enzymes An enzyme is an organic catalyst that is mostly made up of proteins and is produced by living cell organisms. Substances needed for an enzyme reaction are called substrates. Substrates will bind with enzymes at a specific site (active site) and form an enzymesubstrate complex. Enzyme nomenclature: Name of enzyme is derived by adding '-ase' to the name of the substrate it catalyses. Example: lactase, protease, and amylase. A few enzymes that do not follow this naming system. Example: trypsin, pepsin and renin General characteristics of enzymes: Enzymes are needed in small amounts. Enzymes are not breaking down at the end of the reaction. Action of enzymes is specific due to the presence of active sites. Most of the chemical reactions catalyzed by enzymes are reversible. Enzymes are sensitive to temperature and pH. Some enzymes require cofactors in their activities. Enzymes activities can be slowed or stopped by inhibitors such as lead. Intracellular and extracellular enzymes: Intracellular enzymes Extracellular enzymes Enzymes are synthesized in a cell for their own use. Example: The hexokinase enzyme is used in the glycolysis process during cellular respiration. Enzymes that are secreted outside the cell. Example: The trypsin enzyme is produced by the pancreatic cells and secreted into the duodenum to break down polypeptides. Extracellular action: In the nucleus, the information for the synthesis of enzymes is carried by the DNA in a form of codes. mRNA is formed to translate the codes into a sequence. mRNA leaves the nucleus and binds with ribosome for the synthesis of protein to occur. The synthesized protein is transported enters the lumen of the rough endoplasmic reticulum. The protein is processed and packaged into a transport vesicle which buds off from the rough endoplasmic reticulum to transports the protein to the Golgi apparatus In Golgi apparatus, the protein is modified to form an enzyme and is packaged in a secretory vesicle which transports the enzymes to the plasma membrane. The secretory vesicle will fuse with the plasma membrane to release the enzymes out of the cell. Mechanism of enzyme action: The enzyme represented by a 'lock' The substrate represented by a 'key' Most reactions inside the cell require high activation energy. Activation energy is the energy needed to break the bond in the substrate molecule before reaction can occur. Enzyme function by lowering the activation energy. Factors affecting the activity of enzymes: Factor affecting the activity of enzymes Temperature Enzyme concentration (limiting factor: substrate concentration) Substrate concentration (limiting factor: enzyme concentration) pH Temperature: At low temperature, the rate of enzymatic reaction is low. The rate of enzyme reaction increases as the temperature increases. This is because of the activation energy of the substrate molecules increases. Therefore, more collision between the enzymes substrate molecule increases the formation of an enzyme-substrate complex. The reaction is the maximum at the optimum temperature. After the optimum temperature, the rate of reaction decreases because the enzyme is denatured in which the bonds that form the structure of the enzyme are changed. This causes the active site to lose its shape. Therefore, the enzyme-substrate complex can no longer be formed. pH: Optimum pH is the pH at which the rate of reaction is at the maximum. Small changes in the pH value of a medium will cause the enzyme to be denatured. The shape of the active site will change. Therefore, the enzyme-substrate complex cannot be formed again. Different enzymes have different optimum pH: o The optimum pH of pepsin is pH 2 o The optimum pH of amylase is pH 7 o The optimum pH of trypsin is ph 8.5 Substrate concentration: The higher the concentration of substrate, the higher the rate of reaction as more substrate molecules bind to the active site of the enzymes to form the enzymesubstrate complex. The rate of reaction becomes low when it reaches the maximum point because all of the active sites have been filled up. At this point, the enzyme concentration is the limiting factor. Enzyme concentration: The higher the concentration of enzymes, the higher the rate of reaction as more active sites for substrate molecules to bind to and form the enzyme-substrate complex. The rate of reaction becomes low when it reaches the maximum point because all substrate molecules have bound to the active sites. At this point, the substrate concentration is the limiting factor. 5.3 Applications of Enzymes in Daily Life Immobilized enzymes are enzymes that combine with inert and insoluble substances to increase the resistance of enzymes towards change in factors such as pH and temperature. The enzyme molecules will remain in the same position throughout the catalytic reaction and then be separated easily from its product. Enzyme immobilization technology is used in various industrial application: Digestive enzymes are used in the medical sector. Amylase, lipase, protease, and cellulase in bio detergent. Trypsin enzyme extracts fur from an animal hide to make leather products. Lactase enzymes are used in lactose-free milk.
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