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SCIENCE LECTURE: POINTERS TO REVIEW Gas Exchange and Transport Respiratory System Cardiovascular System Genetics Mendelian Non-Mendelian Pedigree Extinction (the 6 mass extinction events) Photosynthesis Cellul...

SCIENCE LECTURE: POINTERS TO REVIEW Gas Exchange and Transport Respiratory System Cardiovascular System Genetics Mendelian Non-Mendelian Pedigree Extinction (the 6 mass extinction events) Photosynthesis Cellular Respiration TOPIC 1: GAS EXCHANGE AND TRANSPORT → Our bodies use oxygen to transform nutrients from food to energy. → Terrestrial (land) vertebrates have a pair of lungs that allow the exchange of oxygen and carbon dioxide. Meanwhile, fish have gills which have blood vessels that help them obtain oxygen dissolved in water and release carbon dioxide. → Oxygen is delivered to the cells and carbon dioxide is collected from the cells through the heart. Animals with Gills Animals with Lungs Single-loop circulatory system Double-loop circulatory system Lungs Heart → Gills → Cells ↓ ↑ Heart ↓ ↑ Cells In order to survive, plants need O2 and CO2 → Plants respire through stomata in leaves, lenticels, and root hairs. 1. Stomata → The stomata (stoma) are openings or pores on leaves and other parts of the plant. 2. Guard Cells → Guard cells are a pair of bean shaped cells that surround the stoma. → The opening and closing of a stoma is controlled by guard cells. 3. Lenticels → Lenticels are openings on the outer surfaces of woody surfaces.  4. Root Hairs → Gasses can diffuse into and out of root hairs. → Oxygen dissolved in water enters the roots of the plants. Plants have vascular tissues that transport water, sugar, and dissolved minerals TWO TYPES OF VASCULAR TISSUES → Xylem Transports water and dissolved minerals Transpiration creates tension that pulls water up the xylem. → Phloem Transports sugar (dissolved in water) from photosynthetic cells to other parts of the plant for growth and storage. Transpiration creates tension that pulls water up the xylem. Water moves against the force of gravity because of capillary action. → COHESION: water molecules stick together → ADHESION: water molecules stick to xylem walls TOPIC 2: RESPIRATORY SYSTEM How the respiratory system and cardiovascular system work together → The Respiratory and Circulatory Systems work together to maintain homeostasis. - The Circulatory System transports blood and other materials throughout the body. It also supplies cells, carries waste materials, and separates oxygenated and deoxygenated blood. - The Respiratory System is responsible for the gas exchange process wherein it picks up oxygen from inhaled air and takes out carbon dioxide and water. The Process of Breathing (Pathway of Air) Nose/Mouth → Pharynx → Larynx → Trachea → Bronchi → Bronchioles → Lungs → Alveoli Nose/Mouth: Air enters the respiratory system through the nose or mouth. The nose filters, warms, and humidifies the air, while the mouth allows for quicker intake of air when needed. Pharynx: The throat (pharynx) serves as a passageway for both air and food. Air travels down the pharynx to the larynx. Larynx: Also known as the voice box, it directs air into the trachea and prevents food from entering the airway with the help of the epiglottis. Trachea: The windpipe (trachea) is a tube that carries air towards the lungs. It is lined with cilia to trap particles and prevent them from reaching the lungs. Bronchi: The trachea splits into two bronchi, each leading to one lung. These branches carry air into the lungs. Bronchioles: Inside the lungs, the bronchi further divide into smaller branches called bronchioles, which distribute air throughout the lungs. Lungs: The lungs house the bronchioles and alveoli and are the main organs of gas exchange. Alveoli: Tiny air sacs at the end of the bronchioles where oxygen is exchanged for carbon dioxide with the blood in the capillaries. Diaphragm: Although not included in the pathway of air, it is a dome-shaped muscle below the lungs. It contracts during inhalation, pulling downward to expand the chest cavity and draw air into the lungs, and relaxes during exhalation, pushing air out. TOPIC 3: CARDIOVASCULAR SYSTEM Functions of the Cardiovascular System → Transportation Oxygen, food, water, and other materials → Elimination Carbon dioxide and other waste materials Parts of the Cardiovascular System Blood Vessels → These are tubes that carry blood. There are 3 main blood vessels: 1. Arteries: take blood away from the heart and has thick walls that withstand high pressure due to heart pumping. The aorta is the first and largest artery, it carries the oxygen-rich blood from the heart to the rest of the body. 2. Veins: bring blood back to the heart and are thinner than arteries as there is less pressure. It has one-way valves to prevent backflow and keep blood moving upwards. 3. Capillaries: these are the smallest blood vessels which deliver materials and take away waste from individual cells. They only have one-cell thick walls which allows the exchange of gases and materials. Heart → A muscular pump that beats 70-75x per min → Valves are thin flaps of tissue that open and close to help the blood move. ATRIA: receiving chambers VENTRICLE: pumping chambers → Right atrium receives → Right ventricle pumps oxygen-poor blood from oxygen-poor blood into the the body lungs → Left atrium receives → Left ventricle pumps oxygen-rich blood from oxygen-rich blood into the rest the lungs of the body Pulmonary Circulation → between the heart and the lungs Coronary Circulation → in the heart Systemic Circulation → between the heart and the rest of the body Blood → A tissue composed of red blood cells (RBC), white blood cells (WBC), platelets, and plasma. TRANSPORTATION PROTECTION TEMP. REGULATION Oxygen, CO2, nutrients, Fights infections and Helps maintain a steady hormones, waste repairs damaged tissues body temperature Parts of Blood Plasma → Yellowish, liquid part of the blood which carries blood cells, salts, vitamins, sugars, minerals, proteins, and cellular wastes → Where RBC, WBC, and platelets are suspended Red Blood Cells (RBC) → AKA Erythrocytes → Contain hemoglobin, an iron-rich molecule which carries oxygen → Has no nucleus and has a biconcave disk shape White Blood Cells (WBC) → AKA Leukocytes → Protects the body from infections and illnesses by attacking pathogens, but usually only lasts a few days and are constantly replaced Platelets → Irregularly shaped pieces of cells → Plug wounds and stop bleeding → Responsible for blood clotting Antigen → Substance that can trigger the immune system Antibody → Clumping protein that attaches to antigens Rhesus (Rh) Factor → A type of protein that is found on the surface of a RBC TOPIC 4: GENETICS Traits → Characteristic features passed on from parents to offspring through genes. These may be visible or hidden and inherited if inherent and not acquired. Genes → Sections of DNA that contain information about a specific trait of that organism. An individual has 2 copies of each chromosome, one from each parent. Allele → These are variations of a gene. Alleles of the same gene are always found on the same location and/or may contain different information for a trait Genotype → The combination of alleles an organism inherits makes up its genotype. Homozygous Heterozygous Homogenous (DOMINANT) (RECESSIVE) AA Aa aa Phenotype → Refers to how the traits appear or are expressed Dominant Allele Recessive Allele Always expressed Expressed only in the absence → Example: A of a dominant allele → Example: a Phenotype Genotype Type A IAIA, IAi Type B IBIB, IBi Type AB IAIB Type O ii Punnett Square → Shows the probability of all possible genotypes and phenotypes of the offspring. Flower color (A/a) Dominant trait purple Recessive trait white Genotype Phenotype Probability AA purple 0 Aa purple 2/4 = 50% aa white 2/4 = 50% In the 1850s, Gregor Mendel performed controlled breeding experiments with pea plants. → Pea plants reproduce quickly and have easily observable traits → Mendel could control which pair of plants reproduced Segregation → Pairs of alleles are separated when gametes are formed Independent Assortment → Pairs of alleles will be sorted independently of one another when gametes are formed Principle of Dominance → The dominant allele masks the effect of the recessive allele NON-MENDELIAN INHERITANCE Incomplete dominance → When an offspring’s phenotype is a combination of its parents’ phenotypes Codominance → Both alleles can be independently observed in a phenotype Multiple Alleles → A gene may have more than two alleles. More than 3 phenotypes occur and it may occur with codominance or incomplete dominance. Sex-linked → When the allele for a trait is on an X or Y chromosome Sex-influenced → Autosomal traits that are expressed differently in different sexes. Sex-limited → Autosomal traits but expressed in one sex only. Polygenic Inheritance → Occurs when multiple genes determine the phenotype of a trait Pedigree → Tool that shows genetic traits that were inherited by members of a family. Squares represent males, Circles represent females → This allows an individual to determine the risk of developing a disease or if they are a carrier of a disease. TOPIC 5: EXTINCTION Extinction → A species is considered extinct when the entire population no longer exists. Mass Extinction → Occurs when many species become extinct within a few million years or less. Ordovician-Silurian Extinction (440 Mya) → Due to the dropping and rising of the sea levels, caused by the formation and melting of glaciers → 25% of marine families and 60% of the marine general were lost Late Devonian Extinction (365 Mya) → 80% of all species on Earth became extinct → May be due to global cooling and lowering of sea levels → Oxygen levels dropped Permian-Triassic Extinction (250 Mya) → The Great Dying → 96% of all species on Earth became extinct → May be caused by the impact of an asteroid or by volcanic eruptions Triassic-Jurassic Extinction (210 Mya) → 80% of land and marine species were lost → May be caused by a massive lava flood → Increase in carbon dioxide levels acidified the oceans Cretaceous-Tertiary Extinction (65 Mya) → also called Cretaceous-Paleogene → May have been triggered by an asteroid that created the Chicxulub Crater Holocene Extinction (Present) → 12,000 years ago to present →Also called the Anthropocene Extinction → Driven by human activities An endangered species is in danger of extinction while a threatened species is likely to be endangered TOPIC 6: PHOTOSYNTHESIS What is Photosynthesis? → Process by which plants use light energy to produce food. Where does photosynthesis occur? → Spongy mesophyll allow gases to flow through → Gases pass through the stomata → Palisade mesophyll cells capture light energy Stomata (singular: stoma) → Pores found on the leaves, stems, and other parts of the plant. Guard Cells → Guard cells are a pair of bean-shaped cells that surround the stoma. → The opening and closing of a stoma is controlled by guard cells. Chloroplasts contain chlorophyll, which traps and stores light energy.  Process Reactants Products Photosynthesis C20 (Carbon Dioxide) C6H12O6 (Glucose) H2O (Water) O2 (Oxygen) The main pigments of photosynthesis are chlorophyll a and chlorophyll b. → Chlorophyll a: violet-blue and orange-red light → Chlorophyll b: blue and yellow light Light-dependent Reactions 1. Excitation of photosystems by light energy → Occur in the thylakoid membrane 2. Production of ATP via an electron transport chain 3. Reduction of NADP+ and the photolysis of water Products: ATP, NADPH, O2 STEP 1: Photosystems are groups of photosynthetic pigments (including chlorophyll) embedded within the thylakoid membrane → When a photosystem absorbs light energy, delocalised electrons within the pigments become “excited.” They are transferred to carrier molecules within the thylakoid membrane.  STEP 2: → As the electrons are passed through the chain they lose energy, which is used to move H+ ions or protons into the thylakoid. Photophosphorylation - light energy is used to produce ATP (from ADP + Pi) The H+ ions return to the stroma via ATP synthase (chemiosmosis). STEP 3: → Excited electrons from Photosystem I may be transferred to a carrier molecule and used to reduce NADP+, forming NADPH. → The electrons lost from Photosystem II are replaced by electrons released from water via photolysis. Water is split by light energy into H+ ions (used in chemiosmosis) and oxygen (released as a by-product). Light-independent Reactions 1. Carbon Fixation 2. Reduction of G-3-P 3. Regeneration of RuBP Products: C6H12O6, ADP, NADP+ Step 1: Carbon Fixation An enzyme, RuBP carboxylase (Rubisco), catalyses the attachment of a CO2 molecule to ribulose biphosphate (RuBP). → The Calvin cycle begins with a 5C compound called ribulose bisphosphate (or RuBP) → An enzyme, RuBP carboxylase (or Rubisco), catalyses the attachment of a CO2 molecule to RuBP → The resulting 6C compound is unstable, and breaks down into two 3C compounds called glycerate-3-phosphate (GP) → A single cycle involves three molecules of RuBP combining with three molecules of CO2 to make six molecules of GP This forms an unstable 6-carbon compound that breaks down into two 3-carbon compounds. This 3-carbon compound is glycerate-3-phosphate (G3P). Step 2: Reduction of G-3-P Glycerate-3-phosphate (G3P) is converted into triose phosphate (TP) using NADPH and ATP. Reduction by NADPH transfers hydrogen atoms to the compound, while the hydrolysis of ATP provides energy. → Glycerate-3-phosphate (GP) is converted into triose phosphate (TP) using NADPH and ATP → The NADPH and ATP are generated by the light dependent reactions (via non-cyclic photophosphorylation) → Reduction by NADPH transfers hydrogen atoms to the compound, while the hydrolysis of ATP provides energy → As six molecules of GP were produced via carbon fixation, six molecules of TP are similarly produced per cycle The remaining five TP molecules are recombined to regenerate stocks of RuBP (5 × 3C = 3 × 5C). STEP 3: REGENERATION → Of the six molecules of TP produced per cycle, one TP molecule may be used to form half a sugar molecule → Hence two cycles are required to produce a single glucose monomer, and more to produce polysaccharides like starch → The remaining five TP molecules are recombined to regenerate stocks of RuBP (5 × 3C = 3 × 5C) → The regeneration of RuBP requires energy derived from the hydrolysis of ATP LIGHT DEPENDENT: LIGHT INDEPENDENT: Light Dependent Light Independent Reactants NADP+ CO2 ADP + Pi NADPH H2O ATP Products NADPH NADP+ ATP ADP + Pi O2 C6H12O6 TL;DR: PHOTOSYNTHESIS (Simplified) What is it? → A process where plants make their food using sunlight, carbon dioxide (CO₂), and water (H₂O). → It happens in the chloroplasts of plant cells. Where does it happen? → Light-dependent reactions: In the thylakoid membrane of chloroplasts. → Light-independent reactions (Calvin Cycle): In the stroma of chloroplasts. 1. Light-Dependent Reactions What happens? → Sunlight is used to make energy carriers (ATP and NADPH) and oxygen (O₂) as a by-products Where? → Thylakoid membrane (inside the chloroplast). Steps: 1. Light absorption → Chlorophyll absorbs sunlight, exciting electrons in photosystems. 2. Electron Transport Chain → Excited electrons move through a chain, creating energy to pump H+ ions into the thylakoid. 3. ATP Production → H+ ions flow back into the stroma through ATP synthase, producing ATP. 4. NADPH Formation → Electrons are used to convert NADP+ into NADPH. 5. Water Splitting → Water is split into H+ ions, electrons (to replace those lost), and oxygen (O₂) is released. Products: ATP, NADPH, and O₂. 2. Light-Independent Reactions (Calvin Cycle) What happens? → The energy carriers (ATP and NADPH) are used to convert carbon dioxide (CO₂) into glucose (C₆H₁₂O₆). Where? → Stroma (fluid surrounding the thylakoids). Steps: 1. Carbon Fixation → CO₂ combines with a 5-carbon molecule (RuBP) to form a 3-carbon compound (G3P), with help from an enzyme called Rubisco. 2. Reduction → G3P is converted into a higher-energy molecule called triose phosphate (TP) using ATP and NADPH. 3. Regeneration → Most of the TP molecules are recycled to regenerate RuBP, ensuring the cycle continues. → Some TP is used to make glucose. Products: Glucose (C₆H₁₂O₆), ADP, NADP+. TL;DR: Light-dependent reactions: Use sunlight to make energy (ATP and NADPH) and release oxygen. Light-independent reactions: Use ATP and NADPH to turn CO₂ into glucose TOPIC 7: CELLULAR RESPIRATION The Role of oxygen in our bodies → Cellular Respiration It is a process that occurs at the level of cells and happens chemically. Food molecules are broken down using oxygen. Oxygen “unlocks” the energy stored in the nutrients and converts it into “energy” in the form of ATP (Adenosine Triphosphate) which is a kind of energy our body uses in performing all activities. Cellular respiration → A series of chemical reactions that convert energy in food molecules into a usable form called ATP. Aerobic Respiration Anaerobic Respiration Oxygen is present when this form of Oxygen is absent when this form of respiration takes place. respiration takes place. Gases are exchanged in this form of Gases are not exchanged in this form of respiration. respiration. It can be found in the cytoplasm and It can be found only in the cytoplasm. the mitochondria. Glucose breaks down into carbon Glucose breaks down into ethyl alcohol, dioxide and water. carbon dioxide and energy. All higher organisms such as mammals Lower organisms such as bacteria and have this type of respiration. yeast use this type. In other organisms, it occurs during heavy activities.  Oxygen is present when this form of Oxygen is absent when this form of respiration takes place. respiration takes place. Matrix → Space surrounding the inner membrane that contains enzymes. Cristae → Folds in the inner membrane that increases the surface area to maximize energy production. Glycolysis → Glucose is broken down in the cytoplasm. Krebs Cycle /TCA Cycle / Citric Acid Cycle (Matrix) → Citric acid goes through a series of reactions that release energy. Electron Transport Chain (Cristae) → Energy is used to produce ATP. Summary: 1 molecule of glucose (6 C) is broken down into 2 molecules of pyruvate (3 C). 1. Phosphorylation → A hexose sugar (typically glucose) is phosphorylated by two molecules of ATP (to form a hexose bisphosphate) → This phosphorylation makes the molecule less stable and more reactive, and also prevents diffusion out of the cell 2. Lysis → The hexose bisphosphate (6C sugar) is split into two triose phosphates (3C sugars) 3. Oxidation → Hydrogen atoms are removed from each of the 3C sugars (via oxidation) to reduce NAD+ to NADH (+ H+) → Two molecules of NADH are produced in total (one from each 3C sugar) 4. ATP formation → Some of the energy released from the sugar intermediates is used to directly synthesise ATP → In total, 4 molecules of ATP are generated during glycolysis by substrate level phosphorylation (2 ATP per 3C sugar) Products: → 2 pyruvate → 2 NADH → 4 ATP (net: 2 ATP) DEHYDROGENATION: Products: → 2 CO2 → 2 NADH → 2 acetyl-CoA KREBS CYCLE: In the Krebs cycle, citric acid is formed when acetyl CoA transfers its acetyl group to oxaloacetate to make citric acid. Citric acid goes through a series of chemical reactions, forming NADh, FADH2, CO2, and ATP. In the Krebs cycle, acetyl CoA transfers its acetyl group to a 4C compound (oxaloacetate) to make a 6C compound (citrate) → Coenzyme A is released and can return to the link reaction to form another molecule of acetyl CoA Over a series of reactions, the 6C compound is broken down to reform the original 4C compound (hence, a cycle) → Two carbon atoms are released via decarboxylation to form two molecules of carbon dioxide (CO2) → Multiple oxidation reactions result in the reduction of hydrogen carriers (3 × NADH + H+ ; 1 × FADH2) → One molecule of ATP is produced directly via substrate level phosphorylation As the link reaction produces two molecules of acetyl CoA (one per each pyruvate), the Krebs cycle occurs twice → Per glucose molecule, the Krebs cycle produces: 4 × CO2 ; 2 × ATP ; 6 × NADH + H+ ; 2 × FADH2 Products: → 6 NADH → 2 FADH2 → 4 CO2 → 2 ATP ELECTRON TRANSPORT CHAIN → Generating a Proton Motive Force → ATP Synthesis via Chemiosmosis →Reduction of Oxygen STEP 1: GENERATING A PROTON MOTIVE FORCE (PMF) → The hydrogen carriers (NADH and FADH2) are oxidised and release high energy electrons and protons → The electrons are transferred to the electron transport chain, which consists of several transmembrane carrier proteins → As electrons pass through the chain, they lose energy – which is used by the chain to pump protons (H+ ions) from the matrix → The accumulation of H+ ions within the intermembrane space creates an electrochemical gradient (or a proton motive force) STEP 2: ATP SYNTHESIS VIA CHEMIOSMOSIS → The proton motive force will cause H+ ions to move down their electrochemical gradient and diffuse back into matrix → This diffusion of protons is called chemiosmosis and is facilitated by the transmembrane enzyme ATP synthase → As the H+ ions move through ATP synthase they trigger the molecular rotation of the enzyme, synthesising ATP STEP 3: REDUCTION OF OXYGEN → In order for the electron transport chain to continue functioning, the de-energised electrons must be removed → Oxygen acts as the final electron acceptor, removing the de-energised electrons to prevent the chain from becoming blocked → Oxygen also binds with free protons in the matrix to form water – removing matrix protons maintains the hydrogen gradient → In the absence of oxygen, hydrogen carriers cannot transfer energised electrons to the chain and ATP production is halted. Glycolysis Link RXN Krebs Cycle ETC (Electron Transport Chain) Reactants 1 C6H12O6 2 pyruvate 2 acetyl-CoA 10 NADH 2 FADH2 6 O2 Products 2 pyruvate 2 acetyl-CoA 2 ATP 32-34 ATP 2 ATP 2 NADH 6 NADH 6 H2O 2 NADH 2 CO2 2 FADH2 4 CO2 Fermentation is the process of breaking down glucose into simpler substances in the absence of oxygen.  TOTAL ATP PRODUCED Aerobic Anaerobic 36-38 2 TL;DR: CELLULAR RESPIRATION (Simplified) What is it? → A process where cells break down glucose to release energy, which is stored as ATP (usable energy for the cell). Types of Respiration: → Aerobic Respiration (with oxygen): Produces a lot of ATP. → Anaerobic Respiration (without oxygen): Produces less ATP. Stages of Cellular Respiration 1. Glycolysis 2. Krebs Cycle (Citric Acid Cycle) 3. Electron Transport Chain (ETC) 1. Glycolysis What happens? → Glucose is broken down into 2 pyruvate molecules in the cytoplasm. → A small amount of ATP and NADH is produced. Where? → Cytoplasm Steps: 1. Phosphorylation → Glucose is activated by adding two phosphate groups (from 2 ATP molecules). 2. Lysis → The activated glucose splits into two 3-carbon molecules. 3. Oxidation → Hydrogen is removed, forming NADH. 4. ATP Formation → A net of 2 ATP is produced. Products: → 2 Pyruvate → 2 ATP (net) → 2 NADH 2. Krebs Cycle (Citric Acid Cycle) What happens? → Pyruvate is broken down into CO₂ in the mitochondrial matrix. → NADH and FADH₂ (energy carriers) and a small amount of ATP are produced. Where? → Mitochondrial matrix Steps: 1. Link Reaction → Pyruvate is converted into acetyl-CoA, producing CO₂ and NADH. 2. Formation of Citrate → Acetyl-CoA combines with a 4C molecule (oxaloacetate) to form citrate (6C). 3. Decarboxylation → Carbon is removed to release 2 CO₂ per cycle. 4. Oxidation → Hydrogen is removed to form NADH and FADH₂. 5. ATP Formation → A small amount of ATP is directly produced. Products (per glucose molecule): → 4 CO₂ → 2 ATP → 6 NADH → 2 FADH₂ 3. Electron Transport Chain (ETC) What happens? → Energy from NADH and FADH₂ is used to produce a large amount of ATP. → Oxygen is the final electron acceptor and forms water. Where? → Cristae (folds of the inner mitochondrial membrane) Steps: 1. Generating Proton Gradient → NADH and FADH₂ release electrons and protons. → Electrons move through the ETC, pumping H+ ions into the intermembrane space, creating a gradient. 2. ATP Synthesis via Chemiosmosis → H+ ions flow back into the matrix through ATP synthase, generating ATP. 3. Reduction of Oxygen → Oxygen accepts electrons and H+ ions to form water (H₂O). Products: → ~34 ATP → H₂O ATP PRODUCTION (Summary) Stage ATP Produced Glycolysis 2 ATP Krebs Cycle 2 ATP Electron Transport Chain 34 ATP Total (Aerobic) 38 ATP per glucose molecule KEY DIFFERENCES OF AEROBIC AND ANAEROBIC RESPIRATION Aerobic Respiration Anaerobic Respiration Requires Oxygen Does not require Oxygen Produces ~38 ATP Produced 2 ATP End products: CO₂ and H₂O End products: Lactate (animals) or ethanol and CO₂ (yeast) Occurs in cytoplasm and mitochondria Occurs only in cytoplasm