Biology A2

For the OCR Biology A2 course, all 4 sections in this part of the course on one mind map.

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Biology A2 by Mind Map: Biology A2

1. Respiration

1.1. Evidence

1.1.1. Chemiosmosis Flow of protons across a partially permeable membrane - coupled to generation of ATP. Eukaryotes: Inner Mitochondrial Membrane Prokaryotes: Cell surface membrane (may be invaginated to increase S.A. Early Studies (1940s) Thought energy associated with NAD - first stored in a high-energy interm. chemical before being used to make ATP (no investigations found interm.) Peter Mitchell's Chemiosmosis Theory (1961) Realised build up of protons on 1 side of membrane = source of potential energy. AND that their movement down electrochemical gradient could provide energy needed to power formation of ATP from ADP and P. Therefore, IMM = an energy-transducing membrane. Energy released from ETC - pumps H+ to IMS & that they flow back through protein channels attached to enzymes. Kinetic energy of flow (proton motive force) drove ATP formation. Radical theory from idea of high-energy interm. compound, but by 1978, lots of evidence to support theory. Other Studies ATP not made if mushroom-shaped parts of stalked particles (ie ATP synthase enzymes) removed. ATP not made in presence of antibiotic Digomycin - blocks flow of protons through ion channel. In intact mitochondria, pH of IMS is lower than matrix and p.d. is -200mV

1.2. Anaerobic

1.2.1. Why Anaerobic No oxygen Note The need for re-oxidation Note

1.2.2. Lactate Fermentation Process Note Equation Pyruvate-----(Red NAD - NAD)------>Lactate Info When oxygen is available the lactate produced is changed back to Pyruvate making it less wasteful than alcoholic fermentation. The muscles can cope with a build up of lactate however it is the lowered pH that occurs as a result that causes cramp Lactate fermentation occurs in mammals only

1.2.3. Alcoholic Fermentation Equation Pyruvate--(Red NAD - NAD)-->Ethanal--(Red NAD - NAD)-->Ethanol Process Note Info This process cannot occur for too long as mopre than 18% ethanol in the yeast cell and it dies. It produces very little ATP so makers of alcoholic beverages first grow the bacteria under aerobic conditions so the yeast cells grow and then switch them to alcoholic fermentation

1.3. Basic Info

1.3.1. Co-enzymes NAD Structure Function Co-enzyme A Function Structure Why Co-enzymes Enzymes are in general poor at oxidation/reduction reactions yet a large number are needed for respiration thus co-enzymes are needed to facilitate the reactions.

1.3.2. ATP Info ATP structure Def: A phosphorylated nucleotide, the universal energy currency Adenine - nitrogenous base Ribose - Pentose sugar Phosphate groups Image ATP Uses Used in Active transport to resist concentration grapdients. Used in the movement of flagella in bacteria or cilla in the lining of the lungs. Protein synthesis in the endoplasmic reticulum Activation of hormones and the secretion of said hormones (exo/endocytosis) ATP Source From a variety of sources including Glycolysis, Krebs cycle and Oxidative phosphorylation. Releasing energy from ATP Note

1.3.3. Substrates Testing for substrates Respirometers Different Substrates Carbohydrates Definition: A respiratory substrate is an organic substance that can be used for respiration. Protein Lipids

1.3.4. Definition Def: The process by which energy stored in complex organic molecules is used to make ATP Used in Maintaining temperature through the production

1.4. Mitochondria Structure

1.4.1. Size Shape and Distribution Size Very small shape between 0.5-1.0 micrometers in length and this allows a large number to be fitted inside a cell, up to 2500. Shape They are long sausage shaped cylinders to increase surface area and thus overall ATP yield. Distribution Distributed in cells towards an area which requires most ATP such as the ends of synaptic knobs, they are moved there through microtubles

1.4.2. Outer Membrane A normal phospholipid bi-layer that contains channel proteins in it. These channels are important for letting the molecule pyruvate in from the cytoplasm to the Matrix to take part in the Krebs cycle.

1.4.3. Inner Membrane Highly folded Increased surface area increases the maximum ATP yield from oxidative phosphorylation Electron transport Chain Note ATP Synthase Allows diffusion of H+ ions across the membrane through this enzyme, also is used for binding ADP and a phosphate group to produce ATP. These enzymes exist in the membrane with the stalk towards the matrix end. Impermeable to ions This allows a build up of H+ ions in the intermembrane space as a potential source of energy.

1.4.4. Matrix Contains Krebs Cycle reagents such as Oxaloacetate needed for Krebs It contains Mitochondrial DNA for specific enzymes such as ATP synthase which means that Mitochondria can exist without a nucleus and cut down time on DNA transport Contains coenzymes needed for Krebs cycle.

1.5. Process

1.5.1. Glycolysis Stage 1: Phosphorylation Note Stage 2: Splitting Note Stage 3: Oxidation of TP Note Stage 4: Conversion Note Overall 2x Molecules of ATP, 2x molecules of Pyruvate, 2x Reduced NAD

1.5.2. Link Reaction 2 Reactions Decarboxylation, using a decarboxylase enzyme Dehydrogenation, using a dehydrogenase enzyme End Products per molecule of Glucose 2x Reduced NAD 2x CO2 2x Acetate, transported to the Krebs cycle using CoA to form Acetyl CoA Occurs in the Matrix and occurs twice for every molecule of Glucose

1.5.3. Krebs Cycle Stage 1: Acetate + Oxaloacetate --> Citrate Stage 2 --> Various intermediates End Products per molecule of Glucose 6x Reduced NAD 4x CO2 2x Reduced FAD 2x ATP Occurs in the matrix and occurs twice for every molecule of Glucose

1.5.4. Oxidative Phosphorylation Stage 1: Red NAD Note Stage 2: Cytochromes Note Stage 3: Oxidative Phosphroylation Note Stage 4: Final electron acceptor Note

2. Photosynthesis

2.1. Photosynthesis Experiments

2.1.1. Investigating the factors that affect the Rate of Photosynthesis (1) Photosynthometer (light intensity on oxygen produced) Experiment Fill photosynthometer (aka Audus microburette) with tap water Well-illuminated 7cm piece of Elodea - make sure bubbles of gas from stem. Place cut-end upwards into test tube with same water that Elodea was kept in & add 2 drops sodiumhydrogencarbonate soln. Beaker at 20degreesC Light source as close as possible (1/d^2) Acclimatisation: 5-10 mins Position capillary tube over cut end for known period of time (5-10mins), gently pull syringe so air bubble near scale - measure its length x pi r^2 = volume gas collected Gently push plunger so bubble expelled + repeat with different distances Carbon dioxide on O2 produced vary no. of drops of sodium hydrogencarbonate soln Temperature on O2 produced Alter temp of water bath (though not v accurate as warmer water reduces solubility of O2)

2.1.2. Investigating the factors that affect..... (2) Changes in Density of Leaf Discs Drinking straw cut leaf discs from cress cotyledons 5-6 discs in 10cm3 syringe - half-fill syringe with dilute sodium hydrogencarbonate soln Hold syringe upright, finger over end, gently pull out plunger --> pulls air out of air spaces in spongy mesophyll --> increases density therefore sink to bottom of syringe Once all discs sunk, transfer syringe contents to small beaker & using bright light, time how long it takes for 1 disc to float to top (Rate: 1/t) Repeat readings at different light intensities

2.2. Light Dependant Reactions

2.2.1. Non-cyclic Photophosphorylation Thylakoid First photon absorbed by PSII (loss of 2e-) Second photon absorbed by PSI Z-scheme

2.2.2. Cyclic Photophosphorylation Thylakoid Photon strikes PSI

2.3. Light Independent Reactions

2.3.1. Calvin Cycle CO2 in combines Ribulose Biphosphate (RuBP) catalysed by Ribulose Biphosphate Carboxylase (Rubisco) = Glycerate-3-Phosphate (GP) GP reduced by NADPH using energy from ATP hydrolysis Stroma

2.3.2. Where carbon dioxide is fixed & used to build complex organic molecules

2.4. Structure of Chloroplasts

2.4.1. Double membrane ie envelope Inner membrane - transport proteins - control entry/exit substances between cytoplasm & stroma Intermembrane space Outer membrane - permeable to many small ions

2.4.2. Photosystems Primary Pigment Reaction Centre Chlorophyll 'a' Accessory Pigments Chlorophyll 'b' Carotenoids Photosynthetic Pigments: Molecules that absorb light energy. Each pigment absorbs a range of wavelengths in the visible region & has its own distinct peak of absorption. Other wavelengths reflected. Allow maximum absorption light energy

2.4.3. Many grana (each up to 100 thylk membranes) Large S.A. Photosynthetic pigments Electron carriers ATP synthase enzymes Proteins embedded in grana hold photosystems in place

2.4.4. Fluid-filled stroma enzymes catalyse reactions of L.I. stage Surrounds the grana so that the products of the L.D. stage can readily pass into it

2.4.5. Chloroplast DNA & ribosomes Code for & assemble proteins

2.5. Limiting Factors

2.5.1. The factor in a metabolic process that is present at the lowest/least favourable value Carbon dioxide No other limiting factor, rate of photosynthesis increase as CO2 increases High number of stomata open - increased transpiration - plant wilting - stress response - stomata close Light Intensity Rate of Photosynthesis directly proportional 1/d^2 (distance halved, light intensity quartered) Low Temperature Rate of photosynthesis increases

3. Communication and Homeostasis

3.1. The Neuronal System

3.1.1. Sensory Receptors Energy Transducers Rod and cone cells in retina Olfactory cells lining inner surface nasal cavity Pacinian corpuslces in skin Sound receptors in inner ear (cochlea) Taste buds in tongue, hard palate, epiglottis & first part oesophagus Propriocepters

3.1.2. Features of Neurones Very long - A.P. transmitted over long distance Plasma membrane - many gated ion channels - control entry/exit of Na+, K+ and Ca2+ Na+/K+ pumps that use ATP to actively transport 3Na+ OUT of cell and 2K+ INTO Maintain pd across plasma membrane Surrounded myelin sheath - insulates neurone. Nodes of Ranvier - saltatory conduction Cell body - nucleus, many mitochondria & ribosomes Motor neurones - cell body in CNS & long axon carries A.P to effector Sensory neurones - long dendron carrying A.P to cell body (just outside CNS). Short axon to CNS Numerous dendrites connected to other neurones

3.1.3. Resting Potential: Pd across neurone plasma membrane when neurone is at rest (-60mV) Generator Potential: Stimulus causes some Na+ channels open therefore depolarisation Threshold Potential reached (-50mV): Voltage-gated Na+ channels open - large influx

3.1.4. Action Potential transmitted by Local Currents (diffusion of Na+ along neurone) Myelinated: has noR (2-3microm) = saltatory conduction Schwann cell enshrouds neurone Non-myelinated: a long wave Several neurones enshrouded in one loosely wrapped Schwann cell

3.1.5. Synapses AP reaches Synaptic Knob (swelling at end of neurone - mitochondria, Smooth ER, neurotransmitter vesicles, VG Ca2+ ion channels in membrane) AP reaches Synaptic Knob = depolarisation VG Ca2+ channels open - diffusion Neurotransmitter vesicles, fuse, cell surface membrane, exocytosis Diffuse, synaptic cleft, postsynaptic membrane Receptor sites, Na+ channels, open, diffusion, postsynaptic neurone Generator potential/Excitatory Postsynaptic Potential (EPSP) created - sufficient amount combine = AP Acetylcholinesterase enzyme Acetylcholine = Ethanoic Acid + Choline. Diffuse back & recombined using ATP Roles Ensure AP transmitted only 1 direction Several presynaptic neurones can converge to one postsynaptic neurone One presynaptic neurone can diverge to several postsynaptic neurones Can filter out unwanted low-level signals (not enough vesicles will be released) Summation: Several small potential changes can combine to produce 1 larger change in pd - amplifying low-level signals Acclimatisation (running out of vesicles) - prevents overstimulation

3.2. Need for Communication

3.2.1. Multicellular Organisms Complex - range of tissues & organs, many not exposed to ext environment as they are protected by epithelial tissues and organs. E.g. skin and bark Stimulus: Any change in the environment that causes a response. Build up of waste products - toxic. Enzymes require set of conditions to work efficiently - pH, temp, aq, freedom from toxins & excess inhibitors Response: A change in behaviour or physiology as a result of the change in environment. Coordination to ensure different parts body work together effectively Cell Signalling: One cell releases a chemical that is detected by another cell, which responds. Maintaining Body Temperature Ectotherm: Organism that relies on ext sources of heat to regulate body temp. Endotherm: Organism that can use internal sources of heat to maintain its body temp.

3.3. The Endocrine System

3.3.1. Regulation of Blood Glucose The Pancreas The Pancreas has two main functions associated with digestion. Exocrine function Endocrine function Monitoring blood glucose Too High Too Low Processing Blood Glucose Image Stage 1: Beta Cell Structure Stage 2: Glucose breakdown Stage 3: Voltage change Stage 4: Insulin release Diabetes Diabetes Mellitus is a disease that means the body cannot enforce the blood glucose negative feedback loop. This can lead to very high concentrations of blood glucose (Hyperglycaemia) or extremely low levels (Hypoglycaemia) Type I Type II Insulin Source

3.3.2. Regulation of Human Heart Rate The Heart provides substrates and takes away waste fro cell metabolism to occur. The heart has to adapt to different levels of cell metabolism so has to change its behavior accordingly Control of the heart rate occurs in the cardiovascular centre in the medulla oblongata this can change heart rate according to signals centre by various receptors and by transmitting those signals to the heart. The heart can change 3 factors to adapt to change Heart Rate Stroke Volume (Amount of blood per contraction) Strength of contraction Factors that increase Heart Rate Stretching of Carotid Sinus Stretching of muscles Lowered pH Adrenalin secretion

3.3.3. Endocrine Basics An example of hormone use: Adrenalin Functions of the Adrenal Glands How Adrenaline works. Glands Endocrine Exocrine Hormones These are molecular signals released by the endocrine system directly into the blood stream. They act as messengers delivering signals to specific target tissues. There are roughly two types of hormone. Protein hormones which cannot pass through the phospholipid bilayer and steroid hormones which can. Steroid hormones act on the DNA of a cell itself. Hormones work by binding to a specific complimentary receptor found on the surface of a cells membrane. Cells that contain the specific receptor are called the hormones 'target cells' and are target tissues in large quantities.

4. Excretion

4.1. Excretion Basic Info

4.1.1. Definition Excretion is the removal of metabolic waste from the body. This encompasses any substances that are toxic or produced in excess.

4.1.2. Why Excretion is importnant CO2 Respiratory Acidosis Haemoglobin competition Nitrogenous Compounds The body cannot store excess amino acids or proteins but instead of wasting them alters them so they can take part in respiration However this altering (deamination) produces the very toxic Ammonia which is also highly soluble. To get rid of this compound it is first altered to form Urea in the ornithine cycle and is then passed out through the kidneys.

4.2. Liver

4.2.1. Structure Blood flow and the liver Image of the liver connected to the circulatory system. Hepatic Artery Hepatic Vein Hepatic Portal Vein Bile Duct Gall Bladder Arrangement of cells in the liver Imgae of a liver Lobule Cells in the liver are arranged into Lobes to ensure the best contact between blood and hepatocytes. These lobes and then further split into lobules. Hepatocytes Kupffer cells Sinusoid Bile Cannilicus

4.2.2. Functions Control of blood glucose levels, amino acid levels Synthesis or destruction of Red blood cells Storage of vitamins Detoxification The liver uses a variety of enzymes in order to detoxify chemicals that can crop up in our every day diet. Toxins can be rendered harmless by oxidation; reduction; methylation or combination. Detoxification of Alcohol Formation of Urea Deamination The Ornithine Cycle

4.3. Kidney

4.3.1. Water Reabsorbtion Image _ Process Stage 1: Addition of Ions Stage 2: Removal of Ions Stage 3: Altering Concentrations Stage 4: Mass Water Reabsorbtion

4.3.2. Osmoregulation Definition The control of water levels and salt levels in the body. This is important because water is gained and lost through a variety of sources(food, drink, urine or sweating) If water potentials in cells vary too wildly they cannot conduct their functions and die Osmoregulation works as a negative feedback loop which is constantly responding to changes in the normal water potential of blood. Process Stage 1: Detecting WP fluxations Stage 2: Changing ADH levels Stage 3: Altering the permeability of the Collecting Duct Stage 4: Return to normal WP

4.3.3. Kidney Failure Why Kidney Failure occurs Diabetes Mellitus (Both types) Hypertension Infection Dialysis Haemodialysis Peritoneal Transplant Major surgery which requires a new kidney to be placed into the body and attached to a blood supply. This treatment needs to be used in conjuncture with immunosuppressant drugs. Peritoneal Dialysis Vs Haemodialysis Vs Transplant Immunospressants Diet Time consumed Manoeuvrability Quality of Life Surgery

4.3.4. Testing Urine samples Pregnancy testing This processes uses a MONOCLONAL ANTIBODY to bind to a hormone called human chorionic gonadotrophin (hCG) which is produced up to 6 days after pregnancy. The Monoclonal antibody means it will only bind to this protein. Once attached the antibody is tagged to a blue bead which moves up the test. One line is always used as a control, another indicates pregnancy. Anabolic steroid testing Anabolic steroids increase protein synthesis which results in the build up of muscle tissue These steroids always remain in the blood for several days and can easily enter the nephron. They are tested for using gas chromatography Gas chromatography involves the vaporisation of a sample in a gas solvent. As the sample passes down the the apparatus different substances are absorbed at different times. If the steroid is present it will be absorbed at a specific place. The resulting chromatogram is compared with other standards to indicate the presence of a drug

4.3.5. Ultrafiltration Definition Ultrafiltration is filtration at a molecular level where molecules in the glomerulus pass into the Bowman's capsulre Process Stage 1: Endothelium of Capillary Stage 2: Basement membrane Stage 3: Podocytes Image _ Ultrafiltration occurs due to different pressures in the afferent and efferent arterioles. As the efferent arteriole is smaller in diameter than the afferent arteriole, this creates pressure forcing blood plasma in the glomerulus into the Bowman's capsule What is filtered Left in blood Taken out of blood

4.3.6. Selective Reabsorbtion Process Stage 1: Na+ ions are actively transported out of the outer PCT lining into the capillary creating a concentrations gradient in the wall Stage 2: Na+ then flow in through the glomerular filtrate in association with the cotransporters. These cotransporters also bring glucose and other amino acids in with them Stage 3: The amino acids and glucose then diffuses into the capillary as per normal. Image _ Proximal Convuluted Tubule adaptations The lining contains microvilli which helps increase the surface area of the wall and thus the amount of substances that can be reabsorbed at any one time Contransporters in the lining of the wall help transport glucose and other salts across the membrane in facilitated diffusion The outer lining of the tubule contains sodium-potassium pumps that help move ions in order to help facilitated diffusion The cells in the wall contain many mitochondria in order to process the vast amounts of active transport in removing sodium ions from the lining of the PCT

4.3.7. Structure Kidney Capsule Renal Artery/Vein Medulla Cortex Ureter Image Nephron Bowman's Capsule Proximal Convoluted Tubule Loop of Henle Distal Convoluted Tubule Collecting Duct Image