AS Biology Notes PDF

1  Carbohydrates: Monosaccharides: sweet, water soluble, reducing sugars...

1  Carbohydrates: Monosaccharides: sweet, water soluble, reducing sugars Disaccharides: sweet, water soluble, most are reducing (not sucrose) Sucrose: Glucose + Fructose Lactose: Glucose + Galactose Maltose: Glucose + Glucose Polysaccharides: long chains of repeating subunits (monosaccharides) joined by condensation Isomers: same molecular formula but a different structural formula reactions Proteins Polymers made up of amino acids. Triglycerides Fatty acid chains can be saturated (no C=C) or unsaturated (have C=C bonds). The more unsaturated the fatty acid the lower the melting point. Fats are insoluble ion water. A phospholipid General fatty acid has a fatty acid replace with a phosphate group. This means it has a hydrophilic region (phosphate head) and hydrophobic regions fatty acid tail. It is integral in the cell membrane. Glycerol 2 Formation of a triglyceride Globular Proteins The vast majority of proteins are globular, i.e. they have a compact, ball-shaped structure. This group includes enzymes, membrane proteins, receptors and storage proteins. The diagram below shows a typical globular enzyme molecule. It has been drawn to highlight the different secondary structures. Globular Proteins  Have complex tertiary and sometimes quaternary structures.  Folded into spherical (globular) shapes.  Usually soluble as hydrophobic side chains in centre of structure.  Roles in metabolic reactions.  E.g. enzymes, haemoglobin in blood. Fibrous (or Filamentous) Proteins Fibrous proteins are long and thin, like ropes. They tend to have structural roles, such as collagen (bone), keratin (hair), tubulin (cytoskeleton) and actin (muscle). They are always composed of many polypeptide chains. This diagram shows part of a molecule of collagen, which is found in bone and cartilage. Fibrous Proteins  Little or no tertiary structure.  Long parallel polypeptide chains.  Cross linkages at intervals forming long fibres or sheets.  Usually insoluble.  Many have structural roles.  E.g. keratin in hair and the outer layer of skin, collagen (a connective tissue). 3 Describe how enzymes break down substances The effect of pH on the rate of enzyme activity How the shape of the enzyme/protein molecules Lowering the activation energy Changes in the pH af f ect the charges on the R is suited to its function Substrate with a complementary shape to the active groups of the amino acids at the active site Each enzyme/protein has specif ic primary structure enters the active site Interactions between the substrate and enzyme are (amino acid sequence) An enzyme substrate complex is f ormed disrupted this sequence determines where the H-bonds will Active site changes shape to mould around the Enzyme substrate complexes are less likely to f orm f orm during development of the secondary structure substrate (induced f it) More extreme pH conditions can cause the bonds Proteins have a unique tertiary structure (f urther This weakens the bonds in the substrate (lowering (ionic, Hydrogen) holding the tertiary structure to f olding of the secondary structure) held by ionic and activation energy) by stretching and distorting them break hydrogen bonds and if amino acids containing The bonds are broken The enzyme denatures (active site is no longer cysteine are present, disulphide bridges Products leave the active site complementary to the substrate) Globular proteins have an active site with unique Enzyme remains unchanged No enzyme substrate complexes can f orm structure; shape of active site complementary to/ will only f it that of substrate Enzyme substrate complexes can f orm Explain how inhibitors affect enzyme activity There are two types of inhibitor, competitive and non-competitive Competitive inhibitors have a similar shape to the substrate They can enter and bind with the active site The effect of temperature on the rate of an Prevents enzyme substrate complexes f orming enzyme reaction Describe how an enzyme catalyses a condensation The problem can be overcome by increasing the As temperature increases so does the rate of the reaction substrate concentration Enzyme active site has a complementary shape to the reaction as… Non-competitive inhibitors substrate Substrate and enzyme gain K.E and collide more Have a dif f erent shape to the substrate An enzyme substrate complex is formed f requently Bind at a point other than the active site The reactive groups……hydroxyl, hydroxyl/ amino, and More enzyme substrate complexes f orm They cause a change in the shape of the active site carboxylic / hydroxyl and carboxylic are brought close Further increases in the temperature cause bonds Prevent f ormation of enzyme substrate complexes together (ionic, disulphide, hydrogen) holding the tertiary Change in the shape of the active site (induced fit) lowers structure of the enzyme in place begin to break the activation energy The enzyme denatures, Water is removed and a glycosidic, peptide or ester bond The active site no longer complements the substrate forms Products leave the active site No enzyme substrate complexes can f orm The enzyme remains unchanged 4  Explain how the small intestine is adapted to its function in the digestion and absorption of the products of digestion. Large surface area provided by villi and microvilli Thin epithelium gives a short diffusion pathway The dense capillary network for absorbing amino acids and sugars and the lacteal for the absorption of digested fats; ensures a steep concentration gradient is maintained The many mitochondria in the epithelial cells supply ATP/ energy for active transport Carrier proteins (in membranes) provide a path for polar molecules to pass through the membrane. Enzymes built into the epithelial membrane make it more likely for enzyme substrate complexes to form and ensure products for absorption are released close to the carrier and channel proteins Digestion of Carbohydrates and Disaccharides Starch Digestion: Amylase Hydrolyses Glycosidic bonds Producing maltose Maltase hydrolyses maltose to glucose Lactose intolerance Food moves through the Cause: reduced lactase levels as we age digestive system by peristalsis. Symptoms: diarrhoea and gas and cramps Absorption of glucose in intestines Mouth = digestion of carbs Glucose moves into the epithelial cell with sodium Via a symport carrier Stomach = digestion of protein Explanation protein; Duodenum = most digestion, Sodium is removed from the epithelial cell by active transport at the sodium- Gas comes from bacteria breaking down the sugar receives pancreatic juice from potassium pump; pancreatic duct and bile form Maintaining a sodium concentration gradient between the lumen and gall bladder (produced in liver) epithelial cell Diarrhoea: sugar lowers the water potential of Ileum = most absorption Glucose moves into blood by facilitated diffusion the lumen compared to epithelial cells, water Colon = absorption of water and And is carried away in the Heaptic portal vein moves into the lumen by osmosis minerals 5 6  Membrane and Movement The membrane is a phospholipid bilayer Where the hydrophobic tails point inwards and the hydrophilic heads face outwards The membrane contains two types of proteins Intrinsic proteins (allow transport of water soluble molecules): spanning the entire bilayer Extrinsic proteins: found on one side of the membrane Most molecules move across the membrane by diffusion down a concentration gradient Small molecules (water/gases) and lipid soluble molecules diffuse between the phospholipids Polar molecules require channel or carrier proteins to move them Channels are water filled pores that can be open at all times or they can be gated (voltage/ligand gated) Carrier proteins have a specific binding site for the molecules/ions This can be facilitated diffusion, a passive (no ATP required) process Some molecules are actively transported across the membrane (against the concentration gradient) This requires ATP (released in respiration) The ATP changes the shape of the protein to move the molecule across the membrane Describe the structure of a cell membrane and phospholipids. Described as fluid mosaic. How the membrane regulates the movement of substances into and out of cells. Fluid: molecules within the membrane able to move; Non-polar/lipid soluble molecules move through phospholipid bilayer; How plasma membrane is adapted for its Small molecules/water/gases move through phospholipid layer/bilayer; Mosaic: mixture of phospholipid and protein functions. Ions/water soluble substances move through channels in proteins; Phospholipid bilayer (as a barrier); Some proteins are gated; Double layer of phospholipid molecules; Reference to diffusion; Forms a barrier to water soluble but allows Phospholipid consists of glycerol; Carriers identified as proteins; non-polar substances to pass so maintains To which are joined two fatty acids; Carriers associated with facilitated diffusion; a different environment on each side And a phosphate; Carriers associated with active transport/transport with ATP/pumps; (compartmentalisation) formed by condensation reaction Different cells have different proteins; Bilayer is fluid: can bend to take up Phosphate head is hydrophilic/polar Correct reference to cytosis; different shapes for phagocytosis and form Fatty acid tail is hydrophobic vesicles the phospholipids are arranged as bilayer in membrane; How proteins are arranged in a plasma membrane and role in transport Channel proteins (intrinsic): let water 1 Some proteins pass right through membrane; soluble/substances through (facilitated Heads on the outside and tails on the inside; 2 Some proteins associated with one layer; diffusion) 3 Involved in facilitated diffusion; Intrinsic proteins molecules pass through entire bilayer 4 Involved in active transport; Carrier proteins (intrinsic): allow facilitated Some of the proteins have channels/pores; 5 Proteins act as carriers; diffusion and active transport Some have specific binding sites and are carrier proteins 6 Carrier changes shape / position; Extrinsic proteins: act in cell recognition, 7 Proteins form channels / pores; act as antigens or receptors; Extrinsic proteins only in one layer 8 Protein allows passage of water soluble molecules / Cholesterol: regulates fluidity / increases Those on the outer side often act as receptors for hormones charged particles / correct named example; stability; Molecules can move in membrane/dynamic/membrane contains Describing the fluid-mosaic structure of a membrane cholesterol; Phospholipids and proteins; Many of the proteins and phospholipids have carbohydrates Phospholipid bilayer: Arrangement of phospholipid molecules ‘Tails to tails’; Molecules can move in membrane; 7 attached forming glycolipids and glycoproteins that make up the Intrinsic proteins extend through bilayer: Channel and carrier proteins Glycocalyx Extrinsic proteins in outer layer only: Act as antigens, receptors Glycoproteins and glycolipids form glycocalyx Presence of cholesterol to help regulate fluidity  The proteins usually span from one side of the phospholipid bilayer to the other (integral proteins), but can also sit on one of the surfaces (peripheral proteins). They can slide around the membrane very quickly and collide with each other, but can never flip from one side to the other. The proteins have hydrophilic amino acids in contact with the water on the outside of membranes, and hydrophobic amino acids in contact with the fatty chains inside the membrane. The phospholipids are arranged in a bilayer (i.e. a double layer), with their polar, hydrophilic phosphate heads facing out towards water, and their non-polar, hydrophobic fatty acid tails facing each other in the middle of the bilayer. This hydrophobic layer acts as a barrier to most molecules, effectively isolating the two sides of the membrane. Different kinds of membranes can contain phospholipids with different fatty acids, affecting the strength and flexibility of the membrane, and animal cell membranes also contain cholesterol linking the fatty acids together and so stabilising and strengthening the membrane. 8 9 10 Diffusion: net movement of molecules form a high concentration to a low concentration Lipid soluble molecules can diffuse easily though the phospholipid bilayer along with small hydrophilic molecules like water, carbon dioxide and oxygen Facilitated diffusion: a passive process, moving large, hydrophilic molecules down the concentration gradient. The molecules cannot pass though the hydrophobic bilayer and must enter/exit the cell through channel proteins or carrier proteins that are specific to the molecules. Active transport Moves a molecule against the concentration gradient (low to high) Requires a specific protein carrier Energy/ATP is used to change the shape of the protein Energy is released in respiration Rate of movement of molecules in facilitated diffusion is limited by the availability of carrier/channel proteins in the membrane. As concentration increase rate will eventually level out as the channels or carriers are working at their maximum rate/ fully occupied. 11  Mechanism of the heart beat Some key facts to learn Cardiac muscle is myogenic The SAN Valves in the heart and blood vessels prevent back flow Sends a wave of electrical activity (depolarisation) across the Tricuspid valve is on the right side of the heart atria Bicuspid valve is on the left side of the heart This triggers atrial systole These two valves are called the atrioventricular valves The impulse is relayed to the ventricles through the AVN These valves are prevented from inverting as they are attached to the papillary Passing down to the apex of the heart along the bundle of His muscle in the ventricle walls, by tendinous cords The impulse spreads along the ventricle walls via the purkyne fibres Semilunar valves are located between the ventricles and the aorta and pulmonary The ventricles contract from the bottom artery. Rare for arteries to have valves The AVN delays ventricular systole to allow them to fill up Pulmonary artery carries deoxygenated blood to the lungs. Rare for arteries to carry with blood deoxygenated blood Double circulation: blood flows through Pulmonary vein carries oxygenated blood to the heart from the lung, rare for vein to the heart twice for one circuit of the have oxygenated blood. body, needs re-pumped after losing pressure in the lungs Deoxygenated blood returns via the vena cava to the RA (1). Atrium contracts blood through tricuspid into RV (2). Ventricle contracts and tricuspid shuts so blood enters the pulmonary artery (3) Blood returns to the LA (4) via the pulmonary vein. The LA contracts and blood forced through the bicuspid valve into the LV (5). The LV contracts and the bicuspid shuts and oxygenated blood flows into the aorta (6) The left ventricle has a thicker, more muscular wall than the right ventricle as it has to pump blood around the whole When ventricular pressure > atrial pressure (1) the body, so must generate a higher pressure. atrioventricular valves shut to prevent backflow, this is the The stroke volume is the volume of blood pumped in each beat. Both the heart rate and the first sound in the heart beat (lub) Cardiac Output: is the amount of blood flowing through the heart each stroke volume can be varied by the body. When When the ventricular pressure < arterial pressure (3) the minute. It is calculated as the product of the heart rate and the stroke the body exercises the cardiac output can semilunar valves shut, this is the second sound of the heart volume: increase dramatically so that beat (dup) Cardiac output = heart rate x stroke volume Oxygen and glucose can get to the muscles faster QRS = electrical activity in the ventricles, occurs just before Carbon dioxide and lactate can be carried away ventricle pressure increases 12 The heart rate can be calculated from the pressure graph by measuring from the muscles faster P = electrical activity in atria and P→Q = time delay due to the time taken for one cardiac cycle and using the formula: Heat can be carried away from the muscles AVN Heart rate (beats/minute) = 60 ÷ time for 1 cycle faster 13  Describe how atheroma may form and lead to a myocardial infarction Cholesterol deposited in the artery wall This atheroma narrows lumen of the artery This creates turbulence and can damage to lining of artery Turbulence increases risk the of blood clot (thrombus) The blood clot may break off (embolus) And lodge in coronary artery; Reduced blood supply to heart muscle; Reduced oxygen supply; Reduced respiration Leads to death of heart muscle Atheroma: How atheroma causes an aneurysm Fatty material within walls of arteries; A build-up of cholesterol Vessels narrow; in the artery wall Blood pressure rises; Weakened blood vessels may burst; Smoking decreases conc. of antioxidants in blood: this increases the damage done to artery walls; raises the number of platelets in the blood and makes them more sticky :more blood clots are likely to form; causes constriction of coronary arteries: raises blood pressure and damage to the artery lining carbon monoxide combines with haemoglobin so less available to transport oxygen blood pressure increased: due to increased heart rate Fat Salt blood cholesterol level increases; Increased salt concentration in blood LDLs transport cholesterol in the blood; decreases water potential of the blood LDLs deposit cholesterol in arteries water moves into the blood atheroma formed blood pressure increased blood pressure increased, turbulence makes clotting more likely 14 There are thousands of different kinds of cell, but the biggest division is between the cells of the prokaryote kingdom (the bacteria) and those of the other four kingdoms (animals, plants, fungi and protoctista), which are all eukaryotic cells. Prokaryotic cells are smaller and simpler than eukaryotic cells, and do not have a nucleus. Prokaryote = without a nucleus Eukaryote = with a nucleus To see cells we need microscopes, like a light microscope. To see the ultrastructure of a cell (the organelles inside) we need electron microscopes. If given a scale bar as below then the formula to use is Actual length of scale bar Magnification = Representative length of the scale bar Ensure you work in the same units × 10 × 1000 × 1000 Cm → mm → µm → nm 20µm 20m Cytoplasm Resolution: how close 2 points can be to each other and still be distinguished as 2 separate points. A B Electron microscopes have a higher resolution than (light microscopes, as they use electrons that have a shorter wavelength than light Shorter wavelengths (like electrons) allow better resolution than longer wavelengths (like light). Explain the advantages and limitations of using a transmission electron microscope How to use a microscope Advantages to measure the size of an 1 TEM uses (beam of) electrons; object. Capsule Cell wall Ribosomes Genetic material 2 These have short wavelength; 3 Allow high resolution/greater resolution/Allow more detail to Measure with an eyepiece be seen/greater useful magnification; graticule If no scale bar is given then the formula to use is Disadvantages Calibrate with the stage Image Size 4 Electrons scattered (by molecules in air); mcirometer (an object of a Magnification = 5 Vacuum established; known size) Actual Size of image 6 Cannot examine living cells; 7 Lots of preparation/procedures used in preparing specimens/ fixing/staining/sectioning; Repeat and calculate an Ensure you work in the same units and then convert to the units 8 May alter appearance/result in artefacts; average 9 very thin specimens 15 they want at the end 10 black and white, images Magnification and Resolution Magnification simply indicates how much bigger the image is that the 1. Using a Magnification Factor original object. It is usually given as a magnification factor, e.g. x100. By Image length = 40 mm using more lenses microscopes can magnify by a larger amount, but the The magnification = ×1000 image may get more blurred, so this doesn't always mean that more detail can be seen. The actual length is 40/1000 = 0.04mm Resolution is the smallest separation at which two separate objects can be Usually convert this to μm = 40 μm distinguished (or resolved), and is therefore a distance (usually in nm). The resolution of a microscope is ultimately limited by the wavelength of light used (400-600nm for visible light). To improve the resolution a shorter wavelength Estimation of size of light is needed, and sometimes microscopes have blue filters for this It is possible to estimate the size of a structure seen with a microscope by comparing the image with a known purpose (because blue has the shortest wavelength of visible light). linear scale. Two pieces of apparatus are commonly used: · a graticule (eyepiece micrometer) · a stage micrometer. Light Microscopes A stage micrometer is a slide with a fine scale of known dimension etched onto it. An graticule is a fine scale that fits inside an eyepiece lens. This is shown in Fig 3. These are the oldest, simplest and most widely-used form of microscopy. Specimens are illuminated with light, which is focused using glass lenses and viewed using the eye or photographic film. Specimens can be living or dead, but often need to be coloured with a coloured stain to make them visible. Many different stains are available that stain specific parts of the cell such as DNA, lipids, cytoskeleton, etc. Electron Microscopes This uses a beam of electrons, rather than electromagnetic radiation, to "illuminate" the specimen. This may seem strange, but electrons behave like waves and can easily be produced (using a hot wire), focused (using electromagnets) and detected (using a phosphor screen or photographic film). A beam of electrons has an effective wavelength of less than 1nm, so can be used to resolve small sub-cellular ultrastructure. The development of the electron microscope in the 1930s revolutionised biology, allowing organelles such as mitochondria, ER and membranes to be seen in detail for the first time. There are two kinds of electron microscope. Transmission electron microscopes (TEM) work much like a light microscope, transmitting a beam of electrons through a thin specimen and then focusing the electrons to form an image on a screen or on film. This is the most common form of electron microscope and has the best resolution (