Biology Unit 1

Biology Unit 1

Microscopes
1. Optical (light)
  1. Although it has lower resolution and lower magnification, it does have advantages over EM.
    1. It's cheaper (£150)
      1. Specimen can be dead or alive
        Natural colours are seen
2. Electron Microscope
  1. Scanning EM
    1. Where electrons bounce off the surface of the object
    2. Provides a 3D image
    3. Benefits comapared to TEM
      1. 3D imaging
        Allows you to view the surface rather than the sliced inside
        Thin sections dont need to be prepared
        This needs to happen with TEM.
        It may mean that when analysing a slide, the shape that you see ma appear to be different to what you were expecting due to the angle at which the thin section was cut
  2. Transmission EM
    1. Where electrons go through the organism
    2. Provides higher reolution and higher magnificaton than SEM
    3. Benefits compared to SEM
      1. Higher resolution reached
        Higher magnification reached
  3. Limitations in general of the EM:
    1. Expensive (£1 million)
      1. A vacuum required so living organisms cant be viewed
        Only get black and white pictures
        Harsh prep may mean result in artefacts, which are structures that weren't found in the original specimen
        Complex staining method is required.
3. Maginification- The number of times the lens makes the image bigger than the object
  1. Higher for the elcetron microscope
4. Resolution- The ability of the lens to distinguish between object that are close together
  1. Higher for the electron microscope
    1. This is because the electron beam has a shorter wavelength than light and so it has a higher resolving power.
Cells- structure, function etc.
1. Eukaryotic cells contain nucleus and other membrane bound organelles
  1. Prokaryotic cells do not contain a nucleus and other membrane bound organelles. They have circular DNA.
2. Nucleus
  1. Mitochondria
    1. Rough endoplasmic reticulum
      1. Smooth endoplasmic reticulum
        Golgi apparatus
        Lysosomes
        Cell membrane
        Ribosomes
        Consists of 2 subunits, larger and a smaller one
        Its function is to produce proteins
        It is partially permeable
        Controls the entry and exit of substances in and out of the cell
        A membrane bound sac filled with digestive enzymes and of acidic pH.
        It gets rid of unwanted structures in the cell
        A network of flattened membranesand vesicles
        It transports and chemically modifies substances such as glycoproteins. It is also invloved in secretion and also produces lysosomes
        Is involved in the production and transportation of lipids.
        A network of membranes without ribosomes
      2. A network of membrane covered in ribosomes.
      3. It transports the proteins made by the ribosomes
    2. Where aerobic respiration occurs. Produces ATP and releases energy
    3. Also consists of an envelope. The folded part is called the crista. It also contains a solution called matrix.
  2. Controls the activities of the cell and contains genetic info
  3. Consists of a nucleolus, nuclear membrane and nuclear pores(allows exchange between nucleus and cytoplasm)
3. Separating organelles
  1. Occurs by cell fractionation and ultracentrifugation
    1. 1. The tissue is homogenised in a blender. This will break open the cell to release it's contents.
      1. Placed in an ice-cold solution to reduce enzyme activity without denaturing them
      2. Placed in an isotonic solution to prevent osmotic damage (bursting)
      3. Placed in a buffer solution to prevent the enzymes denaturing
      4. 2. The resulting homgenate is then filtered off to remove any unbroken cells
        3. It is then centrifuged, meaning spun at high speed for a certain amount of time
        The most dense organelle will sink to the bottom during this and form a pellet
        The first pellet will be the nucleus. Then you'll get the mitochondria if you're looking at an animal cell or chlorplasts if you're looking at a plant cell. Then you should get ribosomes and membranes
        4. The supernatant found above the pellet will be poured off so that it can be centrifuged again at higher speeds and for longer
The Cell Membrane
1. The function of the cell surface membrane in to control what eneters and exits the cell
  1. It's partially permeable
2. Composition
  1. Phopholipids
    1. The phospholipid contains a glycerol molecules, 2 fatty acid tails on one side and a phosphate group on the other side.
      1. It is often represented like so:
        The 'head' i.e. the gylcerol and the phospahte group are hydrophilic, i.e. water loving, bevause they're polar
        The tail, consisting of the fatty acids are hydrophobic i.e. water hating because they're non-polar
        Because of these two properties, the phospholipids are arranged as a bilayer
        This is important so that the hydrophobic head faces both aquatic environments (cytoplasm and tissue fluid) and the hyrdrophilic tail faces neither
    2. Function: It acts as a barrier to prevent large, charged or water soluble molecules through e.g. sodium ions.
      1. However, small, uncharged and lipid soluble molecules such as oxygen may enter through the gaos in the fluid bilayer.
    3. Simple Diffusion
      1. This is a passive process so nor energy is required from ATP. Particles rely on their own kinetic energy
      2. It is defined as the net movement of substances from an area of high concentration to an area of low concentration through a partially permeable membrane
        i.e. It moves down a concentration gradient.
      3. It occurs through movement through the phospholipid bilayer. They molecules have to be small, uncharged and lipid soluble.
      4. Ficks Law: Rate of diffusion is proportional to (surface area x difference in concentration gradient) / thickness of exchange surface
        Therefore, in order to have the highest rate of diffusion, you need:
        A large surface area
        Large difference in concentration gradient
        Short diffusion pathway
        High temperature (more kinetic energy)
      5. Osmosis
        Water Potential
        This is a measure of the tendency of water to move and leave a system
        Units: kPa
        Thw water potential of pure water is 0
        Therefore, the water potential of a solution must be negative
        The reason for this is because in a solution, water molecules move less freely because theyre attracted to the solute. Therefore their tendency to move and leave a place is lower and so the water potential must be lower
        This depends on pressure potential (+) and solute potential (-)
        This is defined as the movement of particles from a less negative water potential to a more negative water potential through a partially permeable membrane
  2. Cholesterol
    1. Found between the phospholipids or proteins.
      1. Helps to keep the mebrane fluid and stable
  3. Proteins
    1. Extrinsic
      1. Goes halfway through the membrane
        Act as receptors. They have a specific shape, so that only a molecule of complemetary shape can bind to the protein.
        Binding will cause changes to take place in the cell e.g. cause the release of a hormone
    2. Intrinsic
      1. Goes all the way through the membrane
        These act as protein carriers or channels and they transport SPECIFIC substances through the mebrane by either facilitated diffusion or active transport
        Facilitated Diffusion
        This is also a passive process where molecules use their own kinetic energy
        The same rules apply for facilitated diffusion as it also depends on Fick's law
        However, it also depends on the number of protein carriers present
        It requires the use of a protein carrier
        The solute will only bind to the protein carrier if it has a complementary shape to it
        The protein will begin to change shape, using its own kinetic energy
        Solute will be released on the other side and the protein carrier will reutrn to its original shape
        Active Transport
        This is the movement of particles against a concentration gradient i.e. from a low concentration to a high concentration
        The process will require energy from ATP.
        It also requires a protein carrier, and the solute needs to be of complementary shape to the protein carrier
        Once binding has taken place, the carrier will change shape using the energy released by ATP
        Solute will be released on the other side and protein carrier returns to original shape
  4. Carbohydrates
    1. Found ON some of the protein or phospholipids
      1. Protein + Carbohydrate = Glycoproteins
      2. Lipid + Carbohydrate = Glycolipid
    2. Only found on the outer layer, next to the tissue fluid
    3. Function: Cell recognition
3. Often described as the 'Fluid Mosaic' model.
  1. This is because the phospholipid bilayer is continously moving making it fluid
    1. An the mosaic refers to the pattern and arrangement of the phospholipids and the proteins
Biochemistry
1. This is the study of chemicals and reactions in the body.
  1. Most common element;
    1. Carbon
    2. Oxygen
    3. Hydrogen
    4. Nitrogen
2. Carbohydrates
  1. Contain Carbon, Hydrogen and Oxygen.
    1. Has a unique property: The hydrogen and oxygen are found in 2:1 rations. Only in carbohydrates.
  2. Monomer: Monosaccharide
    1. All end in '-ose'
    2. They are all sugars, because they dissolve in water to form a sweet solution
      1. These are used to build bigger macromolecules through condensation reactions
        All monomers are reducing sugars, and so can be tested with the beneducts test:
        You heat with benedicts for 10 minutes and you should get a brick red precipitate.
    3. Example: Glucose
      1. α Glucose
        Has the OH group at the BOTTOM
      2. β Glucose
        Has the OH group at the TOP
      3. A respiratory substrate and it has 2 isomers
      4. C6H12O6
      5. Other examples: Fructose and Galactose
  3. 2 monomers: Disaccharide
    1. Are also reducing sugars and so can be tested with Benedict's.
    2. Where 2 monomers are joined by condensation reaction
      1. e.g. Maltose (2 α Glucose)
        Other examples
        Sucrose (fructose+glucose)
        Transport compound in plants
        Lactose (glucose+galactose)
        Sugar found in milk
        The bond formed is called a glycosidic bond
  4. Many monomers: Polysaccharide
    1. Many monosaccharides joined together through condensation reactions
    2. They're NOT sugars as they're insolube in water
    3. Example: Starch (α glucose)
      1. Test: Add few drops of iodine
        Turns from yellow to blue-black
      2. It's a major energy store in plants
      3. Straight chained
      4. Branch chained
      5. Hydrogen bonds between the glucose molecules holds its specific shape
      6. Its a good energy store because:
        Insolube: doesn't affect water potential
        Coiled and compact, more stored in a small volume
        Readily broken down by enzymes
3. Lipids
  1. Also contain Carbon, Hydrogen and Oxygen. However, they dont have any unique properties
    1. They're made up of fatty acids and glyrcerol.
      1. A triglyceride looks like this:
        It contains a glycerol molecule ( CH2OHCHOHCH2OH) and a fatty acid molecule (RCOOH)
        Saturated: no double bonds in HC chain
        Unsaturated: Double bonds in the HC chain
        Forms an Ester bond
  2. Functions
    1. Energy store
    2. Insulation
    3. Protection
    4. Phospholipids
  3. Test:
    1. Dissove in ethanol, add a few drops of water and you should get an emulsion
4. Proteins
  1. Belong to a macromolecular group called the polypeptides
  2. Test:
    1. Add sodium hydroxide then a few drops of copper sulphate solution and the colour should go purple
  3. Structure:
    1. When it condenses, it forms a peptide bond
    2. Condensation occurs between the H on NH2 and the OH on acid group
  4. Primary
    1. Refers to the number and sequence of amino acid chain
    2. Peptide Bond
  5. Secondary
    1. Peptide + Hydrogen bonds
    2. Describes the coiling and folding of structure into α helix and β pleated sheet. Hydrogen bonds hold the shape together.
    3. Called Fribrous Proteins
  6. Tertiary
    1. Peptide + Hydrogen + Ionic + Disulphide
    2. Refers to the extensive coiling and folding of the chain into a complex, compact 3D shape. This creates a specific shape for things like enzymes.
    3. Globular Proteins
  7. Quaternary
    1. A protein that consists of more than one polypeptide chain.
    2. Peptide + Hydrogen + Ionic + Disulphide
    3. e.g. Haemoglobin (4)
5. Condensation: The joining of two monomers by the removal of water, and the formation of a bond
  1. Hydrolysis: The separation of two or more monomers through the addition of water. Also requires the use of enzymes
6. Test for non-reducing sugars: Boil with dilute HCL, cool, then neutralise with NaHCO3. Then do benedicts.
Enzymes
1. These are globular proteins (tertiary)
2. They are biological catalysts that speed up hydrolysis reactions
3. Enzymes have an acitve site that is a specific shape. Only a substrate of complememntary shape will bind to the active site to form the Enzyme-Substrate complex
4. They break down bigger molecules into smaller ones
5. They work by lowering the activatiomn energy required for the reaction.
6. Lock and Key theory
  1. The idea that the substrate has to be an exact complementary shape to active site in order to bind.
7. Induced Fit theory
  1. The idea that the substrate isn't an exact complementary shape and so as it binds, the active site changes shape slightly, putting a strain on the substrate which makes it easier to break.
8. Factors affecting enzyme activity
  1. Temperature
    1. As you increase the temperature, the rate of enzyme activity will increase due to more frequent and succesful collisions (more kinetic energy)
      1. After optimum temperature is reached, the rate decreases. This is because the enzyme has been denatured as broken hydrogen bonds have cause a change in the shape of the active site.
  2. pH
    1. The rate of enzyme activity will be highest when optimum pH is reached.
      1. Once you go past optimum temperature, the enzyme will become denatured because broken ionic bonds have meant that active site has changed shape so the ES complex can't form.
  3. Substrate Concentration
    1. At first, as you increase the substrate concentration, the rate of enzyme activity will also increase as their are more substrates to form ES complexes with.
      1. However, as you increase the substrate concentration even more, the rate becomes constant. This is because all the enzymes are currently occupied.
        Enzyme conc is the limiting factor here
      2. Substrate concentration is the limiting factor
  4. Inhibitor
    1. Competitive
      1. This is where the inhibitor has a similar shape to the correct substrate and can also bind to the enzyme and block it.
        Degree of inhibition depends on the relative concentration of inhibitor compared to substrate.
    2. Non-competitive
      1. This is where the inhibitor binds to a site OTHER than the active site, and this causes the active site to change shape so the ES complex can't form.
The Digestive System
1. This involves the breakdown of bigger, insoluble molecules, to smaller, soluble molecules that can be absorbed and assimilated
  1. This is done by enzymic hydrolysis
2. The following processes occur:
  1. 1. Ingestion: Where food is taken in the mouth; the first interface with the environment
    1. 2. Digestion: where bigger insoluble molecules are broken down into smaller soluble ones that can be absorbed and used.
      1. Absorption: This is where the small soluble molecules are taken up through the lining of the small intestine
        Egestion: the substances that can't be digestied pass through the large intestine and out the anus. You also get things like enzymes or cells that have been scraped from the gut lining as well as bacteria in the form of faeces.
        Adaptations:
        Many mitochondria: releases energy from ATP for active transport.
        Microvilli: gives a large surface area for the diffusion of nutrients.
        The soluble molecules can be absorbed into the body cells by:
        Facilitated Diffusion
        Active transport
        Co-Transport
        This is how glucose enters the cells.
        It co-transports with sodium ions. This means that they move together into the protein carrier. (Facilitated diffusion)
        For this to occur, a concentration gradient needs to be maintained.
        This is done by acitvely pumping out Na+ ions into the blood and thus maintaining a low concentration gradient of Na+ ions inside the cell.
        Na+ ions will want to enter by facilitated diffusion from a high concentration to a low concentration, co-transporting glucose moleucles with it.
3. Digestion of carbohydrates.
  1. We need to know about the breakdown of carbohydrates in tthe body. Example:
    1. Starch---->Maltose---->Glucose by amylase and then maltase.
      1. 1. Amylase is found the the saliva, produced by the salivary gland. It starts off the proces of enzymic hydrolysis, but is rarely completed because of swallowing.
        2. Pancreatic amylase is found in the pancreas. Hydrolysis is completed here and maltose is produced.
        2. The maltose then flows down the duodenum (First 30cm of the small intestine)
        The enzyme maltase is located on the surface of the epithelial cells in the small intestine. This is so that the products (Glucose) are produced on the surface of the cells and are ready for immediate absorption.
  2. Sucrase hydrolyses sucrose to glucose and fructose
  3. Lactase will hydrolyse lactose into glucose and galactose
4. Issues/Problems
  1. Lactose Intolerance
    1. The sugar Lactose found in milk is hydrolysed with the help of the enzyme lactase into glucose and galactose.
      1. Some people dont have this enzyme and so can't break down lactase.
        This lactase remains in the gut lumen. This makes the water potential of the gut lumen more negative.
        Water will leave the surrounding cells and enter the gut lumen by osmosis
        This will lead to diarrhoea
  2. Cholera.
    1. It is caused by a bacterium
      1. Bacteria are prokaryotic
        They have no nucleus
        They have circular DNA
        Contain plasmids which are cicular loops of DNA
        They have a capsule which offers protection
        They have a flagellum which allows movement
        Smaller ribosomes
        They have a cell wall (not cellulose).
        No membrane bound organlelles
    2. The bacterium produces toxins
      1. A poisonous chemical
      2. The toxins cause chloride ions to be secreted from the cells into the lumen
        This then makes the water potential more negative than the surrounding cells
        Water enters from cells into the gut lumen by osmosis
        This will lead to diarrhoea
    3. Symptoms:
      1. Diarrhoea
      2. Cramps
      3. Vomiting
      4. Extreme Dehydration
      5. Fever
    4. Treatment
      1. Oral Rehydration Solution
        Contains water aswell as glucose, sodium ions, chloride ions, potassium ions etc.
        More energy, and it reverses the water potential gradient so water will be drawn back in by osmosis and will rehydrate the patient.
        Can be given as a drip but this requires specially trained people.
        Can also be given as a powder made by adding sterile water
        Sterile becasue you dont want to make them ill again.
The Heart
1. Circulation System
  1. Heart
    1. Its job is to pump blood around the body.
      1. The upper chambers of the heart are known as atria
        The lower chambers are known as the ventricles
        The left side deals with Oxygenated blood
        The right side deals with Deoxygenated blood
        Atrioventricular valves are found between the atria and the ventricles
        The semi-lunar valves are found between the ventricles and arteries.
        Tendons attatched to the valves are there to prevent the valve turning inside out.
        The valves are there to ensure blood flows in one direction and prevents backflow.
    2. The septum is a sheet of thick muscle in the middle of the heart to prevent the mixing of oxygenated and deoxygenated blood.
    3. The thickest muscle is found on the left side of the heart near the ventricle to allow the most forceful contraction
  2. Blood
    1. A fluid containing plasma and red and white blood cells
  3. Blood Vessels
    1. These are tubes that blood flows through.
    2. Arteries/arterioles: Carry blood Away from the heart
      1. Coronary arteries: supply the blood with glucose and oxygen. They branch from the aorta.
    3. Veins/venules: Carry blood too the heart
    4. Capillaries: Allow an exchange of substances between blood and cells
  4. Blood circulation
    1. Oxygenated blood enters the left atrium through the pulmonary vein.
      1. It goes down to the left ventricle and then up and out the aorta then around the body
        Deoxygenated blood now enters the right atrium through the vena cava
        It goes down to the right atrium and then up and out the pulmonary artery to be removed by the lungs
2. Cardiac Cycle
  1. Diastole
    1. The relaxation of the heart
  2. Systole
    1. The contraction of the heart
  3. Blood will always move from a region of high pressure to a region of low pressure.
    1. Also, when the muscle contracts, volume decreases and pressure increases
  4. The atrium goes into systole, forcing blood to move into the ventricle from high pressure to low pressure
    1. The ventricle then goes into systole. Pressure is now higher in the ventricle than in the atria.
      1. The tendency of blood would be to move back into the atrium from a high pressure to a low pressure
      2. AV valves are now closed to prevent backflow
      3. Pressure continues to increase untill it is greater than the pressure in the arteries.
        SL valves open
        Ventricular diastole occurs, and the pressure in the artery increases above ventricular pressure
        SL valves shut
        The tendenecy of blood would be to move back into the ventricle from a higher pressure to a low pressure.
        Meanwhile, pressure in a atria is slowly building up, not because it's contracting but because it's filling with blood from the pulmonary vein
        This pressure forces the AV valves to open and blood fills the ventricle causing its pressure to build up again
        Atrium starts contracting and the cycle starts again
        Atrium in diastole at this stage
    2. AV valves open
  5. Heart rate per minute = 60/ time taken for one cycle
3. Control of the Heartbeat
  1. The cardiac muslce is myogenic, meaning that the electrical activity required for it to contract starts from within the heart itself.
    1. SAN- The pacemaker. It's a group pf specialised cells found in the right atrium.
      1. It sends out a wave of electrical activity which enables the atria to start contracting
        AVN- Also a group of specialised cells found between the atria.
        It's job is to detect the wave of electrical activity and delay it to allow the atria to finish contracting before the ventricles start to contract.
        The wave of electrical activity is then sent down the purkyne fibres. These are collectively called the bundle of His.
        They take they wave of electrical activity down to the apex of the heart. From here the electrical activity spreads up and out over both ventricles.
        It causes the ventricles to contract from the base upwards.
        This then means blood is forced up towards the arteries.
4. Cardiac Output = Stroke Volume x Heart Rate
  1. Stroke Volume is the volume of blood pumped out the ventricle per contraction
    1. Athletes, who have more muscle around their ventrilce, may have a higher stroke volume.
  2. Heart Rate: Contractions per minute
Gas Exchange
1. Gas exchange occurs by diffusion
  1. Therefore all things relating to ficks law apply
2. A thin exchange surface is achieved as the alveolar epithelium consists of a single layer of squamous cells. As does the capillary endothelium
3. There are many alveoli to allow a large surface area
4. A differrence in concetration gradient is mainatined by:
  1. Being well ventilated
    1. Inspiration:
      1. 1. Muscles of the diaphragm contract making it a flatter shape.
        The intercostal muscles contract and the ribcage moves up and out.
        This increases the volume and decreases the pressure below atmospheric pressure
        Air is forced in from a high pressure to a low pressure
    2. Expiration:
      1. 1. Muscles of the diaphragm relax making it dome shaped.
        The intercostal muscles relax and the ribcage moves down and in.
        This decreases volume and increases the pressure above atmospheric pressure
        Air is forced out from a high pressure to a low pressure
  2. Having a continuous supply of blood
5. Structure of the Lungs:
  1. Lungs are found in thorax; the upper part of the body
  2. It's protected by the rib cage, and between the ribcage you find the intercostal muscles.
  3. The diaphragm separates the thorax from the abdomen
  4. Air enters through the treachea, which splits into bronchi, which splits into smaller bronchioles and at the end of these you find the alveoli. The alveoli also contain elastic tissue that stretch when you breathe in and recoil when you breathe out
6. Pulmonary Ventilation: Tidal Volume x Ventilation rate
  1. Tidal volume is the volume of gas exchanged per breath
    1. Ventilation is the amount of breaths per minute
      1. Pulmonary ventilation is the total volume of gas exchanged per minute

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