Topic 3 - Cells

• Microscopes are instruments that produce a magnified image of an object. An object is the material placed under the microscope, whilst the image is how the material appears when put under the microscope.
• Light microscopes use a pair of convex glass lenses to view images with a maximum resolution of 0.2 micrometers. Resolution of a microscope is the minimum distance apart that two objects can be in order for the microscope to distinguish them as separate objects. Light microscopes don't have a very good resolution since light beams have a long wavelength.
• Magnification is defined as how many times bigger an image is than an object in terms of a microscope. Magnification has the equation IMAGE SIZE/OBJECT SIZE = MAGNIFICATION.
• Resolution of a microscope (the resolving power) is dependent on the wavelength and type of radiation used. The lower the value of the resolution, the better the resolution is. An image with a high resolution will be more clarified, clear and precise. Magnification of a microscope can be increased, however every microscope has a maximum resolution. Up until this limit, the image will become more detailed, but after the limit, the image will become more blurry.
• Cell fractionation is the process where cells are broken up and the subcellular organelles are separated out. This is used to study the structure and function of subcellular organelles by obtaining large numbers of isolated organelles.
• Before cell fractionation, the tissue is placed in a cold, buffered solution of the same water potential as the tissue. The water potential prevents organelles from swelling and bursting due to osmotic gain/loss of water. The solution is buffered to ensure that the pH doesn't fluctuate and affect organelle structure/enzyme function. The solution is cold to reduce enzyme activity that could damage organelles.
• Cell fractionation occurs across two stages : homogenisation and ultracentrifugation. Homogenisation involves breaking up cells using a homogeniser (blender). The resultant fluid (homogenate) is then filtered to remove any whole cells and large pieces of debris. Ultracentrifugation involves using a centrifugal force to separate the fragments within the homogenate via a centrifuge machine (spins tubes at high speed).
• Ultracentrifugation involves a tube of filtrate being spun at low speed in a centrifuge. The nuclei (heaviest organelles) are forced to the bottom of the tube. Next, the fluid at the top of the tube (supernatant) is removed, leaving the nuclei sediment. The supernatant is put into a tube, and spun at a medium speed. The next heaviest organelles (mitochondria) are forced to the bottom of the tube, and the supernatant is removed. This process is repeated for all organelles.
• Ultracentrifugation depends on the varying speed of the centrifuge in order to isolate certain organelles. The speed is measured in revolutions/min. A low speed for a heavy organelle (the nucleus) would be about 1000 r/m. A medium speed for less heavy organelles (mitochondria) would be about 3500 r/m. A high speed for light organelles (lysozymes) would be about 16500 r/m.
• Electron microscopes use a beam of electrons that are focused by electromagnets to produce an image. An advantage of electron microscopes over light is that electron beams have a shorter wavelength, so have a higher resolution. Therefore, they are more effective than light microscopes. However, a disadvantage of electron microscopes is that they require near-vacuum conditions (electrons are absorbed/deflected by air molecules), meaning live specimen can't be viewed.
• There are two types of electron microscope : transmission electron microscope (TEM) and scanning electron microscope (SEM). Artefacts are things that may result from the way the specimen is prepared that show up in the image which don't actually exist on the object.
• Transmission electron microscope (TEM) : Electron gun fires a beam that is focused onto a specimen by a condenser electromagnet. The beam passes through a thin section of the specimen, and parts of the specimen will absorb electrons and appear dark. Other parts allow electrons to pass through and appear light (contrast). An image is produced on the screen, and can be photographed to produce a photomicrograph.
• The resolution of a transmission electron microscope is 0.1 nm, however two factors can limit this. Firstly, difficulties preparing the specimen can limit the resolution. Also, the higher energy electron beam may destroy the specimen.
• One limitation of transmission electron microscopes is that the whole system must be in a vacuum (can't view live specimen). Also, a staining process is required, yet the TEM can't produce a coloured image. The specimen must also be extremely thin to allow the electron beam to penetrate and form a 2D image. Furthermore, the image may still contain artefacts that aren't actually on the specimen.
• Scanning electron microscope (SEM) : uses a beam of electrons (fired from above the object) to pass across the surface of the object and scatter, and the pattern of scattering builds up a 3D image depending on the contours of the specimen. An SEM has a slightly worse resolution (20 nm) than the TEM, however it is still better than a light microscope.
• An eyepiece graticule is a glass disc that is placed in the eyepiece of a microscope, with a scale etched into it.
• A stage micrometer is a microscope slide with a scale etched into it (typically the scale is 2 mm long with subdivisions as small as 0.01 mm).
• The scale on an eyepiece graticule cannot be used directly to measure object size under a microscope's objective lens, since each objective lens will magnify to a different degree. The graticule must be calibrated for a specific objective lens.
• The ultrastructure of a cell is the unique internal structure of specific cells that make them adapted for their function. Eukaryotic cells contain a nucleus and membrane-bound organelles, whereas prokaryotic cells do not.
• The nucleus of the cell contains the organism's hereditary information and controls cell activities. It is typically 10-20 micrometers in diameter, and is made up of the nuclear envelope, nuclear pores, nucleoplasm, chromosomes and the nucleolus.
• The nuclear envelope is a double membrane that surrounds the nucleus, and it's outer membrane is continuous with the endoplasmic reticulum. It controls the entry and exit of materials in and out of the nucleus, and contains the reactions within the nucleus.
• The nuclear pores allow the passage of large molecules (e.g. mRNA) to leave the nucleus. There are around 3000 nuclear pores in each nucleus.
• Nucleoplasm is a granular, jelly-like material that makes up the bulk of the nucleus. The chromosomes contain protein-bound, linear DNA. The nucleolus is a spherical region within the nucleus, and it manufactures ribosomal RNA and assembles ribosomes.
• The nucleus has three fundamental functions : firstly to act as a cellular control centre by producing mRNA and tRNA in order for protein synthesis to occur. Also, the nucleus retains the genetic material of the cell as DNA/chromosomes. Finally, the nucleus manufactures ribosomal RNA and ribosomes (in the nucleolus).
• The mitochondria are oval organelles, and are bound by a double membrane called the envelope. The double membrane allows the entry and exit of materials, and the inner of the two membranes folds to form projections called cristae inside the mitochondria. The cristae provide a large surface area for enzymes and other proteins involved in aerobic respiration.
• The matrix fills the rest of the mitochondria, and contains proteins, lipids, ribosomes and DNA that allow the mitochondria to manufacture their own proteins.
• Mitochondria are the site of aerobic respiration, and are therefore responsible for the production of ATP (adenosine triphosphate). In cells that have a high metabolic rate, lots of mitochondria are needed to supply the cells with ATP energy.
• Chloroplasts are disc-shaped organelles that carry out photosynthesis. Chloroplasts are made up of the chloroplast envelope, grana (thylakoid stacks) and stroma.
• The chloroplast envelope is a double plasma membrane which surrounds the organelle. It is highly selective. The grana are stacks of up to 100 thylakoid discs (which contain the chlorophyll pigment). Some thylakoids have tubular extensions, which allow them to join up with thylakoids in adjacent grana. Grana carry out the first stage of photosynthesis : light absorption.
• The stroma of a chloroplast is a fluid-filled matrix where the second stage of photosynthesis, synthesis of sugars, occurs.
• Chloroplasts have adaptations for their role in photosynthesis. Firstly, the membranes of the grana provide a large surface area for the attachment of chlorophyll, electron carriers and enzymes that carry out the first stage of photosynthesis. Next, the stroma fluid contains all enzymes required to carry out the second stage of photosynthesis. Chloroplasts also contain DNA and ribosomes to quickly manufacture proteins needed in photosynthesis.
• The endoplasmic reticulum is a 3D system of sheet-like membranes, which spread throughout the cytoplasm of cells. The membranes enclose a network of tubules and flattened sacs called cisternae. It is made up of the rough endoplasmic reticulum (RER) and the smooth endoplasmic reticulum (SER).
• The rough endoplasmic reticulum (RER) is a series of flattened sacs enclosed by a membrane with ribosomes on it's surface. It has two functions : to provide a large surface area for protein/glycoprotein synthesis, and to provide a pathway for the transport of materials throughout the cell. Essentially, it specialises in folding and processing proteins made on the ribosomes.
• The smooth endoplasmic reticulum (SER) is a system of membrane-bound sacs. The SER has no ribosomes on it's surface, and has a more tubular appearance than the rough endoplasmic reticulum. It has two functions : to synthesise/store/transport lipids, and to synthesise/store/transport carbohydrates. Cells that manufacture lots of lipids and carbohydrates have an extensive endoplasmic reticulum.
• The Golgi apparatus is a series of fluid-filled, flattened and curved sacs (cisternae) with vesicles surrounding the edges. The Golgi apparatus processes/packages lipids and proteins. Often, the Golgi apparatus modifies proteins by adding non-protein components to them, and labels them in order for them to be transported correctly. Once sorted, modified proteins/lipids are transported in Golgi vesicles, which are pinched off from the ends of the cisternae.
• The Golgi apparatus has five main functions : to add carbohydrate to protein to form glycoproteins, to produce secretory enzymes, to secrete carbohydrates , to transport/modify/store lipids, and to form lysosomes.
• Lysosomes are vesicles containing digestive enzymes bound by a single membrane, including proteases, lipases and lysozymes. Lysosomes isolate these enzymes from the rest of the cell before releasing them (e.g. in phagocytes).
• Lysosomes have four main functions : to hydrolyse material ingested by phagocytes, to release enzymes to outside a cell (exocytosis) to destroy material around the cell, to digest worn out organelles and release their useful chemicals, to completely break down cells after they have died (autolysis).
• Ribosomes are made up of two sub units (one large, one small) which contain ribosomal RNA and protein. They are the site of protein synthesis. There are two types of ribosome : 80S and 70S. 80S ribosomes are found in eukaryotes, and are around 25nm in diameter. 70S ribosomes are smaller, and found in prokaryotes/mitochondria/chloroplasts.
• The plant cell wall is a rigid outer covering made of microfibrils of cellulose, embedded in a matrix. It consists of multiple polysaccharides. There is a thin layer, the middle lamella, which marks the boundary between adjacent cell walls and cements adjacent cells together.