Topic 3: Cell structure

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Methods of studying cells: Microscopy

Microscopes are used to produce a magnified image of an object. Magnification is how many times bigger the image is compared to the actual object. 

Magnification= size of image/ size of real object

Resolution or resolving power is the minimum distance apart that two objects have to be in order for them to appear as separate items. This depends on the wavelength or form of radiation used. In a light microscope, this is about 0.2 um. Greater resolution means greater clarity so the image produced is more precise. Increasing magnification does not always increase resolution- the image may get bigger but the object will just be more blurred. 

        equivalent in metres 

km= 10-3                               m= 1 

mm=103                                   um= 106   

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Methods of studying cells: Cell fractionation

The process where cells are broken up and the different organelles they contain are separated out. Before it can begin, the tissues is placed in a solution that is:

  • Cold- to reduce activity of enzymes that might break down the organelles 
  • Isotonic- to prevent organelles bursting or shrinking due to osmotic gain or loss of water 
  • Buffered- so that pH does not fluctuate. This could alter the structure of the organelles or affect the functioning of enzymes

There are two stages: 

1) Homogenation: cells are broken up by a blender or homogeniser which breaks the cell and releases the organelles. The resultant fluid (homogenate) is filtered to remove large pieces of debris and any complete cells 

2) Ultracentrifugation: fragments in the homogenate are separated in a centrifuge. The heaviest organelles, the nuclei are extracted from the first sediment/pellet. The fluid at the top of the tube (supernatant) is removed leaving the sediment and is transferred to another tube and spun at a faster speed than before. Sediment 2 contains mitochondria, lysosomes and chloroplasts; Sediment 3 contains small vesicles; sediment 4 contains ribosomes. 

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How electron microscopes work

Electrons are beamed at the object, which is placed in a vacuum to prevent interruptions in the flow of electrons by air particles. They are focused using magnetic condensers because electrons are negatively charged, unlike in a light (optical) microscope which uses lenses to focus light rays. The intermediate image is formed and is focused onto a flourescent screen using magnetic projectors. 

The electron beam has a very short wavelength and so the microscope can resolve objects well. It has high resolving power. 

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The Scanning electron microscope

SEM- scanning electron microscope

  • A beam of electrons is directed onto the specimen from above and it is passed back and forth across a portion of the specimen in a regular pattern. 
  • The electrons are scattered by the specimen- the pattern of which is due to the contours of the specimen surface.
  • Using computer analysis of the scattered electrons and secondary electrons produced, a 3D image is made. 
  • The basic SEM has a resolving power of 20nm and magnification of x100 000
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The Transmission electron microscope

TEM- transmission electron microscope

  • Electron gun produces a beam of electrons  focused onto the specimen by a condenser magnet from below. The beam passes through a thin section of the specimen. Parts that absorb electrons appear dark and those that allow the electrons to pass through appear light. 
  • A 2D image is produced on a screen and this can be photographed to give a photomicrograph. 
  • Resolving power is 0.1nm, which cannot always be achieved in practice because of difficulties preparing the specimen and higher energy electron beam is required and this may destroy the specimen. 
  • The magnification is x500 000 
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Limitations of electron microscopes

All electron microscopes

  • Whole system must be in a vacuum so living specimens cannot be observed 
  • A complex staining process is required and even then image may not be in colour

TEM

  • Specimens must be extremely thin to allow electrons to penetrate 
  • The image may contain artefacts (things that result from the way the specimen is prepared) which may appear on the finished photomicrograph but are not part of the natural specimen. It is therefore not always easy to be sure that what is seen on the photomicrograph really exists in that form. 
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Microscope measurements and calculations

Measuring cells 

An eyepiece graticule is a glass disc with a scale etched onto it (which is typically 10mm long) that is placed in the eyepiece of a (light) microscope and used to measure the size of objects. This cannot be used directly to measure the size of objects under a microscope's objective lens because each lens will magnify to a different degree. It must be calibrated for that particular objective lens and once calibrated, it can remian in position for future use given that the same objective lens is used. Record the results of calibration for a particular objective lens and leave this attached to the microscope, which will save you having to recalibrate each time. 

Calibrating the eyepiece graticule

A stage micrometer is needed for this. It is a slide with a scale etched onto it usually 2mm long and its smallest subdivisions are 0.01mm (10um). Line the stage micrometer with the eyepiece graticule to find out how much each unit on the micrometer scale is equivalent to on the eyepiece graticule. The scale for different objective lenses can be calculated by dividing the differences in magnification. e.g. if an objective lens magnifying x40 gives calibration of 25um per graticule unit, then an objective lens magnifying x400 (10 times greater) means each graticule unit is equivalent to 25um/10 = 2.5um  

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The Nucleus

  • Contains the organism's hereditary material and retains genetic material of the cell in the form of DNA and chromosomes
  •  10-20 um in diameter
  • Acts as the control of the cell through the production of mRNA and tRNA hence protein synthesis. 
  • Manufacures rRNA and ribosomes
  • Nuclear envelope: Double membrane that surrounds the nucleus. Its outer membrane is continuous with endoplasmic reticulum and often has ribosomes on its surface. It controls the entry and exit of materials in and out of the nucleus and contains the reactions taking place within it 
  • Nuclear pores: Allow the passage of large molecules such as mRNA out of the nucleus
  • Nucleoplasm: Granular, jelly-like material that makes up the bulk of the nucleus 
  • Chromosomes: consist of protein-bound, linear DNA. These are called histones. 
  • Nucleolus: Small spherical region in the nucleoplasm that manufactures rRNA (ribosomal) and assembles the ribosomes. They may be more than one in a nucleus. 
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The Mitochondrion

Mitochondria are the sites of aerobic respiration (Krebs cycle and oxidative phosphorylation). They are therefore responsible for the production of the cell's energy (ATP) from respiratory substrates such as glucose. Their numbers are high in cells that have a high level of metabolic activity therefore require plentiful supply of ATP, e.g. epithelial (for active transport) and muscle cells. 

  • Double membrane: Controls entry and exit of material. The inner of the two membranes is folded to form extensions known as cristae. 
  • Cristae: Provide a large surface area for the attachment of enzymes and other proteins involved in respiration
  • Matrix: Makes up the remainder of the mitochondrion. It contains protein, lipids, ribosomes and DNA that allows the mitochondria to control the production of some of their own proteins. Many enzymes involved in respiration are found in the matrix. 
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Chloroplasts

  • Chloroplast envelope: Double plasma membrane surrounding the organelle. It is highly selective in what is allowed to enter and leave the chloroplast.
  • Grana: Stacks of discs (thylakoids) where the first stage of photosynthesis- the light dependent reaction, (light absorption) occurs.  Within thylakoids is chlorophyll. Some of them have tubular extensions (lamellae) that join up with thylakoids in adjacent grana
  • Stroma: Fluid-filled matrix where the second stage of photosynthesis- the light independent reaction, (synthesis of sugars) occurs. Within them are a number of other structures such as starch grains. 

Adaptations to their function of harvesting sunlight and carrying out photosynthesis: 

  •  Granal membranes provide large surface area for the attachment of chlorophyll, electron carriers and enzymes that carry out the first stage of photosynthesis. These chemicals are attached to the membrane in a highly ordered fashion. 
  • Fluid of the stroma has all the enzymes needed to make sugars in the second stage 
  • Contain DNA and ribosomes so can quickly and easily manufacture their own proteins for photosynthesis 
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Endoplasmic reticulum

ROUGH ENDOPLASMIC RETICULUM (RER): Has ribosomes on the outer surface of the membranes. Its functions are to:

  • Provide large surface area for the synthesis of proteins and glycoproteins 
  • Provide a pathway for the transport of materials, especially proteins, throughout the cell. 

SMOOTH ENDOPLASMIC RETICULUM (SER): Lacks ribosomes on its surface and is often more tubular in appearance. Its functions are to: 

  • Synthesise, store and transport lipids 
  • Synthesise, store, and transport carbohydrates 

Cells that manufacture and store large quantities of carbohydrate, proteins and lipids have a very extensive ER. e.g. liver and secretory cells- epithelial cells lining the intestines. 

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Golgi Apparatus

Structure

  • Similar to SER but is more compact. It consists of flattened sacs (cisternae), with vesicles. Proteins and lipids produced by the ER are passed through the Golgi body in a strict sequence. It modifies the proteins, adding non-protein components e.g. carbohydrates and labels them allowing them to be sorted and sent to the correct destinations. Once stored, the modified proteins and lipids are transported in vesicles. Vesicles can move to the cell surface and fuse with the membrane, releasing their contents to the outside. 

Functions:

  • Add carbohydrate components to proteins to form glycoproteins 
  • Produce secretory enzymes such as those secreted by the pancreas
  • Secrete carbohydrates such as those used in making cell walls in plants 
  • Transport, modify and store lipids 
  • Form lysosomes. 

It is well developed in secretory cells such as the epithelial cells lining the intestines

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Lysosomes

They are formed when the vesicles produced by the Golgi apparatus contain enzymes such as proteases and lipases. They also contain lysozymes- enzymes that hydrolyse the cell walls of certain bacteria. They isolate these enzymes from the rest of the cell before releasing them, either to the outside or into a phagocytic vesiscle within a cell. 

Functions are to:

  • Hydrolyse material ingested by phagocytic cells, e.g. white blood cells and bacteria
  • Release enzymes to the outside of the cell (exocytosis) in order to destroy material around the cell
  • Digest worn out organelles so that useful chemicals they are made of can be re-used 
  • Completely break down cells after they have died (autolysis)

They are abundant in secretory cells. 

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Ribosomes

Small cytoplasmic granules found in all cells. They may occur in the cytoplasm or be associated with the RER. There are two types: 

  • 70S- found in prokaryotic cells, mitochondria and chloroplasts, is slightly smaller. 
  • 80S- found in eukaryotic cells. 

Ribosomes have two subunits- one large and one small, each of which contains ribosomal RNA and protein. 

They are the site of protein synthesis. 

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Cell Wall

Structure:

  • Consist of microfibrils of the polysaccharide cellulose, embedded in a matrix. 
  • Thin layer called the middle lamella, which marks the boundary between adjacent cell walls and cements adjacent cells together. 

Function of the cellulose cell wall:

  • Provides mechanical strength in order to prevent the cell bursting under the pressure created by the osmotic entry of water 
  • To give mechanical strength to the plant as a whole 
  • To allow water to pass along it and so contribute to the movement of water through the plant 
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Vacuole

A fluid-filled sac bounded by a single membrane. The membrane is called a tonoplast. In mature plant cells, there is usually one large central vacuole. It contains a solution of mineral salts, sugars, amino acids, wastes and sometimes pigments. 

Functions:

  • They support herbaceous plants, and herbaceous parts of woody plants by making cells turgid 
  • The sugars and amino acids may act as a temporary food store
  • Pigments may colour petals to attract pollinating insects
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Prokaryotic cells

Bacteria.

  • Cell wall made of murein- physical barrier that excludes certain substances and protects against mechanical damage and osmotic lysis 
  • Capsule- protects bacterium from other cells and helps groups of bacteria to stick together for further protection 
  • Cell-surface membrane- acts as a differentially permeable layer, which controls entry and exit of chemicals 
  • Circular DNA- possess the genetic information for the replication of bacterial cells
  • Plasmid- possesses genes that may aid in the survival of bacteria in adverse conditions, e.g. produces enzymes that break down antibiotics. 
  • Have no nuclei, only an area where DNA is found
  • No membrane bound organelles 
  • DNA is not associated with proteins 
  • No chloroplasts, only bacterial chlorophyll associated with the cell-surface membrane in some bacteria 
  • 70S ribosomes only
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Viruses

  • Acellular (not consisting of cells), non-living particles 
  • Smaller than bacteria 
  • Contain nucleic acids such as DNA or RNA but can only multiply inside living host cells. 
  • Nucleic acid enclosed in a protein coat- capsid
  • Some viruses like HIV are surrounded by a lipid envelope or the capsid has attachment proteins, which allow the virus to identify and attach to a host cell
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Mitosis

Mitosis is division of a cell that results in each of the two daughter cells having the same number of  chromosomes as the parent cell (diploid) , each with identical DNA to the parent cell. 

It is always preceded by interphase- where DNA is replicated, organelles synthesised and spindle fibres formed. It is a continuous that can be divided into four stages: 

  • Prophase: chromosomes become visible and condensed (shorter and thicker). The centrioles, from which spindle fibres develop, move to opposite poles of the cell. The nucleolus disappears and the nuclear envelope disintegrates leaving the chromosomes free in the cytoplasm of the cell. 
  • Metaphase: Chromosomes are made up of two chromatids and are joined up at the centromere. Spindle fibres attach to the centromere, causing the chromosomes to line up along the equator of the cell. Each chromatid has DNA identical to that of the parent cell. 
  • Anaphase: The centromere holding the two sister chromatids together breaks down and spindle fibres contract, pulling the sister chromatids to opposite poles of the cell. Energy for this process is provided by the mitochondria, which gather around the spindle fibres. If cells are treated with chemicals that destroy the spindle, the chromosomes remain at the equator, unable to reach the poles. 
  • Telophase and cytokinesis: Chromosomes reach poles and become indistinct (longer and thinner) finally disappearing and leaving only widely spread chromatin. The spindle fibres disintegrate and the nucleolus and nuclear envelope reform. The cytoplasm divides in a process called cytokinesis
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Importance of mitosis

  • Growth- mitosis ensures that all cells resulting from the fusion of gametes are identical to the original cell so the individual resembles its parents 
  • Repair- if cells are damaged or die, it is important that new ones have an identical structure and function to those lost 
  • Asexual reproduction 
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The cell cycle and cancer

The cell cycle has 3 stages:

  • Interphase- organelles and proteins are synthesised, DNA is replicated,  proteins needed for the spindle fibres are made. 90% of the cycle is interphase. 
  • Nuclear division- mitosis/meiosis 
  • Cytokinesis 

Cancer is a result of damage to genes that regulate mitosis and the cell cycle. This leads to uncontrolled growth and division of cells, which results in the development of a tumour. The treatment of cancer involves killing dividing cells by blocking part of the cell cycle so that division and hence cancer growth, stops. Drugs used in chemotherapy work by preventing DNA from replicating or inhibiting the metaphase stage of mitosis by interfering with the formation of spindle fibres. Such drugs also affect cell cycles of normal cells but since cancer cells divide more rapidly, they are more affected. 

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