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Methods of Studying Cells

Magnification - how many times bigger the image is when compared to the object 

Magnification= Image / Size of the Real Object 

Resolution - the minimum distance apart that two objects can be in order for them to appear as separate items

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Cell Fractionation

The process where cells are broken up and the different organelles they contain are seperated out 

The tissue is placed in a solution which is:

  • Cold - to reduce enzyme activity that might break down organelles 
  • Same water potential - to prevent organelles bursting or shrinking as a result of osmotic gain or loss 
  • Buffered - so that the pH does not fluctuate. Any changes in pH could alter the structure of the organleels or affect the functioning enzymes 

Homogenation - cells are broken up by a homogeniser (blender) to release the organelles from the cell. The resultant fluid in then filtered to remove any complete cells or large pieces of debris 

Ultracentrifugation - process by which the fragments in the homogenate are separated in a centrifuge. The heaviest organelles (nuclei) are forced to the bottom where they form a pellet. The fluid is then spun again at a faster speed where the mitochondria is forced to the bottom

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The Electron Microscope

  • Use electrons to form an image 
  • Have a higher resoultion giving more detailed pictures 

Light Microscopes 

  • Use light to form an image 
  • Has a poor resolution due to a long wavelength 

Transmission Electron Microscope 

  • Use electromagnets to focus a beam of electrons through a specimen 
  • Denser parts of the specimen appear darker 
  • Whole system is under a vacuum so live animals can not be observed 
  • Specimen must be extremely thin 

Scanning Electron Microscope 

  • Has a lower resolving power than TEM
  • Whole system is under a vacuum so live animals can not be observed 
  • Specimen must be extremely thin 
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The Nucleus

The Nucleus contains the organism's hereditary material and controls the cell's activities. The parts are:

  • The nuclear envelope is a double membrane that surrounds the nucleus. It outer membrane is continuous with the endoplasmic reticulum of the cell and often has ribosomes on its surface and controls the entry and exit of materials out of the nucleus 
  • Nuclear pores allow the passage of large molecules, such as mRNA out of the nucleus 
  • Nucleoplasm is the granular jelly material that makes up the nucleus 
  • Chromosomes consist of protein-bound, linear DNA 
  • The nucleolus manufactures rRNA and assembles the ribosomes 

The functions of the nucleus are to:

  • Act as the control centre of the cell through the production of mRNA and tRNA and protein synthesis
  • Retain the genetic material of the cell in the form of DNA and chromosomes 
  • Manufactures rRNA and ribosomes 
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The Mitochondrion

They are made up of the following structures:

  • Around the organelle is a double membrane that controls the entry and exit of material
  • The inner of the two membranes is folded to form cristae which provide a large surface area for the attachment of enzymes 
  • The matrix makes up the remainder of the mitochondrion and contians proteins, lipids, ribosomes and DNA that allows the mitochondria to control the production of their proteins

Mitochondria are the sites of the aerobic stages of respiration

They are responsible for the production of the energy-carrier molecule ATP

High numbers of mitochondrion are found where there are high levels of metabolically activtiy e.g. muscle and epithelial cells 

Epithelial cells require a lot of ATP in the process of absorbing substances from the intestines by active transport 

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There main features:

  • The chloroplast envelope is a double membrane that surround the organelle and is highly selective to what it allows to enter and leave the cell 
  • The grana are stacks of discs structures called the thylakoids
  • Within the thylakoid is the photosythetic pigment chlorophyll 
  • The stroma is a fluid-filled matrix where the second stage of photosynthesis happens 

Chloroplast are adapted to their functions of carrying out photosynthesis in the following ways:

  • Granal membranes provide a large surface area for the attachment of chlorophyll and the enzymes that carry out the first stage of photosynthesis
  • The fluid of the stroma possesses all the enzymes needed to make sugars in the second stage of photosynthesis
  • Chloroplasts contain both DNA and ribosomes so they can quickly and easily manufacture some of the proteins needed for photosynthesis 
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Endoplasmic Reticulum

Rough Endoplasmic Reticulum (RER)

  • Has ribosomes present on the outer surface of the membrane 
  • Provides a large surface area for the synthesis of proteins and glycoproteins 
  • Provide a pathway for the transport of materials, especially proteins, thoughout the cell 

Smooth Endoplasmic Reticulum (SER) 

  • Lacks ribosomes on its surface and is often more tubular in appearance
  • Synthesise, stores and transports lipids 
  • Synthesis, stores and transports carbohydrates 

Cells that manufacture and store large quantities of carbohydrates, proteins and lipids have a very extensive ER. E.g. liver and secretory cells 

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Golgi Apparatus

  • Consists of a stack of membranes that make up flattened sac
  • Have small rounded hollow structures called vesicles 
  • The golgi modifies these proteins often by adding non-protein component such as carbohydrates 
  • Labels the protein allowing them to be accurately sorted and sent to their correct destinations 

The functions of the Golgi apparatus are to:

  • Add carbohydrates to proteins to form glycoproteins 
  • Produce secretory enzymes
  • Secrete carbohydratyes 
  • Transport, modify and store lipids 
  • Form lysosomes 

The Golgi apparatus is well developed in secretory cells such as the epithelial cells in the intestines 

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  • Formed when the vesicles produced by the Golgi apparatus contain enzymes like lipases 
  • Lysosomes isolate these enzymes from the rest of the cell before releasing them, either to the outside or into a phagocytic vesicle 

The functions of lysosomes are to:

  • Hydrolyse material ingested by phagocytic cells such as white blod cells and bacteria 
  • Release enzymes to the outside of the cell in order to destory material around the cell 
  • Digest worn out organelles so that the useful chemicals they are made of can be reused 
  • Completely break down cells after they have died 

Lysosomes are found in secretory cells such as the epithelial cells and phagocytic cells 

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Ribosomes and Vacuoles


  • Small cytoplasmic granules found in all cells 
  • May occur in the cytoplasm or be associated with the RER

There are two types of ribosomes:

  • 80S - which are found in eukaryotic cells 
  • 70S - found in prokaryotic cells 


  • A fluid-filled sac bounded by a single membrane called a tonoplast 
  • Contains mineral salts, sugars, amino acids, wastes and pigments 

Plant vacuoles serve a variety of functions:

  • They support herbaceous plants, and hearbaceous parts of woody plants by making cell turgid 
  • The sugars and amino acids may act as a temporary food store 
  • The pigments may colour petals to attract pollinating insects 
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Cell Wall

  • Consists of microfibrils of the polysaccharide starch embedded in a matrix 
  • Cellulose microfibrols have considerable strenght and contribute to the overal strenght of the cell wall

Cell walls have the following features:

  • They consist of a number of polysaccharides 
  • There is a thin layer, called the middle lamella, which marks the boundary between adjacent cell walls 

The functions of the cellulose cell walls are:

  • To provide mechanical strenght in order to prevent the cell bursting under the pressure created by the osmotic entry of water 
  • To give mechanical strenght to the plant as a whole 
  • To allow water to pass along it and so contribute to the movemnet of water through the plant 
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Structure of a Bacterial Cell

  • Some prokaryotes have a capsule made up of secreted slime. This helps to protect bacteria from attack by cells of the immune system 
  • The cell wall supports the cell and prevents it from changing shape. It is made of a polymer called murein which is a glycoprotein 
  • The plasma membrane is mainly made out of lipids and proteins. It controls the movement of substances into and out of the cell 
  • The cytoplasm of th prokaryotic cell has no membrane bound organelles. It has smaller ribosomes
  • Plasmids are small loops of DNA. These contain thing like antibiotic resistance and allow themselve to reproduce 
  • They have cirucular DNA that floats free in the cytoplasm and is not attached to any proteins
  • The flagellum is a long-hair like structure that rotates to make the prokaryotic cell move. Not all prokaryotes have a flagellum  
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Virus Structure

Viruses are acellular, non-living particles 

They contain nucleic acids such as DNA or RNA as genetic material but can only multiple inside host cells 

The nucleic acid is enclosed in a protein coat called the capsid

Some virues are further surrounded by a lipid envelop that has attachment proteins 

Attachment proteins are essential to allow the virus to identify and attach to a host cell

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Interphase - the cell carries out normal functions, but prepares to divide. The cell's DNA is unravelled and replicated and the organelles are also replicated 

Prophase - the chromosomes condense, by getting shorter and fatter. Tiny bundles of protein called centrioles start moving to opposite ends of the cell, forming a network of protein fibres called the spindle. The nuclear envelope breaks down and chromosomes lie free in the cytoplasm

Metaphase - the chromosome line up along the middle of the cell and become attached to the spindle by their centromere

Anaphase - the centromeres divide, separating each pair of sister chromatids. The spindles contract pulling chromatid to opposite poles of the spindle making them appear V shaped 

Telophase - the chromatids reach the opposite poles of the spindle. They uncoil and become long and thin again so are called chromosomes. A nuclear envelopr forms around each group so there are two nuclei. The cytoplasm divides and there are now two daugther cells the are genetically identical 

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Cell Division in Prokaryotic Cells

Cell division in prokaryotic cells takes place by a process called binary fission as follows:

  • The circular DNA molecule replicates and both copies attach to the cell membrane 
  • The plasmids also replicate 
  • The cell membrane begins to grow between the two DNA molecules and begins to pinch inward, dividing the cytoplasm 
  • A new cell wall forms between the two molecules of the DNA 

Replication of Viruses 

Viruses use their attachment proteins to bind to complementary receptor protein on the surface of a host cell.They then injecct their nucleic acid into the host cell so it starts producing the viral components, nucleic acids, enzymes and structural proteins 

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The Cell Cycle

The cell cycle has three stages:

1) Interphase - which occupies most of the cell cycle and is sometimes known as the resting phase because no division takes place 

2) Nuclear division - when the nucleus divides either into two or four 

3) Division of the cytoplasm - which follows nuclear division and is the process by which the cytoplasm divides to produce two new cells or four new cells

Treatment of Cancer 

Often involves killing dividing cells by blocking a part of the cell cycle disrupting the cell division. Drugs used to treat cancer usually disrupt the cell cycle by:

  • Preventing DNA from replicating 
  • Inhibiting the metaphase stage of mitosis by interfering with the spindle formation
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Structure of Cell Surface Membranes (1)

Phospholipids - have hydrophilic heads on both phospholipid layers that point to the outside of the cell-surface membrane which are attracted by water on both sides. The hydrophobic tails of both layer point into the centre of the cell-membrane which are repelled by water

Lipid soluble material moves through the membrane so the functions of phospholipids are to:

  • Allow lipid-soluble substancw to enter and leave the cell 
  • Prevent water-soluble substances entering and leaving the cell 
  • Mak the membrane flexible and self-sealing 

Proteins - can be embedded in the phosopholipid bilayer in two main ways:

  • Some proteins occur in the surface of the bilayer and never extend completely across it. They act to either give mechanical support or as cell receptors for hormones
  • Other proteins completely span the phospholipid for one side to the other. Some are protein channels and some are carrier proteins
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Structure of Cell Surface Membranes (2)

Cholesterol - occur within the phospholipid bilayer of the cell-surface membrane and add strenght. Cholesterol are very hydrophobic so pull together fatty acid tails of the phospholipd molecules limiting movement. They also make the membrane less fluid at high temperatures and prevent leakage of water and dissolved ions from the cell

Glycolipids - made up of a lipid and carbohydrate. They acts as recognition sites, help maintain the stability of the membrane and help cells to attach to one another so form tissues

Glycoproteins - a carbohydrate chain attached to an extrinsic protein. They act as recognition sites, help cells to attach to one another so form tissues and allows cells to recognise one another e.g. lymphocytes can recognise an organism's own cells

Permeability of the membrane

  • Not soluble in lipids and therefore cannot pass through the phospholipid bilayer
  • Too large to pass through the channels
  • Of the same charge of the protein channels so are repelled
  • Polar making it difficult to pass through the phospholipid bilayer
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Diffusion - the net movement of molecules or ions from a region where they are more highly concentrated to one where their concentration is lower until evenly distributed 

Facilitated Diffusion

  • Facilitated diffusion is a passive process which relies on the inbuilt motion of the diffusing molecules 
  • There are two proteins called protein channe;s or carrier proteins 

Protein Channels - form hydrophilic channels across the membrane. They allow specific water-soluble ions to pass through. Channels are selective as ions bind to change shape in a way that closes it to one side of the membrane and opens it to the other side 

Carrier Proteins - involves carrier proteins that span the plasma membrane. When a protein is present it causes the shape to change so the ion can fit inside. The molecules move from a region where they are highly concentrated to one of lower concentration 

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Osmosis - the passage of water from a region where it has a higher water potential to a region where it has a lower water potential through a selectively permeable membrane 

Water potential is the potential of water molecules to diffuse out of or into a solution

Pure water has the highest water potential. All solutions have a lower water potential than pure water 

If two solutions have the same water potential they're said to be isotonic 

The Rate of Osmosis Depends on:

  • The water potential gradient 
  • The thickness of the exchange surface 
  • The surface area of the exchange surface 
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Active Transport

Active transport - the movement of molecules or ions into or out of a cell from a region of lower concentration to a region of higher concentration using ATP and carrier proteins 

1) Two protein molecule bind to a carrier protein 

2) The ATP binds to the protein causing it to split into ADP and a phosphate molecule causing the molecule to change shape then ADP then recombines with a phosphate molecule to make ATP

Factors Affecting Rates

  • The speed on individual carriers 
  • The number of carrier proteins present 
  • The rate of respirationin the cell and the availabilty of ATP

Sodium Potassium pump 

  • Sodium ions are actively transported into the blood causing sodium ions to diffuse into the epithelial cell via sodium-glucose co-transporter proteins 
  • Co-transporter proteins carry glucose increasing glucose concentration 
  • Glucose diffuses out of the blood by facilitated diffusion
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Defence Mechanisms

Non-Specific - response is immediate and the same for all pathogens 

Non-specific responses include:

  • Physical barrier e.g. skin 
  • Phagocytosis 

Specific - response is slower an specific to each pathogen 

Specific responses include:

  • Cell-mediated response (T lymphocytes)
  • Humoral response (B lymphocytes)
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  • Chemical products of pathogens or dead, damaged and abnormal cells act as attractants, causing phagocytes to move towards the pathogen 
  • Phagocytes have several receptors on their cell-surface membrane that recognise, and attach to, chemicals on the surface of the pathogen 
  • They engulf the pathogen to form a vesicle, known as a phagosome 
  • Lysosomes move towards the vesicle and fuse with it 
  • Enzymes called lysozymes are present which destroy ingested bacteria by hydrolysis of their cell walls
  • The soluble products from the breakdown of the pathogen are absorbed into the cytoplasm of the phagocyte 
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T Lymphocytes and Cell Mediated Immunity

Antigens - any part of an organism or substance that is recognised as non-self by the immune system and stimulates an immune response 

Cell Mediated Immunity 

1) Pathogens invade body cells or are taken in by phagocytes 

2) The phagocyte place the antigens from the pathogen on its cell surface membrane 

3) Receptors on a specific helper T cell fit exactly onto these antigens 

4) This attachment activates the T cell to divide rapidly by mitosis and form a clone of genetically identical cells 

5) The cloned T cells develop into memory cells that enable a rapid response to future infections by the same pathogens, stimulate phagocytes to engulf pathogens by phagocytosis, stimulate B cells to divide and secrete their antibody and activate cytotoxic T cells 

Cytotoxic T cells kill cells by producing a protein called perforin that makes holes in the cell surface membrane. These holes mean the cell membrane becomes freely permeable to all substances and the cell dies 

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B Lymphocytes and Humoral Immunity

1) The surface antigens of an invading pathogen are taken up by a B cell

2) The B cell processes the antigens and presents them on its surface

3) Helper T cells attach to the processed antigens on the B cell activating them

4) The B cell is now activated to divide by mitosis to give a clone of plasma cells

5) The cloned plasma cells produce and secrete the specific antibody that exactly fits the antigen

6) The antibody attaches to antigens on the pathogen and destroys them

7) Some B cells develop into memory cells that can respond to further infections

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Antibodies - proteins with specific binding sites synthesised by B cells

Structure of Antibodies

  • Made up of four polypeptide chains (heavy chains and light chains)
  • Has a specific binding site known as an antigen-antibody complex
  • The binding site is different on each antibody so is called the variable region
  • The rest of the antibody is known as the constant region

Destruction of Antigens

  • Agglutination of bacterial cells making it easier for phagocytes to locate as they are less spread out within the body
  • They serve as makers to stimulate phagocytes to engulf the bacterial cells attached

Monoclonal Antibodies

  • An antigen is added to a well and the patients blood plasma is added so their antibodies bind to the antigen
  • A secondary antibody is added and attaches to the patients antibodies
  • A solution is added with an enzymes that produces a colour is the antigen is detected
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Immunity - the ability of an organism to resist infection

Passive Immunity

  • Produced by the introduction of antibodies into the individuals
  • No direct contact is needed with the pathogen or antigen
  • Antibodies are not produced so no memory cells are made so there is no lasting immunity

Active Immunity

  • Produced by stimulating the production of antibodies by the individuals' own immune system
  • Direct contact with the pathogen or antigen
  • Long lasting
  • Can include the body forming its own antibodies naturally or inducing the immune response
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Features of a Successful Vaccination Programme

  • Must be economically available in sufficient quantities to immunise the vulnerable population
  • Very few side effects
  • Means of producing, storing and transporting the vaccine must be available
  • Must be a means of administering the vaccine
  • Must be possible to vaccinate the vast majority of the population to produce herd immunity (making it difficult for the pathogen to spread as the vaccinated population are unlikely to come into contact with an infected person)

Why Vaccines don't Eliminate Disease?

  • Fails to induce immunity in certain individuals
  • May develop the disease immediately after vaccination before immunity levels are high
  • The pathogen mutates frequently (antigenic variability)
  • Certain pathogens hide from the immune system
  • May have objections against vaccinations
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Structure of HIV

  • Outside is a lipid envelope in which attachment proteins are embedded
  • Inside the envelope is a capsid that encloses two strands of RNA and reverse transciptase

Replication of HIV

  • HIV enters the bloodstream and circulates around the body
  • A proteins on the HIV readily binds to a protein which is found on helper T cells
  • The protein capsid fuses with the cell surface membrane. The RNA and enzymes enter the helper T cell
  • The HIV reverse transcriptase converts the virus's RNA into DNA which is inserted into the nucleus
  • The nucleus creates mRNA containing the new instructions for viral protein and RNA
  • The HIV particles break away with a piece of its cell surface membrane surrounding them which forms their lipid envelope
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