3.2.3 Transport across cell membranes

Okay so the basic structure of cells is covered in 3.2.1.1 and 3.1.1.2. Here, I will cover the arrangement/movement/structure of the cell surface membrane:

• phospholipids
• hydrophilic heads point outward and hydrophobic tails point inward creating a phospholipid bilayer
• lipid soluble material moves through the membrane via this bilayer
• this bilayer:
• allows the movement of lipid-soluble material
• prevents water-soluble substances entering/leaving
• makes the membrane flexible and self-sealing
• proteins
• These are interspersed throughout the cell surface membrane embedded in the phospholipid bilayer in two main ways:
• some occur in the surface of the bilayer and never extend completely across it. These either act to give mechanical support to the membrane or (in conjunction with glycolipids) as cell receptors for molecules such as hormones
• others span the membrane. Protein channels form water-filled tubes to allow water-soluble ions to diffuse across whilst protein carriers bind to ions/molecules and change shape in order to move these molecules across the membrane.
• provide structural support
• allow active transport (carrier proteins)
• act as channels to transport water-soluble substances across (channel proteins)
• form cell-surface receptors for identifying cells
• help cells adhere to each other
• act as receptors (e.g for hormones)
• glycoproteins
• carbohydrate chains attached to many extrinsic proteins on the outer surface of the cell membrane
• act as cell-surface receptors for hormones and neurotransmitters
• help cells attach to one another forming tissues
• allow cells to recognise one another e.g lymphocytes can recognise an organism's own cells
• glycolipids
• made up of carbohydrate covalently bonded with a lipid. The carbohydrate section extends into the phospholipid bilayer where it acts as a cell-surface receptor for specific chemicals
• act as recognition sites
• help to maintain the stability of the membrane
• help cells to attach to one another forming tissues
• cholesterol
• this restricts the movement of other molecules making up the membrane
• the fluid-mosaic model
• the way in which the various molecules are combined into the structure of the cell-surface membrane is known as the fluid-mosaic model:
• fluid because the individual phospholipid molecules can move relative to one another giving the membrane a flexible structure that is constantly changing shape
• mosaic because the proteins that are embedded in the phospholipid bilayer vary in shape/size/pattern similar to the tiles of a mosaic

The permeability of the cell-surface membrane is as follows. Substances can't enter if they are:

• not soluble in lipids (cannot pass through bilayer)
• too large (cannot pass through channels)
• of the same charge (they will be repelled)
• electrically charged (this means they are polar). In this case they have difficulty passing through the non-polar hydrophobic tails in the phospholipid bilayer

Movement across membranes occurs by: 
• simple diffusion (involving limitations imposed by the nature of the phospholipid bilayer) 
• facilitated diffusion (involving the roles of carrier proteins and channel proteins) • osmosis (explained in terms of water potential) 
• active transport (involving the role of carrier proteins and the importance of the hydrolysis of ATP)
• co-transport (illustrated by the absorption of sodium ions and glucose by cells lining the mammalian ileum). 

Simple diffusion
This is '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'. It is a passive process

Facilitated diffusion
So we know that only small non-polar molecules can diffuse across the cell-surface membrane. The movement of charged ions and polar molecules is facilitated by protein channels and carrier proteins. It only occurs at specific points along the membrane (where these proteins are situated) and, like simple diffusion, also occurs down a concentration gradient. It is also passive.

• Protein channels form water-filled hydrophilic channels across the membrane that allow specific water-soluble ions to pass through. They are selective and open in the presence of a specific ion (in this way they have control of entry/exit of substances in/out of the membrane). The ion binds to the protein causing it to change shape in a way that closes it to one side of the membrane and opens it to the other side.
• Carrier proteins bind with a specific molecule (e.g glucose) and change their shape in such a way that the molecule is released to the inside of the membrane.

Osmosis
This is '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 electively permeable membrane'. It is important to realise that the highest value water potential can be is 0kPa (pure water) and anything not pure water has a negative water potential. Osmosis is essentially the diffusion of water molecules. 

In animal cells, when water enters the cell swells and bursts, when water leaves the cell shrinks. In plant cells when water enters the cell becomes turgid, when water leaves the shell becomes plasmolysed (at the same water potential the condition is incipient plasmolysis).

Active transport
This is 'the movement of molecules or ions into or out of a cell from a region of higher concentration to a region of lower concentration using ATP and carrier proteins'. ATP is used to directly move molecules/individually move molecules using a concentration gradient which has already been set up by direct active transport (this is co-transport):

• the carrier proteins that span the membrane bind to a molecule/ion (the molecule/ion binds to the receptor site)
• on  the inside of the cell/organelle ATP binds to the protein causing it to split into ADP + Pi. This causes the protein molecule to change shape opening to the opposite side of the membrane
• the molecule/ion is released to the other side of the membrane
• the phosphate molecule is released from the protein which causes the protein to revert to its original shape

Co-transport 
Sometimes more than one molecule/ion may be moved in the same direction at the same time by active transport. Occasionally a molecule/ion is removed at the same time one is assed. An example of this is the sodium-potassium pump. Sodium ions are actively removed from the cell/organelle while potassium ions are actively taken in from the surroundings.


Cells may be adapted for rapid transport across their internal or external membranes by an increase in surface area of, or by an increase in the number of protein channels and carrier molecules in, their membranes. 


Differences in.....

• increased surface area = larger area for diffusion
• increased number of channel/carrier protein = more placed for facilitated diffusion/active transport to occur
• a larger difference in concentration gradient/water potential means a faster rate of transport

......and vice versa.

3.2.2 All cells arise from other cells

Eukaryotic organisms
In multicellular organisms not all cells retain the ability to divide. Eukaryotic cells that to retain the ability to divide show a cell cycle. Cell division can occur by mitosis or meiosis. Mitosis produces two daughter cells that have the same number of chromosomes as the parent. We will cover mitosis in this section. Meiosis produces four daughter cells each with half the number of chromosomes of the parent cell. Meiosis is covered in section 3.4.3.

Mitosis can be split into 5 stages:

Interphase
Mitosis is proceeded by a period during which the cell is not dividing (this is interphase). Here, DNA replication occurs. The two copies of DNA remain joined at the centromere.
Prophase

• Chromosomes first become visible by shortening and condensing
• (in animals) centrioles move to opposite ends/the poles of the cell
• spindle fibres develop from each centriole. These span the cell from pole to pole and are collectively called the spindle apparatus.
• the nucleolus disappears and the nuclear envelope breaks down leaving the chromosomes free in the cytoplasm.
• the chromosomes are drawn towards the equator by spindle fibres attached to the equator

Metaphase

• the chromosomes can now be seen to be made up of two chromatids (each an identical copy of the DNA from the parent cell unless mutation occurs)
• chromosomes arrange themselves along the equator of the cell

Anaphase

• centromeres divide in two and spindle fibres pull the individual chromatids apart
• chromatids more to their respective poles and are now referred to as chromosomes (energy provided by mitochondria situated around the centrioles)

Telophase (+ cytokinesis)

• chromosomes reach their respective poles and become longer and thinner and disappear altogether leaving widely spread chromatin
• spindle fibres disintegrate

NOTE: Mitosis is a controlled process. Uncontrolled cell division can lead to the formation of tumours and of cancers. Many cancer treatments are directed at controlling the rate of cell division.

We need to be able to calculate mitotic index:

mitotic index = number of cells in mitosis x 100 / total number of cells

Prokaryotic cells
These divide by binary fission:

• The circular DNA molecule replicates and both copies attach to the cell membrane
• the plasmids replicate (a variable number)
• the cell membrane begins to grow between the two DNA molecules and begins to pinch inward, dividing the cytoplasm in two
• a new cell wall forms between the two molecules of DNA dividing the original cell into two identical daughter cells (each with a single copy of the circular DNA and a variable number of copies of the plasmids).

Viruses

Viruses do not undergo cell division. They inject their nucleic acid into a host cell infecting it. The host cell replicates the viral particles.

3.2.1.2 Structure of prokaryotic cells and of viruses

Prokaryotic cells
Prokaryotic cells are much smaller than eukaryotic cells. They also differ from eukaryotic cells as they:

• lack membrane-bound organelles
• have smaller (70S) ribosomes
• have no nucleus (instead they have a single circular DNA molecule that is free in the cytoplasm and not associated with proteins)
• a cell wall containing murein (a glycoprotein)

Some prokaryotic cells might additionally have:

• one or more plasmids
• a capsule surrounding the cell
• one or more flagella

Viruses
These are acellular non living particles. They are smaller than bacteria (20-300nm) and contain nucleic acids (DNA or RNA) as genetic material. They can only multiply inside a host cell. The nucleic acid is enclosed in a protein coat (a capsid). Some viruses are further surrounded by a lipid envelope (e.g HIV). The lipid envelope/capsid has attachment proteins which allow the virus to identify and attach to a host cell.

3.2.1.3 Methods of studying cells Content

This section is all about microscopes. The material we put under the microscope is the object, the appearance of this material when viewed under the microscope is the image. The magnification of an object is how many times bigger the image is when compared to the object:

magnification = size of image / size of object

NOTE: remember to keep the units of measurement the same!

Resolution is different to magnification. The resolution of a microscope is the minimum distance apart that two objects can be in order for them to appear as separate items. The resolving power depends on the wavelength/form of radiation emitted from the microscope. Increasing the magnification will increase the size of an object but not necessarily the resolution (every microscope has a limit resolution).

Okay so there are three types of microscope we use to study cells: the optical/light microscope, the transmission electron microscope, and the scanning electron microscope. We need to know the principles and limitations of using each one:

• The light microscope
• can only distinguish between objects more than 2μm apart due to the long wavelength of light.
• the transmission electron microscope
• can be focused by electromagnets as electrons are negatively charged
• can resolve objects that are just 0.1nm apart
• beams pass through a thin section of the specimen. Parts of this specimen absorb electrons and appear darker (other parts allow the electrons to pass through and so appear bright)
• an image is produced on a screen which can be photographed to produce a photomicrograph
• the resolving power (0.1nm) cannot always be achieved due to difficulties in preparing the specimen/the high energy electron beam may destroy the specimen
• the main limitations are as follows:
• whole system must be in a vacuum (living specimens cannot be observed)
• image produced is black and white
• a complex staining process is required
• specimen must be extremely thin
• image may contain artefacts
• 2D image produced
• the scanning electron microscope
• can be focused by electromagnets as electrons are negatively charged
• can resolve objects that are 20nm apart
• directs a beam of electrons on to the surface of the specimen from above (rather than penetrating from below). The beam is passed back and forth across a portion of the specimen in a regular pattern - the electrons are scattered depending on the contours of the specimen surface.
• A 3D image is produced by computer analysis of the pattern of scattered electrons and secondary electrons produced.
• the main limitations are as follows:
• whole system must be in a vacuum (living specimens cannot be observed)
• image produced is black and white
• a complex staining process is required
• image may contain artefacts

Cell fractionation
This is used to obtain large numbers of isolated organelles. It is the process whereby cells are broken up and the different organelles are separated out. Before cell fractionation can occur the tissue is placed in a cold buffered solution of the same water potential. this is because:

• cold to reduce enzyme activity that might break down the organelles
• is of the same water potential to prevent organelles bursting/shrinking as a result of osmotic gain/loss of water
• buffered so that the pH does not fluctuate.

The two stages of cell fractionation are homogenation and ultracentrifugation:

• homogenation
• cells are broken up by a homogeniser which releases the organelles from the cell. The resultant fluid is known as a homogenate and is filtered to remove any complete cells/large pieces of debris
• ultracentrifugation
• this is the process by which the fragments in the filtered homogenate are separated in a machine (a centrifuge). this spins the tubes of homogenate at very high speeds which creates a centrifugal force:
• the tube of filtrate is placed in the centrifuge and spun at slow speeds
• the heaviest organelles are forced to the bottom and form a pellet
• the supernatant is removed
• the supernatant is transferred to another tube and spun in the centrifuge at a faster speed than before
• the next heaviest organelles are forced to the bottom
• etc

3.2.1.1 Structure of eukaryotic cells

Each type of cell has a special internal structure suited to its job. This is known as the cell ultrastructure. Eukaryotic cells have a distinct nucleus and membrane bound organelles. The most important stuffs in the cell are as follows:

• cell-surface membrane (covered in 3.2.3)
• nucleus (containing chromosomes, consisting of protein-bound, linear DNA, and one or more nucleoli) 
• this contains the organisms hereditary material, manufactures rRNA and ribosomes, and acts as the control centre of the cell through the production of mRNA and tRNA (hence protein synthesis)
• has a nuclear envelope (double membraned) whose outer surface is continuous with the endoplasmic reticulum. This controls the entry/exit of materials in and out of the nucleus
• Nuclear pores allow the passage of large molecules
• The nucleoplasm makes up the bulk of the nucleus (granular jelly-like material)
• Chromosomes consist of protein (histone) bound linear DNA
• mitochondria
• These are the sites of the aerobic stages of respiration so are responsible for the production of ATP.
• These are double membraned. This controls entry and exit of material. The inner membrane is folded to form cristae which provide a large surface area for attachment of enzymes involved in respiration (respiration occurs on the mitochondrial membrane)
• The matrix contains proteins, lipids, ribosomes, and DNA which allows the mitochondria to control the production of some of their own proteins.
• chloroplasts (in plants and algae)
• These are organelles that carry out photosynthesis
• the chloroplast envelope is a double plasma membrane that surrounds the organelle. Being highly selective, it controls what enters and exits the chloroplast
• the grana are stacks of up to 100 disc like structures (thylakoids). Within thylakoids there is chlorophyll (the photosynthetic pigment). The granal membranes provide a large surface area for the attachment of chlorophyll/electron carriers/enzymes that carry out the light-dependant reactions
• the stroma is a fluid-filled matrix where the second stage of photosynthesis occurs. The stroma contains other structures such as starch grains. The stroma possesses all the enzymes needed to make sugars in the second stage of photosynthesis.
• They contain DNA and ribosomes to quickly and easily manufacture some of the proteins needed for photosynthesis
• Golgi apparatus and Golgi vesicles
• This is similar to the SER but is more compact. It consists of a stack of membranes that make up flattened sacs (cisternae) will vesicles (small rounded hollow structures called vesicles).
• The proteins and lipids produced by the ER are passed through the Golgi apparatus which modifies the proteins (e.g adding prosthetic components) and labels them allowing them to be accurately sorted and sent to their correct destinations. Once sorted the proteins and lipids are transported in Golgi vesicles.
• The Golgi apparatus can:
• add carbohydrate to proteins to form glycoproteins
• produce secretory enzymes
• secrete carbohydrates 
• transport, modify, and store lipids
• form lysosomes
• lysosomes (a type of Golgi vesicle that releases lysozymes) 
• lysosomes are formed when the vesicles produced by the Golgi apparatus contain enzymes (e.g proteases and lipases).
• They hydrolyse material ingested by phagocytic cells
• they release enzymes to the outside of the cell (exocytosis) to destroy external material
• they digest worn out organelles
• they completely break down cells (autolysis)
• ribosomes 
• small cytoplasmic granules with two subunits - one small and one large. Each subunit contains rRNA and protein. They are the site of protein synthesis.
• may be associated with the RER
• 80S are larger and occur in eukaryotic cells
• 70S are smaller and occur in prokaryotic cells, mitochondria, and chloroplasts
• rough endoplasmic reticulum and smooth endoplasmic reticulum
• This is a system of membranes that spread through the cytoplasm of the cells. It is continuous with the outer membrane and encloses a network of tubules and flattened sacs called cisternae
• The rough endoplasmic reticulum has ribosomes present on the outer surface of the membranes. It provides a large surface area for the synthesis of proteins and glycoproteins and provides a pathway for the transport of materials through the cell (especially proteins)
• The smooth endoplasmic reticulum lacks ribosomes on its surface and might be more tubular in appearance. It synthesises, stores, and transports lipids and carbohydrates.
• cell wall (in plants, algae and fungi)
• consists of microfibrils (cellulose) embedded in a matrix. microfibrils have considerable strength and so contribute to the overall strength of the cell wall
• The cell wall consists of a number of polysaccharides (such as cellulose) and there is a thin layer (the middle lamella) which marks the boundary between adjacent cell walls and cements adjacent cells together
• The cell wall provides mechanical strength in order to prevent the cell bursting under changing osmotic pressure, gives mechanical strength as a whole to the plant, allows water through to contribute to the movement of water through the plant
• cell vacuole (in plants)
• a fluid-filled sac bounded by a single membrane (tonoplast)
• contains a solution of mineral salts, sugars, amino acids, wastes, and sometimes pigments such as anhthocyanins
• they support herbaceous plants by making cells turgid
• the sugars and amino acids can act as a temporary food store
• the pigments may colour petals which might attract pollinating insects

In complex multicellular organisms, eukaryotic cells become specialised for specific functions. Specialised cells are organised into:

• tissues
• for working efficiency cells are often aggregated together. A collection of similar cells that perform a specific function is known as a tissue. Examples include:
• Epithelial tissue
• xylem
• organs
• tissues are aggregated into organs. It therefore follows that an organ is a combination of tissues that are coordinated to perform a variety of functions (although they often have one predominant major function). Examples include:
• the stomach
• a leaf
• systems
• organs work together as a single unit known as an organ system. Examples include:
• the digestive system
• the respiratory system
• the circulatory system

3.2.4: Cell recognition and the immune system (Viruses (HIV) and ELISA testing)

HIV (human immunodeficiency virus) is a virus which causes AIDS (acquired immune deficiency syndrome) by attacking helper T cells and interfering with their function, reducing the amount of T helper cells in the blood. Without a sufficient number of T helper cells the immune system cannot stimulate enough B cells to produce enough antibodies to combat pathogens/enough cytotoxic T cells to kill infected cells. This means the body is unable to produce enough of an immune response, and this also makes the patient more susceptible to cancers and other infections. It is these infections/diseases that cause death, not the AIDS itself.

HIV belongs to a group of viruses known as retroviruses. The structure:

• Lipid envelope
• Attachment proteins
• Capsid
• Two single strands of RNA
• Enzymes (including reverse transcriptase which catalyses the production of DNA and RNA)

HIV cannot replicate itself as it is a virus. It replicates by...

• HIV enters the bloodstream and circulates around the body
• A protein on HIV binds to a protein on helper T cells
• The capsid fuses with the cell-surface membrane of the T helper cell
• RNA and enzymes enter the T helper cell and the reverse transcriptase converts the viral RNA into DNA (so the host cell can read it).
• This DNA is inserted into the host cells DNA in the nucleus. This DNA creates mRNA which contains instructions for creating new viral proteins and RNA for the new HIVs
• mRNA passes out of the nucleus and it is read and proteins are made
• HIV particles break away from the T helper cell and take a piece of it's cell-surface membrane with it which forms the new lipid envelope.

We also need to know about ELISA testing, not sure where to put it so here it is:

ELISA (enzyme linked immunosorbant assay) uses antibodies to quantify the amount of a protein in a sample. It is useful in both allergen and drug tests. Here is an example of how it works when testing for antigens:

• Apply a sample to the surface of a slide
• Wash the surface to remove any unattached antigens
• Add the antibody that is specific to the antigen, leave for a little bit so the two can bind together
• Wash the surface (again) to remove excess/unbound antibodies
• Add a second antibody that has an enzyme attached to it. This will bind with the first antibody
• Add the colourless substrate of the enzyme
• When the enzyme acts on the substrate, colour is produced
• The amount of antigen present is proportional to the intensity of the colour of the final solution.

Unfortunately, we cannot use antibiotics against viruses. This is because one way in which viruses work is by inhibiting enzymes required for the synthesis of peptide cross-bridges in cell walls. This means that, in bacteria, they can no longer withstand osmotic pressure as their cell wall is very weak and they burst. However, viruses do not have a cell wall. They also do not have any metabolic mechanisms that the antibiotic might be able to disrupt.

3.2.4: Cell recognition and the immune system (Vaccination and immunity)

Immunity is the ability of an organism to resist infection. It can take two forms:

• Active immunity: This is produced by stimulating the production of antibodies by the individuals own immune system by direct contact with the pathogen/antigen. It is generally longer lasting but takes time to develop. There are two kinds of active immunity:
• Artificial active immunity: occurs from immunisation (vaccination). Involves inducing an immune response in an individual without suffering the disease. E.g injecting a dead/inactive form of the pathogen
• Natural active immunity: results from an individual becoming infected with a disease. E.g if I was to obtain a cold my plasma B cells would produce antibodies
• Passive immunity: This is produced by the introduction of antibodies into individuals from an outside source - direct contact with the antigen/pathogen is not required and immunity develops immediately. However, as the body is not producing its own antibodies, the antibodies are not replaced and no memory cells form. This means that immunity is not long lasting. Examples include anti-venom given to victims of snake bites, and antibodies given to baba from mama.

Vaccination involves stimulating an immune response by injecting/swallowing a vaccine. A vaccine contains one or more types of antigen of the appropriate disease. The initial (primary) response is only little but memory cells are produced (this is the important bit!!). These memory cells remain in the blood (humour) and divide, by mitosis, producing plasma B cells and more memory cells if a future infection is detected.

Vaccines must be economically available in sufficient quantities to immunise at least most of the vulnerable population. There must also be few side affects and a means of producing/storing/transporting/administering the vaccine.

Herd immunity

This arrises when a large proportion of the population has been vaccinated. For a pathogen to spread, it must be passed from person to person in close proximity. Since the vast majority of the population are immune, it is very unlikely that a susceptible person comes into contact with another susceptible person - this means that those not vaccinated are still protected from the disease. It is important as not all of the community may be vaccinated. For example, babies are not vaccinated as their immune systems are still developing, individuals may be allergic to an ingredient in the vaccine.

NOTE: it is important to understand that vaccination does not eliminate a disease. For example, as mentioned above, not all individuals can be vaccinated. Also, someone may obtain the disease straight after vaccination when their immunity is not high enough. Also, antigenic variability. 

Vaccine ethics:

Some individuals may have objections to vaccinations for religious/ethical/medical reasons...

• Vaccines have side effects that may cause long term harm
• How should we test vaccines?
• Is it acceptable to involve the use of animals in the production and development of existing/new vaccines?
• It is right that, in the interest of everyone's health, all of the population should be vaccinated (regardless of religious reasons etc)? - basically, should vaccination be compulsory?
• Should expensive vaccination programmes be stopped if the disease is almost eradicated?

3.2.4: Cell recognition and the immune system (B lymphocytes, humoral immunity, and antibodies)

Humoral immunity is called humoral immunity because it involves antibodies and antibodies are soluble in blood and tissue fluid (humour).

There are many different types of B lymphocyte, each produces andifferent antibody in response to a specific antigen. Here's how:

• An antigen (on the surface of a pathogen/foreign cell/toxin, for example) enters the blood/tissue fluid, there will be a B cell that has a complimentary antibody on it's surface
• The antibody attaches to this antigen
• The antigen enters the B cell (by endocytosis)
• The B cell presents the antigien on it's surface (this is also known as 'processing')
• T helper cells (a type of T lymphocyte) binds to the processed antigens and stimulated the B cells to divide by mitosis (clonal selection) to form a clone of identical B cells which all produce the antibody that is specific to the foreign antigen.

Often, some pathogens have many different antigens so many different B cells make clones at the same time. As each clone produces one specific antibody, the antibodies are referred to as monoclonal antibodies. Each clone develops into either:

• Plasma cells: these secrete antibodies (usually) into blood plasma. They survive for only a few days but can make around 2000 antibodies per second (that's quick). These antibodies lead to the destruction of the antigen therefore plasma cells are responsible for the immediate defence of the body against infection. 
• Memory cells: these are responsible for the secondary immune response. They live considerable longer than plasma cells but do not produce antibodies. Instead, they divide rapidly into plasma cells and more memory cells when they encounter the same pathogen once again (e.g a new infection but of the same infection......did that make sense?????not sure lol). The plasma cells they produce in turn produce antibodies to fight the new infection and the new memory cells circulate in the blood and tissue fluid (humour). Because of this, memory cells provide long-term immunity against the original infection. An increased quantity of antibodies is secreted faster the second time round ensuring that the infection sis destroyed before it can cause any/much harm.

NOTE: The production of antibodies and memory cells is known as the primary response.

To summarise, the overall response of B cells:

• Surface antigens of invading pathogen are taken up by a B cell
• The B cell processes the antigens and presents them on its surface
• helper T cells attached to the processed antigens, activating the B cells
• The B cells are stimulated to divide (by mitosis) forming clones of the B cell with the complimentary antibody
• These clones either form plasma or memory cells
• The cloned plasma cels secrete antibodies to attach to and destroy the pathogen
• The cloned memory cells can respond to future infections by dividing rapidly and developing into plasma cells which produce complimentary antibodies (the secondary immune response)

So, what actually are antibodies?

Antibodies are proteins with specific binding sites synthesised by plasma B cells when the body is infected by non-self material. The antibody reacts with a complimentary antigen by binding to it. Each antibody has two specific and identical binding sites. They are made of proteins which leads to a massive variety of antibodies.

They are made up of four polypeptide chains. Two are long (heavy chains) and two are shorter (light chains). As mentioned above, each antibody has a specific binding site that fits very precisely onto a specific antigen forming an antigen-antibody complex. This binding site is different on different antibodies and is therefore known as the variable region (the rest of the antibody is the constant region - this binds to receptors on cells such as B cells).

Antibodies do not directly destroy the antigen, they just prepare it for destruction. If the pathogen is a bacterial cell, the antigen can prepare it in one of two ways:

• Cause agglutination (clumps of the bacterial cell form, making it easier for the phagocytes to locate them as they are less spread out)
• Act as markers that stimulate phagocytes to engulf the bacterial cell to which they are attached (phagocytosis)

It is of medical value if we can produce a single type of antibody outside of the cell, these are known as monoclonal antibodies. Some uses of monoclonal antibodies are:

• Direct/indirect monoclonal antibody therapy.
• Monoclonal antibodies are produced that are specific to cancer cells (for example)
• These antibodies are administered to a patient and attach themselves to the receptors on the cancer cells
• They block the chemical signals that stimulate the uncontrolled growth of the cancer cells.
• The advantages of this is that, since antibodies are highly specific and not toxic, they lead to fewer side effects than other forms of therapy (e.g chemo/radiotherapy)
• Indirect monoclonal antibody therapy involves attaching a cytotoxic/radioactive drug to the antibody, therefore the cell that the antibody attaches to dies
• They can be used in small doses which is cheaper and less invasive and reduces the side effects of other drugs that may be used alternatively
• Medical diagnosis
• They are used for the diagnosis of hepatitis/chlamydia/influenza infections as they produce a much more rapid result than conventional methods of diagnosis
• One example is prostate cancer: men with prostate cancer often produce higher numbers of PSA (prostate specific antigen). By using a monoclonal antibody that reacts with this antigen is is possible to obtain a measure of the amount of PSA in a mans blood. Whilst this does not diagnose the disease it gives a good indication/early warning that the cancer may be present
• Pregnancy testing
• Placenta produces a hormone known as hCG (human chorionic gonadatrophin). This is present in mamas urine
• Monoclonal antibodies linked to coloured particles are present on home pregnancy tests
• If hCG is present it binds to these antibodies and the hCG-antibody complex moves along the strip creating a coloured line

Monoclonal antibody ethical issues:

• Monoclonal antibody production involves inducing mice with cancer to create tumour cells
• There have been some deaths associated with the use of monoclonal antibodies and multiple sclerosis treatment
• in March 2006 six healthy volunteers trialed a new monoclonal antibody and within minutes suffered multiple organ failures, although all survived.
• Monoclonal antibodies have been used successfully to treat a number of diseases

3.2.4 Cell recognition and the immune system (T lymphocytes and cell-mediated immunity)

An antigen is any part of an organism/substance that is recognised as non-self (foreign) by the immune system and stimulates an immune response. The presence of an antigen stimulates the production of antibodies.

As mentioned in 3.2.4 Defence mechanisms, immune responses such as phagocytosis are non-specific. Specific responses are slower but can provide longer lasting immunity. The type of response (humoral or cell-mediated) displayed depends on the white blood cell present. There are two types of lymphocyte:

• B lymphocytes (mature in the bone marrow, think B for Bone). These are associated with humoral immunity (immunity involving antibodies present in body fluids or humour such as blood plasma)
• T lymphocytes (mature in the thymus gland, thing T for Thymus). These are associated with cell-mediated immunity/cellular response (immunity involving body cells).

Cell mediated immunity/cellular response:

Invader cells have different antigens on their surface to antigens on self-cells. T lymphocytes can distinguish invader cells from normal cells because:

• Phagocytes that have engulfed and hydrolysed a pathogen (phagocytosis) present some of a pathogen's antigens on their own cell surface membrane
• Body cells invaded by a virus present viral antigens on their own cell surface membranes
• Transplanted cells from individuals of the same species have different antigens on their cell-surface membrane
• Cancer cells present antigens on their cell surface membrane

Cells that display foreign antigens on their surface are known as antigen-presenting cells as they can present antigens of other cells on their own cell surface membrane.

T lymphocytes differ from B lymphocytes as T lymphocytes will ONLY respond to antigens that are present on a body cell (rather than within body fluids). The receptors on T each T cell responds to a single antigen. It follows that there is a vast number of T lymphocytes, each responding to one antigen. The 'method' of cell-mediated immunity/cellular response is:

• Pathogens are taken in by phagocytes
• The phagocyte places antigens from the pathogen on its cell-surface membrane
• Receptors on a specific helper T cell fit onto these antigens
• This attachment activated the T cells to divide rapidly by mitosis and form a clone of genetically identical cells (clonal selection)
• These cloned T cells can either:
• Develop into memory cells that enable a rapid secondary response (for if the pathogen invades the body once again)
• Stimulate phagocytes to engulf pathogens by phagocytosis
• Stimulate B cells to divide and secrete their antibody
• Activate cytotoxic T cells. Cytotoxic T cells kill abnormal body cells/infected body cells by producing the protein perforin that makes holes in the cell-surface membrane meaning the membrane becomes freely permeable to all substances and the cell dies.

NOTE: The action of T cells is most effective against viruses as viruses replicate inside other cells.

Okay so i'm not too sure where to slot this next bit in but it's in the spec so i'll just put it here:

The effect of antigen variability on disease and disease prevention. Antigenic variability means that the antigens on the surface of the pathogen are constantly changing so, every time you're infected, you're immune system will not have the memory cells with complimentary antibodies, so the above process will have to start all over again. This means there will not be a rapid secondary response to the pathogen ( as it is technically a different pathogen). Therefore, even if you were vaccinated against the 'old' pathogen, since it's antigens have changed you're vaccine will not prevent you against infection. The common cold is a good example here, everyone gets infected pretty frequently (well, I do anyway). This is because each time you get infected with a slightly different pathogen, so you don't have the built up immune responses to immediately fight against it.

3.2.4: Cell recognition and the immune system (defence mechanisms)

Cell recognition:

It is important to recognise these as millions of humans die each year from infectious diseases.

To defend the body, lymphocytes (a type of white blood cell) must be able to recognise your own cells from 'bad' cells, such as pathogens. Each type of cell has specific molecules on its surface that identify it. These molecules (for example, proteins) enable the immune system to identify:

• Pathogens
• Cells from other organisms of the same species
• Self-cells (your own body cells)
• Toxins
• Abnormal body cells (e.g tumours/cancers)

Proteins are the most important cell identification molecules as they have a highly specific tertiary structure and enormous variety and therefore make it easy to distinguish one cell from another.

This response is very effective, but may be potentially dangerous to patients who, for example, have had an organ transplant. The immune system may recognise these cells as non-self and attempt to destroy them. To minimise the effect of tissue rejection, donor tissues are matched as closely as possible to the cells of the recipient (for example, an organ from a relative) and also immunosuppressant drugs are often administered to reduce the level of immune response that may occur.

There are millions of types of lymphocytes in out body's. There is a high probability that, when a pathogen enters the body, one of these lymphocytes has a protein on its surface that is complementary ti one of the proteins on the pathogen. When an infection occurs, the one that is present with the complimentary protein to the pathogen will be stimulated to divide, building up its numbers to a level where it is effective in destroying the infection. This is known as clonal selection.

But how to lymphocytes recognise self cells (cells belonging to the body)?

Basically, in the fetus the lymphocytes are constantly colliding with other cells. Here, infection is rare as mama protects baba (and the placenta also protects baba). This means that lymphocytes will collide almost exclusively with self cells. The lymphocytes that have receptors that are complementary to self cells are suppressed or die. This means that the only remaining lymphocytes are those that might be complimentary to foreign material. (also, in adults lymphocytes produces in bone marrow will initially only encounter self cells and any that are complimentary undergo apoptosis before they mature).


An infection: an interaction between a pathogen and the body's defence mechanisms

If the individual recovers from the disease the body's defence mechanisms seem better prepared for a second infection from the sam pathogen - often killing it before the patient is aware they have been infected. This is known as immunity.

The body has a range of different defences to protect itself from pathogens. These defence mechanisms can be split into specific and non-specific responses:

Specific: response is slower and specific to each pathogen

• Cell-mediated immunity (T lymphocytes)
• Humoral immunity (B lymphocytes)

Non-specific: response is immediate and the same for all pathogens

• Physical barrier (skin)
• Phagocytosis

Phagocytosis

Should the physical barrier line of defence fail, next up is phagocytosis. Basically, phagocytes ingest and destroy the pathogen before it can cause harm (well, it doesn't always work hence we have cell-mediated/humoral responses as a back up, but this is worth a try first):

• Chemical products of pathogens attract the phagocytes
• The phagocytes have several receptors on their cell-surface membrane that recognise and attach to chemicals on the pathogens surface
• The phagocyte then engulfs the pathogen forming a vesicle (in this instance, the vesicle is also known as a phagosome)
• Inside the phagocyte, lysosomes move towards the vesicle and fuse with it
• Lysozymes from the lysosome destroy the bacteria by hydrolysing their cell walls
• The soluble products are absorbed into the cytoplasm of the phagocyte

This is pretty cool tbh