Section 2: Cell Structure: Mrs Williams

Object: material that is put under the microscope 

Image: apperance of this material when veiwed under the microscope 

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

Magnification= size of image / size of real object 

It 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 or radiation. 

The greater the resolution the greater clarity is has and the image produced is clearer and more precise. 

Increasing the magnification increases the size of an image but not the resolution. 

It is where the cells are broken up and the different organelles they contain can be separated. 

It shows organelles is great detail. 

Before undergoing this; it has to go through this: 

• cold- reduce enzyme action that might breakdown organelles 
• Same water potential- prevents organelles bursting or shrinking due to osmosis gain or loss 
• Buffered- pH does not fluctuate as it could alter the structure or affect functioing of enzymes 

The two stages of Cell Factionation:

• Homogenation: cells are broken up in a homogeniser (blender)= releases the organelles and the homogenate (fluid) is filtered to remove any complete cells and large peices 
• Ultracentrifugation: Fragments in the filtered homogenate are separated in a centrifude (machine)
• Spins tubes at high speeds 
• Heaviest organelles, the nuclei are forced to the bottom (sediment)
• The fluid at the top is removed and left with the sediment 
• Then it is tranferred and spun even faster and the heaviest organelles are put to the bottom and this process is repeated 

• Nucleur Envelope: double membrane that surrounds the nucleus, it is continuous in the endoplasmic reticculum and has rribosomes on its surface. It controls entry and exit of materials 
• Nucleur Pores: allows the passage of large molecules out of the cell. 
• Nucleoplasm: jelly like substance that makes up the bulk of the nucleus 
• Chromosomes: consists of protein bound linear DNA 
• Nucleous: manufactures ribosomal RNA and assembles the ribosomes 

Other functions:

• Control centre 
• genetic material 
• manufacture ribosomal RNA and ribosomes 

Structures:

• Double membrane: entry and exit of material. Inner of the two membranes is folded to form extensions known as a cristae 
• Cristae: extensions in the inner membrane= provide large surface area for the attachment of enzymes and other proteins involved in respiration 
• Matrix: contains proteins, lipids, ribosomes and DNA= production of their own proteins. Also contain ezymes 

Sites of aerobic stages of respiration and are responcible for the production of energy- carrier molecule= ATP that can be used in things such as active transport 

Carry out photosynethis. 

Structures:

• Chloroplast envelope: double plasma membrane that surrounds the organelle. Seletive to entry and exit of molecules. 
• Grana: stacks of thylakoids, light aborbance  
• Thylakoids: contains the photosyntheis pigment= chlorophyll  
• Stroma: fluid filled matrix that does the syntheis of sugars 

Functions and how they have adapted:

• membranes provide large surface areas for the attachment of chlorophyll 
• Fluid of the stoma= processes all the enzymes needed for sugars 
• Chlroplasts contain DNA and ribosomes so manufacture of proteins is quick 

Two types:

• Rough endroplasmic reticulum: 
• ribsomes present on outer surface of membranes 
• provide a large surafce area for syntheis of proteins and glycoproteins 
• pathway for transport of materials e.g. proteins 

• Smooth Endoplasmic Reticulum: 
• lacks ribsomes on its surface. More tubular appearance
• syntheises, stores and transports lipids 
• Syntheises, stores and transports carbohydrates 
• Allows manufacture and store of carbohydrates, proteins and lipids 

• It consists of a sack of membranes made up of flattened sacks. 
• The proteins and lipids that are produced by the endoplasmic reticulum are passed through here in strict sequences
• It modifies the proteins and can also add non-proteins such as carbohydrates 
• It also labels them so they are sent to the right destinations 

Functions: 

• add carbohydrate to proteins to form glycoproteins 
• produce secretory enzymes 
• secrete carbohydrates 
• transports, modify and stores lipids 
• form lysosomes 

Formed in the vesicles of the gogli apparatus, contain enzymes such as protease and lipases. 

They also contain lysozymes enzymes that hydroysise the cell walls of bacteria 

Functions:

• hydrolyse material ingested by phagocytic cells
• release enzymes
• digest worn out organelles
• break down cells after they die 

Two types: 

• 80s- found in eukaryotic cells (e.g. plants)
• 70s- found in prokaryotic cells (e.g. bacteria) 

Contains two parts (both contains ribosomal RNA and protein 

Site of protein syntheis. 

Consists of microfibrils of the polysaccharide celluose embedded in the matrix. 

• Microfibrils have alot of strength 

Features:

• number of polysaccharides such as celluose 
• middle lamella that marks the boundry between cell walls and cements cells together 

Functions: 

• mechanical strength to prevent cell from bursting under pressure 
• strength as a whole 
• allows water to pass through 

Made up of: celluose and glycoproteins or both. 

Fungi contain chitin instead of celluose which is also a polysaccharide (nitrogen containing) 

Membrane= tonoplast 

It contains a solution of: salts, sugars, amino acids, wastes and pigment 

Functions:

• make the cell turgid 
• sugars and amino acids are a tempory food store 
• pigments may colour petals for attracting insects 

Each specilised cell has evolved more or fewer of certain organelles and structures to suit the role it carries out. 

Embryo= idnetical cells- then as it matures each cell takes on its own individual characteristics that suit its function 

All cells are produced by mitotic divisions from the fertilised egg. 

It has genes but only a few are switched on (expressed)= specilised 

Epitheial Cells 

• sheets of cells 
• line surafces of organs
• protective or secretory function 

Xylem 

• transport water and mineral ions 
• mechanical support 

Organ System: 

• Digestive System: digests and processes food. Organs such as salivary glands, oesophagus, stomach etc
• Respirtory System: breathing and gas exchange. Organs such as trachea, bronchi and lungs 
• Circulatory System: pumps and circultates blood. Made up of the heart, arteries and veins 

Eukaryotic: larger and have a nucleus bounded by nucleur membranes (envelope)

Prokaryotic: cells are smaller and have no nucleus or nucelur envelope 

Differences: 

• prokaryotic cells have smaller ribosomes 
• Prokaryotic cells have an capsule and eukaryotic cells dont have one 
• Prokayotic cells may have plasmids and eukaryotic cells dont have any plasmids 

Mitosis= produces two daughter cells that have the same number of chromosomes as the parent cell and each other 

Meiosis= produces four daughter cells, each with half the number of chromosomes of the parent cell

Mitosis= it is always done in the period during which the cell is not dividing (interphase)

Interphase= period during which the cell is not dividing but DNA is replicating 

Phophase= replicate chromosomes (thicken and shorten) 

Metaphase= replicated chromosomes line up down the middle of the cell 

Anaphase= replications of the chromsomes are pulled apart from each other towards opposite poles of the cell 

Telophase= two new nuclei are formed 

Cytokesis= cytoplasm divides 

Importance of Mitosis: 

• Growth 
• Repair 
• Reproduction 

Spindle role= separation of centromere

• Cancer is a group of diseases caused by as growth disorder of cells 
• As a result of damage of the genes that regulate mitosis and the cell cycle
• Leads to uncontrolled growth and division of cells 
• A group of abnormal cells is called a tumour that constantly expands in size

Treatment: 

• Involves killing dividing cells by blocking a part of the cell cycle 
• This disrupts the cell cycle and cell division 

Phospholipids: 

• Form a bilayer 
• hydrophilic heads of both phospholipids layers point to the outside of the cell surface membrane (attracted by water) 
• Hydrophobic tails of both phospholipid layers point to the centre (repel water) 

Functions:

• allow liid soluble substances to enter and leave the cell 
• prevent water soluble substances entering and leaving the cell 
• flexible and self-sealing 

They are embedded in the phospholipid bilayer in two ways: 

• surface of bilayer; act as mechanical support to membrane, receptors for molecules such as hormones 
• Span the the phospholipid bilayer. Some are protein channels (water filled tubes to allow water soluble ions to diffuse across). Carrier proteins (bind to ions or molecules like glucose and amino acids then change shape in order to move these molecules across the membrane 

Function: 

• structural support 
• act as channels transporting water soluble substances 
• allow active transport across the membrane through carrier proteins 
• act as receptors on surface 
• help stick together

• add strength 
• very hydrophobic (repel) 
• prevent water loss and dissolved ions as they are hydrophobic 
• pull together the fatty acid tails of phospholipid molecules, limiting their movement but without making it too rigid

Functions:

• reduce lateral movement 
• make membranes less fluid at high temps 
• prevent leakage of water and dissolved ions 

Made up of carbohydrate covalently bonded with a lipid. 

• acts as a receptor for specific chemcials 

Functions: 

• Recognition sites 
• maintain the stability of the membrane 
• help cells attach to one another= tissues 

• act as receptors for hormones and neurotransmitters 

Functions:

• recognition sites 
• help cells attach to one another
• allows cells to recognise each other e.g. lymphocytes 

Controls movement of substances in and out of the cell 

Do not freely diffuse because: 

• not soluble in lipids and therefore cannot pass through the layer
• too large to pass through the channels 
• same charge of the protein channels so they are repelled 

• Fluid= individual phospholipid molecules can move relative to one another= flexibility 
• Mosaic= proteins that are embedded into it; vary in shape, pattern etc. Micture of phospholipids and proteins 

• Passive transport (energy is natural, inbuilt motion rather than from an external source) 
• particles are constantly in motion due to kenetic energy 
• No set pattern of motion 
• Bouncing off each other are the molecules 

Definition= net movement of molecules or ions from a region of high concentration to low concentration. 

Non-polar= oxygen and carbon dioxide (easily diffuse through as they are small) 

Movement of larger molecules, charged molecules and polar molecules are made easier by transmembrane channels and carriers that span the membrane. 

• Passive process 
• Relies on inbuilt motion and kenetic energy 
• Occurs at specific points on the membrane where special protein molecules are. 

= protein channels and protein carriers

Hydrophilic channels (attract water) 

• They allow the movement of water soluble ions to pass through 
• They are seletive to specific ions 
• Therefore there is control over entery and exit of ions 
• The ion binds to the protein causing it to change shape, opens and closes at one end at a time 

When a molecule is specific to the proetin it binds to it. 

This causes it to chnage shape and the molecule is released inside the membrane 

No external energy is needed and only use kenetic energy. 

Defination= the passage of water from a region where it has a higher water potential to a region of lower water potential through a slectively permaeable membrane. 

Water potential is created by the water molecules and is measured in pascals. Pure water has 0 water potential. 

It follows that:

• addition of a solute to water will lower its water potentialWater potential of a solution must always be less than zero (negetive value) 
• Water and solute are in random motion due to kenetic energy 

The movement of molecules or ions into or out of the cell from a region of low conc to high conc using ATP and carrier proteins. 

Active Transport ATP is used to: 

• directly move molecules 
• moves molecules using the concentration gradient which has already been set up by direct active transport= co-transport 

How it differs from metabolic energy: 

• ATP is needed (transfer of energy)
• Against the concentration gradient 
• Carrier proetin molecules needed 
• Very selective process 

It is an intrinic transmembrane protein. 

The pump actively transports sodium ions out of the cell and pottassium ions into the cell. Moved against the concentration gradients. 

This process requires ATP (Transfer of energy)

Increasing rate of movement: 

• microvilli= finger like projections that provide more surface area for insersion of carrier proteins; facilitated diffusion, diffusion and active transport can take place. 
• Increase the number of protein channels and carrier proteins= increase their density

Co-transport involves the movement of two molecules through a carrier protein at the same time. 

In the small intestine sodium and glucose ions diffuse into the epitheial cells through the same carrier protein at the same time. 

A combination of active transport and co-transport ensure that all the glucose is absorbed into your body: 

(As relying on diffusion to absorb glucose and amino acids from the blood would reach equilibrium in the small intestine and glucose would be lost in faeces. 

• Sodium ions are actively transported into the blood using the sodium potassium pump 
• This decreases the concnetration of sodium ions into the epitheial cells and maintains a concnetration gradient between the cell and the lumen of the small intestine
• Sodium ions diffuse into the epitheial cells through the co-transporter protein, bringing a glucose molecule with them (or amino acid) 
• Glucose diffuses into the body through a channel protein via faciliated diffusion 

This is an example of indirect active transport as ATP is used to set up a sodium ion gradient which is subuquently used to actively transport glucose into the epithial cells 

• The lining of the small intestine is folded into finger like projections called Villi which increase the surface area 
• The epitheial cells of the small intestine are lined with projections called microvilli which increase the surface area of the cells 
• The epitheial cells have a very large number of transport proteins to increase the rate of diffusion and active transport 
• Carbohydrates and proteins are being continuosly digested which helps to maintain a high concentration gradient 
• The blood is constantly being recirculated and placed which also helps maintain a high concentration gradient 
• Epithelial cells contain reasonably high number of mitrocondrian to produce the ATP required or active transport 

The binding site of the co-transporter molecule is complimentary to shape of the glucose and sodium ion. 

The binding of glucose and sodium ion to the trasnporter leads to a change in the co-transporters shape. 

This moves glucose and sodium into the cell. 

• Skin forming a barrier to the entry of the pathogens and phagocytosis 

White Blood Cells: Two forms: 

• T-lymphocytes 
• B-lymphocytes 

It must be able to disiguish the bodies own cells from the foreign cells or the lymphocytes would destroy the organisms own tissues. 

Self or non-self have specific molecules on its surface that identify it. 

Proteins= they have a variety and highly specific teritary structure. This variety of the specific of 3D structure distrguishes one cell from another. 

Protein molecules allow the immune system to identify: 

• Pathogens 
• non-self material
• Tozins including those produced by certain pathogens
• Abnormal body cells suh as cancer cells 

The immune system recognosies these as non-self even through they have come from individuals of the same species. And it attempts to destroy the transplant. 

To reduce this: 

• matched quite closely as possible to those of the recipient; best matches are relatives that are gentically close 
• Drugs are often used to reduce the level of the immune responce 

There are so many different types of lymphocytes there is a high propibility that when a pathogen gets into the body, these lymphocytes will have a protein on its surface that is complimentary to one of the proteins of the apthogen= recognise the pathogen then the lymphocytes multiply in order for them to destroy it= clonal selection.

This explains the lag time between expesure to the pathogen and bodys defences bringing it under control

• Lymphoytes are constanly colliding with other cells (own material) 
• Produced in the bone marrow 
• Some will have receptors that exactly fit those of the bodys own cells 

Two types of white blood cell: 

• Lymphocyte= immune responce 
• Phagocytes= ingest and destroy the destroy the pathogen by a process called phagocytosis before it can called harm

Explained below:

• Chemicals, dead or damaged cells aact as attractants causing phagocytes to move towards the pathogen 
• Receptors of the surface recognise and attach to chemicals on the surface of a pathogen 
• They engulf the pathogen to form a vesicle known as a phagosome 
• Lysosomes move towards the vesicle and fuse with it
• Enzymes are called lysozymes are presnet within the lysosome. These lysozymes destroy ingested bacteria by hydroysis of their cell wall 
• Soluble products from the breakdown of the pathogen are absorbed into the cytoplasm of the phagocyte

Antigens are proteins that are partof the cell surface membranes onr cell walls of invading cells. The presence of antigens triggers the production of an antibody as part of the bodies defence system. 

Immune responces such as phagocytes are non-specific and occur whatever the infection. The body also has specific responces that react to a specific antigens. These are slower in action at first but can providelong term immunity. 

It depends on the type ona type of white blood cell called lymphocyte. 

There are two types of lymphocytes with its own immune responce: 

• B lymphocytes: humoral immunity; immunity involving antibodies that are present in body fluids or blood plasma, mature in the bone marrow 
• T lymphocytes: mature in the thymus gland, cell mediated immunity; immunity involving body cells

they respond no non-self material but also cells from the same species because they are genetically different. They have diffrent antigens on their cell-surface membrane from antigens on organisms own cells. 

T cells can distinguish these invader cells from normal cells because:

• phagocytes when engulfed a pathogen can present pathogens antigens on their own surface 
• body cells invaded by a virus present viral antigens on own surface 
• transplated cells from same species have different antigens on surface 
• cancer cells are different from body cells and present antigens on surface 

Antigen-presenting cells; cells that display foreign antigens on own surface 

(t cells will only respond to antigens on surface and not those in body fluids)= cell-mediated responce 

• Pathogens are engulfed by phagocytes 
• They present the forgein antigens on surface 
• Receptors on specific T helper cell fit onto antigen 
• Activates t cell to divide rapidly (mitosis) and form clones 

Cloned T cells then: 

• develop to memory cells= rapid responce to future infections
• stimulate phagocytes to engulf pathogen 
• stimulate b cells to divide and produce antibodies 
• Activate cytotoxic t cells to kill infected cells by making holes in membrane 

They kill infected cells by producing a protein (perforin) that makes holes in surface membrane. 

=membrane becomes permeable to substnaces and dies as a result,this prevents them from multiplying and infecting more cells 

Involves antibodies (soluble in fluid)

The antigen on the pathogen is complimentary to the antibody= antigen enters b cells by endocytosis and is presented on its surface for which the cytotoxic cell binds to and stimulates the b cell to divide to form a clone which antibody is specific to the forgein antigen.=CLONAL SELECTION 

Toxins: acts as a antigen: clone of b cells produce specific antibody= monoclonal antibodies: cells produced develop into two types of cells: 

• Plasma Cells= secrete antibodies, lead to destruction of antigen= primary responce 
• Memory cells= circulate in fluids and when come across same antigen they divide rapidly and develop into plasma cells and more memory cells. = secondary defence for future infection. 

Proteins with specific binding sites syntheised by b cells that produce the specific antibody. 

Antibodies are made up of 4 polypeptide chains. 

• 1= heavy chains 
• 2= lighter chains 
• each antibody have a specific binding site that fits onto a specific antigen= antigen-antibody complex 
• Binding site is different on each sntibodies= called the variable region 

Each binding site consists of a sequence of amino acids 

Rest of the antibody is known as the= constant region- binds to receptors on cells such as b cells 

Antibodies do not destroy the pathogen but prepare it to be. 

Two ways:

• Agglutination= clumps cells together (easier for phagocytes), act as markers for phagocytes 

Each antigen will induce a different b cell to multiply and form a clone of itself. 

^This can be used in medical ways so a single antibody can be isolated and cloned 

This can have many functions and uses in medicine. 

This can be used to target specific substances and cells. e.g cancer cells= attach to surface of cancer cells and block the chemical signals thatt stimulate uncontrolled growth 

Advantages: 

• Non toxic 
• Highly specific 
• =fewer side affects but in smaller doses 

Or radioactive and cytotoxic cells (indirect) can be attached that kills the cells. 

The placenta produces a hormone called hCG that is found in the urine. 

Monoclonal antibodies are attached to to coloured partices that binds to the antibodies and creates coloured lines if the hormone is present. 

• use of mice that is considered harmful as they are induced with cancer cells that causes suffering 
• Deaths have been associated (making sure patients are sure of the risks) 
• Testing for saftey is dangerous: suffering in patients in trials, raises issues about conduct of drug trials 

We must balence the advantages with the disadvantages 

Two forms: 

• Passive immunity: Outside source which doesn't have any contact with the pathogen. This is not produced by the individual themselves; so no memory cells are formed and antibodies are not replaced when broken down 
• Active Immunity: is produced by stimulating the production of antibodies by own individuals immune system. Also has direct contact with the pathogen but takes time for immunity. 

Two types of active immunity: 

• natural= infected under normal situations 
• Artifical= vaccination by inducing an immune responce without suffering to the symptoms of disease. Small amount induced. Memory cells are induced for future infection 

• available in suffient quanities to immunise most of the population 
• Must be few side affects 
• Producing, storing and transporting the vaccine= available 
• Appropriate time= training staff 
• Vaccinate most of population to produce herd immunity 

Suffifient amount of the population is vaccinated to make it difficult for the pathogen to spread the population. 

Means unvaccinated people are protected too. 

It is important as it is never possible to vaccinate the whole population. 

• Fails to induce immunity 
• Individuals may develop disease immediatly after vaccinated before immunity levels are high enough to prevent it
• Pathogen may mutate= new antigens on pathogen that are not recognised by immune system= antigenic variability and this is why people may become re infected 

• Have side affects 
• Who should they be tested on? 
• Is it acceptable to trial vaccines without known risks 
• Expensive 

• Lipid envelope: embedded with attachment proteins 
• Capsid: two single strands of RNA and enzymes 
• Enzymes: reverse transcriptive because it cataylses the production of DNA from RNA- this is carried out by transcriptase 
• Retoviruses= presence of a reverse transpripase that has the ability to make DNA from RNA 

Replication: It cannot replcate itself but uses genetic material to instruct the host cell to produce the compounents required to make a new HIV:

• Enters the bloodstream and circulates body
• Protein attachs to another protein called CD4 and can also attach to t helper cells 
• Capsid fuses with surface membrane and the RNA and enzymes enter the t helper cell 
• Reverse transpritase converts viruses RNA into DNA 
• DNA is moved into t helper cells nucleus and is inserted 
• It then creates RNA (messenger) using enzymes that has intructions to make new viral proteins and the RNA to go to the new HIV 
• Passes out and uses proetin synethis to make HIV 
• The HIV breaks away from cell with peice of its membrane which forms the lipid envelope 

HIV attacks the t helper cells and it causes aids by killing or interfering with t helper cells. 

T helper cells are important in carrying out cell mediated immunity and without suffient numbers they cannot stimulate b cells to produce antibodies or cytotoxic cells that kills pathogens. 

The body is then not able to produce immune responces and this causes other problems and person will eventually die. 

HIV does not kill directly but inferfers with immune system that prevents it from working proper;y. 

Uses antibodies to detect and have quanity of specific proteins. 

Method: 

• Apply sample to surface to which all antigens in smaple will attach 
• Wash surface to remove any unattached antigens 
• Add the antibody (specific) and leave to bind 
• Wash again 
• Add second antibody that binds to first antibody (second has a enzyme attached to it) 
• Add colourless substrate of enzyme and if enzymes attach they present colour 
• Amounts of antigens is reliative to the amount of colour that develops 

This can be used to detect HIV and pathogens of diseases and testing of drugs and allergen tests 

• Viruses rely on host cells to carry out infection so lack own metabolic structures that antibiotics could disrupt. 
• Viruses also have a protein coat rather than murein cell wall and so don't have sites where antibiotics can work. 
• Viruses are within the organisms own cell so antibiotics cannot reach them