Topic 2A - Cell Structure and Division - complete

- prokaryotic organisms are prokaryotic cells (i.e. theyre singled-celled organisms) and eukaryotic organisms are made up of eukaryotic cells
- eukaryotic cells are complex and include all animal and plant cells, as well as all cells in algae and fungi
- prokaryotic cells are smaller and simpler, e.g. cells are smaller and simpler, e.g. bacteria
- both types of cells contain organelles
- organelles are parts of cells and each one has a specific function

- eukaryotic cells are generally more complicated than prokaryotic cells
- they have a range of organelles:
1 - plasma (cell surface) membrane
2 - rough endoplasmic reticulum
3 - nucleolus
4 - nucleus
5 - smooth endoplasmic reticulum
6 - lysosome
7 - ribosome
8 - nuclear envelope
9 - golgi apparatus
10 - cytoplasm
11 - mitochondrion

- plant cells have all the same organelles as animal cells, but with a few added extras:
- a cellulose cell wall with plasmodesmata ('channels' for exchanging substances with adjacent cells)
- a vacuole (compartment that contains cell sap)
- chloroplasts

- algal cells are a lot like plant cells
- they have the same organelles, including a cell wall and chloroplasts
- algae carry out photosynthesis, like plants, but can be single-celled or multicellular

- fungal cells are also a lot like plant cells, but with two key differences:
- their cell walls are made of chitin, not cellulose
- they dont have chloroplasts (because they dont photosynthesise)
- fungi include mushrooms and yeast

- the membrane found on the surface of animal cells and just inside the cell wall of other cells
- its made mainly of lipids and protein
- it regulates the movement of substances into and out of the cell
- it also has receptor molecules on it, which allow it to respond to chemicals like hormones

- a large organelle surrounded by a nuclear envelope (double membrane), which contains many pores
- the nucleus contains chromosomes (which are made from protein-bound linear DNA) and one or more structures called a nucleolus
- the nucleus controls the cell's activities (by controlling the transcription of DNA)
- DNA contains instructions to make proteins
- the pores allow substances (e.g. RNA) to move between the nucleus and the cytoplasm
- the nucleolus makes ribosomes 

- they're usually oval shaped
- they have a double membrane
- the inner membrane is folded to form structures called cristae
- inside is the matrix, which contains enzymes involved in respiration
- this is the site of aerobic respiration, where ATP is produced
- they're found in large numbers in cells that are very active and require a lot of energy

- a small, flattened structure found in plant and algal cells
- its surrounded by a double membrane, and also has membranes inside called thylakoid membranes
- these membranes are stacked up in some parts of the chloroplast to from grana
- grana are linked together by lamellae -- thin, flat pieces of thylakoid membrane
- this is the site where photosynthesis takes place
- some parts of photosynthesis happen in the grana
- other parts happen in the stroma (a thick fluid found in chloroplasts)

- a group of fluid-filled, membrane-bound flattened sacs
- vesicles are often seen at the edges of the sacs
- it processes and packages new lipids and proteins
- it also makes lysosomes

- a small fluid-filled sac in the cytoplasm, surrounded by a membrane and produced by the golgi apparatus
- stores lipids and proteins made by the golgi apparatus and transports them out of the cell, viathe cell-surface membrane

- a round organelle surrounded by a membrane
- no clear internal structure
- type of Golgi vesicle
- contains digestive enzymes called lysozymes
- kept separate from the cytoplasm by the surrounding membrane
- can be used to digest invading cells or to break down worn out components of the cell

- a very small organelle that either floats free in the cytoplasm or is attached to the rough endoplasmic reticulum
- its made up of proteins and RNA
- its not surrounded by a membrane
- the site where proteins are made

RER
- a system of membranes enclosing a fluid-filled space
- the surface is covered with ribosomes
- folds and processes proteins that have been made at the ribosomes

SER
- similar to RER but with no ribosomes
- synthesises and processes lipids

- a rigid structure that surrounds cells in plants, algae and fungi
- in plants and algae its made mainly on the carbohydrate cellulose
- in fungi, its made of chitin
- supports cells and prevents them from changing shape

- a membrane-bound organelle found in the cytoplasm of plant cells
- it contains cell sap which is a weak solution of sugar and salts
- the surrounding membrane is called the tonoplast
- helps to maintain pressure inside the cell and keep the cell rigid
- this stops plants wilting
- also involved in the isolation of unwated chemicals inside the cells

- in multicellular eukaryotic organisms, cells become specialised to carry out specific functions
- a cells structure helps it to carry out its function
- depending on what job it does, a specialised cell can look very different to the 'normal' cells (i.e. animal, plant, algal and fungi)
- example: epithelial cells in the small intestine are specialised to absorb food efficiently
- the walls of the small intestine have lots of finger-like projections called villi
- these increase surface area for absorption
- the epithelial cells on the surface of the villi have folds in their cell-surface membranes called microvilli
- microvilli increase surface area even more
- they also have lots of mitochondria to provide energy for the transport of digested food molecules into the cell

- in multicellular eukaryotic organisms, specialised cells are grouped together to form tissues
- a tissue is a group of cells working together to perform a particular function
- different tissues work together to form organs
- different organs make up an organ system

- for example, epithelial cells make up epithelial tissue
- epithelial tissue, muscular tissue and glandular tissue (which secretes chemicals) all work together to form the stomach (an organ)
- the stomach is part of the digestive system - this is an organ system made up of all the organs involved in the digestion and absorption of food (including the small intestine, large intestine and liver)

- prokaryotic cells are smaller and simpler than eukaryotic cells
- bacteria are examples of prokaryotic cells

Cytoplasm
- has no membrane bound organelles
- it has ribosomes but they're smaller than those in a eukaryotic cell

Plasma Membrane
- is mainly made of lipids and proteins
- controls the movement of substances into and out of the cell

Cell Wall
- supports the cell and prevents it from changing shape
- made of a polymer called murein
- murein is a glycoprotein (a protein with a carbohydrate attached)

Capsule
- made up of secreted slime
- helps to protect bacteria from attack by cells of the immune system
Plasmids
- small loops of DNA that arent part of the main circular DNA molecule
- plasmids contain genes for things like anibiotic resistance, and can be passed between prokaryotes
- plasmids are not always present in prokaryotic cells and some have several
DNA
- prokaryotic cells dont have a nucleus so DNA floats free in the cytoplasm
- its circular DNA, present as one long coiled-up strand
- not attached to any histone proteins
Flagellim
- long, hair-like structure that rotates to make the prokaryotic cell move
- not all prokaryotes have a flagellum
- some have more than one

- viruses are acellular meaning they're not cells
- viruses are just nucleic acids surrounded by protein and they arent alive
- they're even smaller than bacteria 
- unlike bacteria, viruses have no plasma membrane, no cytoplasm and no ribosomes
- all viruses invade and reproduce inside the cells of other organisms
- those cells are known as host cells
- viruses contain a core of genetic material - either DNA or RNA
- the protein coat around the core is called the capsid
- attachment proteins stick out from the edge of the capsid
- these attachment proteins let the virus cling on to a suitable host cell

- in binary fission, the cell replicates its genetic material before physically splitting into two daughter cells
1 - the circular DNA and plasmid(s) replicate. the main DNA loop is only replicated once, but plasmids can be replicated lots of times
2 - the cell gets bigger and the DNA loops move to opposite poles of the cell
3 - the cytoplasm begins to divide and new cell walls begin to form
4 - the cytoplasm divides and two daughter cells are produced. each daughter cell has one copy of the circular DNA, but can have a variable number of copies of the plasmid(s)

1 - viruses use their attachment proteins to bind to complementary receptor proteins on the surface of host cells
2 - different viruses have different attachment proteins and therefore require different receptor proteins on host cells. as a result, some viruses can only infect one type of cell while others can infect lots of different cells
3 - because they're not alive, viruses dont undergo cell division. instead they inject their DNA or RNA into the host cell. this hijacked cell then uses its own 'machinery' (e.g. enzymes, ribosomes) to replicate the viral particles

- magnification is how much bigger the image is than the specimen (the sample you're looking at)
- the formula is: magnification = size of image/size of real object
- for example, if you have a magnified image that's 5mm wide and your specimen is 0.05mm wide, then the magnification is 5/0.005 = x100

- resolution is how detailed the image is
- OR how well a microscope distinguishes between two points that are close together
- if a microscope lens cant separate two objects, then increasing the magnification wont help

- use light to form an image
- they have a maximum resolution of about 0.2 micrometres
- this means that you cant use an optical microscope to view organelles smaller than 0.2 micrometres
- this includes ribosomes, the endoplasmic reticulum and lysosomes
- you may be able to make out the mitochondria (but not in perfect detail) and you can see the nucleus
- the maximum useful magnification of an optical microscope is about x1500

- they use electrons to form an image
- they have a higher resolution than optical microscopes
- therefore they give a more detailed image and can be used to look at more organelles
- they have a maximum resolution of about 0.0002 micrometres, which is about 1000 times higher than optical microscopes
- the maximum useful magnification of an electron microscope is about x1500000

- a micrometre is three orders of magnitude smaller than a millimetre
- one micrometre = 0.001 mm
- to convert from micrometres to mm, divide by 1000

- TEMs use electromagnets to focus a beam of electrons, which is then transmitted through the specimen
- denser parts of the specimen absorb more electrons, which make them look darker on the image produced
- TEMs are good because they give high resolution images, so you can see the internal structure of organelles like chloroplasts
- however, they can only be used on thin specimens 

- SEMs scan a beam of electrons across the specimen
- this knocks off electons from the specimen, which are gathered in a cathode ray tube to form an image 
- the images you end up with show the surface of the specimen and they can be 3D
- SEMs are good because they can be used on thick specimens
- however, they give lower resolution images than TEMs

- start by pipetting a small drop of water onto the slide (a ***** of clear glass or plastic)
- then use tweezers to place a thin section of your specimen on top of the water drop
- add a drop of a stain
- stains are used to highlight objects in a cell
- for example, eosin is used to make the cytoplasm show up
- iodine in potassium iodide solution is used to stain starch grains in plant cells
- finally, add the cover slip (a square of clear plastic that protects the specimen)
- to do so, stand the slip upright on the slide, next to the water droplet
- then carefully tilt and lower it so it covers the specimen
- try not to get any air bubbles under there as they'll obstruct your view of the specimen

- can be done in several different ways, e.g. by vibrating the cells or by grinding the cells up in a blender
- this breaks up the plasma membrane and releases the organelles into solution
- the solution must be kept ice-cold to reduce the activity of enzymes which break down organelles
- the solution should also be isotonic
- this means it should have the same concentration of chemicals as the cells being broken down to prevent damage to the organelles through osmosis
- a buffer solution should be added to maintian the pH

- next, the homogenised cell solution is filtered through a gauze to separate any large cell debris or tissue debris
- for example, connective tissue, from the organelles
- the organelles are much smaller than the debris, so they pass through the gauze

- after filtration, you're left with a solution containing a mixture of organelles
- to separate a particular organelle from all the others, you use ultracentrifugation
1 - the cell fragments are poured into a tube. the tube is put into a centrifuge and is spun at a low speed. the heaviest organelles, like nuclei, get flung to the bottom of the tube by the centrifuge. they form a thick sediment at the bottom (the pellet). the rest of the organelles stay suspended in the fluid above the sediment (the supernatant)
2 - the supernatant is drained off, poured into another tube, and spun in the centrifuge at a higher speed. again, the heaviest organelles, this time the mitochondria, form a pellet at the bottom of the tube. the supernatant containing the rest of the organelles is drained off and spun in the centrifuge at an even higher speed
3 - this process is repeated at higher and higher speeds, until all the organelles are separated out. each time, the pellet at the bottom of the tube is made up of lighter and lighter organelles
- from heaviest to lightest, the organelles are seperated in this order: nuclei, chloroplasts (if applicable), mitochondria, lysosomes, endoplasmic reticulum and finally ribosomes

- in mitosis, a parent cell divides to produce two genetically identical daughter cells (they contain an exact copy of the DNA of the parent cell)
- mitosis is needed for the growth of multicellular organisms and for repairing damaged tissues
- in multicellular organsisms, not all cells keep their ability to divide
- the ones that do, follow a cell cycle which mitosis is apart of 
- the cell cycle consists of a period of cell growth and DNA replication called interphase
- mitosis happens after that
- interphase (cell growth) is subdivided into three separate growth stages
- these stages are called G1, S and G2

- the cell carries out normal functions, but also prepares to divide
- the cell's DNA is unravelled and replicated to double its genetic content
- the organelles are also replicated so it has spare ones
- its ATP content is also increased
- as mitosis begins, the chromosomes are made of two strands joined in the middle by a centromere
- the seperate strands are called chromatids
- there are two strands because each chromosome has already made an identical copy of itself during interphase
- when mitosis is over, the chromatids end up as one-strand chromosomes in the daughter cells

- the chromosomes condense, getting shorter and fatter
- tiny bundles of protein called centrioles start moving to opposite ends of the cell, forming a network of protein fibres across it called the spindle
- the nuclear envelope (the membrane around the nucleus) breaks down and chromosomes lie free in the cytoplasm

- the chromosomes (each with two chromatids) line up alsong the middle of the cell and become attached to the spindle by their centromere

- the centromeres divide, separating each pair of sister chromatids
- the spindles contract, pulling chromatids to opposite poles (ends) of the spindle, centromere first
- this makes the chromatids appear v-shaped

- the chromatids reach the opposite poles on the spindle
- they uncoil and become long and thin again
- they're now called chromosomes again
- a nuclear envelope forms around each group of chromosomes, so there are now two nuclei
- the cytoplasm divides (cytokinesis) and there are now two daughter cells that are genetically identical to the original cell and to each other
- mitosis is finished and each daughter cell starts the interphase part fo the cell cycle to get ready for the next round of mitosis

Example: A scientist observes a section of growing tissue under a microscope. He counts 100 cells undergoing mitosis. Of those, 10 cells are in metaphase. One complete cell cycle of the tissue lasts 15 hours. How long do the cells spend in metaphase? Give your answer in minutes.
1 - the scientist has observed that 10 out 100 cells are in metaphase. This suggests that the proportion of the time the cells spend in metaphase must be 10/100th of the cell cycle
2 - you're told that the cell cyle in these cells lasts 15 hours. That's (15x60=) 900 minutes
3- so the cells spend: (10/100) x 900 = 90 minutes in metaphase

- cancer is the result of uncontrolled cell division
- mitosis and the cell cycle are controlled by genes
- normally, when cells have divided enough times to make enough new cells, they stop
- if there's a mutation in a gene that controls cell division, the cells can grow out of control
- the cells keep on dividing to make more and more cells, which form a tumour
- cancer is a tumour that invades surrounding tissue
- some treatments for cancer are designed to control the rate of cell division in tumour cells by disrupting the cell cycle. this kills the tumour cells
- these treatments don't distinguish tumour cells from normal cells though and will kill normal body cells that are dividing
- however, tumour cells divide much more frequently than normal cells, so the treatments are more likely to kill tumour cells
- one cell cycle target of cancer treatment is G1. some chemical drugs (chemo) prevent the synthesis of enzymes needed for DNA replication. if these aren't produced, the cell is unable to enter the synthesis phase. this disrupts the cell cycle and forces the cell to kill itself.
-radiation and some drugs damage DNA. at several points in the cell cycle (including just before and during S phase) the DNA in the cell is checked for damage. if severe damage is detected, the cell will kill itself - preventing further tumour growth

- wear gloves, a jacket and goggles
- Cut 1cm from the tip from a growing root (e.g. of an onion). It needs to be he tip because that's where growth occurs, and so that's where mitosis takes place
- Perpare a boiling tube containing 1 M hydrochloric acid and put it in a water bath at 60^oC
- Transfer the root tip into the boiling tube and incubate for about 5 minutes
- Use a pipette to rinse the root tip well with cold water. Leave the tip to dry on a paper towel
- Place the root tip in a microscope slide and cut 2mm from the very tip of it. Get rid of the rest
- Use a mounted needle to break the top open and spread the cells out thinly
- Add a few drops of stain and leave it for a few minutes. The stain will make the chromosomes easier to see under a microscope. There are lots of different stains you can use
- Place a cover slip over the cells and push down firmly to squash the tissue. This will make the tissue thinner and allow light to pass through it. Don't smear the cover slip sideways or you'll damage the chromosomes
- Now you can look at all the stages of mitosis under an optical microscope.

- start by clipping the slide you've prepared onto the stage
- select the lowest-powered objective lens (lowest magnification)
- use the coarse adjustment knob to bring the stage up to just below the objective lens
- look down the eyepiece (which contains the ocular lense)
- use the coarse adjustment knob to move the stage downwards, away from the objective lens until the image is roughly in focus
- adjust the focus with the fine adjustment knob, until you get a clear image of what's on the slide
- if you need to see the slide with greater magnification, swap to a higher-powered lens and refocus

- if you're asked to draw cells undergoing mitosis under the microscope, make sure you write down the magnification the specimen was viewed under
- also, label your drawing

- the mitotic index is the proportion of cells undergoing mitosis
- you can calculate the mitotic index of your cells using the formula:

mitotic index = number of cells with visible chromosomes / total number of cells observed

- this lets you work out how quickly the tissue is growing and if there's anything weird going on
- a plant root tip is constantly growing, so you'd expect a high mitotic index (i.e. lots of cells in mitosis)
- in other tissue samples, a high mitotic index could mean that tissue repair is taking place of that there is a cancerous growth in the tissue

- this is where the eyepiece graticule and stage micrometer come in
- an eyepiece graticule is fitted onto the eyepiece
- its like a transparent ruler with numbers, but no units
- the stage micrometer is placed on the stage - it is a microscope slide with an accurate scale (it has units) and it's used to work out the value of the divisions on the eyepiece graticule at a particular magnification
- this means that when you take the stage micrometer away and replace it with the slide containing your sample, you'll be able to measure the size of the cells
EXAMPLE
- line up the eyepiece graticule and the stage micrometer
- each division on the stage micrometer is 0.1 mm long
- at this magnification, 1 division on the stage micrometer is the same as 4.5 divisions on the eyepiece graticule
- to work out the size of one division on the eyepiece graticule, you need to divide 0.1 by 4.5 (one division on eyepiece graticule = 0.1/4.5 = 0.022mm)
- so if you look at a cell under the microscope at this magnification and its 4 eyepiece divisions long, you know it measures: 4 x 0.022 = 0.088 mm 

- if you're given an image of cells under the microscope in the exam, you can calculate their actual size using this formula:

actual size = size of image / magnification

EXAMPLE
if the image of a cell measures 5mm and the magnification is x100, then the actual size of the cell will be: 5/100 = 0.05mm

- artefacts are things that you can see down the microscope that aren't part of the cell or specimen that you're looking at
- they can be anything from bits of dust, air bubbles and fingerprints, to inaccuracues caused by squashing and staining your sample
- artefacts are usually made during the preparation of your slides and shouldn't really be there at all - artefacts are especially common in electron micrographs because specimens need a lot of preparation before you can view them under an electron microscope
- the first scientists to use these microscopes could only distinguisg between artefacts and organelles by repeatedly preparing specimens in different ways
- if an object could be seen with one preparation technique, but not another, it was more likely to be an artefacts than an organelle