M2- Chapter 2 - Basic components of living systems Flashcards
What is the cell theory
- Both plants and animal tissue is composed of cells
- Cells are the basic unit of all life
- Cells only develop from existing life
3 types of microscopes
- Light microscope
- Scanning Electron Microscope (uses a beam of electrons to produce an image.)
- Laser scanning confocal microscope (it can use 2D images to create a 3D visual of the structure by using a pinhole to block out-of-focus light.)
2 lenses on a light microscope
Eyepiece
Objective
They allow higher magnification and reduced chromatic abberation (when different wavelengths of light move through slightly different angles, creating a blurry image)
2 knobs
- coarse adjustment - moves stage up and down.
2. fine focus- literally fine tunes the focus.
Sample preparation
- dry mount
- wet mount
- squash slides
- smear slides
Dry mount
The specimen has to be cut to thin slices, a technique called sectioning. No staining, just put a coverslip on top.
Wet mount
Use water or immersion oil to introduce pressure
The coverslip must be placed at an angle to reduce the chances of air bubbles.
Ideal for aquatic
Squash slides
Wet mount is prepared
a lens tissue is used to gently press the cover slip down.
For specimens that require a delicate touch
Smear slides
You use the side of another slide to create a smooth, thin coat of liquid such as blood to view cells
Stain prep
- Allow to air dry
2. Pass through a flame
Staining techniques
- Negative staining
- Gram stain
- Acid fast
Negative staining
Dyes that are negatively charges are repelled by the negatively charged cytosol. So the actual cells are left unstained, creating a contrast.
Gram stain
used to identify gram+ and gram-
1. apply crystal violet
2. then iodine
3. then wash it out with alcohol
Gram+ will retain the purple stain but gram- won’t because it has thinner cell walls and will lose the dye.
It is then stained with safranin dye causing the bacteria to look red
Examples of negatively charged dyes
Congor red or Nigrosin
Acid fast technique
Differentiate species of Mycobacterium from all other.
1. A lipid-solvent is used to carry carbolfuchsin dye.
2. All cells are washed with a dilute acid-alcohol solution.
Mycobacterium will retain the C.F dye (red). All other bacteria are exposed to methylene blue stain.
Risk management
Many stains are toxic or irritant
Carry out a risk assessment.
CLEAPPS provides framework for students.
What is the size of the ribosomes in a prokaryote
70S
Compared to a larger 80S in eukaryote
Cell wall for different organisms
Plant - cellulose
Fungi - chitin
Animals - none
cell wall structure
A thick layer outside the cell membrane. It gives strength but are freely permeable to solutes. In plants, they are made up of cellulose. They have 3 layers: primary cell wall, the secondary cell wall and the middle lamella. In fungi, they are made up of chitin.
Nucleus structures
Surrounded by a nuclear envelope, which is a double membrane with nuclear pores.
Smooth Endoplasmic Reticulum structure
Series of flattened membrane channels without ribosomes attached
Ribosomes structure
the sites of protein synthesis. They are composed of protein and RNA, and are manufactured in the nucleolus of the nucleus. They are often found in groups called polysomes. All eukaryotic ribosomes are of the larger, “80S”, type.
Flagella and cilia structure
Flagella are longer than the cell and cilia are identical in structure. They are much smaller and there are usually very many of them.
Mitochondria structure
This is a sausage-shaped organelle which is surrounded by a double membrane
Rough Endoplasmic Reticulum structure
Series of flattened membrane channels studded with ribosomes.
Chloroplasts structure
Bigger and fatter than mitochondria with a double membrane, they also have a third membrane called the thylakoid membrane. The thylakoid membrane is folded into thylakoid disks, which are then stacked into piles called grana. The space between the inner membrane and the thylakoid is called the stroma.
Plasma membrane structure
This is a thin, flexible layer round the outside of all cells made of phospholipids and proteins
Lysosomes structure
These are small membrane-bound vesicles formed from the RER containing a cocktail of digestive enzymes.
Vesicles structure
Series of flattened membrane vesicles, formed from the endoplasmic reticulum.
Nucleus function
Inside it is the nucleoplasm, which has chromatin (DNA/ protein complex in a 1:2 ratio containing the genes). During cell division, the chromatin becomes condensed into discrete observable chromosomes. The nucleolus is responsible for making the ribosomes. The pores are large holes that contain proteins that control the exit of substances (like RNA)
mitochondria function
where aerobic respiration happens in eukaryotic cells. the outer membrane in highly folded into cristae (gives it a large surface area). The inside part is called the mitochondrial matrix (contains small circular strands of DNA). the inner membrane is studded with stalked particles, which are the site of ATP synthesis.
Chloroplasts function
The thylakoid membrane contains chlorophyll and other photosynthetic pigments arranged in photosystems, together with stalked particles, and is the site of photosynthesis and ATP synthesis. They also contain starch grains, ribosomes and circular DNA.
Vacuoles function
Involved in synthesising and transporting materials, mainly lipids and carbohydrates, needed by the cell.
Rough ER function
The attached ribosomes synthesise proteins, which are processed here (e.g. by enzymatically modifying the polypeptide chain, or adding carbohydrates), before being exported from the cell via the Golgi Body.
The Golgi apparatus function
It takes proteins from the RER to the cell membrane to take outside the cell. Parts of the RER contain proteins that can fuse with one side of the Golgi body membranes. However, the other side small vesicles bud off and move towards the cell membrane, where they fuse and release their contents by exocytosis (basically throwing out its contents outside the cell)
exocytosis
simple taking contents out of a cell
Lysosomes function
They are used to break down unwanted chemicals, toxins, organelles or even whole cells, so that the materials may be recycled. They can also fuse with a feeding vacuole to digest its contents.
centrioles function
Before each division the centriole replicates itself and the two centrioles move to opposite ends of the cell, where they initiate the spindle that organises and separates the chromosomes. As part of the cytoskeleton, microtubules and their motor proteins are involved in maintaining cell shape, movement of vesicles and movement of chromosomes. the nuclear membrane disintegrates just before cell division takes place, and this is why the centrioles are outside the nucleus.
Flagella and cilia function
This is a flexible tail present in some cells and used for motility. It is an extension of the cytoplasm, surrounded by the cell membrane, and is full of microtubules and motor proteins so is capable of complex swimming movements. Cilia may be either stationary or motile.
Plasma membrane function
It separates the contents of the cell from the outside environment, and controls the entry and exit of materials. It also contains receptors for recognition of various chemicals e.g. hormones, antibodies.
Cell wall function
Used to give a cell strength and rigidity. There are often channels through those belonging to plant cells called plasmodesmata, which link the cytoplasm of adjacent cells.
They prevent the cell from bursting and they allow turgidity.
What is cellulose
A complicated carbohydrate
Vacuoles
They contain cell sap. They are very important in the maintenance of turgor, so the cell contents stay pushed against the cell wall and keep it rigid. The membrane of the vacuole is called the tonoplast, which is selectively permeable.
Chloroplasts- more information
They are responsible for photosynthesis. They have a fluid called stroma inside. They also have a network of membranes, which form flattened sacs called thylakoids. Many thykaloids stacked together is called a granum. The grana are joined together by membranes called lamellac. The grana contain the chlorophyll pigment.
what is magnification
How many times larger the image is than the object being viewed
What is resolution
The ability to see the individual structures as separate entities
What does the resolution depend on
The diffraction of the light as is spreads through the sample. The structures are quite close together and the light reflected can overlap, causing a loss of data as it can’t be seen clearly
How can you increase resolution
By using a electron beam rather than a light beam. This is because they have a wavelength that is 1000 times shorter. This allows it to focus more into a specific part.
Eyepiece graticule
It is fitted into the eyepiece lens. It is just a line with 100 divisions on it. There are no units, you have to work out how much each division is in units by calibrating it, using a stage micrometer
Disadvantages of electron microscope
Expensive
Big + bulky
Electron beam can lead to artefacts
TEM
Transmission Electron Microscope
A beam of electrons is passed through the specimen
SEM
Scanning Electron Microscope
A beam of electrons is sent across the surface of the specimen.
It can create 3D images.
Sample prep for electron mic.
There needs to be a vacuum inside the microscope to focus the beam. The specimen must be fixed using chemicals or freezing, staining with heavy metals and dehydration with solvents.
TEM: set in resin and stained again
SEM: may be fractured and then coated with heavy metals on the inside
Identifying artefacts
ex:
They found inside foldings and they thought it was part of the structure. However, it disappeared in specific conditions, making it an artefact
LSCM
Laser Scanning Confocal Microscope
They use fluorescent lights, which has a higher light intensity.
There is a single spot of focused light which is sent from a laser. It reflected off of a dichroic mirror (a beamsplitter) Then it goes to the specimen. The emitted light from the specimen is filtered through a pinhole aperture. Light is reflected/ radiated on the focal plane.
What is fluorescence
The absorption and re-radiation of light
3D and 2D on LSCM
2D images are made when only 1 focal point is used, but when more than 1 is used, 3D images can be made.
Dichroic mirror
This is used in LSCM. It reflected 1 wavelength (from the laser) and all others are allowed to just go through. The position of the 2 pinholes means the light from the laser follows the same path as the light radiated from the sample. This gives them the same focal point.
advantages of light micrososcopes
Quick Easy to use Small and portable Cells are alive Vacuum not required
What is the resolution of light microscopes
200nm
Resolution of TEM
0.5nm
Magnification of TEM
500,000
Resolution of SEM
3-10nm
Steps in making a protein
- The nucleus is the site of where ribosomes are made (nucleolus).
- Some ribosomes will stay inside the nucleolus to make other proteins. Others will leave to go to the Rough ER, and will attach to the other membrane of the ER.
- The proteins are transported to the Golgi Body from the Rough ER by vesicles.
- At the Golgi Body, the proteins are processed, modified and packaged into other vesicles. Some proteins even have sugars added on to make glycoproteins.
- The vesicles will travel from the Golgi Body as they are ‘pinched’ off towards the plasma membrane.
- At the plasma membrane, the vesicles will fuse with the plasma membrane, and as they do so, undergo exocytosis, where the contents of the vesicles are thrown outside of the cell.
What is the cytoskeleton
The cytoplasm has a network of protein threads running through it. This is called the cytoskeleton
What does the cytoskeleton do
Supports the cell’s organelles (because everything stays in place because of it)
Allows organelles to move in the cell (such as the movement of chromosomes during mitosis)
Maintains the shape of the cell
Allows the cell to move around (the flagella)
Allows the cell to change shape (ex: cytokinesis)
What are the 3 things the cytoskeleton is made up of
Microtubules
Microfilaments
Intermediate fibres
Microtubules
Found in all eukaryotic cells, and are involved with mitosis, cell motility and maintenance of the cell. They are made up of strands of globular proteins, called Actin. They act as a track for transport for vesicles and organelles. They also make up spindle fibres and polymerise.
Microfilaments
They are made up of 2 intertwined strands of globular proteins, called Actin. They act as a track for transport for vesicles and organelles. They also make up spindle fibres and polymerise. Fibres that can contract, made of actin and are responsible for cytokinesis.
Intermediate fibres
Gives strength
They are made up of long fibres or polymers and subunits.
how can you calibrate an eyepiece graticule
For each magnification:
find 2 lines that line up on the stage micrometer and the eyepiece graticule.
Then, the
distance on stage micrometer/ units on the eyepiece graticule
gives you what distance each eyepiece unit is worth.
What is a stage micrometer
It is just a slide that you put in to measure the sample size. Usually, it is 1mm long. This means it is 1000 micrometers, and therefore as there are 100 divisions on it,each division is worth 10 micrometers.
