Final Exam Part 1 Flashcards
What is cell biology
Cell biology is the study of the structure and function of the cell, which is the basic unit of life. structures and organelles chemical composition life cycle interactions
How did people first discover that organisms were made of cells?
- Nobody knew until microscopes were invented.
- 1600s - when people first started to see cells. Robert Cooke – coined the term cells.
- Looked at a piece of cork sliced into thin slices. He saw thin shapes – slices through cork show the patterns of the cell walls of dead cells.
- Piece of dead material. When he named cells he was comparing to honeycomb – physical similarities in structure.
- Next step in recognising cells are alive – van Leeuwenhoek – a business man. Got into the lens making business – good at it – 275x magnification.
- He looked at scraping off tooth tartar – bacteria etc. he saw little things moving around. He called these animalcules.
- The connection between these tiny animals cells and the cells dead that Cooke had seen wasn’t made until 150 years later.
- The ideas that cells make up everything came from Schwann and Schleiden. Studying animal and plant cells.
- Published a paper – microscopic investigations of the similarities, structures and development of animals and plants. First idea that the units that make up animals and plants are the same and then this was extended to all life.
- They came up with the cell theory.
Three basic tenants of cell theory
- All organisms are composed one or more cells. Single celled organisms and lots of cells stacked together to make one large cell.
- Cells are the smallest living units of all living organisms. The cell is considered alive and reproduce on its own. The structures within the cell, if take out of the cell, would die - they depend on the cell.
- Cells don’t spontaneously arise. They come about from divisions of previous cells. Idea coined by Raspial.
Important parameters of light microscopy
- Magnification
Resolution – if you have two points how big do they need to be to distinguish them as two separate points.
The higher your magnification, the better the resolution but only to a certain point. Just because we make something bigger doesn’t mean we can see everything – limited resolution.
Contrast – important that the features stand out against the background. Doesn’t matter how good resolution and magnification are if the features don’t stand out you won’t be able to see them.
People use stains to get around this. Can stain the nuclei, proteins, membranes. Might need to permeabilise the cells, the cells might need to be dead to get the stain in - can be a limitation.
Looking at live cells – innovations that allow us to see cells without needing to use stains. These use different properties of light. The cell is composed of a jelly like substance like water – but more jelly like than a liquid. More viscous.
Light can interact with the cell differently than it interacts with the water – diffracts differently. So it means you can start to see the edges of the cell a bit nicer.
Fluorsence microscopy
Specific kind of light microscopy.
Uses florescence stain – a stain that you excite with a specific wavelength of light and it will emit a specific wave length of light. You can look at just that wavelength and take away the background from your cells.
You can stain the different parts of the cell different colours. The stains may need to be absorbed by the cell – might be a live or dead cell. In some cases they might be florescent proteins that are inside the cell. In that case you can look at live cells.
Light microscopy – resolution is limited by the size of the wavelength of light. The wavelength of light is 0.2 mincrons. If you want to look at features samaller than that, because light is bigger than those features it wont be able to tell you anything.
Super-resolution florescence microscopy is a new innovation that allows a better resolution to look at smaller things. One trick is to have two objects close to each other and have a fluorescent dye on both of them. If the dye is visible at the same time, you wont see them as two different particles – but the dyes are flashing dyes so you can have one dye on at one time and with a computer you can look at that light beam and find the centre of the light beam and take a picture. Then you rake a picture of the other molecule when that light beam is flashing. Then on the computer you can reconstruct where the particles are relative to each other.
Electron microscopy
If we want to look at organelles, protein structures or small bacteria you can use electron microscopy.
Electrons are particles – electrons can also be considered to be a wave – so they have a wavelength and the wavelength is much smaller than the wavelength of light if we use electrons in our sample instead of light beams we can resolve much smaller features. The electron microscope looks very similar to a light microscope – shine an electron beam on your sample, in some places it will get absorbed, that will appear dark in your image, and in some places it will pass through which will appear light in your image.
Scanning electron microscopy (SEM)
SEM – used to look at at surfaces – electrons are bounced off a surface. The image is reconstructed where those electrons came from.
Study surfaces of objects by measuring the scattered electrons.
Scattered electrons – electrons are bounced off a surface and then measured. Samples need to be coated with a conductive material. Usually using gold to coat the samples so the samples are usually dead.
Transmission electron microscopy (TEM)
TEM – to look inside things. The electron beam passes through the sample and we see where its absorbed more or less.
For looking into a sample. For whole cells we need to slice them thin so that light can pass through.
Centriole – part of where microtubules grow from.
Viruses – too small so have to use an electron microscope image.
Sliced and prepared in various ways – measured in a vacuum – so the cells are also dead.
Cyro transmission electron microscopy (cyro-EM)
Looking at small things – beyond cells. People want to look at protein structures (really small) but under a microscope – the conditions, all the atoms are very dynamic – the bonds are moving, and stretching so the image will be blurred out because everything is moving all the time. So the samples are frozen at really low temperatures. Which means tou can take images of proteins and reconstruct the structures.
The three domains of life
- Eukarya – plants, animals, fungi.
- Bacteria
- Archaea – are different from bacteria – also single celled but they are fundamentally very different.
Archaea
Associated with being organisms that survive in extreme environments. Hot springs, salt lakes, underwater sea vents. Extremophiles.
Which domains of life are more closely related?
Eukarya and archae are more closely related to eachother than they are to bacteria.
Differences between eukaryotic cells and prokayotic cells
- Prokaryotes – cells that lack a nucleus.
- Eukaryotes – contain a nucleus.
- Nucleus is where the DNA is contained.
- Prokayptes have DNA but its not isolated within a membrane bound organelle.
- Prokaryotes
- lack a nuclues
- circular chromosomes
- no organelles
- smaller
- not multicellular
- Eukaryotes
- Have a nucleus
- Linear chromosomes
- Organelles
- Larger
- Can be multicellular
Prokaryotes and eukaryotes - multicellular or unicellular?
bacteria and archaea
animals, fungi, plants, protists.
- Prokaryotes
- bacteria - unicellular
- archaea - unicellular
- Eukaryotes
- animals - multicellular
- fungi - multi or unicellular
- plants - multicellular
- protists - mostly unicellular.
Structure and things in a eukaryotic cell.
Draw it!
- Ribosomes – translation. Ribosomes are found in the cytoplasm and in the endoplasmic reticulum which is joined onto the nucleus.
- ER – sorts and produces proteins.
- Mitochondria – produces ATP.
- Golgi apparatus – also involved in sorting or proteins.
- Plastids – chloroplasts – in a plant cell. Chloroplasts do photosynthesis.
- Lysozomes – found in animal cells – breaking down stuff in the cell – proteins, lipids carbs, recycle them to make new stuff.
- Cell wall – animals don’t have a cell wall.
- Vacuoles – plants in fungi. Vacuole and lysozyme are similar.
- Membrane proteins
- Cytoskeleton – filaments that help to shape the cell into its correct shape. Found in all eukaryotes.
Structure and things in a prokaryotic cell.
Draw it!
- Circular chromosomes.
- Ribosomes
- Mitochondria
- Plasmids
- Cell wall
- Flagella
Viruses
- Viruses are not cells.
- very small
- packages of DNA or RNA surrounded by a protein coat.
- they lack a membrane and are not cells.
- they “live a borrowed life” - requrire cells to replicate
- generally not considered living organisms.
Compartments in the animal cell
- Nucleus - where the cell stores its DNA
- Plasma membrane - the cell’s external membrane
- ribosome - where proteins is synthesised
- endoplasmic reticulum - first organelle in the secretary pathway
- golgi apparatus - second organelle in the secretary pathway
- mitochondria - cellular power plant
- cytoskeleton - cells internal scafolding
- peroxisome
Plant cell compartments
- mostly everthing that the animal cell has plus:
- cell wall - to provide rigidity
- vacuole - storage and maintenance of call shape.
- chloroplasts for photosynthesis.
Prokayotic cell compartments
- Membrane
- Cell wall
- Dna inside – not in a membrane bound organelle.
- Ribosomes
- Cytoplasm
- Everything that occurs in the cell, happens in the cytoplasm
- Flagella. – for movement
- Pilli/cilia – for movement
- Lack a nucleus and membrane cound organelles.
Genome sizes
Smallest genome withn the vertebrates – hummingbirds. Flying creatures – tend to have smaller genomes because if you need to fly quickly – evolutionary the organisms have got rid of everything that’s not 100% essential. Got rid of the genes that are not 100% needed.
Compared to a kiwi – which doesn’t fly, no need to save on weight. It’s the bird with the largest genome of 1.7 billion base pairs. Can afford to have a larger amount of base pairs.
How do we get 2m of human DNA into a cell?
- by supercoiling
- Supercoiling – a coil that’s coiled again and again.
- chromosomal packing of succesive rounds of coiling and looping.
Supercoiling process
- DNA – some proteins called histones package the dna. They form complexes by 8 of them grouping together to form a ‘bead’ and the dna wraps around the histone ‘nugget’ proteins twice. Then the beads coil around each other ot get into a more compact form – the beads are called the nucleosomes.
- The coils of coils then form a 30 nanometre wide fibre which get looped into big loopy structures compacting them into a three hundred nanometre wide fibre and then one final round of looping makes a compact chromosome. A chromosome is the most compact form of DNA we can have in a cell.
- Our chromosome is made up of about 50% protein. This material made up of protein and DNA wrapped around each other is called chromatin. The complex of DNA and protein together – chromatin. The condensed form of chromatin only exists during cell division.
- We need to be able to access the DNA for life processes. Regions of the DNA are compact and other regions are more loose. When the cell is about to divide it will go into a more compact form because it wants to separate its chromosomes into two pieces and it doesn’t want them to be tangled up.
- The histone proteins that make up the proteins that the DNA is wrapped around help to compact the DNA but also play a role in controlling which sections of the DNA can be open, read and transcribed. the tails on the histones are where the histones get modified – other proteins will recognise the tails and bind onto them and then force that bit of the DNA open.
The nuclear envelope
- The nuclues is an organelle surrounded by a lipid membrane called the nuclear envelope.
- The nuclear envelope is a double membrane.
- The lipids in the membrane have a head group and tails. The head groups are hydrophilic heads – charged so they like to interact with water. The tails of the lipids in the bilayer are hydrophobic – don’t like water. The tails line up with each other.
- The nucleus has two rows of membranes. 4 layers of lipids surrounding the nucleus. Two lipid bilayers. Called a double membrane. Also sometimes called the nuclear envelope.
