Title: InkBiology / Cells, microscopy and biological organisation
On every note of this deck, unless a note says otherwise:
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Front: DEFINE
Define: Lysosome.
Back: A vesicle containing hydrolytic enzymes, bounded by a single membrane, which digests worn-out organelles and engulfed material.

Front: DEFINE
Define: Organ system.
Back: A group of organs working together to perform an overall life function.

Front: DEFINE
Define: Crista.
Back: A fold of the inner mitochondrial membrane, giving a large surface area for the electron transport chain.

Front: DEFINE
Define: Specialised cell.
Back: A cell whose structure is adapted to one particular function.

Front: DEFINE
Define: Capsule.
Back: A layer of slime outside the cell wall which retains water, aids attachment and gives some protection from phagocytosis.

Front: DEFINE
Define: Reverse transcriptase.
Back: An enzyme carried by retroviruses such as HIV which catalyses the synthesis of DNA from an RNA template.

Front: DEFINE
Define: Differentiation.
Back: The process by which a cell develops the structures and characteristics needed to carry out a particular function, through some genes being expressed and others not.

Front: DEFINE
Define: Pluripotent.
Back: Able to develop into any cell type in the body, but not into the placenta. Found in embryonic stem cells in the blastocyst.

Front: DEFINE
Define: Magnification.
Back: How many times larger the image is than the actual object. A ratio, with no units.

Front: DEFINE
Define: Virus.
Back: An acellular infectious particle consisting of nucleic acid within a protein capsid, sometimes with a lipid envelope, which can only replicate inside a host cell.

Front: DEFINE
Define: Tissue.
Back: A group of similar cells working together to perform a particular function.

Front: DEFINE
Define: Nucleolus.
Back: A dense region within the nucleus where ribosomal RNA is made and ribosomes are assembled.

Front: DEFINE
Define: Ribosome.
Back: A structure of ribosomal RNA and protein, in two subunits, with no membrane, which is the site of translation. 80S in eukaryotic cytoplasm, 70S in prokaryotes and in mitochondria and chloroplasts.

Front: DEFINE
Define: Nuclear envelope.
Back: The double membrane surrounding the nucleus, continuous with the endoplasmic reticulum and perforated by nuclear pores.

Front: DEFINE
Define: Nucleoid.
Back: The region of a prokaryotic cell occupied by its circular DNA, with no surrounding membrane.

Front: SPOT THE ERROR
Say what is wrong with this claim:
A neurone kept the nerve genes and lost the rest, and that is how it differs from a red blood cell.
Back: Nothing is discarded. Almost every nucleated cell holds a complete genome, so a cell in your retina carries the insulin gene and never uses it. What differs between cell types is which genes are transcribed.

Front: DEFINE
Define: Stage micrometer.
Back: A slide bearing a scale of known length, used to calibrate an eyepiece graticule for one particular objective lens.

Front: DEFINE
Define: Eyepiece graticule.
Back: A ruled scale in the eyepiece whose divisions have no fixed length until it is calibrated.

Front: DEFINE
Define: Rough endoplasmic reticulum.
Back: Flattened membrane sacs with ribosomes attached, which make and transport proteins for export or for membranes.

Front: DEFINE
Define: Totipotent.
Back: Able to develop into any cell type in the organism and into the extra-embryonic tissues such as the placenta. Found in the zygote and the cells of the first few divisions.

Front: CHECK YOURSELF
A patient is treated with an antibiotic for a bacterial chest infection and recovers. Two months later she has influenza, and asks for the same antibiotic. Explain, in terms of cell structure, why it will not help her, and why some bacterial infections no longer respond to it either.
Back: An antibiotic works by attacking a structure or process that bacteria have and human cells do not. Many, penicillin among them, prevent the cross-linking of murein in the bacterial cell wall, so a dividing cell builds a wall too weak to resist the water entering by osmosis and bursts. Others bind to the 70S ribosome and block translation, leaving the 80S ribosomes in her cytoplasm alone. That second selectivity is real but not perfect, because her mitochondria carry ribosomes of prokaryotic ancestry, remodelled but still similar enough for some of these drugs to touch, which is one reason drugs of this class can have side effects the wall-builders do not.
Influenza is a virus. It has no cell wall to weaken, no ribosomes to block and no metabolism to interfere with. It is acellular, and its proteins are made on the ribosomes of her own infected cells. There is nothing there for the drug to act on, so it can do nothing but disturb the useful bacteria she already has.
Resistance in bacteria is a separate matter and comes largely from plasmids. A mutation producing an enzyme that breaks the antibiotic down gives its carrier a selective advantage whenever the drug is present, and because such genes often sit on plasmids they can be passed directly between bacteria rather than only to daughter cells.
That is why a resistant strain can appear in a population within months, and why prescribing an antibiotic for a viral infection makes the problem worse without treating anything.

Front: DEFINE
Define: Prokaryotic cell.
Back: A cell with no nucleus and no membrane-bound organelles, whose DNA is a single circular molecule free in the cytoplasm.

Front: DEFINE
Define: Plasmid.
Back: A small circular molecule of DNA, separate from the main chromosome, which replicates independently and often carries genes such as antibiotic resistance.

Front: DEFINE
Define: Capsid.
Back: The protein coat surrounding a virus's genetic material.

Front: SPOT THE ERROR
Say what is wrong with this claim:
Bacteria are simple cells and viruses are just very small bacteria.
Back: A virus is not a small bacterium. It has no cytoplasm, no ribosomes, no membrane of its own and no metabolism: it cannot make a protein, respire or divide. That is why antibiotics work on bacteria and do nothing whatever to viruses.

Front: SPOT THE ERROR
Say what is wrong with this claim:
A microscope that magnifies more shows you more.
Back: Magnification is how much bigger; resolution is how much detail there is to enlarge. A light microscope cannot separate two points closer than about 0.2 µm, so enlarging past that gives a bigger blur and nothing new.

Front: DEFINE
Define: Attachment protein.
Back: A protein on a virus's surface with a shape complementary to a receptor on its host cell, which determines which cells it can infect.

Front: DEFINE
Define: Resolution.
Back: The minimum distance between two points at which they can still be distinguished as separate. A length, and smaller is better.

Front: DEFINE
Define: Smooth endoplasmic reticulum.
Back: Membrane sacs without ribosomes, which synthesise lipids and steroids and store calcium ions.

Front: DEFINE
Define: Organelle.
Back: A structure inside a cell with a distinct function, usually but not always surrounded by its own membrane.

Front: DEFINE
Define: Organ.
Back: A structure made of several different tissues working together to perform a particular function.

Front: CHECK YOURSELF
A cell taken from the pancreas secretes digestive enzymes. Describe the path taken by one of those enzyme molecules from the gene that codes for it to the moment it leaves the cell, naming every organelle involved and saying what each contributes.
Back: The gene is transcribed in the nucleus. Messenger RNA is made against the DNA template and, once processed, is exported through a nuclear pore, whose machinery passes mRNA out while the chromosomes stay put.
In the cytoplasm the mRNA binds to a ribosome attached to the rough endoplasmic reticulum. Translation assembles the polypeptide, and the chain is fed into the cisterna as it grows, so the enzyme is inside the membrane system from the moment it exists.
A transport vesicle pinches off the rough ER and carries the enzyme to the Golgi apparatus, where it is modified, commonly by having sugar groups added, then sorted and packaged. It folded in the ER as it was made, so what the Golgi does is finish it and address it, not shape it.
A secretory vesicle buds from the other face of the Golgi and moves to the cell-surface membrane, where the two membranes fuse and the enzyme is released outside. That last step is exocytosis, and it needs ATP, which is why a secretory cell like this one is also rich in mitochondria.

Front: DEFINE
Define: Multipotent.
Back: Able to develop into a limited range of cell types. Found in adult stem cells, such as those in bone marrow which produce the blood cells.

Front: DEFINE
Define: Artefact.
Back: A structure seen in a prepared specimen that was not present in the living cell, produced by the preparation or imaging process.

Front: DEFINE
Define: Ultrastructure.
Back: The detail of a cell's internal structure as revealed by an electron microscope.

Front: CHECK YOURSELF
Cells lining the trachea and cells lining the alveoli both come from the same fertilised egg and carry the same DNA, yet one is a tall cell covered in cilia and the other is so flat it is barely visible in section. Explain how this difference arises and why each shape suits where the cell is.
Back: Both cells hold a complete copy of the genome. The difference comes from gene expression: in each cell only the genes needed for that cell type are transcribed, and the rest stay switched off. Which genes those are was determined during development by the signals each cell received, including its position in the growing airway, and the pattern is then inherited by its daughter cells.
The ciliated cell in the trachea has expressed the genes for the proteins that build cilia and for the mitochondria that power them. Its job is to keep the airway clean: goblet cells among the epithelium secrete mucus that traps dust and bacteria, and the coordinated beating of the cilia sweeps that mucus up to the throat, away from the lungs.
The squamous cell in the alveolus has done the opposite and become as thin as a cell can be. Its job is to be got through. Oxygen and carbon dioxide diffuse across the alveolar wall, and rate of diffusion falls as the distance rises, so a wall one flattened cell thick keeps the path as short as possible.
Neither cell could do the other's job, and neither can change into the other, because differentiation is very hard to reverse once the pattern of expression is fixed.

Front: SPOT THE ERROR
Say what is wrong with this claim:
A cell is a bag of jelly with organelles floating loose in it, each one a separate gadget doing its own job.
Back: They are not separate gadgets. The nuclear envelope runs straight on into the endoplasmic reticulum, and a protein bound for export passes from rough ER to Golgi to vesicle to the surface without crossing a membrane. Each shape is built for its job, and the pairing is what earns marks.

Front: DEFINE
Define: Empty magnification.
Back: Enlarging an image beyond the detail its resolution contains, so nothing further becomes visible.

Front: CHECK YOURSELF
A student photographs a cell through a light microscope, then enlarges the photograph on a computer until the whole image is a metre wide. She says she has now magnified the cell about ×20 000, so she should be able to see its ribosomes. Explain why she will not.
Back: Her arithmetic is fine and her conclusion is wrong, because magnification and resolution are different quantities and only one of them has changed.
Enlarging the photograph raises the magnification but cannot add detail that the original image never contained. The detail was fixed at the moment the light microscope formed the image.
That limit comes from the wavelength of visible light, roughly 400 to 700 nm. Two points closer than about 0.2 µm cannot be resolved, so they merge into one. A ribosome is around 25 nm across, some eight times smaller than the limit, so it was never separately recorded.
All the enlargement does is make the same blur bigger, which is what empty magnification means. To see ribosomes she needs a shorter wavelength, and that means an electron microscope.

Front: DEFINE
Define: Cytoplasm.
Back: Everything inside the cell-surface membrane except the nucleus: the cytosol and the organelles suspended in it.