Week 1 Flashcards
What is an example of an archaea extremophile?
Thiomargarita namibiensis- in oceans but not harmful, it is almost a cm
What are some adaptations of Archaea ?
-proteins fold differently to avoid denaturation at high temperatures
- thermostable enzymes
What biotechnical applications use extremophiles ?
-polymerase chain reaction
-biofuels
-biomining
-carotenoid production
-detergents
What thermophile produces taq polymerase for pcr?
Thermus aquaticus
Do archaea have peptidoglycan in their cell walls?
No
What are the components of a prokaryotic cell?
-pili
-nucleoid
- ribosomes
-plasma membrane
-cell wall
-capsule
-flagella
What are the most common bacterial shapes?
-cocci ( spherical )
-bacilli ( rod shaped )
-spirochetes ( helical )
What is the function of bacterial pili?
-help bacteria stick to their substrate or to each other
How does a flagellum allow for movement?
Oxidises ATP by pumping H+ outside of the cell, generating a gradient, diffusion of teh H+ back into the cell wall, turns hook causing filament to turn and propel
How do pili help with antibiotic resistance?
- pili allow bacteria to stick together and conjugate , sharing genetic material
Is it gram - or + which has Teichoic acids? Which - or + is antibiotic resistance?
Positive
Gram negative - antibiotics cannot target the peptidoglycan wall
What are the bacteria ( + ) that are responsible for tetanus , botulism, pneumonia?
-clostridium tetani
-clostridium botulinum
- streptococcus pneumoniae
What - bacteria cause infectious blindness, cholera, plague ?
Chlamydia trachomatis
Vibrio cholerae
Yersinia pestis
What are the medical advantages of bacteria?
Large production of proteins
Drug screening tests and diagnostics
What are the agricultural advantages of bacteria ?
Introduction of a new gene in plant chromosome
Example - purple tomatoes have high anthocyanin
Environmental advantages of bacteria?
Bioremediation – removes pollutants, industrial by-products, oil spills
Industrial advantages of bacteria?
Lactic bacteria develop the flavour and colour of foodstuff
Improve the storage longevity of wines
What are autotrophs ? Heterotrophs ?
AUTOTROPHS: Producers – make their own food – plants, algae, bacteria
HETEROTROPHS: Consumers – consume producers/consumers – mammals
What are some examples of why we use microscopy in research ?
Cell culture
Colocalisation of proteins
Host-pathogen interactions
Abundance of proteins after stimulation
Proliferation or cell death markers
Frequency of cell types in a sample
What cells does the SARS Cov2 virus affect?
SARS cov 2 infection induces the dedifferentiation of multiciliated cells and impairs mucociliary clearance
Who was the father of microscopy ?
Robert Hooke
When was the electron microscope developed?
1930s
What is the resolution of electron and light microscopes?
0.2 micrometer limit of light
0.08 nm resolution limit of electrons
What are 2 key differences between Dissecting and Compound brightfield light microscopes ?
-dissecting : surface features , 70x magnification
-compound brightfield , in depth features , 400-1000x magnification
What are the stages of light microscope sample preparation?
-whole mounts
-tissue sections
-dehydration and clearing
-embedding
-sectioning
-staining
What does advanced light microscopy allow the observation of ? What generates the contrast?
Transparent living cells
Light phase shifts induced by specimen
What does confocal microscopy use?
Lasers and special optics for ‘optical sectioning’
Only regions within a narrow depth of focus are imaged
What microscopy techniques remove the resolution limit, to allow an even higher resolution for images?
-deconvolution microscopy —- algorithms remove out of focus light and this sharpens the image and improves resolution
-super resolution gathers light from individual fluorescent molecules and records their position. Combining information from these individual molecules breaks the resolution limit
How does a TEM work ?
Electron gun: usually a heated tungsten filament which produces electrons by thermionic emission
Electron beam passes through the specimen
The image is focused and magnified by magnetic objective and projector lenses
The electron image is converted into a visible image by a fluorescent screen, which is viewed through a glass window.
Photographs can be taken using a digital camera
The whole inside of the microscope is kept at a high vacuum during operation
How is a TEM sample produced?
Whole mounts: Bacteria and viruses can be examined directly
Tissue sections
Fixation: Usually in Glutaraldehyde (protein crosslinking) followed by a second fixation step in Osmium Tetroxide (lipid crosslinking)
Dehydration: In an ethanol series
Embedding: Specimens for TEM are embedded in plastic resins such as Epoxy resins.
Sectioning: 50nm thick sections are cut using a ultramicrotome.
Staining: Biological tissue has little contrast under the electron beam, so heavy metal stains such as lead are used to improve contrast
How is a SEM sample made?
Biological samples must be fixed and dried before being examined in the SEM under vacuum
Fixation: The same fixatives are used as with TEM preparation
Dehydration: The water is replaced with Ethanol
Critical Point Drying: This technique allows all the ethanol to be removed from the sample in a way that minimises shrinkage
“if a defined amount of gas at a given temperature is subjected to increasing pressure, its volume will become increasingly compressed”
https://caic.bio.cam.ac.uk/electron-microscopy/SpecimenPrep/CPD
Coating Specimens are coated with a thin layer of gold to protect them from electron beam damage
What are the uses for cell fractionation ?
Protein Enrichment
Enrich target proteins and improve detection of low abundance protein
Protein Characterization
Identify the subcellular localization of a protein
Protein Translocation
Monitor translocation of cell signalling molecules from the cytoplasm to the nucleus
What is phase contrast microscopy ?
Enhances contrast in unstained cells by amplifying variations in density within specimen, useful for unpigmented cells
How does fluorescent microscopy work ?
Fluorescent substances absorb short wavelength radiation, UV and emit longer wavelength radiation, visible light. Often the fluorescence is added by tagging with fluorescent molecules.
What do plant cells have that animal cells don’t?
-chloroplasts
-central vacuole and tonoplast
-cell wall
-plasmodesmata
What do plant cells not have that animal cells do?
-lysosomes
Centrioles
Flagella
What is the function of plasmodesmata ?
Perforations in the cell membrane allowing for diffusion of moelcules
What 2 bacterial types are thought to have been incorporated into cells in the endosymbiotic theory ?
Aerobic bacterium - mitochondria
Cyanobacterium - chloroplast
What is the difference between the Davison-Danielli and Fluid mosaic model Singer Nicholson model ?
Fluid mosaic has proteins nestled into membrane amongst phospholipid , whereas Davison-Danielli , there was 2 protein layers, above and below phospholipid bilayer
What are glycolipids mainly used for ?
Cellular recognition / identification
what is Glycocalyx in the membrane useful for ?
Identifying self and foreign cells , different in everyone
What are flipase and flopase used for?
Enables opposite phospholipids to flip-flop , which is rare but requires enzymes
What is the effect of cholesterol at high and low temperatures?
High - dec distance between PLs , dec fluidity
Low- inc distance between PLs, inc fluidity
How do we carry out freeze-fracture electron microscopy ?
Fixation and preservation with glycerol
Rapid Freezing – liquid nitrogen
Fracturing – under pressure using a liquid nitrogen cooled microtome
Replication
Replica cleaning
What are the functions of membrane proteins?
Transport
Enzymatic activity
Signal transduction
Intercellular joining
Cell-cell recognition
Attachment to the cytoskeleton and extracellular matrix
What is cystic fibrosis caused by ? Recessive or dominant ? Causes what ?
Defective chloride channel
Autosomal recessive
Viscous mucus , individual prone to infections
What co-receptor does HIV need to infect a cell? Individuals that lack this are what?
CCR5
Resistant to HIV
What are the 4 types of tissue?
Connective
Epithelial
Muscle
Nervous
What are most epithelial cells fastened together?
Where are they ?
What do they protect against ?
2 types ?
Desmosome junctions
Covers outside of body , lines organs and cavities
Mechanical injury , microbes , fluid loss
Simple ( one layer ) , stratified ( several layers )
What are the types of epithelial cells?
Cuboidal epithelial
Simple columnar
Simple squamous
Pseudostratified columnar epithelium
Stratified squamous epithelium
What is dense connective tissue made from ?
Extarcelluklar matrix with few cells e.g bone tendon , ligaments . Fibrous proteins ( collagen and elastin ) , ground substance usually proteoglycans
What does loose connective tissue connect, and what does it include ?
Glands and epithelia , basal lamina
What is the basic structural unit of collagen ?
Triple helix
What are the 3 vertebrate muscle types ?
Skeletal , smooth , cardiac
What cells nourish , insulate and replenish neurons ?
Glial cells / glia
What direction do dendrites conduct the impulse ?
Towards the nerve body
What are some shared characteristics between Archaea and bacteria ?
Both lack a nuclear envelope
Both lack membrane organelles
Both have a circular chromosome
What are some shared characteristics between Eukarya and Archaea ?
Both lack peptidoglycan in their cell walls
Both have several kinds of RNA polymerase
Both have methionine as their initiator amino acid for protein synthesis
Both have histones (some archaea not all )
Give an example of a filamentous virus
Tobacco mosaic virus
What 4 groups are viruses broken into structurally ?
Filamentous
Spheroid viruses
Enveloped viruses
Tailed spheroid virus
What is an example of a spheroid virus, an enveloped virus and a tailed spheroid virus ?
Spheroid - adenoviruses which cause viruses such as gastroenteritis and keratoconjunctivitis
Enveloped - lipid enveloped viruses such as influenza and coronaviruses
Tailed spheroid viruses - e.g lambda phage
Who invented gram staining ?
Hans Christian Gram
what residues of lysosome enzyme proteins are phosphorylated in the cis Golgi?
Mannose residues
What is the order of electron carrier proteins in the electron transport chain ?
Flavoprotein
Iron-sulphur protein
Ubiquinone
Cytochromes ( 4 organic rings surrounded by an iron atom like Hb)
