Week 1 Flashcards
What is an example of an archaea extremophile?
Thiomargarita namibienisis - found in the ocean, unharmful
What archaea are adapted to high temperature?
Thermophile
Membrane is adapted to remain fluid at increased temperature,
Enzyme structure adaptation to prevent denaturing,
Proteins fold different to withstand extreme temperatures
What biotechnical application can extremophiles be used for?
- PCR
- Biofuels
- Biomining
- Carotenoid production (uses halophiles)
- Detergents
What thermophile can be used during polymerase chain reaction?
Thermus aquaticus
(Used as a heat resistant enzyme, Taq DNA polymerase)
Components of prokaryotic cells?
Pili
Nucleoid
Ribosomes
Plasma Membrane
Cell Wall
Capsule
Flagella
Cytoplasm
(Classified by shape)
Prokaryotic cell components: Nucleoid
Contains circular DNA, no nuclear membrane
What are the most common shape of bacteria?
Cocci
Bacilli
Spirochetes
Prokaryotic cell components: Plasma membrane
Has the same basic structure of all biological membranes
Some prokaryotes have infoldings of the plasma membrane which contain specialised enzymes that perform specific functions (eg cyanobacteria have thylakoids)
How does the flagella allow for movement?
Movement by a rotatory motor
Oxidises ATP by pumping H+ out of the cell, generating a gradient, diffusion of these H+ back into the cell, turs the Hook which causes filament to turn and propel
What are autotrophs
(Modes of nutrition)
Producers - make own food - pants, algae, bacteria
What are heterotrophs?
Modes of nutrition)
Consumers - consume producers/consumers - mammals
What is photo?
Modes of nutrition)
Use light
What is chemo?
Modes of nutrition)
Use molecules/compounds
What are Eukaryotes: modes of nutrition?
Photoautotrophs and chemoheterotrophs
What are prokaryotes: mode of nutrition?
Chemoautotrophs, chemoheterotrophs, photoautotrophs and photoheterotrophs
Examples of extremophiles, adapted to pH
Hyperacidophile
Acidophile
Neutrophile
Alkaliphile
Hyperalkaliphile
Examples of extremophiles, adapted to temperature
Psychrophile
Mesophile
Thermophile
Hyperthermophile
Examples of extremophiles, adapted to salinity (salt)
Non-halophile
Halotolerant
Halophile
Extreme halophile
Examples of extremophiles, adapted to pressure
Barotolerant
Barophile
Hyperbarophile
Examples of extremophiles, adapted to water activity
Xerophile
What is a polyextremophile
An archaea/extremophile with tolerance or preference to multiple parameters combined
Prokaryotic cell components: Cytoplasm
Contains ribosomes and little else
Prokaryotic cell components: Flagella
Some prokaryotes have flagella which is composed of the protein flagellin
Prokaryotic cell components: Pili
Composed of the protein Pilin and help bacterial stick to their substrate or to each other.
They extend to attach onto other bacteria and stick together bacteria and conjugate, sharing genetic material
Prokaryotic cell components: Capsule
Many bacteria have this, and is usually composed of polysaccharides
What is the function of the prokaryotic cell wall?
Protects cell against mechanical and osmotic shocks
Composed of the molecule peptidoglycan
Can be divided up into two types: Gram+ and Gram-
Features of gram+ cell wall?
Peptidoglycan = thick (20-80nm)
Cell wall structure = Simple, single layer
Teichoic acids = present
Lipopolysaccharide = Absent
Gram stain = Purple
Antibiotic resistance = susceptible
Features of a gram- cell wall?
Peptidoglycan = thin (<10nm)
Cell wall structure = Complex, double layer
Teichoic acids = absent
Lipopolysaccharide = present
Gram stain = Pink
Antibiotic resistance = resistant
Example of gram+ bacteria?
Clostridium tetani (tetanus)
Clostridium botulinum (botulism)
Streptococcus pneumoniae (pnumonia)
Example of gram- bacteria
Chlamydia trachomatis (common cause of infectious blindness)
Vibro cholerae (cholera)
Yersinia pestis (plague - ‘black death’)
Medical Advantage of Bacteria in biotechnology
Bacteria can be used to produce large quantities of proteins cheaply for therapeutic use, eg insulin
Drug screening tests and diagnotics
Agricultural Advantage of Bacteria in biotechnology
Introduction of a new gene in plant chromosome
Eg purple tomatoes have high anthocyanin
Environmental Advantage of Bacteria in biotechnology
Bioremediation - removes pollutants, industrial by-products, oil spills
Industrial Advantage of Bacteria in biotechnology
Lactic bacteria develop the flavour and colour of foodstuff
Improve the storage longevity of wines
Photoautotroph major nutritional modes
Energy source: Light
Carbon source: CO2, HCO3- or related compound
Types of organisms: Photosynthetic prokaryotes (eg cyanobacteria, plants, certain protists)
Chemoautotroph major nutritional modes
Energy source: Inorganic chemicals (eg H2S, NH3 or Fe2+)
Carbon source: CO2, HCO3- or related compound
Types of organisms: Unique to certain prokaryotes (eg Sulfolobus)
Photoheterotroph major nutritional mode
Energy source: Light
Carbon source: organic compounds
Types of organisms: unique to certain aquatic and halophile prokaryotes (eg Rhodobacter, Chloroflexus)
Chemoheterotroph major nutritional modes
Energy source: Organic compounds
Carbon source: Organic compounds
Types of organisms: many prokaryotes (eg Clostridium) and protists; fungi; animals; some plants
Features of a filamentous virus?
Nucleic acid is arranged in a helix, with the protein sub-units surrounding and stabilizing it.
Eg Tobacco mosaic virus
Features of a Spheroid virus?
Nucleic acid is considered inside a protein envelope which is usually organised into a multisided geometric shape
Eg adenovirus - different types cause illness ranging from Gastroenteritis to Keratoconjunctivitis
Features of an enveloped virus?
Have lipid envelopes
Including influenza and coronavirus
Features of a Tailed spheroid virus?
Basically a spheroid virus with a tail
eg the lambda phage
When was the light microscope invented?
17th century, allowing individual cells to be visualised
when was the electron microscope developed?
20th century, allowing cell organelles and molecules to be visualised and studies
What cells does the SARS CoV2 virus affect?
Induces the dedifferentiation of multiciliated cells and impairs mucociliary clearance
Who is the father of microscopy
Robert Hooke
1665 Robert Hooke published what?
A collection of essays under the title Micrographica.
One gave detailed description of a section of cork, in which Hooke described seeing honeycomb of chambers - called cells.
1675 Dutchman Anton Van Leewenhoekk improved what?
Art of polishing lenses.
His best microscopes were able to resolve to about 1.5 microns - he was able to report what he described as a host of little animals in a drop of rain water, (protozoa) and was later on described the existence of bacteria
What happened in the 19th century? (microscopy)
Maximum theoretical resolution of the light microscope was attained (about 0.25 microns)
In 1930s, electron microscope was developed allowing cell organelles to be seen. Ultrastructure was coined to describe the level of detail obtainable with the EM.
Define magnification
The ratio of an object’s image size to its real size
Define resolution
The measure of the minimum distance of two distinguishable points
(the closest two points can be, and still be resolved as being separate.)
Define contract in terms of microscopy
Visible differences in brightness or colour between parts of the sample
What are the types of light microscopes?
Dissecting (view surface features, 70x mag)
Compound brightfield (View indepth features, 400-1000x mag) (most common)
Others include: florescent, phase/differential contrast and confocal microscopes
Features of the light microscope? (top to bottom)
Ocular lens (eyepeice)
Focal plane of objective lens
Reflective prism
Objective lenses
Specimen on stage
Condenser lenses
Base with light source
Lamp field stop
What is the major advantage and disadvantage of the light microscope?
+ = Ability to image living things
- = Limited resolution eg best resolution is 0.2 microns. (Only way to improve this, is to use a shorter wavelength of radiation)
Whole mounts?
(Light microscope sample prep)
Small relatively transparent specimens mounted directly onto slides
Tissue sections?
(Light microscope sample prep)
most tissues need to be sectioned before they can be examined
Fixation?
(Light microscope sample prep)
Involves using chemical fixatives to prevent cell autolysis and preserve structure of the tissue
Dehydration and clearing?
(Light microscope sample prep)
Removes water from tissue in prep for wax impregnation
Embedding?
(Light microscope sample prep)
Specimen is infiltrated with molten wax, after transferred to a mould
Sectioning?
(Light microscope sample prep)
Thin sections approx 5 microns thick are cut on a microtome, and collected onto a glass slide
Staining?
(Light microscope sample prep)
Wax removed and the tissues stained with a clolour dye such as Eosin (cytoplasm) or haematoxylin (nuclei)
List the different ways of Light microscope sample preparation?
Whole mounts,
Tissue sections,
Fixation,
Dehydration and clearing,
Embedding,
Sectioning,
Staining
What does advanced light microscopy do?
(Phase-contrast and Differential-interference contrast microscopy)
Permits observation of transparent living cells
Light phase shifts induced by specimen are used to generate contract
Phase contrast (refracted and unrefracted light)
Differential interference contract (two light beams)
Brightfield (unstained specimen) light microscopy?
Passes light directly through specimen; unless cell is naturally pigmented or artificially stained, image has little contrast.
Brightfield (stained specimen) light microscopy?
Staining with various dyes enhances contrast, but most staining procedures require that cells be fixed (preserved)
Florescence light microscopy?
Shows locations of specific molecules in the cell.
Florescent substances absorb short-wavelength, ultraviolet radiation and emit longer-wavelength, visible light.
Fluorescing molecules may occur naturally in specimen but more often are made by tagging molecules of interest with florescent molecules
Phase-contrast light microscopy?
Enhances contrast in unstained cells by amplifying variations in density within specimen; especially useful for examining living, unpigmented cells
Differential-interference-contrast (Nomarski) light microscopy?
Like phase-contrast microscopy, it uses optical modifications to exaggerate differences in density
Confocal light microscopy?
Uses lasers and special optics for ‘optical sectioning’. Only regions with narrow depth of focus are imaged.
Regions above and below the selected plane appear black rather than blurry.
Microscope typically used with fluorescently stained specimens.
Example of green fluorescent protein (GFP) discovered by Shimomura et al
Aequorea Victoria (crystal jelly) is a bioluminescent hydrozoan
Light microscopy of three-dimensional objects?
(Confocal scanning microscopy.)
Generates 3D images of living cells,
Removes out-of-focus images = optical sectioning
Can look inside thick specimens (eggs, embryos, tissues)
How does deconvolution microscopy ‘break the resolution limit’
Algorithms remove out of focus light and sharpens the image, improving resolution
How does super resolution ‘break the resolution limit’
Gathers light from individual fluorescent molecules and records their positions.
Combining information from these individual molecules breaks the resolution limit
Features of an electron microscope?
Developed in 1930s,
Short wavelength, so better resolution than light microscope (0.08nm),
Kept under a vacuum and can be focused by magnetic fields
What are the two main types of an electron microscope?
Transmission and Scanning
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
TEM microscope sample preparation process?
Whole mounts
Fixation
Dehydration
Embedding
Sectioning
Staining
Whole mounts: TEM microscope sample preparation process?
Bacteria and viruses can be examined directly
Tissue sections
Fixation: TEM sample prep
Usually in Glutaraldehyde (protein crosslinking) followed by a second fixation step in Osmium Tetroxide (lipid crosslinking)
Dehydration: TEM sample prep?
In an ethanol series
Embedding: TEM sample prep?
Specimens for TEM are embedded in plastic resins such as Epoxy resins.
Sectioning: TEM sample prep?
50nm thick sections are cut using a ultramicrotome.
Staining: TEM sample prep
Biological tissue has little contrast under the electron beam, so heavy metal stains such as lead are used to improve contrast
What does cell fractionation allow?
Major organelles to be individually separated out, so they can be studied in isolation
First stage of cell fractionation?
Cells are homogenised to release the organelles
How does cell fractionation work?
Differential centrifugation is used to isolate cell components on the basis of size and density by using increasing durations and g forces
What are the three main 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)
Features of the SEM
So called because the electron beam is scanned across the specimen. Used for looking at the surface of specimens
The top part to the microscope is similar to a TEM
Its called a Scanning Electron Microscope as the electron beam is Scanned across the surface of the specimen.
Electrons are reflected from the surface of the specimen, collected by a electron detector and converted into an electronic signal which is displayed on a screen.
The image on the SEM represents the topology of the sample. The great depth of focus of the SEM gives images a 3-D appearance
How is a SEM sample prepped?
Biological samples must be fixed and dried before being examined in the SEM under vacuum
Fixation (same as TEM)
Dehydration (H2O replaced with ethanol)
Critical Point Drying (Allows all ethanol to be removed from sample in a way that minimises shrinkage)
Coating: Specimens coated with a thin layer of gold to protect them from electron beam damage
True or False
Eukaryotic cells have several specialized organelles including numerous internal membranes together termed the endomembrane system.
True
List the organelles of an animal cell
Rough and smooth ER,
Flagellum,
Peroxisome,
Microvilli
Cytoskeleton (Microfilaments, intermediate filaments, microtubules),
Lysosome,
Mitochondrion,
Plasma membrane,
Golgi apparatus,
Ribosome,
Nucleus (Chromatin, nucleolus, nuclear envelope)
What is the function of the cytoskeleton? (eukaryote)
Gives the cell structure and shape and adapts in response to stimuli so can generate cell movement
What is the function of chromatin? (eukaryote)
Helps DNA bind by the use of histone
Function of the flagellum? (eukaryote)
Help absorption and molecular acquisition, and aids movement within the gut
What is the role of the plant cell wall?
The plant cell wall maintains the cell shape and prevents mechanical damage. This cell wall is composed of cellulose fibres embedded in a protein/polysaccharide matrix consisting mainly of hemicellulose and pectin
What are the components of a plant cell?
Nucleus (Chromatin, Nucleolus, Nuclear envelope),
Centrosome,
Golgi apparatus,
Mitochondrion,
Peroxisome,
Plasma membrane,
Cell wall,
Plasmodesmata,
Chloroplast,
Cytoskeleton (Microfilaments, Intermediate filaments, Microtubules),
Tonoplast,
Central vacuole,
Ribosomes,
Smooth and Rough ER
What is the role of the Peroxisome (eukaryotic cell)?
Lipid metabolism,
Detoxification,
Oxidative reactions
What is the role of the plasmodesmata (plant cell organelle)?
Pores in the cell membrane allowing diffusion of molecules from one cell to another, also aids communication between cells.
Components of the plant cell vacuole?
Cytosol, Tonoplast, Cell wall, Chloroplast.
Usually 10-15 microns wide.
Where is mRNA synthesised in a eukaryote?
inside the nucleus from a DNA template and released into the cytoplasm via the nuclear pores where it controls protein synthesis.
What does the plasma cell membrane control in eukaryotic cells?
Controls the entry of nutrients and the exit of waste products. Maintains the electrolyte balance in the cell. Acts as sensor to external signals
What is the role of the Glycocalyx in the phospholipid bilayer?
Enables self and foreign cell/molecule identification. Controlling what enters and exits the cell!
What are the three major types of lipids in cell membranes?
Phospholipids,
Cholesterol,
Glycolipids
What is the role of filipase and flopase in a bilayer?
Enable opposite phospholipids to flip-flop, which is rare and requires enzymes.
Low vs High temperature on the fluidity of membranes without cholesterol
Low = phospholipids cluster together, Low fluidity
High = Phospholipids more distant, high fluidity
Low vs High temperature on the fluidity of membranes with cholesterol
Low = Increases distance between phospholipids, increases fluidity
High = Decreases distance between phospholipids, decreases fluidity
How often do lipid molecules exchange places with adjacent lipid molecules?
over 1000,000 times a second. Lipid molecules also rotate rapidly about their axis
What does high cholesterol do within phospholipid membranes?
increases membrane stability by interacting with phospholipid molecules.
What are trans membrane proteins?
A polypeptide chain of membrane proteins that often cross the lipid bilayer several times.
They are amphipathic
How are peripheral membrane proteins associated with the bilayer?
by non-covalent linkages and are easily dislodged
How can shape and distribution of membrane proteins be observed?
By using freeze fracture electron microscopy
What is freeze-fracture electron microscopy?
Specialized preparation technique by flash-freezing the samples which splits the membrane along the middle of the phospholipid bilayer
What can be used as evidence for the drifting of membrane proteins?
Mouse cell with membrane proteins + Human cell with membrane proteins –> Hybrid cell after being mixed for one hour.
Demonstrates movement of membrane proteins and how dynamic a membrane can be!
What are receptor sites of a membrane?
the exterior region of a transmembrane protein may act as a receptor for a chemical messenger such as a hormone or growth factor.
What proteins within the bilayer allow the cell to attach to the extracellular matrix?
Integrins (have structural roles)
What is the role of cell junctions in the bilayer?
Tight junctions are present between some cell types. They act to separate the apical and basal membranes which have different functions.
What are 6 functions of membrane proteins?
Transport,
Enzymatic activity,
Signal transduction,
Intercellular joining,
Cell-cell recognition,
Attachment to the cytoskeleton and extra cellular matrix (ECM)
What causes cystic fibrosis?
a defective chloride ion channel (a transmembrane protein).
This is an autosomal recessive disease.
What does cystic fibrosis result in?
The failure of the chloride channel results in a build-up of viscous mucus within the lungs making the individual prone to infections.
It appears to be an ideal disease to treat with gene therapy, but progress has been much slower than expected.
What glycoprotein co-receptor must be present along with CD4 receptor for HIV to infect a cell?
co-receptor CCR5.
HIV cannot enter the cells of resistant individuals that lack normal CCR5 co-receptors.
Name four types of tissue that make up organ systems?
Connective
Epithelial
Muscle
Nervous
What does epithelial tissue consist of?
What cell junctions does it have?
Consists of sheets of tightly packed cells, it covers the outside of the body and lines organs and cavities inside the body.
Fastened together by Desmond one junctions and sealed with tight junctions
For example, the inner surface of the digestive tract and respiratory tract, and the outer surface of the body.
How are epithelial cells fastened together and sealed?
fastened together via desmosome junctions and sealed via tight junctions to withstand stresses and strains.
Role of epithelial tissue within the body?
protects against mechanical injury and also provides a barrier against microbes and fluid loss.
They can be simple (one layer thick) or stratified (several layers thick)
What are the 5 types of epithelial tissue?
- Cuboidal
- Simple columnar
- Pseudostratified columnar (look like something but are something else)
- Simple squamous (usually when quick diffusion of substances are needed)
- Stratified squamous (main purpose is for protection)
What is connective tissue?
Main role of connective tissue is mechanical strength binds and support for other tissues.
It consists of an extracellular matrix through which cells are sparsely scattered.
Can be dense or loose (also blood and adipose)
Dense connective tissue?
Has great mechanical strength and elasticity. Consists of just extracellular matrix with relatively few cells
Eg cartilage bond and tendon.
what is dense connective tissue made of?
- Fibrous proteins (mainly collagen and elastin)
- Ground substance usually proteoglycans
What is loose connective tissue?
holds small glands and epithelia together and includes the basal lamina of cells.
what is the main component of dense connective tissue?
collagen
What is the role of muscle tissue?
The role of muscle tissue is support and movement. Muscle consists of long excitable cells, which contain large numbers of actin and myosin filaments
Muscle tissue fibre is divided into myofibrils, that contain what two types of filaments?
- Thin filaments composed of actin
- Thick filaments composed of myosin
These two types of filaments slide past each other during contraction. The regular arrangement of the filaments along the myofibrils creates a banding pattern. Each band is termed a sarcomere.
Name 3 vertebrate muscle types and its responsibility?
Skeletal muscle = voluntary movement
Smooth muscle = involuntary movement (present in most of the body eg blood vessels, gut, etc)
Cardiac muscle = Contraction of the heart
Features of the nervous tissue?
Senses stimuli and transmits signals throughout the animal
Neurons, or nerve cells, that transmit nerve impulses
Glial cells, or glia. That help nourish, insulate and replenish neurons
What is the nervous tissue’s functional unit?
The neuron or nerve cell. Its role is communication at synapses
What does the nervous tissue consist of, what are the functions?
- A cell body or soma and two or more nerve processes (eg dendrites, that conduct impulses towards the nerve)
- Axons transmit impulses away from the heart
- Schwann cells wrap around an axon to form multi-layered membrane sheath providing insulation.
Some of the functions of the eukaryotic organelles are performed in bacteria by the….
Plasma membrane
Electron microscope can magnify an object typically….
Hundreds of thousands times bigger
The genetic material of which kind of cells is included in a single, circular molecule of DNA devoid of any histone protein?
Bacteria
The interior of eukaryotic cells contain numerous membrane-bound structures that together are called….
Endomembrane system
