definitions for prelim Flashcards
Hazard
Anything that poses a potential threat to the individual or environment.
This can include toxic or corrosive chemicals, heat or flammable substances, pathogenic organisms and mechanical equipment.
Risk
The likelihood of harm arising from exposure to the hazard
Risk assessment
Involves identifying control measures to minimise the risk.
Control measures?
include using appropriate handling techniques, protective clothing and equipment and aseptic technique
Linear dilution?
Series differs by an equal interval
Serial/log dilution?
Series differs by a constant proportion
Colorimetry?
Used to quantify concentration and turbidity by measuring absorbance of specific wavelengths.
Buffer?
Used to control pH
Addition of acid or alkali has small effects on the pH of a buffer and keeps it constant.
Centrifugation?
Separates substances in liquid by differing density
Pellet?
Larger and denser materials settle here.
Supernatant?
Liquid that is less dense remains here.
Paper Chromatography?
Separates differing substances e.g. amino acids and sugars.
The mixture to be separated is dotted at the bottom of the chromatography paper. A solvent is run through the dots and separates by differing solubility,
Thin Layer chromatography?
Separates different substances e.g. amino acids and sugars. Same principle of paper chromatography except the paper is replaced by an un reactive substance placed on a glass/plastic plate.
Affinity chromatogrpahy?
Separates protein and purifies them.
Target and non-target proteins are passes through a matrix causing target proteins to have a high affinity for it. The target proteins attach to the matrix and non-target proteins to be washed out
Gel electrophoresis?
Separates proteins and nucleic acids.
Charged macromolecules move through an electric field applied to a gel matrix.
Native Gels?
Separate proteins by shape, size and charge.
Native gels do not denature the molecule so separates by shape, size and charge.
SDS-PAGE?
Separates proteins by size alone.
Give all molecules an equally negative charge and denatures them separating them by size.
Isoelectric Point (IEP)?
pH at which a soluble protein has no net charge and will precipitate out of solution.
Proteins IEP’s can be used to separate in electrophoresis as they will stop migrating at the proteins IEP as the pH gradient has not net charge.
Aseptic technique?
Eliminates unwanted microbial contaminants when culturing micro-organisms.
Involves the sterilisation of equipment and culture media by heat or chemical means and subsequent exclusion of microbial contaminants.
Growth factors?
Proteins that promote cell growth and proliferation. Growth factors are essential for the culture of most animal cells.
Primary cell lines?
Can divide a limited number of times until they die.
Tumour cell lines?
Can perform unlimited cell divisions
Vital Staining?
Required to identify and count viable cells.
Serial dilution is often needed to achieve a suitable colony count.
Haemocytometer?
Estimate cell numbers in a liquid culture.
Proteome?
Entire set of proteins expressed by the genome.
This is larger than the genome because more than one protein can be expressed by one gene due to alternative RNA splicing.
Non-coding RNA genes?
Genes that do not code for proteins.
They can produce rRNA, tRNA and RNA molecules.
Endoplasmic reticulum (ER)
Forms a network of membrane tubules continuous with the nuclear membrane.
Where lipid synthesis takes place.
Golgi apparatus?
A series of flattened membrane discs.
Lysosomes?
Membrane-bound organelles containing a variety of hydrolases.
Hydrolases?
Digest proteins, lipids, nucleic acids and carbohydrates.
Vesicles?
Trnasports materials between membrane compartments.
Signal sequence?
A short stretch of amino acids at one end of the polypeptide being synthesised and determines the eventual location of a protein within a cell.
Post translational modification?
Altercation of the protein after translation.
Involves either the addition of chemical groups and proteolytic cleavage.
Proteolytic cleavage?
Involves removing some of the protein allowing it to fold and form its final active conformation. e.g. digestive enzymes that need to be activated.
Proteins?
Polypeptide chain of amino acid monomers
Acidic protein?
Negatively charged e.g. COO or COOH
Basic protein?
Positively charged (NH2 or NH3)
Polar protein?
Differing charges OH
Hydrophobic?
Hydrocarbon
Polypeptide?
Several amino acids linked by peptide bonds.
Primary structure?
sequence in which the amino acids are synthesised into the polypeptide
Secondary structure?
Hydrogen bonding along the backbones of the protein strand results in secondary structure - alpha helices, parallel or antiparallel beta pleated sheets or turns.
Tertiary structure?
The polypeptide folds into a tertiary structure. This conformation is stabilised by interactions between R-groups: Hydrophobic interactions, ionic bonds, London dispersion forces, Hydrogen bonding, disulfide bridges
Quarternary structure?
Exists in proteins with two or more connected polypeptide subunits. The subunits are linked by bonding between their R groups not involved in tertiary structure.
Quaternary structure describes the spatial arrangement of the subunits.
Prosthetic group?
a non-protein unit tightly bound to a protein and necessary for its function.
The ability of haemoglobin to bind to oxygen is dependent upon the non-protein haem group.
Ligand?
A substance that binds to a protein.
R-groups not involves in protein folding can allow binding to ligands
The binding of ligands causes change to the conformation of the protein causing a functional change in the protein.
Modulators?
Regulate the activity of the enzymes when they bind to the allosteric site.
Positive modulators?
Increase the enzyme’s affinity for the substrate.
Negative modulators?
Decreases the enzyme’s affinity for the substrate
Protein Kinases?
Catalyse the transfer of a phosphate group to other proteins
Protein Phosphatase?
Catalyse the removal of a phosphate group to other proteins.
Integral proteins?
Interact extensively with the hydrophobic region of the membrane phospholipids.
They are transmembrane proteins.
Peripheral Proteins?
Have hydrophilic R groups on their surface and are bound to the surface of membranes mainly by ionic and hydrogen bond interactions.
Interact with the surface of integral proteins
Phospholipid bilayer?
A barrier to ions and most uncharged polar molecules.
Some small molecules, such as oxygen and carbon dioxide pass through the bilayer by simple diffusion.
Facilitated diffusion?
Passive transport of substances across the membrane through specific transmembrane proteins.
Channels?
Multi-subunit proteins with the subunits arranged to form water-filled pores that extend across the membrane.
Ligand-gated channels?
Controlled by the binding of signal molecules
Voltage-gated channels?
Controlled by changes in ion concentration
transporter proteins?
Bind to the specific substance to be transported and undergo a conformational change to transfer the solute across the membrane.
Active transport?
Uses pump proteins that transfer substances across the membrane against their concentration gradient.
Metabolic energy required.
ATPases?
Hydrolyse ATP
Ion pumps?
Use energy from the hydrolysis of ATP to establish and maintain ion gradients.
Sodium-Potassium pumps?
Transports ions against a steep concentration gradient using energy directly from ATP hydrolysis.
Actively transports sodium ions out of the cell and potassium ions into the cell.
Cytoskeleton?
Gives mechanical support and shape to cells.
Microtubules?
Hollow cylinders composed of the protein tubulin. They radiate form the microtubules organising centre (MTOC) or centrosome. It controls the movement of membrane bound organelles and chromosomes.
Interphase?
Involves growth and DNA synthesis during G1, S and G2
Cytokineis?
Division of cytoplasm
Prophase?
DNA condenses into chromosomes consisting of two sister chromatids. Nuclear membrane breaks down. Spindle fibres extend from MTOC by polymerisation and attach to chromosomes via kinetochores.
Metaphase?
Chromosomes are aligned at the metaphase plate.
Anaphase?
Spindle fibres shorten by depolymerisation and sister chromatids are separated and chromosomes are pulled to opposite poles
Telophase?
Chromosomes decondense and nuclear membranes form around them
Checkpoints?
Are mechanisms within the cell that assesses the condition of the cell during the cell cycle and halt progression to the next phase until certain requirements are met.
Retinoblastoma (Rb)
Acts as a tumour suppressor by inhibiting the transcription of genes that code for proteins needed for DNA replication.
G1 Checkpoint
Checks for sufficient cell size.
G2 checkpoint
Checks for success of DNA replication and any damage to DNA is assessed
p53
Triggered by DNA damage. Stimulates DNA repair, arrest the cell cycle or cause cell death.
Metaphase checkpoint?
Progression is halted until the chromosomes are aligned correctly on metaphase plate and attached to spindle microtubules.
Proto-onco gene
A normal gene involved in control of cell growth or division. Can mutate to form a tumour promoting onco gene.
Apoptosis
Programmed cell death
External death signals
Molecules bind to a surface receptor protein and trigger a protein cascade within the cytoplasm
Internal death signals
Resulting from DNA damage causes activation of p53 tumour-supressor protein.
Caspases
Types of protease enzyme that causes the destruction of cell.
Point count
Involves the observer recording all individuals seen from a fixed point count location
Quadrats
Of suitable size and shape or transects are used for plants and other sessile or slow-moving organisms
Capture techniques
traps and nets used for mobile species
Taxonomy
Involves the identification and naming or organisms and their classification into groups based on shared characterisitcs
Morphology
Internal and external structures of an organism
Phylogenetics
The study of the evolutionary history and relationships among individuals or groups of organisms. Uses heritable traits such as morphology, DNA, sequences and proteins structure to make inferences about an organisms, evolutionary history and create a phylogeny.
Nematodes
Round worm
Arthropod
Joint-legged invertebrates
Chordatas
Mammals, birds, fish vertebrae
Model organism
Those that are either easily studied, or have been well studied. Information obtained can be applied to other species that are difficult to study.