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.
E. coli
Bacterium
Arabidopsis Thaliana
Plant
C. Elegans.
Nematode
Drosphilia melanogaster.
Arthropod
Indicator species
Presents, absence or abundance can give information of the environments qualities, such as presence of pollutant
Mark and recapture
Used to estimate population size where
N = population
M = sample of population captured, marked and released
C =number, captured in second sample
R =number, recaptured marked in second sample
Assume:
All individuals have equal chance of capture
No immigration or emigration
All individuals that are released and marked can mix fully and randomly with total population
Latency
The time between the stimulus occurring and the response behaviour
Frequency
The number of times of behaviour occurs within the observation period
Duration
The length of time each behaviour occurs during observation period
Ethogram
Lists species specific behaviours to be observed in recorded in the study.
Time budget
Record the duration of each of the behaviours in the ethogram together with a total time of observation allows the proportion of time spent on each behaviour to be calculated in the time budget.
Anthropomorphism
Attributing human characteristics to non-human species. It can lead to invalid conclusions..
Evolution
The change over time in the proportion of individuals in a population, differing in one or more inherited traits
Mutation
A random change to the DNA that can be harmful, neutral or may be beneficial
Natural selection
Nonrandom, increasing the frequency of DNA sequences the increase survival
-Populations produce more offspring, then environment can support
-Variation amongst offspring as a result of mutations
-There are selection pressures
-Individuals with a selective advantage, survive to reproduce, and pass unfavourable alleles to their offspring
-Those favourable alleles confer an advantage to the next generation and become more frequent
Selection
Results in the nonrandom increase in the frequency of advantageous, alleles and nonrandom, decrease in the frequency of deleterious alleles
Selection pressures
Environmental factors that influence which individuals in a population pass on their alleles
Sexual selection
The nonrandom process involving the selection of alleles increase the individuals chances of mating and producing offspring. may lead to sexual dimorphism.
Male to male rivalry
Large size and weaponry increases access to females through conflict
Female choice
Females assessing the fitness of males
Genetic drift
Occurs when chance events cause unpredictable fluctuations in allele frequencies from one generation to the next.
More important in small populations as alleles are more likely to be lost from the gene pool
Founder effect
The isolation of a few members of a population from a large population
Bottlenecks
Occur when a population size is reduced for at least one generation
Hardy Weinberg principle
States that in the absence of evolutionary influences, allele and genotype frequencies in a population will remain constant over the generations
Assume
-,No natural selection
-Random mating
-,No mutation
-Large population size
-,No gene flow
Fitness
A measure of the tendency of some organisms to produce more surviving offspring than competing members of the same species. Indication of an individuals ability to be successful at surviving, and reproducing.
Absolute fitness
The ratio between the number of individuals of a particular genotype after selection to those before selection
=1 then stable
> 1 increase in genotype
<1 decrease in genotype
Relative fitness
Ratio of the number of surviving offspring per individual of a particular genotype to the number of surviving offspring per individual of the most successful genotype.
Co- evolution
The process by which two or more species, evolve in response to selection pressures imposed by each other.
Symbiosis
Co evolved intimate relationships between two members of two different species.
Mutualism
Both organisms in the interaction are interdependent on each other for resources or services. Both organisms gain from the resources.
Commensalism
Only one organism benefits
Parasitism
The parasite benefits in terms of energy and nutrients, and a hostess harmed as a result of the loss of these resources
Red Queen hypothesis
States that in a Co-evolutionary relationship changes in the traits of one species can act as aselection pressure on the other species.
Asexual reproduction
Just one parent can produce daughter cells and establish a colony of virtually unlimited size overtime
Parthenogenesis
Reproduction from a female gamete without fertilisation
Meiosis
The division of the nucleus that results in the formation of haploid gametes from a diploid gametocyte
Homologous chromosomes
Chromosomes of same size, same centromere position, and with the sequence of genes at the same loci
Chiasmata
Form at point of contact between nonsister chromatids of a homologous pair in sections of DNA are exchanged
Linked genes
Those on the same chromosome
Crossing over
Results in the new combinations of alleles of these genes. Crossing over of DNA is random and produces genetically different recombinant chromosomes
Independent assortment
Each pair of chromosomes is positioned independently of the other pairs, irrespective of a maternal or paternal origin
Heterogametic
Males lack most of the corresponding homologous alleles on the shorter Y chromosome
Homogametic
One of the two X chromosomes present in each cell is randomly in activated at an early stage of development.
X-chromosome inactivation
Process by which most of one X chromosome is an activated. This prevents a double dose of gene product which could be harmful.
Hermaphrodites
Species that have functioning male and female reproductive organs in individuals
Parental investment
All the costs that the parents incur during the reproductive strategy and paternal care of offspring.
Female investment
In the egg structure in non-mammals, or in the uterus and during gestation in mammals
Monogamy
The mating of a pair of animals to the exclusion of all others
Polygamy
Individuals of one sex have more than one mate
Polygyny
One male mates exclusively with a group of females
Polyandry
One female meets with a number of males in the same breeding season
External fertilisation
Occurs when fertilisation takes place outside an organisms body. Gamemetes are released into water and sperm, swim or a carried by the currents to the eggs.
Internal fertilisation
The eggs are retained within the reproductive tract of the female, until after they have been fertilised by sperm inserted into the female by the male.
Courtship
Especial behaviour in animals that attracts a number of the opposite sex in leads to mating
Sign stimulus
A trigger that provokes a behavioural response
Fixed action pattern
Intrinsic behavioural response triggered by a very specific stimulus once triggered the fix action pattern can’t be stopped midstream must be played to completion.
Sexual dimorphism
Occurs an animals were, there is a physical difference between males and females of the same species
Lekking
Males gather to display a Lek were female choice occurs.
Ecological niche
Multidimensional summary of the tolerances and requirements of a species
Fundamental niche
Species occupies that niche in the absence of an interspecific competition.
Realised niche
Occupied in response to interspecific competition
Competitive exclusion
As a result of intraspecific competition or two niches are so similar that one declines to local extinction
Resource partitioning
Realise nieces are sufficiently different potential competitors can coexist
Scientific cycle
Observation construction of hypothesis, experimental design, gathering and recording data, analysis of data, evaluation, conclusion, and re-forming a hypothesis if necessary
Null hypothesis
Proposes that there will be no statistically significant effect as a result of the experiment treatment
Peer review
Critical evaluation by specialists with expertise in the relevant field
Review articles
Summarise current knowledge and recent findings in a particular field
Legislation
Limits the potential for the misuse of studies and data.
Human study consideration
Informed consent, the right to withdraw data, confidentiality
Reliability
Consistent values in repeat an independent replicates
Reliable results, reduce the effect of atypical results and can be increased by having it large sample size.
Accuracy
Data or means of data sets are close to the true value
Precision
Measure values are close to each other
Pilot study
Used to help plan procedures, assesses validity and check techniques. Evaluation and modification of experimental design. Ensures an appropriate range of values for the independent variable.
Independent variable
Variable changed in a scientific experiment. On the x axis
Dependent variable
Variable being measured in a scientific experiment.
Multifactorial
Involves a combination of more than one independent variable or combination of treatment.
Observational studies
Good at detecting correlation but does not test the hypothesis so they are less useful at testing causation
Correlation
Where there is a relationship between variables
Causation
When changing the independent variable causes the effect noted in the dependent variable.
Confounding variables
Variables other than the independent variable that affects the dependent variable. Must be kept constant or monitored.
Negative control
Provides results in the absence of a treatment
Positive control
A treatment that is included to check that the system can detect a positive result when it occurs.
Placebos
Included as a treatment without the presence of the independent variable being investigated
Placebo effect
A measurable change in the dependent variable being investigated as a result of patients expectations rather than changes in the independent variable.
In vitro
Refers to the technique of performing a given procedure in a controlled environment outside of a living organism
In vivo
Refers to the experimentation using a whole living organism
Representative sample
Should share the same mean and the same degree of variation about the mean as the whole population
Random sampling
Members of the population have an equal chance of being selected
Systematic sampling
Members of the population are selected at regular intervals
Stratified sampling
The population is divided into categories that are then sampled proportionally.
Qualitative data
Subjective and descriptive
Quantitative
Measured objectively usually with a numerical value
Ranked data
Refers to the data transformation in which numerical values are replaced by their rank when the data are sorted from lowest to highest.
Correlation
An association and does not imply causation. Causation exists if the changes in the values of the independent variables are known to cause changes to the value of the dependent variable.
Positive correlation
When an increase in one variable is accompanied by an increase in the other variable.
Negative correlation
Exists when an increase in one variable is accompanied by a decrease in the other variable
Aim
Links the independent and dependent variable together
Method seciton
Contain sufficient information to allow another investigator to repeat the work
Experimental design
Address the intended aim and test the hypothesis.
Statistical tests
Used to determine whether the differences ebtween means are unlikely or liekly to have occurred by chance
Electrochemical gradient
the concentration gradient and the electrical potential difference combine to form the electrochemical gradient.
Glucose Symport
Transports sodium ion and glucose at the same time in the same direction. Sodium enters the cell down the concentration gradient and glucose enters the cell against its concentration gradient.
Receptor molecules of target cells
Proteins with a binding site for a specific signal molecule
Extracellular signalling molecules
Multicellular organism coordinate their communication using this.
Examples include steroid hormones, peptide hormones and neurotransmitters.
RNA Viruses
RNA viruses are called retroviruses. RNA retroviruses use the enzyme reverse transcriptase to form DNA which is then inserted into the genome of the host cell.
Viral life cycle
- Infection of host cells with viral genetic material
- Host cell enzymes replicate viral genome
- Transcription of viral genes
- Translation of viral proteins
- Assembly of new viral particles
- Release of new virus particles.
Transmission
The spread of parasites to host.
Virulence
The harm caused to a host species by a parasite.
Physical barrier
Epithelial cells line organs and gland that create a physical barrier that blocks the entry of parasites.
Chemical secretion
Hydrolytic enzymes in mucus, saliva and tears destroy bacterial cell walls.
Phagocytosis
Phagocytes destroy parasites by phagocytosis. Phagocytes engulf parasites and enclose them in a vesicle. Parasites contain lysosomes which fuse to the vesicle. Lysosomes contain powerful digestive enzymes that destroy parasites.
Natural Killer cells
Natural killer cells can identify and attached to viral infected cells. Chemicals are released that lead to cell death by inducting apoptosis.
immunoassay
Immunoassay techniques are used to detect and identify specific proteins
monoclonal antibodies
These techniques use stocks of antibodies
with the same specificity
Bright field microscopy
Bright-field microscopy is commonly used to
observe whole organisms, parts of
organisms, thin sections of dissected tissue
or individual cells
Fluorescence microscopy
Fluorescence microscopy uses specific
fluorescent labels to bind to and visualise
certain molecules or structures within cells or
tissues
Transcription factors
proteins that when
bound to DNA can either stimulate or inhibit
initiation of transcription
Hydrophobic signalling molecules
Hydrophobic signalling molecules can diffuse
directly through the phospholipid bilayers of
membranes, and so bind to intracellular
receptors
hormone
response elements (HREs)
The hormone-receptor complex binds to
specific DNA sequences called hormone
response elements (HREs). Binding at these
sites influences the rate of transcription, with
each steroid hormone affecting the gene
expression of many different genes
Hydrophilic signalling molecules
Hydrophilic signalling molecules bind to
transmembrane receptors and do not enter
the cytosol
G-proteins
G-proteins relay signals from activated
receptors (receptors that have bound a
signalling molecule) to target proteins such
as enzymes and ion channels.
Type 1 diabetes
failure to
produce insulin (type 1)
Type 2 diabetes
loss of receptor
function (type 2)
Resting membrane potential
Resting membrane potential is a state where
there is no net flow of ions across the
membrane
action potential
An action potential is a wave of electrical
excitation along a neuron’s plasma membrane
Depolarisation
Depolarisation is a change in the membrane
potential to a less negative value inside
Rods
Rods function in dim light but do not allow
colour perception
Cones
Cones are responsible for
colour vision and only function in bright light.
retinal
the light-sensitive molecule retinal.
opsin
combined with a membrane protein retinal to form the photoreceptors of the eye
photoexcited rhodopsin
Retinal absorbs a photon of light and
rhodopsin changes conformation to
photoexcited rhodopsin. Photoexcited rhodopsin activates a G-protein, called transducin
transducin
which activates the
enzyme phosphodiesterase (PDE)
PDE
catalyses the hydrolysis of a molecule
called cyclic GMP (cGMP)
Reversed sexual dimorphism
When the normally inconspicuous female is larger or more ornate than the male.
Female choice
involves females assessing
honest signals of the fitness of males
Honest signals
Honest signals can indicate favourable
alleles that increase the chances of survival
of offspring (fitness) or a low parasite burden
suggesting a healthy individual.
Transmission
Transmission is the spread of a parasite to a
host
Virulence
Virulence is the harm caused to a host
species by a parasite
