Definitions Unit 4 Flashcards
Autotrophic
Organisms that make complex organic compounds from simple compounds in the environment
Photosynthesis
The process by which living organisms, particularly plants and algae, capture the energy of the Sun using chlorophyll and use it to convert carbon dioxide and water into simple sugars
Heterotrophic
Organisms that obtain complex organic molecules by feeding on other living organisms or their dead remains
Adenosine triphosphate (ATP)
A nucleotide that acts as the universal energy supply in cells. It is made up of the base adenine, the pentose sugar ribose and three phosphate groups
ATPase
The enzyme which catalyses the formation and breakdown of ATP, depending on the conditions
Adenosine diphosphate (ADP)
A nucleotide formed when a phosphate group is removed from ATP, releasing energy to drive reactions in the cell
Reduction/oxidation reactions (redox reactions)
Reactions in which one reactant loses electrons (is oxidised) and another gains electrons (is reduced)
Electrón transport chain
A series of electron-carrying compounds along which electrons are transferred in a series of oxidation/ reduction reactions, driving the production of ATP
Chloroplast envelope
The outer and inner membranes of a chloroplast including the intermembrane space
Grana
Layers of thylakoid membranes within a chloroplast
Thylakoids
Membrane discs found in the grana of a chloroplast
Lamellae
Extensions of the thylakoid membranes which connect two or more grana and act as a supporting skeleton in the chloroplast; they maintain a working distance between the grana so that these receive the maximum light and function as efficiently as possible
Stroma
The matrix which surrounds the grana and contains all the enzymes needed to complete the process of photosynthesis and produce glucose
Chlorophyll α
A blue-green photosynthetic pigment, found in all green plants
Chlorophyll β
A yellow-green photosynthetic pigment
Carotenoids
Photosynthetic pigments consisting of orange carotene and yellow xanthophyll
Phaeophytin
A grey pigment which is produced by the breakdown of the other photosynthetic pigments
Absorption spectrum
A graph showing the amount of light absorbed by a pigment against the wavelength of the light
action spectrum
A graph demonstrating the rate of photosynthesis against the wavelength of light
Rf value
The ratio of the distance travelled by the pigment to the distance travelled by the solvent alone when pigments are separated by chromatography
Photosystem l (PSI)
A combination of chlorophyll pigments which absorbs light of wavelength 700nm and is involved in cyclic and non-cyclic photophosphorylation
Photosystem ll (PSII)
A combination of chlorophyll pigments which absorbs light of wavelength 680nm and is involved only in non-cyclic photophosphorylation
Light-dependent reactions
The reactions that take place in the light on the thylakoid membranes of the chloroplasts; the reactions produce ATP and break down water molecules in a photochemical reaction, providing hydrogen ions to reduce carbon dioxide and produce carbohydrates
Light-independent reactions
The reactions that use the reduced NADP and ATP produced by the light-dependent stage of photosynthesis in a pathway known as the Calvin cycle; this occurs in the stroma of the chloroplast and results in the reduction of carbon dioxide from the air to cause the synthesis of carbohydrates
Photochemical reaction
A reaction initiated by light
Cyclic photophosphorylation
A process that drives the production of ATP; light-excited electrons from PSI are taken up by an electron acceptor and transferred directly along an electron transport chain to produce ATP, with the electron returning to PSI
Non-cyclic photophosphorylation
A process involving both PSI and PSII in which water molecules are broken into smaller units using light energy to provide reducing power to make carbohydrates and at the same time produce more ATP
Photolysis
The breaking down of a molecule into smaller units using light
Calvin cycle
A series of enzyme-controlled reactions that take place in the stroma of chloroplasts and result in the reduction of carbon dioxide from the air to bring about the synthesis of carbohydrate
Ribulose bisphosphate (RuBP)
A 5-carbon compound that combines with carbon dioxide from the air in the Calvin cycle to fix the carbon dioxide and form a 6-carbon compound
Ribulose bisphosphate carboxylase/oxygenase (RUBISCO)
A rate-controlling enzyme that catalyses the reaction between carbon dioxide/oxygen and ribulose bisphosphate
Glycerate 3-phosphate (GP)
A 3-carbon compound thought to be the result of breakdown of a theoretical highly unstable 6-carbon compound formed as a result of the reaction between RuBP and carbon dioxide in the Calvin cycle
Glyceraldehyde 3-phosphate (GALP)
A 3-carbon sugar produced in the Calvin cycle using reduced NADP and ATP from the light-dependent stage; GALP is the key product of photosynthesis and is used to replace the RuBP needed in the first step of the cycle, in glycolysis and the Krebs cycle, and in the synthesis of amino acids, lipids, etc. for the plant cells
Photorespiration
The alternative reaction catalysed by RUBISCO in a low carbon dioxide environment which uses oxygen and releases carbon dioxide, making photosynthesis less efficient
Gluconeogenesis
The synthesis of glucose from non-carbohydrates
Limiting factor
The faster needed for a reaction to progress that is closest to its minimum value
Abundance
The relative representation of a species in a particular ecosystem
Ecosystem
An environment including all the living organisms interacting within it, the cycling of nutrients and the physical and chemical environment in which the organisms are living
Habitat
The place where an organism lives
Microhabitat
A small area of a habitat
Population
A group of organisms of the same species, living and breeding together in a habitat
Population
A group of organisms of the same species, living and breeding together in a habitat
Community
All the populations of all the different species of organisms living in a habitat at any one time
Niche
The role of an organism within the habitat in which it lives
Predator
An organism which hunts and eats other organisms
Predator
An organism which hunts and eats other organisms
Abiotic factors
The non-living elements of the habitat of an organism
Biotic factors
The living elements of a habitat that affect the ability of a group of organisms to survive there
Prey
An organism which is hunted and eaten by other organisms
Prey
An organism which is hunted and eaten by other organisms
Biosphere
All of the areas of the surface of the Earth where living organisms survive
Biomes
The major ecosystems of the world
Succession
The process by which the communities of organisms colonising an area change over time
Succession
The process by which the communities of organisms colonising an area change over time
Colonisation
The process by which new species spread to new areas
Opportunists/pioneer species
Species which are the first to colonise new or disturbed ecosystems
Climax community
A self-sustaining community with relatively constant biodiversity and species range. It is the most productive group of organisms that a given environment can support long term
Climatic climax community
The only climax community possible in a given climate
Plagioclimax
A climax community that is at least in part the result of human intervention
Microclimate
A small area with a distinct climate that is different from the surrounding area
Edaphic factors
Factors that relate to the structure of the soil
Leaching
The loss of minerals from soil as water passes through rapidly
Density-independent factors
Factors affecting the number of organisms occupying a niche which are the same regardless of population size
Density-dependent factors
Factors affecting the number of organisms occupying a niche which are dependent on the number of organisms in a specific area
Intraspecific competition
Competition between members of the same species for a limited resource
Interspecific competition
Competition between different species within a community for the same resources
Abundance
The relative representation of a species in a particular ecosystem
Distribution
Where a species of organism is found in the environment and how it is organised
Quadrat
A sample area used in practical ecology, often measured using a square frame divided into sections that you lay on the ground
Individual counts
A measure of the number of individual organisms in an area
Percentage cover
The area covered by the above-ground parts of a particular species
ACFOR scale
A simple scale used to describe the abundance of a species in a given area
Line transect
A way of collecting data more systematically; a tape is stretched between two points and every individual plant (or animal) that touches the tape is recorded
belt transect
When two tapes are stretched out and the ground between them surveyed or a tape stretched out and quadrats are taken at regular intervals
Spearman’s rank correlation coefficient
A statistical tool used to test whether two variables are significantly correlated
Student’s t-test
A statistical test that allows you to judge whether any difference between the means of the two sets of data is statistically significant
Chi squared test
A statistical test that enables you to determine whether there is a statistically significant association between the distribution of two species
Null hypothesis
The hypothesis that any differences between data sets are the result of chance
Significant
Not due to chance
Food chain
A simple way of modelling the feeding relationships between a series of organisms in an ecosystem
Trophic level
A term which describes the position of an organism in a food chain or web and its feeding relationship with other organisms
Producers
Organisms that make food by photosynthesis or chemosynthesis
Primary consumers
Organisms that eat producers, either plants or algae
Secondary consumers
Animals that feed on primary consumers
Tertiary consumers
Animals that feed on secondary consumers (i.e they eat other carnivores); they are usually the top predators in an area
Decomposers
The final trophic level in any set of feeding relationships; these are the microorganisms such as bacteria and fungi that break down the remains of animals and plants and return the mineral nutrients to the soil
Pyramid of numbers
A model of feeding relationships that represents the numbers of organisms at each trophic level in a food chain
Pyramid of biomass
A model of feeding relationships that represents the biomass of the organisms at each trophic level in a food chain
Pyramid of biomass
A model of feeding relationships that represents the biomass of the organisms at each trophic level in a food chain
Pyramid of energy
A model of feeding relationships that represents the total energy store of the organisms at each trophic level in a food chain
Secondary production
The process of making new animal biomass from plant material that has been eaten
Gross primary productivity (GPP)
In plants, the rate at which light from the Sun catalyses the production of new plant material, measured as gm -2 year-1, gCm -2 year-1or kJm-2 year -1
Net primary productivity (NPP)
The material produced by photosynthesis and stored as new plant body tissues; that is, NPP=GPP - R (where R = losses due to respiration)
Carbon cycle
A series of reactions by which carbon is constantly recycled between living things and the environment
Carbon sink
A reservoir where carbon dioxide is removed from the atmosphere and locked into organic or inorganic compounds
Greenhouse gases
Gases found in the atmosphere, including carbon dioxide, methane and water vapour, which are involved in the greenhouse effect
Greenhouse effect
The process by which gases in the Earth’s atmosphere absorb and re-radiate the radiation from the Sun, which has been reflected from the Earth’s surface, maintaining a temperature at the surface of the Earth that is warm enough for life to exist
Global warming
A measurable increase in the temperature of the Earth’s atmosphere or temperature at the surface of the Earth
Climate
The average weather in a relatively large area (such as a country) over a long period of time
Weather
The conditions in the atmosphere at a particular time (for example, if it is sunny or windy or rainy when you go outside)
Climate change
A large-scale change in global or regional weather patterns that happens over a period of many years
Interglacials
The relatively warm periods between ice ages
Dendrochronology
The dating of past events using tree ring growth
Calibration
Checking the measurement values given by one system of measurement against another of known accuracy
Anthropogenic
Produced by people
Correlation
A strong tendency for two sets of data to vary together
Causal relationship
One event happens as a direct result of another, with a clear mechanism by which one factor causes a given change
Extrapolate
Apply already known trends to unknown situations to predict what will happen
Temperature coefficient (Q10)
A coefficient showing the effect of temperature on the rate of a reaction
Optimum temperature
The temperature at which an enzyme works most efficiently
Denature
To cause permanent changes in a protein by too high a temperature
Allopathic speciation
An evolutionary process that occurs when populations become physically or geographically isolated
Sympatric speciation
An evolutionary process that occurs when organisms become reproductively isolated by mechanical, behavioural or seasonal changes
Sustainability
The production of a decent standard of living for everyone now, without compromising the needs of future generations or the ecosystems around us
Sustainable resources
Resources which can be grown and used in a sustainable way
Biofuels
Fuels produced directly or indirectly from biomass
Reforestation
The replanting of trees in an area where trees have been lost
Pathogens
Microorganisms that cause disease
Tobacco mosaic virus (TMV)
A virus that infects the leaves of tobacco plants and other closely related species, and causes a mosaic patterning which can reduce the yield
Capsid
The protein coat of a virus
Capsomeres
The repeating protein units that make up the capsid of a virus
Virus attachment particles (VAPs)
specific proteins (antigens) that target proteins in the host cell surface membrane
Envelope
A coat around the outside of a virus derived from lipids in the host cell
DNA viruses
Viruses that have DNA as the genetic material
RNA viruses
Viruses that have RNA as the genetic material
Retrovirus
A special type of RNA virus that controls the production of DNA corresponding to the viral RNA, and inserts it into the host cell DNA
Reverse transcriptase
an enzyme synthesised in the life cycle of a retrovirus which makes DNA molecules corresponding to the viral RNA genome
Human immunodeficiency virus (HIV)
A retrovirus that causes AIDS
Plasmid
small, circular piece of DNA that codes for a specific characteristic of the bacterial phenotype
Vector
Living organisms or environmental factors which transmit pathogens from one host to another
Provirus
The DNA that is inserted into the host cell during the lysogenic pathway of reproduction in viruses
Latent
The state of the non-virulent virus within the host cell
Lysogeny
The period when a virus is part of the reproducing host cell, but does not affect the host adversely
Exocytosis
The energy-requiring process by which a vesicle fuses with the cell surface membrane so the contents are released to the outside of the cell
Binary fission
Asexual reproduction in bacteria in which the bacteria split in half
Generation time
The time span between bacterial divisions
Lag phase
When bacteria are adapting to a new environment and are not reproducing at their maximum rate
Log phase/ exponential phase
When the rate of bacterial reproduction is close to or at its theoretical maximum, repeatedly doubling in a given time period
Stationary phase
When the total growth rate is zero as the number of new cells formed by binary cells is equal to the number of cells dying due to factors including competition for nutrients, lack of essential nutrients, an accumulation of toxic waste products and possibly lack of, competition for, oxygen
Death phase/ decline phase
When reproduction has almost ceased and the death rate of cells is increasing so that the population number falls
Sterile
A term used to describe something that is free from living microorganisms and their spores
Nutrient medium
A substance used for the culture of microorganisms, which can be in liquid form (nutrient broth) or in solid form (usually nutrient Agar)
Nutrient broth
A liquid nutrient for culturing microorganisms, commonly used in flasks, test tubes or bottles
Liquid culture
Growing microorganisms in a nutrient broth in a flask or test tube rather than on an agar plate
Nutrient agar
A jelly extracted from seaweed and used as a solid nutrient for culturing microorganisms, commonly used in Petri dishes
Selective medium
A growth medium for microorganisms containing a very specific mixture of nutrients, so only a particular type of microorganisms will grow on it
Inoculation
The process by which microorganisms are transferred into a culture medium under sterile conditions
Haemocytometer
A thick microscope slide with a rectangular indentation and engraved (marked) grid of lines that is used to count cells
Turbidimetry
A method of measuring the concentration of a substance by measuring the amount of light passing through it
Turbid
A term used to describe something that is opaque because of suspended matter
Dilution plating
A method used to obtain a culture plate with a countable number of bacterial colonies
Total viable cell count
A measure of the number of cells that are alive in a specific volume of a culture
Communicable
Diseases caused by pathogens which can be passed from one organism to another
Bacterial flora
The combination of different species of microorganisms found in or on a specific region of the body
Sebum
An oily substance produced by the skin which contains chemicals that inhibit the growth of microorganisms
Lysozymes
Enzymes found in tears and other body secretions that are capable of destroying microbial cell walls
Endotoxins
Lipopolysaccharides that are an integral part of the outer layer of the cell wall of Gram-negative bacteria and act as toxins to other cells
Exotoxins
Soluble proteins produced and released into the body by bacteria as they metabolise and reproduce in the cells of their host; these proteins act as toxins in different ways
Lipopolysaccharides
Chemicals made up of a combination of lipids and polysaccharides (complex carbohydrates)
Primary infection
The initial stage of tuberculosis, when M. Tuberculosis has been inhaled into the lungs, invaded the cells of the lungs and multiplied slowly, often causing no obvious symptoms of disease
Tubercule
A localised mass of tissue containing dead bacteria and macrophages formed as a result of a healthy immune response to an infection by M. tuberculosis
Acquired immunodeficiency syndrome (AIDS)
The disease which results from the destruction of the T helper cells as a result of infection with HIV
Human immunodeficiency virus (HIV)
A retrovirus that causes AIDS
HIV positive
Someone who has antibodies to HIV in their blood, indicating that they have been infected with the virus and so are at risk of passing it on to other people
Anti-retroviral drugs
Drugs which are effective against retroviruses such as HIV
Antigens
Glycoproteins, proteins or carbohydrates on the surface of cells, toxins produced by bacterial and fungal pathogens, and some whole viruses and bacteria that are recognised by white blood cells during the specific immune responses to infection; they stimulate the production of an antibody
leucocytes
white blood cells which are larger than erythrocytes and can squeeze through tiny blood vessels as they can change their shape; there are around 4000-11000 leucocytes per mm3 of blood and there are several different types which carry out different functions in the body
granulocytes
leucocytes with granules that absorb stain in the cytoplasm of the cells; this makes them visible under the microscope; they have lobed nuclei and are involved in the non-specific responses to infection
neutrophils
the most common type of leucocyte; they engulf and digest pathogens by phagocytosis
eosinophils
leucocytes important in the non-specific immune response against parasites, in allergic reactions and inflammation, and in developing immunity to disease
basophils
leucocytes with a two-lobed nucleus; they produce histamines involved in inflammation and allergic reactions
agranulocytes
leucocytes with round nuclei but without granules in their cytoplasm; they are involved in the specific immune response to infection
monocytes
the largest of the leucocytes, they can pass from the blood into the tissues to form macrophages
macrophages
cells that engulf pathogens by phagocytosis as part of the specific immune system
lymphocytes
small leucocytes with very large nuclei that are vitally important in the specific immune response of the body; they make up the main cellular components of the immune system; they are made in the white bone marrow of the long bones
inflammation
a common, non-specific response to infection involving the release of histamines from mast cells and basophils; this causes the blood vessels to dilate producing local heat, redness and swelling
mast cells
cells found in the connective tissue below the skin and around blood vessels; they release histamines when the tissue is damaged
histamines
chemicals released by the tissues in response to an allergic reaction
antibodies
glycoproteins that are each produced in response to a specific antigen
fever
a raised body temperature, often in response to infection
phagocytosis
the process by which a cell engulfs another cell and encloses it in a vesicle to digest it
phagocyte
cell which engulfs and digests other cells or pathogens
phagosome
the vesicle in which a pathogen is enclosed in a phagocyte
cytokines
molecules which signal between cells; they have several roles in the immune system, including stimulating other phagocytes to move to the infection site
interferons
chemicals produced by cells in very small amounts when invaded by viruses; interferons act to prevent the viruses invading other cells
immune response
the specific response of the body to invasion by pathogens
B cells
lymphocytes that are made and mature in the bone marrow; once they are mature, they are found in the lymph glands and free in the body
immunoglobulins
antibodies
B effector cells
lymphocytes that are made and mature in the bone marrow which divide to form the plasma cell clones
plasma cells
cells that produce antibodies to particular antigens at a rate of around 2000 antibodies per second
B memory cells
lymphocytes that are made and mature in the bone marrow and that provide the immunological memory to a specific antigen; they allow the body to respond very rapidly to the same pathogen carrying the same antigen a second time
T cells
lymphocytes made in the bone marrow that mature and become active in the thymus gland
T killer cells
lymphocytes that mature in the thymus gland and produce chemicals that destroy pathogens
T helper cells
lymphocytes that mature in the thymus gland and are involved in the process that produces antibodies against the antigens on a particular pathogens
opsonins
chemicals which bind to pathogens and label them so they are more easily recognised by phagocytes
T memory cells
very long-lived cells which constitute part of the immunological memory
major histocompatibility complex (MHC) proteins
proteins that display antigens on the cell surface membrane
antigen-presenting cell (APC)
a cell displaying an antigen/ MHC protein complex
clone
a group of genetically identical cells which are all produced from one cell
clonal selection
the selection of the cells that carry the right antibody for a specific antigen
plasma cell clones
clones of identical plasma cells that all produce the same antibody
agglutination
the grouping together of cells caused when antibodies bind to the antigens on pathogens
opsonisation
a process that makes a pathogen more easily recognised, engulfed and digested by phagocytes
neutralisation
the action of antibodies in neutralising the effects of bacterial toxins on cells by binding to them
Natural active immunity
When the body produces its own antibodies to an antigen encountered naturally
Natural passive immunity
When antibodies made by the mother are passed to the baby via the placenta or mother’s milk
Immunisation
The process of protecting people from infection by giving them passive or active artificial immunity
Vaccination
The introduction of harmless forms of organisms or antigens by injection or mouth to produce artificial immunity
Artificial passive immunity
When antibodies are extracted from one individual and injected into another ( e.g. one form of the tetanus vaccine)
Artificial active immunity
When the body produces its own antibodies to an antigen acquired through vaccination
Attenuated pathogens
Viable pathogens tat have been modified so that they do not cause disease but still cause an immune response that results in the production of antibodies and immunity
Herd immunity
When a high proportion of a population is immune to a pathogen, usually through vaccination, thus lowering the risk of infection to all, including those not vaccinated
Antibiotic
A drug that either destroys microorganisms or prevents them from growing and reproducing
Selective toxicity
A substance that is toxic against some types of cells or organisms but not others
Penicillin
The first antibiotic discovered; it is a bactericidal and affects the formation of bacterial cell walls
Bacteriostatic
the inhibits the growth of bacteria
Tetracycline
A bacteriostatic antibiotic that inhibits protein synthesis
Bactericidal
Kills bacteria
Antibiotic resistant
A microorganism that is not affected by an antibiotic (even one that may have been effective in the past)
Methicillin-resistant Staphylococcus aureus (MRSA)
a strain of S.aureus that is resistant to several antibiotics, including methicillin
Clostridium difficile
A type of bacterium that often exists in the intestines and causes no problems unless it becomes dominant as a result of antibiotic treatment that has removed or damaged the normal gut flora
Hospital-acquired infections (HAIs)
Infections that are acquired by patients while they are in hospitals or care facilities; these infections may be the result of poor hygiene or the result of antibiotic treatment; the pathogens may be antibiotic resistant
Nitrogen cycle
The recycling of nitrogen between living things and the environment by the actions of microorganisms
Forensic science
The application of scientific techniques to the investigation of a crime
Rigor mortis
Temporary muscle contraction causing the body to become rigid after death
Forensic entomology
The study of insect life relating to crime
Exons
The coding regions of DNA (the genes)
Introns
The large, non-coding regions of DNA that are removed before messenger RNA is translated into proteins
DNA sequencing/ gene sequencing
The analysis of the individual base sequence along a DNA strand or an individual gene
DNA profiling
The identification of repeating patterns in the non-coding regions of DNA
Polymerase chain reaction (PCR)
The process used to amplify a sample of DNA (to make more copies of it very rapidly)
Amplified
The process by which DNA is replicated repeatedly (using the polymerase chain reaction) to produce a much bigger sample
Micro-satellite
A section of DNA with a 2-6 base sequence repeated 5 to 100 times
Mini-satellite
A section of DNA with a 10-100 base sequence repeated 50 to several hundred times
Restriction endonucleases
Enzymes used to cut up strands of DNA at particular points in the intron sequences
Recognition site
Specific base sequences where restriction endonucleases cut the DNA molecule
Short tandem repeats
Micro-satellite regions that are widely used in DNA identification of suspects; statistically, the chance of two people matching on 11 or more sites is so small that it is considered to be reliable evidence in court
