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higher biology - unit 2
Terms in this set (262)
all the chemical reactions taking place within a cell
most chemical reactions occur as part of integrated and interconnected pathways, catalysed by enzymes
is a degradation reaction that releases energy
bio-synthesis reaction that uses energy
catabolic and anabolic reactions are usually closely ______________ and therefore often rely on one another
___ acts as an important means of energy transfer between reactions
most metabolic pathways have both ___________ ____ ______________ steps
reversible and irreversible
what does the irreversible conversion of glucose to intermediate 1 mean?
this allows a concentration gradient to be maintained which promotes the diffusion of glucose into the cell
what does the reversible conversion of intermediate 1 to intermediate 2 mean?
if there is more of intermediate 2 made that the body requires it can be converted back into intermediate 1 and be used in an alternative pathway
are pathways that exists through substances that allow certain stages controlled by enzymes to be bypassed
example of alternative pathway in glycolysis
through substance called sorbital, allows enzyme stages A,B and C to be passes
the cell membrane
separates the intracellular environment from the extracellular environment
the cell membrane ___________ the flow of materials into and out of the cell
Two examples of organelle bounded by double membrane
Mitochondria and chloroplasts, inner membrane acts as highly metabolic membrane surfaces
-allow metabolic activity to be localised to compartments within the cell
-used to separate or keep together metabolites
-provide surfaces for metabolic pathways
proteins embedded in membranes allow various functions to be carried out
transport molecule that contains pores, the provide channels for specific substances to diffuse across membrane
the movement of molecules and ions across the cell membrane from a low to high concentration, against concentration gradient
enzymes in membrane
some protein molecules are embedded in membrane of phospholipids, enzymes catalyse the steps in a metabolic process essential to cell
protein pores allow ___________ diffusion
pumps allow __________ _____________
enzymes in membrane __________ reactions
smaller compartments have __________ volume to surface area ratio
high surface area of membranes allows:
the high concentration of substances to be maintained and faster reaction rates to be achieved
how does high surface area of membranes allow high concentration of substances to be maintained?
as they are involved in the active transport of substances
how does high surface area of membranes allow faster reactions rates to be achieved?
as they can provide surfaces for metabolic reactions
the amount of chemical change per unit of time
the energy required to achieve the transition state and start a chemical reaction
enzymes ________ the activation energy and by doing so increase the reaction rate
an attraction or force between particles that cause them to combine
the substrate binds readily to the enzyme because it has ________ ___________ for the active site
the product is released because it has a _____ __________ for the active site
orientation of reactants
if two or more substances are involved in the reaction, the shape of the active site ensure that they come together in the best orientation to facilitate the chemical reaction
activation energy diagram enzymes
induced fit of enzymes
when the active site changes shape to create a tighter fit around substrate, returns to original shape after product is released
ways of increasing rate of enzyme activity
- changing temperature towards optimum
- changing pH towards optimum
- increasing substrate concentration
ways of decreasing substrate concentration
- changing temperature away from optimum
- changing pH away from optimum
- decreasing substrate concentration
- use of an inhibitor
why does the reaction rate increase as the substrate concentration increases?
because more of the available active sites can become occupied by substrate molecule
when does the reaction rate become constant
when the concentration is reached whereby all active sites are occupied
in a metabolic pathway the product of each enzyme reaction is the ___________ for the next
the direction in which the reaction proceeds at any given time depends on the _____________ ___ _________ and product present
concentration of substrate
metabolic pathways can be controlled by ______________ _______ __________________ signalling molecules
intracellular and extracellular
multi enzyme complexes
enzymes are often grouped together so metabolites can be quickly transferred from one enzyme to the next
to control a metabolic pathway the rate of ____________ __________ must be controlled
some enzymes are only synthesised by cells the they are actually required, how is this done?
achieved by switching the gene on and off temporarily
other enzymes that are synthesised all of the time the gene is permanently switched __
inhibitor on enzyme activity
completely changes the active site so no matter how much you increase substrate concentration it wont increase enzyme activity
slowly the substrates out compete the inhibitor so it will increase to same end point as having no inhibitor but slower
competitive inhibitors bind on the _______ _____ of the enzyme
structure of ATP
composed of one molecule of adenosine bonded to three molecules of inorganic phosphate
importance of ATP
it is the link between catabolic and anabolic reactions, it also provides energy for other cellular processes e.g. active transport
what is phosphorylation?
the addition of a phosphate group to a molecule
what is an example of phosphorylation?
the regeneration of ATP
phosphorylation is a common mechanism used to __________ __ _________ proteins within a cell
activate or deactivate
the phosphate from phosphorylation can be supplied by the breakdown of _____
a series of metabolic pathways which brings about the release of energy which is stored as ATP
cellular respiration is _________ to many other pathways
respiration pathways are present from all _______ domains of life
are involved in glycolysis and the citric acid cycle, they remove H+ ions and electrons from compounds
what happens to the H+ ions and electrons after they are removed by dehydrogenase enzymes?
then passed to coenzymes NAD or FAD
what are the H+ ions and electrons used for?
to generate ATP during ATP synthesis
first stage of respiration
second stage of respiration
the citric acid cycle
third stage of respiration
the electron transport chain (ETC) and ATP synthesis
what happens during glycolysis?
-occurs in cytoplasm
-intermediates are phosphorylated before ATP is generated
-NET gain of 2ATP
what happens during the citric acid cycle?
-occurs in the matrix of the mitochondria
-acetyl coenzyme A combines with oxaloacetate
-citrate is formed
-H+ ions and electrons are accepted by NAD and FAD
-2ATP and CO2 is generated
what happens during the electron transport chain and ATP synthesis?
-receives H+ ions and electrons from coenzymes NAD and FAD
-is a collection of proteins present on the inner membrane of the mitochondria
how much ATP is generated through aerobic respiration?
what are the two stages of glycolysis?
-energy investment phase
-energy payoff phase
what happens in energy investment phase?
the intermediates are phosphorylated and 2 molecules of ATP are used to provide phosphates for the phosphorylation
what happens in the energy payoff phase?
4 molecules of ATP are produced and the hydrogen ions and electrons are released and accepted by NAD
NET gain of glycolysis?
what happens during breakdown of pyruvate?
pyruvate is broken down into an acetyl group and carbon dioxide, the acetyl group combines with a molecule of coenzyme A and produces acetyl coenzyme A, more hydrogen ion and electrons are released and accepted by NAD
what happens to the carbon dioxide from the breakdown of pyruvate?
it is released as a by product
where does the electron transport chain occur?
inner membrane of the mitochondria
what do the NADH and FADH2 also release doing ETC?
high energy electrons which provide energy for the active transport of H+ ions across the membrane
what happens to the electrons after they come out of ETC?
they combine with oxygen, the final electron acceptor, and at the same time oxygen combines with a pair of hydrogen ions to form water
what happens during ATP synthesis?
hydrogen ions that have been pumped across membrane diffuse back into the matrix of the mitochondria through protein ATP synthase causing part of protein to spin, enzyme ATP synthase is able to catalase regeneration of ATP from ADP+Pi
what happens if oxygen is absent, for animals?
the pyruvate is converted into lactate (lactic acid)
what happens if oxygen is absent, for plants and yeast ?
the pyruvate is converted into ethanol and carbon dioxide
overview of respiration
carbohydrate stored by plants
carbohydrate stored by animals
what are starch and glycogen composed of?
chains of glucose molecules
what do starch and glycogen act as?
respiratory substrates as they can be broken down to release glucose as required
other sugar molecules such as maltose and sucrose can also be converted to glucose or intermediates in the _____________ ___________
a molecule of ______ can be broken down into glycerol and fatty acids when required for use as a respiratory substrate
what is glycerol converted into?
what happens to the fatty acids?
they are metabolised into molecular fragments that enter the pathway as acetyl coenzyme A for use in the citric acid cycle
what happens to proteins when required as a respiratory substrate?
proteins in the diet are broken down to their component amino acids, amino acids in excess for body's requirements for protein synthesis undergo deamination forming urea and respiratory pathway intermediates
how are the proteins broke down?
by the action of digestive enzymes
what happens to the respiratory pathway intermediates from proteins?
enter the metabolic pathway and act as respiratory substrates regenerating ATP as before
the energy consumed by an organism per unit time
how can energy consumption be measured indirectly?
-rate of oxygen consumption
-rate of carbon dioxide production
-rate of heat production
measures changes to air being pumped through a sealed chamber for example oxygen and carbon dioxide content and temperature
measures temperature change of water being passed through a sealed chamber
_______ metabolic rates require efficient delivery of oxygen to cells
circulatory system of fish
have a single circulatory system, one atrium on ventricle. The blood is delivered at high pressure to the gills after being pumped from the heart but is at low pressure by the time it reaches the body
circulatory system of amphibians and reptiles
have an incomplete double circulatory system. 2 atriums and one ventricle. some mixing of oxygenated blood from the lungs and deoxygenated blood from body occurs in the ventricle, tissue blood in incompletely oxygenated
circulatory system of mammals and birds
have a complete double circulatory system. 2 atriums and ventricles completely separated by a septum
which is the most efficient circulatory system?
mammals and birds, it enables an endothermic (warm blooded) vertebrate to deliver large quantities of oxygen to respiring tissues which release heat during metabolism and keep its body warm
birds are very active vertebrates and so have a very efficient system of gas exchange that allows them to obtain the large quantities of oxygen needed for their high ____________ _________
birds have a system of large ____ _____ associated with their lungs, which are designed to keep the air flowing through the lungs in one direction rather than having to go in and out by the same route
what happens when a bird breaths in?
fresh air fills its posterior air sacs, stale air moves into the anterior air sacs from the lungs. when the bird breaths out, the fresh air passes from the posterior sacs to the lungs and the stale are passes from the anterior sacs to the outside
lungs of amphibians
They only use their lungs for gas exchange when very active. lungs are small, thin walled and without alveoli. have a relatively smaller surface area for gas exchange compared to mammals.
how do amphibians exchange gas when not active?
through their skin
lungs of reptiles and mammals
lungs with branched system of tubes called bronchioles ending in many thin walled, moist alveoli, providing a large surface area for the efficient exchange of gases.
some organisms show ______________ adaptions that enable them to survive in and exploit low oxygen niches
example of low oxygen niches
-deep in the ocean
how do humans respond to high altitudes?
increase number of red blood cells by up to 20%, takes several weeks for this adapt to take effect
physiological adaptions of diving mammals, such as seals, that allow them to make deep water dives for a long time
one adaption is to slow their heart rate down to conserve oxygen, another is to collapse their lungs as this reduces their buoyancy and allows them to sink quickly, saving energy for hunting.
how do bloodworms survive in low oxygen bottom sediments of fresh water?
their bodies contain haemoglobin, which allows them to absorb oxygen from the limited amount present
the oxygen concentration over time has ________
as oxygen levels increases, so can ____________ _____
what is one way to determine aerobic fitness?
measure the maximum rate as which the body is able to take up and use oxygen, known as VO2 max
what is VO2 max usually measured in?
how do you establish the VO2 max?
a person runs on a treadmill whilst breathing in a measured gas supply, as the intensity of exercise is increased (by increasing speed and gradient of the treadmill) more oxygen is taken in until it reaches a level that does not change, even if the intensity of the exercise is increased
the greater the VO2 max, the ________ the individual
we control the _______________ variable
the dependent variable depends on the __________________
what external abiotic factors can affect an organisms metabolic rate?
organism will be either one of two categories, conformers or ___________
cannot alter their metabolic rate and conform to the condition in the environment, their internal environment is dependent upon the external environment
alter their metabolic rate to maintain a steady state, they regulate their internal environment
conformers have low __________ _____ as they do not expend energy maintaining their internal environment
where must conformers live?
in stable environments as they are less adaptable
how can conformers maintain an optical metabolic rate?
using behavioural responses, for example lizards sunbathe to control body temperature
conformers have a _________ ecological niche
regulators occupy a vast range of __________ _______
example of a conformer
spider crab, pros are that it doesn't need much energy, cons are that it is unable to osmoregulate and dies in water that is less salty that sea water
example of a regulator
shore crab, pros are that animal is able to osmoregualte and survive in estuaries which is less salty than sea water, cons are that it has to find more food to provide energy expended during osmoregulation
to maintain homeostasis, organisms require ____________ ______________
System of maintaining homeostasis in a regulator organism
Use of negative feedback in regulation of body temperature in mammals. Either ectotherms or endotherms
are unable to regulate body temperature
examples of ectotherms
fish, amphibians and reptiles
are able to regulate body temperature, maintain temperature in the best range for enzyme controlled reactions and optimises diffusion rates
diffusion at higher temperatures means more ________ is available
examples of endotherms
mammals and birds
how the hypothalamus controls temperature?
-the skin has thermo receptors that detect changes in the temperature
-nerve impulses sent to the hypothalamus relaying this information
-the hypothalamus also contains thermo receptors
-hypothalamus sends out nerve impulses to effectors to return body temp to normal levels
the two main mechanisms employed by the skin to regulate body temperature in a mammal
the blood vessels that supply blood to the skin dilate (widen), increasing the amount of blood flowing to the skin. this increases the surface area from which heat can be lost to environment by radiation
Blood vessels supplying blood to the skin constrict ( narrow) reducing the amount of blood flowing to the skin. as a result less heat is lost by radiation from the surface of the body
how else does the body cool down?
- sweat glands in the skin secrete sweat which cools the body down when it evaporates from the skin
-decreasing metabolic rate as it reduces the amount of heat energy produced
how else does the body warm up?
-less sweat is produced to conserve heat
-shivering warms the body up, as does increasing the rate of metabolism (generates more heat energy)
how do hairs in the sublayer of the skin help keep heat?
when the body is cold, nerve impulses from the hypothalamus contract the erector pili muscles, causing the hairs to stand up. this traps a layer of air close to the body, which acts as a insulator. more effective in furry animals than in humans
reduction in metabolic rate enables _________ during a period when the cost of continued metabolic activity would be too high
a period of suspended growth and development in response by the organism to tolerate adverse conditions
when an organism becomes dormant before the arrival of the adverse conditions
example of predictive dormancy
many trees respond to decreasing day length and temperatures by shedding leaves and entering dormancy
when an organism becomes dormant after the arrival of the adverse condition
example of consequential dormancy
snails enter dormancy during extremely dry periods
hibernation can be consequential or ________________
what does hibernation allow animals (usually mammals) to survive?
adverse cold conditions
what happens during hibernation?
the animals metabolic rate drops with a resulting decrease in body temperature, heart rate and breathing rate
the bare minimum of energy is used during hibernation for what?
to maintain vital cellular activities using fat stores built over the summer
example of an animal that hibernates
aestivation is an example of ________________ dormancy
what does aestivation allows animals to survive?
periods of excessive drought or heat during the summer
two examples of animals that go through aestivation
crocodiles and land snails
a period of reduced activity and metabolism in organisms as part of a 24 hour cycle. additional decrease in breathing rate, body temperature and heart rate
torpor decreases the rate of ___________ _________________ at a time when searching for food would likely be unsuccessful or risk of predation is too high
what kind of animals is daily torpor often found in?
organisms with high metabolic rate
example of animal that goes through torpor
bats are torpid during the day and feed at night
is the regular movement by the members of a species from one place to another over a relatively long distance
migration avoids ______________ __________ caused by shortage of food and low temperatures by expanding energy to relocate to a more suitable environment
what does long distance migration normally involve?
an annual round trip between two regions that both provide favourable condition for each part of the year
example of birds migrating
artic suka move from one hemisphere of the world to the other
example of butterflies migrating
monarch butterflies migrate north from Mexico to breed int he USA and Canada
when studying long distance migration what do biologists want to find out?
-when the animal migrated
-where they overwintered
-whether or not they returned to their original summer territory
-how long they lived for
specialised techniques for studying migration
-ringing with metal bands
-tracking using transmitters
ringing with metal bands
a metal band carrying a birds individual identification number is attached to birds leg. of the bird is recaptured then its information can be recorded
a small circular tag is attached to the hind wing of a monarch butterfly. this carries a code entered in a database. if the tag is recovered at a later date, the route and distance covered by the butterfly can be determined
the use of bright coloured marks ( and flags on larger birds) has allowed biologists to observe the birds with binoculars without needing to recapture them
tracking using transmitters
lightweight transmitters are glued to the animals body or implanted under its skin. the transmitter emits signals that are picked up by satellites, signals are beamed back to ground stations
advantage of tracking using transmitters
they provide the most accurate information so far on the exact locations of flyways used by birds during their migratory cycle
disadvantage of tracking using transmitters
are expensive and may have a drag effect on some small birds
is inherited and inflexible. this pattern of behaviour is performed in the same way by every member of the species
begins after birth and is gained by experience. it is flexible and occurs as a result of trial and error and the transmission of knowledge and skills among the members of a social group
displacement experiment design
large number of starlings were captured in Holland and taken to Switzerland to be released. Starlings normally migrate from eastern Europe to the northern France in autumn
displacement experiment conclusion
migratory behaviour of the adult birds was based on a combination of both innate and leaned influences. whilst the young birds and their migratory behaviour was purely innate ( arrived in Spain instead of France)
cross fostering experiment design
herring gulls (non-migratory) and less black backed gulls (migratory), their eggs were swapped and migratory behaviour studied
cross fostering experiment conclusion
the black backed gulls raised by non-migratory birds did migrate, so migration is innate behaviour. the helming gulls raised by black-backed gulls did move with their foster parents exhibiting learned behaviour
are organisms that live in extreme conditions. most belong to the domain archaea. many live in hydrothermal vents
these organisms thrive at high temps, thermophile bacteria have heat tolerant enzymes such as heat tolerant polymerase (used in PCR)
these organisms generate their ATP by removing high energy electrons from inorganic molecules such as H2S, they are therefore producers that do not photosynthesise
what are considered microorganisms?
archaea, bacteria and some species of eukaryotes
in general why are microorganisms used?
because of their adaptability, ease of cultivation and speed of growth
microorganisms include species that can sue a wide variety of substances for metabolism and produce a range of __________ from their metabolic pathways
well known products from microorganisms
why microorganisms are useful?
- they are easy to cultivate
-the reproduce and grow quickly
-their food substrate is often a cheap substance (or even a waste product from another source )
-they produce many different useful products
-their metabolism can be manipulated relatively easily
microorganisms are normally grown under controlled conditions in a laboratory, they can be grown in two ways:
- in a growth medium called broth jar
- on a solid medium called agar jelly
large scale industrial processes use _____________ _______ fermenters
all processes will provide the following growth requirements:
- energy source ( chemical or light)
- simple chemical compounds
- suitable environmental condtions
why must simple chemical compounds be provided?
microorganisms being grown in culture must be provided with this for the biosynthesis of more complex molecules
some microorganisms can synthesis all the ____________ ________ e.g. amino acids they require if provided with simple chemical compounds
other microorganisms must be provided with complex compounds as they are unable to synthesis, such as _______ ______ and ____________
fatty acids and vitamins
complex compounds can be found in _______ extract
sulphur is a chemical requirement, where can it be sourced and why is it needed?
can be sourced from a compound containing sulphate group. it is needed for the synthesis of some amino acids
carbon is a chemical requirement, where can it be sourced and why is it needed?
can be sourced from organic compounds such as carbohydrates. needed as organic compounds provide the microbe with energy and raw materials for biosynthesis
factors that need to be controlled:
- sterility (eliminate contaminants)
- concentration of oxygen
- glucose concentration
what does using a fermenter allow?
a variety of environmental conditions to be monitored and controlled. this is done by computers when industrial sized fermenters are used
the time required for a population of unicellular organism to double in number
why does the pattern of growth of a population of microorganisms change over time?
- nutrients provided are used up
- metabolites produced by the microorganisms being secreted (released outside the cell)
growth of microorganism (phases of growth)
little to no increase in cell numbers. the cells are adjusting to growth medium and show increased metabolic activity, they are making substrates and turning on enzymes. flat line
the enzymes may need to be ________ in the lag phase for use in metabolising the new substrates
the cells grow and multiply as maximum rate, providing there is no limiting factor. steep incline line
nutrients begin to run out and/or secondary metabolites produced by the microbe start to build up. at this point the rate of production of new cells is equal to the rate of death of old cells. line is level.
what happens when there is a build up of secondary metabolites?
it can have a toxic effect and causes rate of cell division to decrease
the lack of nutrient substrate and/or the accumulation of high concentration of toxic metabolites leads to death phase. number of cells dying now exceeds the number of new cells being produced. steep decline
total cell count
the number of cells in a culture
viable cell count
the number of living cells in a culture
metabolism can be controlled through the addition of metabolic __________, ____________ or ______________
precursors, inducers or inhibitors
earlier metabolites from the pathway can be added to increase metabolism
example of precursor
metabolite A is increased to produce more of B
addition of the the metabolite receding the one which is required. this helps to ensure the enzyme responsible for releasing the product is kept active
example of inducer
more metabolite B is added to keep enzyme 2 active for producing metabolite C
to reduce the activity or production of the enzyme which would further the pathway past the required product (keep at product not past)
example of inhibitors controlling metabolism
reducing the activity or production of enzyme 3 so there is a build up of metabolite C
production of primary metabolites essential for growth e.g. amino acids
substances produced which are not associated with growth but can confer an ecological advantage
example of secondary metabolite
penicillin, antibiotic stops fungi from getting infected
difference/original x 100
wild strains (wild type)
the phenotype of a species as it occurs in nature
one way wild strains be improved?
selecting particular strains by repeatedly subculturing those with the most desirable characteristics.
__________ ____________ of different strains (sexually reproducing organisms) or encouraging horizontal gene transfer between asexual strains also improves wild strains
increase _____________ (mutation rate) using mutagenic agents such as UV, radiation and mutagenic chemicals also improves wild strains
another way to improve wild strains is by genetic modification using ______________ _____ _____________
recombinant DNA technology
what is recombinant DNA?
DNA created artificially
genetic alteration of bacteria
plasmids and chromosomal DNA can be transferred between cells or taken up from the environment
three ways genetic alteration of bacteria can occur
environmental uptake, when a cell takes up a piece of naked foreign DNA from the remains of a cell that has been destroyed or burst (lysis)
genetic transfer, when a virus containing fragments of foreign DNA injects this DNA into cell , foreign DNA becomes incorporated into the chromosome
genetic transfer, temporary tube form between two bacterial cells, tube allows a copy of genetic material to pass from the donor cell to the recipient cell. formation of bacterial cell that contains new combination of genetic material.
genetic alteration of yeast and fungi
new genotypes can be developed through controlled sexual reproduction
recombinant DNA technology
an enzyme extracted from bacteria which is used to cut up the DNA into fragments
can be fluorescent proteins or genes for antibiotic resistance, scientists can select the cells that are for example glowing green and know they also contain gene of interest
a site that is cut open by restriction enzymes to allow the gene to be transferred or be inserted
a specific short sequence of DNA bases that is cut by restriction enzyme
recombinant plasmids and artificial chromosomes are used as these to carry DNA between organisms
a gene that is used by scientists to identify if recombinant DNA has been taken up into cells
a sequence of DNA that controls the expression of a gene
origin of replication
the site on a plasmid that allows it to control its own replication (self- replication)
DNA that has been created artificially that allows for longer sequences of DNA to be transferred between organisms
combines complementary sticky ends on the vector with the target sequence e.g. seals the gene into the plasmid
what is a limitation of using eukaryotic animal/plant recombinant DNA in prokaryotic cells?
when the eukaryotic gene is expressed in the prokaryotic cells the required polypeptide may fold incorrectly or may lack post translational
why may eukaryotic animal/plant recombinant DNA lack post translation?
as splicing and post translational modification doesn't occur in prokaryotes as they have no introns
how can limitations be reduced?
by using recombinant eukaryotic yeast cells instead of bacteria
sometimes genes that improve the ______________ of the organism can be inserted
how can genes improve yield of a specific protein?
genes that remove inhibitory controls or amplify specific metabolic steps in a pathway can be introduced
genes can also be added that prevent the __________ of the microorganisms in an extern environment (outside of the lab)
genes can be added that make the cell __________ their product into the surrounding medium making it easier to collect
is a source of harm or danger
how is use of microorganisms tightly controlled?
products must meet specific requirements such as:
-they must not cause any risk to staff manufacturing them
-must to safe to use by consumers
-it must be pure and free from microorganisms that could contaminate the environment
the likelihood of that harm occurring
how is the manufacturing of microorganisms controlled?
-the purity of the product must be maintained and checked
-the facilities used must meet safety standards
when an end product inhibits the activity of an enzyme that catalysed a reaction earlier in the pathway that produced it
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