AOS2 Flashcards
what are biomechanical reactions
reactions occurring in cells that lead to the formation of a product from a reactant.
what are reactants
substances (molecules/elements) that are changed from a chemical reaction
what are products
a compound produced from the reactants reacting (from the chemical reaction)
what are biomechanical pathways
a series of linked biomechanical reactions
what is metabolism
The total activity of the reactions of all biochemical pathways in a living organism
what are substrates
a compound on which an enzyme acts
what are the types of biomechanical pathways
- anabolic pathways
- catabolic pathways
what are anabolic pathways (anabolism)
These pathways turn simple molecules into more complex ones
what happens to the energy levels in the anabolic pathways
anabolic pathways are energy-requiring or endergonic
what are catabolic pathways (catabolism)
These pathways break down complex molecules into more simple ones
what happens to the energy levels in catabolic pathways
Catabolic pathways are energy-releasing or exergonic
example of anabolic pathway
Photosynthesis, where glucose molecules are synthesised from carbon dioxide and water using radiant energy from the Sun
example of catabolic pathway
Aerobic cellular respiration, where glucose molecules are broken down into carbon dioxide and water molecules
are enzymes proteins
yes most enzymes are proteins
what are catalysts
factors that increase rate of reaction
are all catalysts enzymes?
no, enzymes are all catalysts but not all catalysts are enzymes
are enzymes specific to reaction?
yes, each different reaction will be catalysed by a specific enzyme
what is activation energy
minimum amount of energy required to initiate a chemical reaction
what is the active site
region of an enzyme that binds temporarily with the specific substrate of the enzyme
what do enzymes do to speed up a reaction
lower activation levels
how do enzymes lower activation levels (2)
- Influence the stability of bonds in the reactants
- Providing an alternative reaction pathway;
how do enzymes bind to substrates (2 steps)
- the enzyme and substrate with join to form the E-S complex (when it binds to the active site)
- the substrate forms weak bonds with particular amino acid residues (in the protein) at the active site.
what are the 3 types of enzyme activity (ways they can bind to substrates)
- substrate specificity
- bond specificity
- group specificity
what is substrate specificity (enzyme activities)
they catalyse one particular substrate only
what is bond specificity (enzyme activities)
they act only on one kind of chemical bond (only peptide bonds)
what is group specificity (enzyme activities)
they act only on particular functional groups present as part of the substrate molecule (-COOH, or -OH)
what are coenzymes
an organic molecule that acts with an enzyme to alter the rate of a reaction
what are cofactors
a non-protein molecule or ion that is essential for the normal functioning of some enzymes
are cofactors and coenzymes the same
no, coenzymes are cofactors but not all cofactors and coenzymes
what are inorganic cofactors
cofactors that do not contain carbon and include metal ions such as magnesium or copper
what are organic cofactors
small non-protein organic molecules that are essential for the function of particular enzymes
what are the 2 types of organic cofactors
- prosthetic groups
- coenzymes
prosthetic groups are ……
cofactors that are tightly bound to an enzyme and are essential for it to function as a catalyst.
what is the difference between prosthetic groups and coenzymes
prosthetic groups are tightly bound to an enzyme, whereas, coenzymes are loosely bound
what are the 5 main coenzymes we focus on
- NAD
- NADP
- FAD
- ATP
- CoA (coenzyme A)
what are the 2 roles of coenzymes to assist enzymes
- transfers of atoms or groups of atoms, such as hydrogens, phosphate groups and acetyl groups
- energy transfers
what are the 2 forms coenzymes can be in (interconvertible forms)
- loaded and
- unloaded
loaded coenzymes main info
they are high in energy and have a group that can be transferred. In simple they are electron donors
unloaded coenzymes main info
they have low energy, and accept groups. In simple they are electron acceptors
what are the 3 factors that impact enzyme activity
- temperature
- pH
- substrate concentration
summary of what happens with varied temperatures for enzyme activity (rate of reaction)
when temperature first increases, the reaction rate also increases. This is because the reactants absorb heat energy and move faster, allowing them to collide and overcome the activation energy.
However, in enzyme-catalysed reactions, this increase only occurs up to the optimum temperature, after which the rate decreases, due to denaturation and the change in enzyme structure.
summary of what happen with varied pH for enzyme activity (rate of reaction)
As pH increases or decreases from optimum pH, the rate of reaction and the activity of an enzyme decreases.
do each enzyme have different optimum pH
yes, each with have different so different graphs with rate of reaction
summary of what happen with varied substrate concentration for enzyme activity (rate of reaction)
the rate of reaction increases with increasing substrate concentration — but only up to a point. Beyond this, any further increase in substrate concentration produces no significant change in reaction rate (active sites are all occupied)
what are enzyme inhibitors
substances that prevent the normal action of an enzyme and therefore slow the rate of enzymes-controlled reactions
what are the 2 types of inhibition
reversible inhibition
irreversible inhibition
what are the 2 types of reversible inhibition
- competitive inhibition
- non-competitive inhibition
what is competitive inhibition
inhibition in which a molecule binds to the active site of a molecule instead of the usual substrate
why does competitive inhibition slow down reaction rate
inhibitor molecules prevent the formation of the E–S complexes (as active site is partially occupied)
what is non-competitive inhibition
inhibition in which a molecule binds to the allosteric site of an enzyme causing a conformation change in the active site
is the active site and an allosteric site the same?
no, allosteric site is somewhere on the enzyme but not the active site itself
why does non-competitive inhibition slow down reaction rate
as the binding of the inhibitor to the allosteric site changes the shape of the enzyme’s active site the E-S complex cannot form
what is irreversible inhibition
occurs when a specific molecule can form a strong covalent bond with an enzyme at its active site, so that the normal substrate is permanently blocked from accessing the active site
what are common irreversible inhibitors?
Heavy metals
what are 3 things that the regulation of rates of reaction does
- prevent waste, such as would occur if pathway products were made in excess of cell requirements
- prevent the build-up in cells of products to potentially harmful levels
- prevent depletion of substrates
what are the 2 types of regulation
- allosteric regulation
- feedback regulation
what is allosteric regulation
control of the reaction rate of enzymes through conformational changes in enzymes. This occurs when a regulator molecule binds to the allosteric site
what can the regulator molecules be (allosteric regulation)
- allosteric inhibitors
- allosteric activators
what does allosteric inhibitors do
their binding produces a change of shape in the enzyme that stops enzyme activity; they act like an OFF switch
what does allosteric activators do
the shape change resulting from the binding produces an increase in enzyme activity; they act like an ON switch
what is feedback regulation
the end product of a metabolic pathway acts as an inhibitor of the key enzyme that catalyses the first step in a pathway.
what is photosynthesis
the process by which plants use the radiant energy of sunlight trapped by chlorophyll to build carbohydrates (glucose) from carbon dioxide and water.
what is the photosynthesis equation
6 carbon dioxide + 6 water = glucose + 6 oxygen (gas)
what are the 2 stages of photosynthesis
- light-dependent stage
- light-independent stage
what is the function of the light dependent stage
to transform sunlight energy that is captured by chlorophyll into the chemical energy of loaded coenzymes
what is the function of the light independent stage
to assemble simple inorganic carbon dioxide molecules into more complex organic glucose molecules
what is another name for the light independent stage
Calvin cycle
where does photosynthesis occur
chloroplasts, in the chlorophyll pigment inside (in the cytosol of plants)
what does chloroplasts enable a plant to do
capture the radiant energy of sunlight, bringing it into cells as the starting point of photosynthesis
what are the 3 main things inside the chloroplasts (not including chlorophyll)
thylakoids
grana
stroma
what are thylakoids
flattened membranous sacs in chloroplasts that contain chlorophyll
what is the grana
stacks of thylakoids are known as grana, where a singular stack is a granum
what is stroma
fluid inside the chloroplasts, containing the enzymes that are involved in calvin cycle
what does the light dependent stage involve
involved in the capture of sunlight and the transformation of its energy to the chemical energy of loaded coenzymes, NADPH and ATP.
where is the light dependent stage occur (c3)
thylakoid (within the grana)
what are the 3 inputs in the light dependent stage
- water
- ADP + Pi
- NADP+
what are the 3 outputs of the light dependent stage
- oxygen
- ATP
- NADPH
summary of what happens in light dependent stage
the energy caught by the chlorophylls make the electrons have high energy (excited) and the splitting of water molecules gives H+ ions (protons).
This then allows NADPH to form as well as ATP
what do the chloroplasts have after the light dependent stage
a supply of high-energy loaded ATP molecules
a supply of high-energy loaded NADPH coenzymes that can act as donors of hydrogen ions and electrons
light dependent equation
water + 18ADP + NADP into 6O2 + 18ATP + NADPH
what happens in the light independent stage
inorganic carbon dioxide molecules (CO2) are built into energy-rich reduced organic molecules, such as glucose (C6H12O6).
where does the light independent stage occur
the stroma
what is required for the light independent stage
Rubisco, and the NADPH (donate H and e-) and ATP (energy source) from the previous stage
what are the 3 inputs of the light independent stage
- ATP
- NADPH
- CO2
what are the 3 outputs of the light independent stage
- ADP + Pi
- NADP+
- Glucose
summary of what happens in light independent stage
inorganic carbon is converted in organic CO2 thru carbon fixation
NADPH donate hydrogens and electrons as molecules are reduced to higher energy levels
ATP supplies energy for anabolic steps
what are the 3 types of plants
C3
C4
CAM
why are there different types of plants
they are categorised into how they fix carbon into glucose
how do C3 plants carry out the Calvin Cycle
These plants carry out the original Calvin Cycle, using Rubisco, and are prone to photorespiration
what are optimal conditions for C3 plants
moist and cool conditions
how do C3 plants use RuBisco
use the Rubisco enzyme to fix inorganic carbon dioxide from the air and it enters the Calvin cycle joined to a carrier molecule (RuBP)
where does the Calvin Cycle take place in C3 plants
in the stroma of the leaf mesophyll cells
Photorespiration definition
a process in which plants take up oxygen rather than carbon dioxide in the light, resulting in photosynthesis being less efficient. (Rubisco takes up O2 instead of CO2)
what does rubisco normally do
the critical enzyme in C3 plants that brings carbon dioxide from the air into the Calvin cycle where the glucose is made
when does photorespiration occur
rubisco binds oxygen rather than carbon dioxide
does photorespiration make glucose
nooooo
why will Rubisco bind to oxygen instead of carbon dioxide
the active site can readily accommodate the oxygen molecules as well as the carbon dioxide molecules, so the two different molecules are in competition for the active site of Rubisco.
2 ways photorespiration arise in C3 plants (increase amount)
- temperature increases
- conditions dry out
why does photorespiration increase as temperature increases
the ability of the Rubisco enzyme to distinguish between carbon dioxide and oxygen decreases and, as a result, Rubisco will increasingly bind oxygen.
why does photorespiration increase as conditions dry out
C3 plants close their stomata to prevent water loss. This closure blocks the entry of carbon dioxide needed as input to the Calvin cycle and limits the exit of oxygen produced
creating a high oxygen low CO2 environment inside the mesophyll cells
how do C4 plants carry out the Calvin Cycle
carry out an adapted Calvin cycle, in which carbon fixation and glucose production occur in different cells
what are optimal conditions for C4 plants
These cells will thrive in warm and tropical regions
what anatomy changes are present in C4 plants (compared to C3 and CAM)
- bundle sheath cells have chloroplasts
- mesophyll cells that are arranged in a close association around the bundle sheath cells
where do the two processes occur in C4 plants
leaf mesophyll cells and bundle sheath cells
what happens in the first process in C4 plants (light dependent stage)
Carbon dioxide is converted into malic acid, in the mesophyll cells
PEP carboxylase catalyses the binding of carbon dioxide to an acceptor molecule (malic acid) (this is called carbon fixation)
what enzyme is used in the first step of C4 plants in photosynthesis
PEP carboxylase
why is PEP carboxylase used instead of RuBisco (C4)
It cannot bind to oxygen so photorespiration cannot happen
what happens in the second process of the C4 plants
Calvin cycle (glucose production) occurs in the bundle sheath cells
produce a steady supply of carbon dioxide from the breakdown of malic acid that raises the carbon dioxide concentration in their leaves. This allows the RuBisco in the bundle sheath cells to bind only to CO2
how do CAM plants carry out the Calvin Cycle
two stages of the Calvin cycle occurring at different times
what are optimal conditions for CAM plants
thrive in hot and arid environments, that are exposed to droughts
when does carbon fixation happen in CAM plants
at night (stomata are open)
when does the Calvin cycle happen in CAM plants
in the day (when the stomata are closed)
where do photosynthesis processes occur in the CAM plants
mesophyll cells
does CAM plants use PEP carboxylase or Rubisco initially
PEP carboxylase
what happens to the malic acid produced in CAM plants when it is night time
it is stored in vacuoles waiting for the stomata to close (day time)
what 3 things will make RuBisco work most efficiently
- carbon dioxide levels in leaves are high
- oxygen levels are low (as happens when water is freely available)
- when temperatures are moderate.
what are the 4 main factors that affect the rate of photosynthesis
- the amount of light reaching their leaves
- the temperature of the environment
- the availability of water
- the concentration of carbon dioxide
what is a limiting factor
any environmental condition that restricts the rate of biochemical reactions in an organism.
what happens to the rate of photosynthesis as light intensity increases
increases as light intensity increases, until it reaches a maximal point.
what is the light saturation point
the point where further increases in light intensity have no effect and the rate of photosynthesis stays constant
why does increased light intensity increase the rate of photosynthesis
more chlorophylls are energised
what does too little or too much water do to the rate of photosynthesis
rate of photosynthesis declines and then stops because closed stomata prevent the uptake of carbon dioxide needed for the Calvin cycle
what does waterlogging do to the rate of photosynthesis
the rate of photosynthesis will also decline and stop because the lack of oxygen for cellular respiration in root cells stops water uptake
what happens to the rate of photosynthesis as temperature increases
As the ambient temperature is increased, the rate of photosynthesis also increases due to an increase in collisions between the reactants and the enzymes involved in photosynthesis. Eventually, as the heat passes a certain threshold, the enzymes start to denature, in which the tertiary structure of an enzyme is lost. This causes the rate to again decrease.
what happens to the rate of photosynthesis as CO2 concentration increases
the rate of photosynthesis will increase until it levels off due to limiting factors
does CO2 concentration impact the light dependent stage and why
no, because CO2 is not apart of the reaction
what is cellular respiration
the process of converting chemical energy into a useable form by cells, typically ATP.
what are the 2 types of cellular respiration
aerobic and anaerobic
what is the equation for aerobic cellular respiration (without coenzymes)
glucose + oxygen arrow carbon dioxide + water + ATP
how many ATP does aerobic respiration make
30-32, 36-38 in optimal conditions
what are the 3 steps of aerobic cellular respiration
- glycolysis
- Krebs cycle
- electron transport chain
what is the main (broad) thing that happens in glycolysis
glucose is broken down into pyruvate
what is the main (broad) thing that happens in Krebs cycle
makes a supply of energy-rich loaded coenzymes
what is the main (broad) thing that happens in the electron transport cycle
transfers energy from electrons supplied by loaded coenzymes to make ATP.
where does glycolysis occur
cytosol
how much ATP is produced from glycolysis
2
what are the 3 inputs in glycolysis
glucose, 2x (ADP + Pi) and 2x (NAD+)
what are the 4 outputs in glycolysis
2x (pyruvate), 2x ATP, 2x (NADH) and two hydrogen ions (protons)
where does the Krebs cycle and electron transport chain occur
mitochondria
where specifically does the Krebs cycle occur
the matrix
what is the matrix of the mitochondria
gel like solution within their inner membrane
where specifically does the electron transport chain happen
the cristae
what does cristae do
It folds in the inner membrane of the mitochondria, it hold enzyme
what happens in between glycolysis and Krebs cycle
pyruvate oxidation
what in summary happens in pyruvate oxidation
pyruvate loses a C and an H atom, forming a 2C acetyl group that is delivered to the Krebs cycle by coenzyme A.
what are the 2 coenzymes that are becoming high in energy in the Krebs cycle
FAD+ and NAD+
what are the 4 inputs in Krebs cycle and pyruvate oxidation
2 x (acetyl CoA (acetyl groups)), 6 x (NAD+), 2 x (FAD) and 2 x (ADP + Pi)
what are the 4 outputs in Krebs cycle and pyruvate oxidation
4 x (CO2), 6 x (NADH), 2 x (FADH2) and 2 x (ATP)
detailed electron transport chain info
Electrons are transferred along enzyme complexes
The first input of high-energy electrons to the ETC comes from loaded NADH coenzymes.
FADH2 also donates its high-energy electrons to an acceptor, but further down the chain.
Oxygen accepts electrons and hydrogen ions, forming water
how is so much ATP produced in the ETC
As electrons transfer from one enzyme complex to the next, the energy released is ultimately used to power the production of ATP from ADP and Pi.
what are the 4 inputs of ETC
6 (oxygen)
26-28 (ADP + Pi)
10 (NADH)
2 (FADH2)
what are the 4 outputs of ETC
6 (water)
26-28 (ATP)
10 (NAD+)
2 (FAD)
which process of aerobic cellular respiration needs oxygen
electron transport chain
what is anaerobic respiration/fermentation
processes that occur without the presence of oxygen, producing a net of 2 ATP molecules
when does anaerobic fermentation occur in humans
occurs in human skeletal muscle cells when the supply of oxygen to the cells by aerobic cellular respiration cannot keep up with their demand for ATP.
where does anaerobic fermentation take place
the cytosol
is the rate of ATP production in anaerobic fermentation higher lower or similar to aerobic respiration
much faster, this is why it is able to produce enough ATP
what are the 2 anaerobic fermentation pathways
- alcohol (ethanol) fermentation
- lactic acid fermentation
what are the 2 processes that occur in both anaerobic fermentation pathways
glycolysis
short add on stage
is glycolysis the same in aerobic and anaerobic cellular respiration
yes
what happens in the add on stage for lactic acid fermentation
pyruvate, ADP and NADH is turned into ATP, lactic acid and NAD+
what happens in the add on stage for alcohol fermentation
alcohol is created, NAH+ is regeneraed for glycolysis again
what are the inputs and outputs of the alcohol fermentation
pyruvate, NADH, ADP
ethanol, CO2, NAD+ 2ATP
what fermentation does yeast and animals use
animals use lactic acid
yeast uses alcohol
what 3 factors affect the rate of cellular respiration
temp
oxygen concentration
glucose concentration
glucose concentration affecting cellular respiration summary
an increase in glucose concentrations leads to an increase in the rate of cellular respiration. This rate eventually levels off from rate-limiting factors
oxygen concentration affecting cellular respiration summary
As oxygen concentration increases, so does the rate of cellular respiration. This eventually levels off due to other factors limiting the rate.
what is biomass
the organic material from plants and animals; it is a renewable source of energy.
what is biofuel
Biofuels are any fuel source derived from biomass.
what is food vs fuel (biofuel sustainability)
world’s population expected to increase, there needs to be a balance between increased production of biofuels and food availability
what is land requirements (biofuel sustainability)
To meet the 2060 target for biofuel production it is estimated an additional 100 million hectares of land will be required
what is energy efficiency (biofuel sustainability)
Creating biofuels from feedstocks is currently an inefficient process. The energy required to produce and then collect the raw materials required is far greater than the fuel produced
