Bio8 Flashcards
8.1 Explain what
metabolic pathways
are
• Metabolic pathways consist of chains and cycles
of enzyme-catalysed reactions
metabolism: sum total of all reactions that occur
within an organism in order to maintain life
-chemical changes in a cell result from a series of
reactions (pathways)
-with each step controlled by a specific enzyme
Metabolic pathways allow for a greater level of
regulation:
-the chemical change is controlled by numerous
intermediates
-typically organised into chains or cycles of
enzyme-catalysed reactions
Examples of chains: Glycolysis (in cell respiration),
coagulation cascade (in blood clotting)
Examples of cycles: Krebs cycle (in cell
respiration), Calvin cycle (in photosynthesis)
8.1 Explain the
function of
enzymes.
Enzymes lower the activation energy of the chemical reactions that they
catalyse
-enzyme binds to a substrate -> stresses and destabilises the bonds in the
substrate
-the substrate binds to the active site and is altered to reach the transition state
-it is then converted into the products, which separate from the active site.
-reduces the overall energy level of the substrate’s transitionary state
-the activation energy of the reaction is therefore reduced. (The net amount of
energy released by the reaction is unchanged by the involvement of the
enzyme.)
-so less energy is needed to convert it into a product and the reaction
proceeds at a faster rate
8.1 Explain enzyme
inhibition.
• Enzyme inhibitors can be competitive or non-
competitive
enzyme inhibitor: a molecule that disrupts the
normal reaction pathway between an enzyme and
a substrate
-prevent the formation of an enzyme-substrate
complex and hence prevent the formation of
product
**may be either reversible or irreversible
depending on the specific effect of the inhibitor
being used
Competitive Inhibition
-involves a molecule, other than the substrate,
binding to the enzyme’s active site
-inhibitor is structurally and chemically similar to
the substrate (hence able to bind to the active
site)
-competitive inhibitor blocks the active site and
thus prevents substrate binding
-as the inhibitor is in competition with the
substrate, its effects can be reduced by increasing
substrate concentration
Noncompetitive Inhibition
-involves a molecule binding to a site other than
the active site (an allosteric site)
-binding of the inhibitor to the allosteric site
causes a conformational change to the enzyme’s
active site
-the active site and substrate no longer share
specificity, meaning the substrate cannot bind
-as the inhibitor is not in direct competition with
the substrate, increasing substrate levels cannot
mitigate the inhibitor’s effect
8.1 Identify one
specific example
for competitive and
non-competitive
inhibition and
explain it.
Relenza (Competitive Inhibitor)
-a synthetic drug designed by Australian scientists
to treat individuals infected with the influenza
virus
-virions are released from infected cells when the
viral enzvme neuraminidase cleaves a docking
protein (haemagglutinin)
-relenza competitivelv binds to the neuraminidase
active site and prevents the cleavage of the
docking protein
-virions are not released from infected cells,
preventing the spread of the influenza virus
Cyanide (Noncompetitive Inhibitor)
-cyanide is a poison which prevents ATP
production via aerobic respiration -> eventual
death
-it binds to an allosteric site on cytochrome
oxidase - a carrier molecule that forms part of the
electron transport chain
-by changing the shape of the active site,
cytochrome oxidase can no longer pass electrons
to the final acceptor (oxygen)
-the electron transport chain cannot continue to
function and ATP is not produced via aerobic
respiration
8.1 Explain how
metabolic pathways
can be controlled
and provide an
example.
• Metabolic pathways can be controlled by end-
product inhibition
End-product inhibition: a form of negative
feedback by which metabolic pathways can be
controlled
-the final product in a series of reactions inhibits
an enzyme from an earlier step in the sequence
-product binds to an allosteric site and
temporarily inactivates the enzyme (non-
competitive inhibition)
-enzyme can no longer function -> reaction
sequence is halted -> rate of product formation is
decreased
**functions to ensure levels of an essential
product are always tightly regulated
-product levels build up -> inhibition -> decreases
the rate of further product formation
-product levels drop -> reaction pathway
proceeds -> the rate of product formation will
increase
• End-product inhibition of the pathway that
converts threonine to isoleucine
Isoleucine: an essential amino acid = not
synthesised by the body in humans (and hence must be ingested)
-in plants and bacteria, isoleucine may be
synthesised from threonine in a five-step reaction
pathway
-in lst step: threonine is converted into an
intermediate compound by an enzyme (threonine
deaminase)
-isoleucine can bind to an allosteric site on this
enzyme and function as a non-competitive
inhibitor
-excess production of isoleucine inhibits further
synthesis, it functions as an example of end-
product inhibition
-feedback inhibition ensures that isoleucine
production does not cannibalise available stocks
of threonine
8.1 Application: Use
of databases to
identify potential
new anti-malarial
drugs.
Malaria is a disease caused by parasitic
protozoans of the genus Plasmodium
the disease is transmitted via mosquito bites
-maturation and development of the parasite in
both human and mosquito host is coordinated by
specific enzymes
-targeting these enzymes for inhibition, new anti-
malarial drugs and medications can be produced
Scientists have sequenced the genome of
infectious species of Plasmodium and used it to
determine the parasite’s proteome
-enzymes involved in parasitic metabolism have
been identified as potential targets for inhibition
-enzymes may be screened against a
bioinformatic database of chemicals to identify
potential enzyme inhibitors
-promising compound identified -> chemically
modified to improve its binding affinity and lower
its toxicity
An alternative method by which potential new
anti-malarial medications can be synthesised is via
rational drug design
-involves using computer modelling techniques to
invent a compound that will function as an
inhibitor
-using combinatorial chemistry, a compound is
synthesised that is complementary to the active
site of the target enzyme
8.2 Give a general
account on how
energy in ATP is
converted for
cellular usage
• Phosphorylation of molecules makes them less
stable
D
phosphorylation: the addition of phosphate to an
organic compound.
-one ATP contains three covalently bonded
phosphate groups (potential energy stored in
bonds)
-phosphorylation makes molecules less stable
and hence ATP is a readily reactive molecule that
contains high energy bonds
-When ATP is hydrolysed (to form ADP + Pi), the
energy stored in the terminal phosphate bond is
released for use by the cell
ATP is synthesised from ADP using energy
derived from one of two sources:
-solar energy - photosynthesis converts light
energy into chemical energy that is stored as ATP
-oxidative processes - cell respiration breaks
down organic molecules to release chemical
energy that is stored as ATP
**
8.2 Explain
glycolysis in cellular
respiration.
• In glycolysis, glucose is converted into pyruvate
in the cytoplasm
-a hexose sugar (6C) is broken down into two
molecules of pyruvate (3C)
1. Phosphorylation
-hexose sugar (typically glucose) is
phosphorylated by two molecules of ATP (to
form a hexose bisphosphate)
-makes the molecule less stable and more
reactive, and also prevents diffusion out of the
cell
-glucose + 2P
2. Lysis
-hexose biphosphate (6C sugar) is split into two
triose phosphates (3C sugars)
3. Oxidation
-H atoms are removed from each of the 3C
sugars (via oxidation) to reduce NAD+ to NADH (+
H+)
-2 molecules of NADH are produced in total (one
from each 3C sugar)
4. ATP formation
-some energy released from the sugar intermediates is used to directly synthesise ATP
-direct synthesis of ATP is called substrate level
phosphorylation
-in total, 4 molecules of ATP are generated
during glycolysis by substrate level
phosphorylation (2 ATP per 3C sugar)
At the end of glycolysis, the following reactions
have occurred:
-glucose (6C) has been broken down into two
molecules of pyruvate (3C)
-two hydrogen carriers have been reduced via
oxidation (2 × NADH + H+)
-net total of two ATP molecules have been
produced (4 molecules were generated, but 2
were used)
• Glycolysis gives a small net gain of ATP without
the use of oxygen
-no 02 = pyruvate is not broken down further and
no more ATP is produced (incomplete oxidation)
-pyruvate remains in the cytosol and is converted
into lactic acid (animals) or ethanol and CO2
(plants and yeast)
-this conversion is reversible and is necessary to ensure that glycolysis can continue to produce
small quantities of ATP
-glycolysis involves oxidation reactions that cause
hydrogen carriers (NAD+) to be reduced
(becomes NADH + H+)
-the reduced hydrogen carriers are oxidised via
aerobic respiration to restore available stocks of
NAD+In the absence of oxygen
-glycolysis will quickly deplete available stocks of
NAD*, preventing further glycolysis
-fermentation of pyruvate involves a reduction
reaction that oxidises NAH (releasing NAD+ to
restore available stocks)
-hence, anaerobic respiration allows small
amounts of ATP to be produced (via glycolysis) in
the absence of oxygen
• Energy released by oxidation reactions is carried
to the cristae of the mitochondria by reduced
NAD and FAD
8.2 Explain the link
reaction
• In link reaction pyruvate is decarboxylated and
oxidised, and converted into acetyl compound
and attached to coenzyme A to form acetyl
coenzyme A in the link reaction
六
Ist stage of aerobic respiration is the link reaction,
which transports pyruvate into the mitochondria.
-pyruvate is transported from the cytosol into the
mitochondrial matrix by carrier proteins on the
mitochondrial membrane
-pyruvate loses a carbon atom (decarboxylation),
which forms a carbon dioxide molecule
-2C compound then forms an acetyl group when
it loses hydrogen atoms via oxidation (NAD+ is
reduced to NADH + H+)
-acetyl compound then combines with coenzyme
A to form acetyl coenzyme A (acetyl CoA)
the link reaction occurs twice per molecule of
glucose
-per glucose molecule, the link reaction produces
acetyl COA (×2), NADH + H+ (2) and CO2 (2)
8.2 Explain the
Krebs Cycle.
• In the Krebs cycle, the oxidation of acetyl
groups is coupled to the reduction of hydrogen
carriers, liberating carbon dioxide
-acetyl CoA transfers its acetyl group to a 4C
compound to make a 6C compound
-coenzyme A is released and can return to the
link reaction to form another molecule of acetvl
COA
-over a series of reactions, the 6C compound is
broken down to reform the original 4C
compound (hence, a cycle)
-2 carbon atoms are released via decarboxvlation
to form two molecules of carbon dioxide (CO2)
-multiple oxidation reactions result in the
reduction of hydrogen carriers (3 × NADH + H+ ; 1
× FADH2)
-1 molecule of ATP is produced directly via
substrate level phosphorylation
**the Krebs cycle occurs twice
Per glucose molecule, the Krebs cycle produces:
4x CO2 ;
2× ATP :
6* NADH + H+ ;
2× FADH2
8.2 Explain the
processes in the
electron transport
chain.
• Transfer of electrons between carriers in the
electron transport chain in the membrane of the
cristae is
coupled to proton pumping.
-hydrogen carriers donate high energy electrons
to the ETC (located on the cristae)
-as the electrons move through the chain they
lose energy, which is transferred to the electron
carriers within the chain
-the electron carriers use this energy to pump
hydrogen ions from the matrix and into the
intermembrane space
-accumulation of H+ ions in the intermembrane
space creates an electrochemical gradient (or a
proton motive force)
-H+ ions return to the matrix via the
transmembrane enzyme ATP synthase (this
diffusion of ions is called chemiosmosis)
-as the ions pass through ATP synthase they
trigger a phosphorylation reaction which
produces ATP (from ADP + Pi)
• Oxygen is needed to bind with the free protons
to maintain the hydrogen gradient, resulting in the
formation of water
-de-energised electrons are removed from the chain by oxygen, allowing new high energy
electrons to enter the chain
-02 also binds matrix protons to form water - this
maintains the hydrogen gradient by removing H+
ions from the matrix
8.2 Skill: Analysis of
diagrams of the
pathways of
aerobic respiration
to deduce where
decarboxylation
and oxidation
reactions occur
Decarboxylation:
-C atoms are removed from the organic molecule
(glucose) to form carbon dioxide
-2 in Link reaction and 4 in Krebs
Oxidation:
-e- and H+ are removed from glucose and taken
up by hydrogen carriers (NADH and FADH2)
-2 NADH in glycolysis
-2 NADH in link reaction
-6 NADH and 2 FADH2 in Krebs
8.2 Skill: Annotation
of a diagram of a
mitochondrion to
indicate the
adaptations to its
function.
List out the
structures of the
mitochondria and its
adaptations.
• The structure of the mitochondrion is adapted to
the function it performs
-eukarvotic cells possess mitochondria - aerobic
prokaryotes use the cell membrane to perform
oxidative phosphorylation
-outer membrane - the outer membrane contains
transport proteins that enable the shuttling of
pyruvate from the cytosol
-inner membrane - contains the electron transport
chain and ATP synthase (used for oxidative
phosphorylation)
-cristae - the inner membrane is arranged into
folds (cristae) that increase the SA:Vol ratio (more
available surface)
-intermembrane space - small space between
membranes maximises hydrogen gradient upon
proton accumulation
-matrix - central cavity that contains appropriate
enzymes and a suitable pH for the Krebs cycle to
Occur
8.3 Outline the
process of
photosynthesis.
Photosynthesis is a two-step process:
• Light dependent reactions take place in the
intermembrane space of the thvlakoids
• Light independent reactions take place in the
stroma.
Step 1: LDR
-light is absorbed by chlorophyll, which releases
energised electrons that are used to produce ATP
(chemical energy)
-electrons are donated to carrier molecules
(NADP+), which is used (along with ATP) in the
light independent reactions
-electrons lost from the chlorophyll are replaced
by water, which is split (photolysis) to produce
oxygen and hydrogen
Step 2: Light Independent Reactions
-ATP and hydrogen / electrons (carried by
NADPH) are transferred to the site of the light
independent reactions
-hydrogen / electrons are combined with carbon
dioxide to form complex organic compounds
(e.g. carbohydrates)
-ATP provides the required energy to power
these anabolic reactions and fix the carbon
molecules together
8.3 Outline light
dependent reaction
in photosynthesis.
-light dependent reactions occur within the
intermembrane space of the thylakoids
-chlorophyll in Photosystems I and Il absorb light,
which triggers the release of high energy
electrons (photo activation)
-excited electrons from Photosystem Il are
transferred between carrier molecules in an
electron transport chain
-electron transport chain translocates H+ ions
from the stroma to within the thylakoid, creating a
proton gradient
-the protons are returned to the stroma via ATP
synthase, which uses their passage (via
chemiosmosis) to synthesise ATP
-excited electrons from Photosystem I are used to
reduce NAD+ (forming NADPH)
-electrons lost from Photosystem I are replaced
by the de-energised electrons from Photosystem
Il
-electrons lost from Photosystem Il are replaced
following the photolysis of water
-products of the light dependent reactions (ATP
and NADPH) are used in the light independent
reactions
8.3 Explain light
dependent reaction
in photosynthesis.
-excitation of photosystems by light energy
-production of ATP via an electron transport
chain
-reduction of NAD+ and the photolysis of water
-light dependent reactions use photosynthetic
pigments (organised into photosystems) to
convert light energy into chemical energy
(specifically ATP and NADPH)
• Absorption of light by photosystems generates
excited electrons
• Transfer of excited electrons occurs between
carriers in thylakoid membranes
Step 1: Excitation of Photosystems by Light Energy
-photosystems are groups of photosynthetic
pigments (including chlorophyll) embedded within
the thylakoid membrane
-photosystems are classed according to their
maximal absorption wavelengths (PS I = 700 nm ;
PS I| = 680 nm)
-when a photosystem absorbs light energy,
delocalised electrons within the pigments become
energised or ‘excited’
-excited electrons are transferred to carrier
molecules within the thylakoid membrane
Excited electrons from Photosvstem I are used to contribute to generate a proton gradient
• ATP synthase in thylakoids generates ATP using
the proton gradient
Step 2: Production of ATP via an Electron
Transport Chain
-excited electrons from Photosystem I (P680) are
transferred to an electron transport chain within
the thylakoid membrane
-as the electrons are passed through the chain
they lose energy, which is used to translocate H+
ions into the thylakoid
-build up of protons within the thylakoid creates
an electrochemical gradient, or proton motive
force
-H+ ions return to the stroma (along the proton
gradient) via the transmembrane enzyme ATP
synthase (chemiosmosis)
-ATP synthase uses the passage of H+ ions to
catalyse the synthesis of ATP (from ADP + Pi)
-above process is photophosphorylation - as light
provided the initial energy source for ATP
production
-newly de-energised electrons from Photosystem
Il are taken up by Photosystem I
• Excited electrons from Photosystem I are used to reduce NADP
• Photolysis of water generates electrons for use
in the light dependent reactions
Step 3: Reduction of NAD+ and the Photolysis of
Water
-excited electrons from Photosystem I may be
transferred to a carrier molecule and used to
reduce NADP+
-forms NADPH - which is needed (in conjunction
with ATP) for the light independent reactions
-electrons lost from Photosystem I are replaced
by de-enerqised electrons from Photosystem Il
-electrons lost from Photosystem Il are replaced
by electrons released from water via photolysis
-H2O is split by light energy into H+ ions (used in
chemiosmosis) and oxygen (released as a by-
product)
• Reduced NAD and ATP are produced in the
light dependent reactions
8.3 Explain
photophosphorylation.
• Photophosphorylation may be either a cyclic
process or a non-cyclic process
Cyclic:
-involves the use of only one photosystem (PS 1)
and does not involve the reduction of NADP+
-when light is absorbed by Photosystem I, the
excited electron may enter into an electron
transport chain to produce ATP
-the de-energised electron returns to the
photosystem, restoring its electron supply (hence:
cyclic)
-electron returns to the photosystem, so NAD+ is
not reduced and water is not needed to replenish
the electron supply
Non-Cyclic
-involves two photosystems (PS I and PS I) and
the reduction of NADP+
-light is absorbed by Photosystem Il, the excited
electrons enter into an electron transport chain to
produce ATP
-photoactivation of Photosystem I results in the
release of electrons which reduce NAD+ (forms
NADPH)
-photolysis of water releases electrons which
replace those lost by Photosystem Il (PS I
electrons replaced by PS I1)
-cyclic photophosphorylation can be used to
produce a steady supply of ATP in the presence
of sunlight
-non-cyclic photophosphorylation produces
NADPH in addition to ATP (this requires the
presence of water)
**only non-cyclic photophosphorylation allows
for the synthesis of organic molecules and long
term energy storage
8.3 Explain light
independent
reactions.
-carboxylation of ribulose bisphosphate
-reduction of glycerate-3-phosphate
-regeneration of ribulose bisphosphate
• In the light independent reactions a carboxylase
catalvses the carboxvlation of ribulose
bisphosphate
Step 1: Carbon Fixation
-Calvin cycle begins with a 5C compound called
ribulose bisphosphate (or RUBP)
-enzyme, RUBP carboxylase (or Rubisco),
catalyses the attachment of a CO2 molecule to
RUBP
-resulting 6C compound is unstable, and breaks
down into two 3C compounds - called
glycerate-3-phosphate (GP)
A single cycle involves three molecules of RuBP
combining with three molecules of CO2 to make
six molecules of GP
• Glycerate-3-phosphate is reduced to triose
phosphate using reduced NAP and ATP
Step 2: Reduction of Glycerate-3-Phosphate
-reduction by NADPH transfers hydrogen atoms
to the compound, while the hydrolysis of ATP
provides energy
-each GP requires one NADPH and one ATP to form a triose phosphate - so a single cycle
requires six of each molecule
• Triose phosphate is used to regenerate RUBP
and produce carbohydrates
• Ribulose bisphosphate is reformed using ATP
Step 3: Regeneration of RuBP
-of the six molecules of TP produced per cycle,
one TP molecule may be used to form half a
sugar molecule
-two cycles are required to produce a single
glucose monomer, and more to produce
polysaccharides like starch
-remaining five TP molecules are recombined to
regenerate stocks of RuBP (5 × 3C = 3 × 5C)
-regeneration of RuB requires energy derived
from the hydrolysis of ATP
