Transcript SAE Competency 3

Competency 3
“You must have knowledge of the
chemical processes of living
things.”
Introduction to Metabolism
Catabolism, Anabolism, & the
Laws of Thermodynamics
Metabolism
• Metabolism is the totality of an organism’s chemical processes,
managing the cellular resources of material and energy
• Metabolic reactions are organized into pathways that are
enzymatically controlled, so that no energy is wasted
• Metabolic reactions may be coupled to drive energy-requiring
reactions in the cell
• In a living cell, break-down and build-up never reach equilibrium
(otherwise the cell would be dead!!!)
• Usually, the products of most reactions will become reactants
within the metabolic pathways for the next reaction
Build-up & Break-down
• Catabolic pathways release
energy from complex
molecules into simpler ones;
free energy is lost & they are
exergonic reactions
• Anabolic pathways consume
energy to make complicated
molecules (ex: stringing
amino acids to make
proteins) These increase
order, & are endergonic
reactions
Types of Energy
• Energy is the capacity to do work
• Kinetic energy is the process of doing
work (energy of motion)
– Thermal energy (heat) is expressed as
measure of the random movement of
molecules
– Light energy from the sun is kinetic energy
which powers photosynthesis
Potential Energy
• Energy that matter
posses because of
location or
arrangement
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– Chemical energy
stored in molecules
because of bond
arrangement
– Object high on a
shelf due to gravity
Potential Energy & Free
Energy
• Objects that have a high degree of order tend to have
more potential energy because of their free energy
available to do work
• Order is the antithesis of entropy- the quantitative
measure of disorder that is proportional to
randomness
– Highly complex macromolecules (ex. Starches) have a lot of
free energy because if we break these down, we end up with
less order, smaller substances with a higher kinetic energy,
thus more random movements to create heat
Are autotrophs really producers?
• No! They are energy
transformers!
• According to the
First Law of
Thermodynamics,
energy can be
transferred and
transformed, but not
created (or
destroyed)
Open & closed systems
• The Second Law of Thermodynamics states that every energy
transfer makes the universe more disordered
• A closed system is a collection of matter under study which is
isolated from its surroundings
• Open systems react with their surroundings, so in living things,
although it make seem that entropy may decrease (making the
system more orderly) but the entropy of the system AND its
surroundings must always increase
– We extract chemical energy from molecules to build our cells, but
release to our surroundings low energy molecules & heat (King of
Entropy)
Organisms live at the Expense of
Free Energy (Just remember: nothing in
life is free..)
• Energy can be transformed, but part is
dissipated as heat
• Heat can only perform work if there is a
temperature gradient
• The Quantity of energy in the universe
is constant, but the Quality is not
• We express the amount of energy that
is available to do work as Free Energy
Free-Energy: Criterion for
Spontaneity
• According to the Gibbs-Helmholtz equation:
• ∆G = ∆H - T∆S;
• G (Gibb’s free energy) is the portion available
to do work & is the difference between the
total energy or enthalpy (H) & the energy
NOT available for doing work (TS- which is a
change in entropy times absolute
temperature in Kelvin)
Significance of free energy
• A spontaneous reaction is one that will occur without
additional energy (exergonic)
• Free energy decreases in a spontaneous process
• Higher temperatures enhance entropy changes;
greater kinetic energy of molecules tend to disrupt
order as collisions increase
• When a reaction reaches equilibrium, ∆G = 0
because there is no net change in the system
• When a reaction is forced away from equilibrium
(requiring energy) the free energy increases & hence
it is endergonic
Free Energy & Metabolism
• Exergonic reactions proceed with a net loss of free
energy
• Products have less free energy than reactants
• Reaction is energetically downhill
• ∆G is negative
Endergonic reactions
• Products store more free energy than the reactants
• They require an input of energy from their
surroundings to proceed; reaction is energetically
uphill & non-spontaneous
• ∆G is positive
What goes up, must come
down
• If chemical process is exergonic, its reverse
in endergonic
– Ex.- For each molecule of glucose oxidized in
exergonic process of cellular respiration, 2870 kJ
are released (∆G = -2870 kJ/mol)
– To produce one mole of glucose, the endergonic
process of photosynthesis requires an energy
input of 2870 kJ (∆G = +2870 kJ/mol)
Energy in the Cell
ATP & Enzymes
ATP powers cellular work
• In cellular metabolism, endergonic reactions are
driven by coupling them to reactions with a greater
negative free energy (exergonic)
• ATP (adenosine triphosphate) is a nucleotide with
unstable phosphate bonds that the cell hydrolyzes for
energy to drive endergonic reactions
• Unstable bonds in the phosphate groups (due to
repelling charges) can be hydrolyzed in an exergonic
reaction making ADP, a more stable molecule (like
relaxing a spring)
ATP is the Source
• Enables mechanical work, such as the beating of cilia
or muscle contraction
• Enables transport work, such as pumping
• Enables chemical work such as polymerization
Energy coupling
• Exergonic hydrolysis of ATP
is coupled with endergonic
processes by transferring a
phosphate group to another
molecule
• Enzymatically controlled
Regeneration of ATP
• ATP is regenerated 10 million times per
second/ per cell
• Reaction is endergonic
• Energy to drive the endergonic
regeneration of ATP comes from
cellular respiration (exergonic)
Enzymes
• Chemical reactions can occur spontaneously
if it releases free energy, but it may be too
slow to be effective
• Enzymes control reaction rates
• They are biological catalysts & are usually
proteins; they don’t change the nature of
reactions, only speed them up
• Are very selective; substrate-specific
• Lower activation energy for a reaction
Activation Energy
• Amount of energy that
reactant molecules
must absorb to start a
reaction
• Thermal energy is
usually enough to break
chemical bonds to form
the transition state, but
at cellular temp.s this is
not enough!
Nutrients
• Nutrients are
substances in food
that are necessary
for normal growth,
maintenance &
repair
• They may be
classified as
carbohydrates,
proteins, or fats
Fats
• Made of long carbon chainshave many bonds which store
LOTS of energy- 9 kilocalories
per gram actually
• May be saturated (only single
hydrogen bonds) or
unsaturated (contain double
bonds)
• Saturated fats are solids at
room temp
• Unsaturated are liquid (oils)
Carbohydrates
• Have the generic formula
CH2O
• Can be classified two
ways:
• Simple monosaccharide
or single sugars, such as
sucrose
• Complex
polysaccharides such as
starch or cellulose, which
is fiber for us
• Both provide FAST
energy
Proteins
• Made up of smaller subunits
called amino acids
• Enzymes, which are
catalysts and speed up
chemical reactions, are all
proteins
• Enzymes chop up nutrients
into small molecules that can
be absorbed into the
bloodstream
Cellular Respiration:
Harvesting Chemical Energy
Breaking bonds is
Spontaneous
• Order is Endergoniclike potential energy; in
large molecules energy
is stored in bonds
• Breaking these bonds
to make smaller
molecules is
spontaneous; -ΔG;
contributes to entropy of
the universe
Order is intrinsically unstable
• Catabolism is the
breaking down of
large organic
molecules to yield
energy
• Most efficient
catabolic pathway is
cellular respiration
Understanding Redox Reactions
•
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•
•
•
“Oil Rig”
Something that is reduced gains electrons
Something that is oxidized looses electrons
The reducing agent is the electron donor
The oxidizing agent is the electron acceptor
Redox Reaction
• Oxygen is one of the most powerful oxidizing agents
due to its electronegativity
• When oxygen pulls electrons toward it, or hydrogen
electrons are transferred, energy is released.
Now, apply it to Glucose…
• C6H12O6 + 6O2 → 6CO2 + 6H2O + Energy
+ Heat
• In this equation, glucose is oxidized…it
looses H electrons & makes carbon dioxide
• Oxygen gas is reduced; being an electron
acceptor, it is an oxidizing agent
• The transfer of the H’s to the O yields energy
How much energy, might you ask…
• Imagine if there were no energy barriers, and
glucose just spontaneously combusted?
• Every time we would eat & breathe, we would
release an enormous amt. of heat!
With no barriers…
• If hydrogens were
just stripped & given
directly to highly
electronegative
oxygen, all energy
would be violently &
immediately be
emitted as heat &
light (akaExplosion)
Obviously, that’s not the case
• Explosions are not occurring
in our body
• Glucose is broken down in a
series of controlled steps
• Each step is catalyzed by a
specific enzyme
• Energy is harnessed in an
electron transport chain
The Bad way vs. The Good
way
Basically…Electron flow goes
• Food enters the system- glucose
• Enzymes known as dehydrogenases (and can you
guess what they do???) remove 2 hydrogens from
the food & transfer them to a very important electron
acceptor called NAD+ (oxidizing agent)
• NAD+ is a key intermediate during respiration
• Dehydrogenases go by many different names- one
for each particular step of respiration
• NAD+ will take two electrons +
one proton to become NADH
• H+ is released in solution
• NAD is a coenzyme; it stands
for Nicotinamide Adenine
Dinucleotide
• From here, the electrons will
go to the electron transport
chain & be pulled to oxygen
which will be released as
water
• Remember- substances such
as FATS that are saturated
with hydrogens make excellent
fuels!
Glycolysis
• Splitting of sugar
• Minor source of ATPaccomplished by
substrate level
phosphorylation (2)
• Yields 2 NADH per
glucose molecule
• Does NOT requireO2;
does NOT produce
CO2- Anaerobic!
Energy investment phase
• Glucose is phosphorylated twice making the
molecule more chemically reactive- takes an
investment of 2 ATP’s with help of enzymes
Energy payoff
• Six-carbon sugar is cleaved making 2-threecarbon sugars, which are actually isomers of
each other
• Glyceraldehyde phosphate is favored & is
removed as fast as it is made, so equilibrium
leans in its favor
• Glyceraldehyde phosphate is oxidized (each
one) to loose one hydrogen each
• These Hydrogens are donated to NAD+ to
give 2 NADH; at the same time, a P is added
to each Glyceraldehyde phosphate
• By substrate
phosphorylation, each
molecule will loose a P
to makes 2 ATP’s
• Enolase removes H2O
to make PEP
(Phosphoenolpyruvate)
a highly unstable
molecule, which then
makes two more ATP’s
+ pyruvate
The Krebs Cycle
• Pyruvates enter mitochondrial matrix through a
transport protein
• The carboxyl group is removed from each as CO2
• 2-carbon fragments then become acetates &
extracted electrons go to NAD+ to make NADH
• Coenzyme A binds to the acetate, making an
unstable acetyl CoA
• Acetyl CoA enters Krebs cycle to be fully
oxidized
• First, oxaloacetate binds to 2-carbon fragment
removing CoA
• Two carbons from the newly formed citrate will
leave as CO2; at same time of release, 2 NAD+
become NADH
• CoA enters cycle again- by substrate
phosphorylation an ATP is made
• H2O is added to cycle to regenerate
oxaloacetate & one more NAD+ is reduced
• At the end of the Krebs
cycle, oxaloacetate is
restored to start cycle again
• We have produced 3 NADH
for EACH molecule of
pyruvate (6 per glucose
molecule)
• 2 ATP were made by
substrate level
phosphorylation
• 2 FADH2 were made (flavin
adenosine dinucleotidesame as NADH but lower
level on electron transport
chain)
• We’ve produced 6 CO2 for
each glucose- hence,
respiration!
Electron Transport Chain
• Structure fits function: Mitochondrial cristae provide space
for many copies of the chain; as we know a typical muscle
cell regenerates ATP at a rate of appx. 10 million
molecules per second; oxidative phosph. accounts for
90% of ATP generated
• NADH donates electron to flavoprotein (first acceptor in
chain)
• Next passes to another protein, then to ubiquinone, the
only non-protein carrier on chain (lipid)
• The remaining electron carriers are cytochromes which
pass electrons downhill to highly electronegative Oxygen
• For every 2 NADH molecules, one O2 molecule is reduced
to 2H2O
Generating ATP
• ATP synthase- protein complex found in inner mitochondrial
membrane that acts as an enzyme to actually generate ATP
• Oxidative Phosphorylation happens by chemiosmosis, where H+
gradient (proton-motive force) couples redox reactions of electron
transport chain
• Each NADH that contributes a pair of electrons to the chain makes
appx. 3 ATP
Efficiency of respiration
• Complete oxidation of a mole of glucose
gives 686 kcal; 36 ATP produced in all
• Phosphorylation of ADP to ATP stores 7.3
kcal per mole ATP
• Efficiency is about 38%; rest is spent on heat
to maintain body temperature, cooling
mechanisms, or just dissipated
• ATP yield is contingent upon adequate supply
of oxygen
In the end
Photosynthesis & Autotrophs
The making of organic food
molecules from inorganic
materials
The Beauty of Nature
• Plants are the base of
the ecological food web
for biosphere
• Autotrophs have the
ability to sustain
themselves using their
chloroplasts
• Heterotrophs rely on
cellular respiration; they
obtain their nutrients
elsewhere
Natural Dynamics
• Nature has balance in that the products
of photosynthesis are the reactants of
cellular respiration
• In a simplistic sense, Photosynthesis:
– CO2 + H2O  (light) C6H12O6 + O2
– Cellular respiration:
• C6H12O6 + O2  CO2 + H2O
Producers vs. Consumers
• Also known as autotrophs,
they produce organic
molecules from inorganic
• Plants rely on CO2, H2O, &
minerals as nutrients
• Require light as an energy
source (photoautotrophic)
• Examples are plants, algae,
some prokaryotes
• AKA heterotrophs
• Must acquire organic
molecules from compounds
produced by other
organisms
• They are unable to
synthesize organic
molecules from raw
inorganic materials
• Include herbivores,
carnivores & decomposers
Special cases
• Photoautotrophs sustain themselves
with energy from sunlight
• Chemoautotrophs get their energy from
the oxidation of inorganic materials in
their environment, such as H2S or NH3
• Examples include Sulfur bacteria or
Giant tube worms
Let There Be Light!
• AKA electromagnetic energy or radiation
• Entire range of radiation is called electromagnetic spectrum;
travels in waves
• Wavelength varies across the spectrum; the shorter the
wavelength (higher frequency) more energy it contains
Light & plants
• Visible light is most
important to us; it is the
light we see (UV light is
dangerous to us) & is
most readily absorbed
by plants
• Ranges from about 380
to 750 nm
• Pigments are light
absorbing substances
Plant pigments
• Plants contain several
types of light absorbing
pigments, including
chlorophyll, carotenoids
& xanthophylls
• All absorb mostly blue &
red light, therefore the
plant reflects green
Parts of the Plant
• All green parts of a plant contain chloroplasts
• Photosynthesis occurs mostly in the leaves
• Chlorophyll is green pigment located in
chloroplasts
• Chloroplasts are found mainly in the
mesophyll of the leaf (interior tissue), each
cell containing 30-40 chloroplasts
Chloroplasts
• CO2 enters leaf via stomata
(pores)
• H2O delivered by means of
veins or vascular bundles
(export sugar to roots too)
• Thylakoid sacs are layered
as grana; chlorophyll is
found in thylakoid
membranes
• Stroma is dense fluid of
c’plast; membranes separate
stroma from thylakoid space
Photosynthesis as a Redox
process
• Recall that respiration is an exergonic process;
energy is released from the oxidation of sugar
• Electron’s associated with sugar’s hydrogens lose
potential energy as carriers transport them to oxygen,
forming water
• Electronegative oxygen pulls electrons down the
transport chain, & potential energy released is used
by mitochondria to produce ATP
• Photosynthesis is endergonic; energy is required to
reduce carbon dioxide
Overview of Photosynthesis
• Occurs in 2 stages:
Light & Dark reactions
(aka Calvin Cycle)
• Light reactions convert
solar energy to
chemical bond energy
in NADPH & ATP
• Calvin cycle involves
carbon-fixation
Light Reactions
• Occur in thylakoid membranes of chloroplasts
• Reduce NADP+ to NADPH
• Light absorbed by c’phyll provides the energy to
reduce NADP+ to NADPH, which temporarily stores
energized electrons from water
• NADP+, a coenzyme similar to NAD+ in respiration, is
reduced by adding a pair of electrons plus a
hydrogen nucleus, or H+
• Gives off O2 as a by-product from split of water
• Generates ATP through photophosphorylation
Products of the Light Reaction
• 1 NADP+ becomes 1 NADPH
• 1 ADP becomes 1 ATP
• 2 H2O become 4 H+ + O2 gas
Pigment Absorption
• A pigment that absorbs all wavelengths of
light appears black
• Absorption spectrum for a pigment in solution
can be determined by using a
spectrophotometer (shows % transmittance)
• Chlorophyll a is light absorbing pigment that
participates directly in light reactions
• Accessory pigments absorb light at different
wavelengths & transfer energy to c’phyll a
Photoexcitation!
• Light is all it takes to get these babies excited!
• Absorbed photons boost one of pigment molecule’s
electrons in its lowest energy state (ground state) to
an orbital of higher potential energy (excited state)
• Pigments have unique absorption spectra because
pigments can only absorb photons corresponding to
specific wavelengths
• Excited state is unstable, so electrons quickly fall
back to ground state orbital, releasing excess energy
in the process
Primary Electron Receptor
• Traps excited state electrons released
from the reaction center chlorophyll
• Transfer of excited state electrons to
primary electron acceptor starts light
reactions
• Energy stored in the trapped electrons
powers the synthesis of ATP & NADPH
in subsequent steps
Electron transport continued
• Photosynthetic membranes use H2O to
replace electrons in chlorophyll; 2 H2O
molecules split to make 4 H+ ions and O2 gas
(released into the air)
• An excess of H+ builds up inside the
photosynthetic membrane, making a voltage
potential (more positive on the inside)
• Voltage potential couples reaction of making
ADP into ATP
Non cyclic electron flow
• Light excites electrons from P700, rxn center in
Photosystem I
• Ultimately stored in NADPH which will be electron
donor in Calvin cycle
• Primary electron acceptor passes excited state
electrons to ferredoxin (Fd), an iron-containing
protein
• NADP+ reductase catalyzes the redox rxn that
transfers these electrons from ferredoxin to NADP+,
producing reduced coenzyme NADPH
• Oxidized P700 c’phyll becomes oxidizing agent as its
electron “holes” must be filled
Restoring electrons
• P680 becomes a strong
oxidizing agent due to
missing electrons
• A water-splitting enzyme
extracts electrons from water
• Oxygen atoms combine to
form O2, which is released
as a gas
Chemiosmosis
• As excited electrons give up energy along the
transport chain to P700, coupling of exergonic flow of
electrons to endergonic rxns phosphorylate ADP to
ATP
• ATP synthase enzyme in thylakoid membrane uses
the proton-motive force to make ATP (called
photophosphorylation since it requires light energy)
Cyclic electron flow
• Uses photosystsem I but not II
• Generates ATP without producing
NADPH or oxygen gas
• Excited electrons leave c’phyll a at the
reaction center, & return to the reaction
center
• Ferredoxin immediately passes the
electrons to transport chain to P700
Calvin Cycle Overview
• Occur in the stroma of the chloroplast
• First incorporate atmospheric CO2 into existing
organic molecules by a process called carbon
fixation, then reduce fixed carbon to carbohydrate
• Reduction of CO2 to sugar requires products of the
light reactions (but not light itself)
– NADPH provides the reducing power
– ATP provides the chemical energy
Differences in Mitochondria &
Chloroplasts
• Mitochondria transfer chemical energy from food
molecules to ATP; high energy electrons extracted by
oxidation of food
• Chloroplasts transform light energy into chemical;
photosystems capture light energy to drive electron
transport chain
• ATP synthase in intermembrane space of
mitochondrial matrix; found in stroma side of
thylakoid compartment
The Calvin Cycle
• Products of light reactions
used to power Calvin cycle
to reduce carbon dioxide to
sugar
• Phase 1: Carbon fixation
• Phase 2: Reduction of 3phosphoglycerate to
glyceraldehyde phosphate
• Phase 3: Regeneration of
starting material, RuBP
Photorespiration
• An evolutiobary relic?
• Reduces yield of photosynthesis
• Consumes oxygen, evolves carbon dioxide,
produces no ATP
• Fostered by hot, dry, bright days since plants
close their stomata to prevent water loss
• Occurs when oxygen concentration is greater
inside the leaf (rubisco accepts oxygen &
transfers it to RuBP)
C4 Plants
• Calvin Cycle occurs in most plants & produces 3phopsphoglycerate, a 3-carbon compound as the first
stable intermediate
• Those plants are called C3 plants (3-C)
• Most important for agriculture are rice, wheat, &
soybeans
• C4 plants preface the Calvin cycle with a 4-C
compound; adaptative pathway because it enhances
carbon fixation under conditions that favor
photorespiration
• Used by several thousand species of plants,
including sugarcane & corn
CAM Plants
• Found in succulent plants
• Stomata open at night & close during day (opposite
of most plants)
• Conserves water during the day, but prevents CO2
from entering leaves
• When stomata open at night, CO2 is taken up &
incorporated into a variety of organic acids; called
Crassulacean Acid Metabolism
• Acids are stored in vacuoles of mesophyll cells until
morning, when light reactions supply ATP & NADPH
for Calvin cycle