Download Week 03 Lecture notes

Learning Objectives
• How do cells store energy?
• How do cells use energy?
• What types of reactions occur in cells?
 Which one requires energy as an input?
 Which one releases energy?
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What is the activation energy of a reaction?
How do catalysts speed up reactions?
How do enzymes work?
What is a biochemical pathway?
How does an enzyme’s environment affect its function?
How does ATP provide energy for the cell?
Learning Objectives
• Consider the location of photosynthesis:
 Where does the light reaction occur? Where is sugar synthesized?
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•
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The flow of energy is the flow of electrons
In very general terms, what does the electron transport system do?
Compare the proton pump to previous membrane transport
mechanisms we’ve looked at
 How does it relate to ATP synthesis?
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Carbon dioxide + water + light = sugar + oxygen + water
Both photosynthesis and cellular respiration use an electron transport
chain
Glycolysis
 Cytoplasm
 Anaerobic—Doesn’t require oxygen
•
What role does fermentation play in metabolism?
Chemical Reactions
• The starting molecules of a chemical reaction are called
the reactants or substrates
• The output molecules from the reaction are called
products
What are the substrates?
What are the products?
Where is the energy?
Is the energy kinetic or potential?
Endergonic vs. Exergonic
There are two kinds of chemical reactions
 endergonic reactions have products with more energy than the
reactants
• these reactions require an input of energy
 exergonic reactions have products with less energy than the
reactants
• these reactions tend to occur spontaneously
Is polysaccharide
formation endergonic
or exergonic?
Exergonic Reactions
Question:
• If exergonic reactions tend to occur
spontaneously, why haven’t they all done so?
Activation Energy
• All chemical reactions require an initial input of
energy called activation energy
 the activation energy initiates a chemical reaction by
destabilizing existing chemical bonds
Catalysis
Reactions become more
likely to happen if their
activation energy is lowered
 this process is called
catalysis
 catalyzed reactions proceed
much faster than noncatalyzed reactions
.
Enzymes
Enzymes are the catalysts used by cells to
perform particular reactions
 enzymes bind specifically to a molecule and
stress the bonds to make the reaction more
likely to proceed
 the active site is the site on the enzyme that
binds to a reactant
 the site on the reactant where the enzyme
binds is called the binding site
Figure 5.5 An enzyme’s shape
determines its activity
Induced fit
How Enzymes Work
• The binding of a reactant to an enzyme
causes the enzyme’s shape to change
slightly
 this leads to an “induced fit” where the
enzyme and substrate fit tightly together as a
complex
 the enzyme lowers the activation energy for
the reaction
 the enzyme is unaffected by the chemical
reaction and can be re-used
Essential Biological Process 5A:
How Enzymes Work
Animation: How Enzymes Work
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Animation: Enzyme Action and the
Hydrolysis of Sucrose
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Inquiry & Analysis
Do Enzymes Physically
Attach to Their
Substrates?
Biochemical Pathways
• Catalyzed reactions
may occur together in
sequence
 the product of one
reaction is the
substrate for the next
reaction until a final
product is made
 the series of reactions
is called a
biochemical pathway
Figure 5.6 A biochemical pathway
Animation: A Biochemical Pathway
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Factors Affecting Enzymes
• Temperature and pH affect enzyme activity
 enzymes function within an optimum temperature
range
• when temperature increases, the shape of the enzyme
changes due to denaturing of the protein chains
 enzymes function within an optimal pH range
• the shape of enzymes is also affected by pH
• most human enzymes work best within a pH range of 6 - 8
– exceptions are stomach enzymes that function in acidic ranges
Figure 5.7 Enzymes are
sensitive to their environment
Why might a human
enzyme need to
function at low pH?
Enzyme Regulation
• Cells can control enzymes by altering their
shape
 allosteric enzymes are affected by the
binding of signal molecules
• some signals act as repressors
– inhibit the enzyme when bound
• other signals act as activators
– change the shape of the enzyme so that it can bind
substrate
Essential Biological Process 5B:
Regulating Enzyme Activity
Enzyme Inhibition
Feedback inhibition is a form of enzyme
inhibition where the product of a reaction acts as a
repressor
 competitive inhibition
• the inhibitor competes with the substrate for the active site
• the inhibitor can block the active site so that it cannot bind
the substrate
 non-competitive inhibition
• the inhibitor binds to the allosteric site and changes the
shape of the active site so that no substrate can bind
Which type of feedback inhibition is more common? Why do you think that
is the case?
Figure 5.8 How enzymes can be
inhibited
Animation: Feedback Inhibition of
Biochemical Pathways
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some animations will not appear until the presentation
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may see blank slides in the “Normal” or “Slide Sorter”
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animations will require the latest version of the Flash
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ATP: The Energy Currency of the
Cell
• The energy from the sun or from food
sources must be converted to a form that
cells can use
 adenosine triphosphate (ATP) is the energy
currency of the cell
Structure of ATP
The structure of ATP suits it as an
energy carrier

each ATP molecule has three
parts
1.
2.
3.
a sugar
an adenine nitrogenous base
a chain of three phosphate
groups


the phosphates are negatively
charged and it takes a lot of
chemical energy to hold them
together
the phosphates are poised to
come apart
ATP Hydrolysis
• When the endmost phosphate group is broken off an
ATP molecule, energy is released
ATP  ADP + Pi + energy
• The Pi represents inorganic phosphate
ATP: Coupled Reactions
• Coupled reactions
 usually endergonic reactions are coupled with the
breakdown of ATP
• more energy than is needed is released by the breakdown of
ATP so heat is given off
• ATP cycles in the cell with respect to its energy
needs
Figure 5.10
The ATP-ADP Cycle
How ATP Is Made
•
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ATP powers many key cell activities
Cells use two processes to convert energy from the sun and from
food molecules into ATP
 photosynthesis
• some cells convert energy from the sun into ATP and then use it to make
sugars that store potential energy
 cellular respiration
• cells break down the potential energy in sugars and convert it ATP
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
TABLE 5.1
How Cells Use ATP Energy to Power Cellular Work
ATP
Table 5.1 How Cells
Use ATP Energy to
Power Cellular Work
P
Product
ATP
ADP
ATP
Reactant
Biosynthesis
Contraction
Chemical Activation
Cells use the energy released from the
exergonic hydrolysis of ATP to drive endergonic
reactions like those of protein synthesis, an
approach called energy coupling.
In muscle cells, filaments of protein repeatedly
slide past each other to achieve contraction
of the cell. An input of ATP is required for the
filaments to reset and slide again.
Proteins can become activated when a highenergy phosphate from ATP attaches to the
protein, activating it. Other types of molecules
can also become phosphorylated by transfer of
a phosphate from ATP.
Outside of cell
Sugar
Outside of cell
Na+
Vesicle or organelle
Other
associated
proteins
Coupled
transport
protein
Ion
pump
Na+–K+
pump
Motor protein
Connector
proteins
ATP
K+
ATP
Inside of cell
ATP
Inside of cell
Microtubule
Importing Metabolites
Active Transport: Na+– K+ Pump
Cytoplasmic Tansport
Metabolite molecules such as amino acids
and sugars can be transported into cells
against their concentration gradients by
coupling the intake of the metabolite to the
inward movement of an ion moving down its
concentration gradient, this ion gradient being
established using ATP.
Most animal cells maintain a low internal
concentration of Na+ relative to their
surroundings, and a high internal concentration
of K+. This is achieved using a protein called the
sodium- potassium pump, which actively pumps
Na+ out of the cell and in, using energy from ATP.
Within a cell’s cytoplasm, vesicles or organelles
can be dragged along microtubular tracks using
molecular motor proteins, which are attached
to the vesicle or organelle with connector
proteins. The motor proteins use ATP to power
their movement.
Cell
Macrophage cell
Actin
ATP
Heat
Flagellum
H2O
ATP
+
ATP
H+ + Pi + ADP
Flagellar Movements
Cell Crawling
Heat Production
Microtubules within flegella slide past each
other to produce flagellar movements. ATP
powers the sliding of the microtubules.
Actin filaments in a cell’s cytoskeleton
continually assemble and disassemble to
achieve changes in cell shape and to allow cells
to crawl over substrates or engulf materials. The
dynamic character of actin is controlled by
molecules bound to actin filaments.
The hydrolysis of the ATP molecule releases
heat. Reactions that hydrolyze ATP often take
place in mitochondria or in contracting muscle
cells and may be coupled to other reactions.
The heat generated by these actions can be
used to maintain an organism’s temperature.
An Overview of Photosynthesis
All of the energy used by almost all living
cells ultimately comes from the sun
 plants, algae, and some bacteria capture the
sunlight energy by a process called
photosynthesis
 only about 1% of the available energy in
sunlight is captured
What biological theme from Chapter 1 does
this relate to?
Overview of Photosynthesis
What other biological theme could we relate this to?
The Chloroplast
Only the leaf cells of plants contain
chloroplasts
 the chloroplast contains internal
membranes called thylakoids
 the stroma is a semi-liquid substance
that surrounds the thylakoids (like the
cytoplasm of the chloroplast)
Why are the
thylakoids green?
Photosystems-Pigments
Embedded in the
thylakoid membrane are
photosystems that
contain pigments
 the primary pigment
molecule in most
photosystems is
chlorophyll
 the pigments act as an
antenna to capture
energy from sunlight
Photosynthesis takes places in three
stages
1. capturing energy from
sunlight
2. using the captured
energy to produce ATP
3. using the ATP to make
carbohydrates from CO2
in the atmosphere
Inside the
chloroplast, but
outside the thylakoid
Photosynthesis: Role of Electrons
Photosystems transfer light energy to electrons
 The flow of energy through the cell is the flow of electrons
 The energy from the electron is used to make ATP (Electron Transport System)
 The electron itself is donated to the formation of glucose
Electrons are transferred from water to glucose
Revisiting our biological theme from Ch.1: The flow of energy
How Plants Capture Energy from
Sunlight
The main pigment in plants is chlorophyll
 Chlorophyll absorbs light at the end of the visible spectrum,
mainly blue and red light
 Chlorophyll pigments and protein molecules occur as complexes
within the thylakoid membrane
 Light energy is first captured by a chlorophyll pigment in a
photosystem
 The energy is passed along to an electron, which subsequently
passes through the electron transport system (ETS)
Figure 6.2 How a photosystem works
ETS
Water
Electron Transport System
• The electron transport system (ETS)
receives the excited electron from the
electron acceptor
 the ETS is comprised of proteins that are
embedded in the thylakoid membrane
 one of these proteins acts as a proton pump
to move a proton from the stroma into the
thylakoid space
 at the end of the ETS, the electron is used to
generate O2
Electron Transport System
Energized electrons are passed through the ETS in the
thylakoid membrane
• Its energy is used to power a “proton pump” that
transports protons against their concentration gradient –
Active transport
How is this like the
sodium-potassium
pump?
Animation: Proton Pump
Please note that due to differing operating systems,
some animations will not appear until the
presentation is viewed in Presentation Mode (Slide
Show view). You may see blank slides in the
“Normal” or “Slide Sorter” views. All animations
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playing each animation. Most animations will
require the latest version of the Flash Player, which
is available at http://get.adobe.com/flashplayer.
ATP synthase
Protons diffuse across membrane (“down” their
concentration gradient) through the enzyme ATP synthase
• Passage of protons through ATP synthase turns it,
catalyzing ATP synthesis.
• ATP and electrons produced by ETS are used to make
glucose in the stroma.
• Energy from the sun is stored by photosynthesis
https://www.youtube.com/watch?v=PjdPTY1wHdQ
Building New Molecules
• The synthesis of sugar
from CO2 employs the
Calvin cycle
 the products of the lightdependent reactions are
used
• ATP energy drives the
cycle
Where Is the Energy in Food?
The energy for living is obtained by breaking
down the organic molecules originally
produced in plants
 the energy invested in building the organic
molecules is retrieved by stripping away
electrons and using them to make ATP
 this process is called cellular respiration
The Food Reaction
• Eukaryotes produce the majority of their ATP by
harvesting electrons from the food molecule glucose:
C6H12O6 + 6 O2  6 CO2 + 6 H2O + energy
• The reactants are glucose and oxygen, and the products
are carbon dioxide, water, and energy (heat or ATP)
• In cellular respiration, oxygen is the final electron
acceptor
Cellular Respiration
• The “opposite” of photosynthesis; high-energy electrons
are harvested by breaking down sugars
• Electrons pass through ETS in mitochondria
 Again, the energy from the electron is used to power proton
pumps and generate a proton gradient across the membrane
 Flow of protons down the gradient through ATP synthase
produces ATP
 This ATP provides the energy for the cell
We’re still following the
flow of energy through the
cell
Figure 7.3 An overview of cellular respiration
Glycolysis
1st step in breakdown of glucose
• Occurs in cytoplasm, not in mitochondria
• Only produces 2 ATP
• 3-carbon sugars produced by glycolysis are then used
by mitochondria
This is the only way
organisms can derive energy
from food in the absence of
oxygen
Acetyl-CoA
• CoA is an important molecule in the Krebs cycle
• As the Krebs cycle proceeds, CoA becomes acetyl-CoA
 If energy is needed, acetyl-CoA is used in production of ATP
 If energy is not needed, acetyl-CoA is used to produce energystoring fat.
Krebs Cycle
• Occurs in mitochondria
• High-energy electrons are harvested from byproducts of
glycolysis
• The energy from the electrons is used by the ETS to
produce lots of ATP (>30)
 Involves proton pumps and ATP synthase
• Carbon dioxide is a byproduct
How does this differ from
photosynthesis?
ETC-Powered Proton Pumps
High-energy electrons are
transferred to a series of
proteins embedded in the
mitochondrial membrane
 Called the electron transport
chain
 Many of the proteins in the ETC
operate as proton pumps,
pumping protons into the
intermembrane space of the
mitochondrion
 The last transport protein
donates the electrons to
hydrogen and oxygen in order
to form water
Figure The electron transport chain
Chemiosmosis ATP
Mitochondria use
chemiosmosis to make
ATP
 as the concentration of
protons builds up in the
intermembrane space, the
protons diffuse back across
the membrane (down their
concentration gradient)
through ATP synthase
channels
 their passage powers the
production of ATP from
ADP
Fermentation
Alternative to Krebs cycle that occurs in absence
of oxygen
 Does not require mitochondria
• bacteria carryout more than a dozen kinds of fermentation
• eukaryotic cells are capable of only a few types of
fermentation
– Ethanol
– Lactic acid
Glucose Is Not the Only Food
Molecule
Cells also get energy from foods other than
sugars
 proteins are first broken down into their individual
amino acids
• deamination removes amino groups so molecules can
take part in the Krebs cycle
 fats are first broken down into fatty acids