bellringer #1… explain the 4 structures of a protein. where are proteins made?
TRANSCRIPT
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BELLRINGER #1…Explain the 4 structures of a protein.
Where are proteins made?
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Answers to Bellringer… Primary= amino acid structure Secondary = alpha helices and beta sheets;
HYDROGEN BONDING creates these folds and coils
Tertiary = forms 3D structure R groups (side chains) on amino acids bind together Ionic bonds, Van der Waals forces, Disulfide
bridges, Hydrogen bonding Quartnary = 2+ polypeptides bond together
(NOT ALL PROTEINS); different protein DOMAINS are created-each can do a different fxn (ex: hemoglobin protein)
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Answers to Bellringer… (Part 2)
Proteins are made on ribosomes FREE RIBOSOMES= make proteins
that are used INSIDE cell ATTACHED RIBOSOMES (to Rough
ER) = make proteins that are shipped out of cell and used elsewhere in organism
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BELLRINGER #2… How do you determine the rate
of reaction for this enzyme?
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http://www.hippocampus.org/Biology;jsessionid=0F877174B8F739BC8C8FE629659CA510
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How does HEAT affect an enzyme?
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How does pH affect an enzyme?
http://www.phschool.com/science/biology_place/labbench/lab2/ph.html
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Chapter 8: Part 1ENERGY
An Introduction to MetabolismAP BiologyMs. Gaynor
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Metabolism An organism’s metabolism transforms
matter and energy follows the laws of thermodynamics
MetabolismSum of ALL of an organism’s
chemical reactions
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Metabolic Pathways
A metabolic pathway has many stepsbegin w/ a specific molecule and
end with a producteach pathway catalyzed by
many different enzymes
Enzyme 1 Enzyme 2 Enzyme 3
A B C D
Reaction 1 Reaction 2 Reaction 3
Startingmolecule
Product
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Metabolic Pathways and Enzyme Inhibition
Competitive inhibitors mimic the substrate and
compete for the active site.Non-competitive inhibitors
bind to enzyme away from active site cause a change in the active site
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Regulation of Enzyme Activity
A cell’s metabolic pathways must be tightly regulatedRegulating enzymes help CONTROL
metabolism
Allosteric Regulationwhen a protein’s function at one
site is affected by binding of a regulatory molecule at another site
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http://bcs.whfreeman.com/thelifewire/content/chp06/0602002.html
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Allosteric Regulation & Enzymes
Regulatory molecules bind to enzyme’s allosteric site changing shape of enzyme.
Allosterically regulated enzymes have a quaternary protein structure
Each subunit of the enzyme has an active site and an allosteric site.
Allosteric activators stabilizes active site
Allosteric inhibitors deactivates active site.
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Negative Feedback inhibition
Active siteavailable
Isoleucineused up by
cell
Feedbackinhibition
Isoleucine binds to allosteric
site
Active site of enzyme 1 no longer binds
threonine;pathway is switched off
Initial substrate(threonine)
Threoninein active site
Enzyme 1(threonine)
Intermediate A
Intermediate B
Intermediate C
Intermediate D
Enzyme 2
Enzyme 3
Enzyme 4
Enzyme 5
End product(isoleucine)
The end product of a metabolic pathway shuts down the pathway
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2 Types Metabolic Pathways
Catabolic pathways Break down complex molecules into
simpler compounds Release energy
Ex: Cellular Respiration Anabolic pathways (“add”)
Build complicated molecules from simpler ones
Sometimes called “biosynthetic pathways”
Consume energyEx: Building protein from amino acids
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Forms of Energy
Energythe capacity to cause changeExists in various forms
thermal (heat)Chemical (potential)kinetic
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2 Main Types of Energy
Kinetic energythe energy of movementType of energy that can do work
Potential energyenergy of position (stored energy)Ex: chemical energy energy stored in
a [ ] gradient, membrane potential *Energy can be converted from one form to
another
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The Laws of Energy Transformation
Thermodynamics study of energy transformations (changes)
Closed vs. open systems Closed isolated from surroundings Open (i.e-organisms) energy can be
transferred from organism to surroundings
Absorb energy (light or chemical from organic molecules) release heat and metabolic waste products (CO2)
2 laws of thermodynamics
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The 1st Law of Thermodynamics
According to the 1st law of thermodynamicsEnergy cannot be created or destroyed
ONLY transferred and transformed
Also known as the principle of energy conservation
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An example of energy conversion
Figure 8.3
First law of thermodynamics: Energy can be transferred or transformed but NeitherNeither created nor destroyed. For example, the chemical (potential) energy in food will be converted to the kinetic energy of the cheetah’s movement in (b).
ChemicalenergyEating
food food has stored
potential energy!
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The 2nd Law of Thermodynamics
According to the 2nd law of thermodynamics With every energy transfer,
entropy is increasedEntropy = disorder (or
randomness) Some energy becomes unusable
released as heat
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An example of 2nd Law of Thermodynamics
Second law of thermodynamics: Every energy transfer or transformation increases the disorder (entropy) of the universe. For example, disorder is added to the cheetah’s surroundings in the form of heat and the small molecules that are WASTE of metabolism.
Heatco2
H2O+
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DECOMPOSITION also increases enthropy
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How is this connected to the 10% rule?
No chemical rxn is 100% efficient b/c not all energy is
converted into work
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2nd Law of ThermodynamicsTOTAL ENERGY =
usable energy + unusable energyPotential/Kinetic+ Heat
Entropy = increase in disorderThe unusable energy
Enthalpy = increase in orderThe usable energyWhen energy is converted from one form to
another, some is becomes unusable!
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Unusable energy usually equal
THERMAL energy (heat)
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Free-Energy known as “G”Free-Energy known as “G”A living system’s free energy
Usable energy that can do work Known as Gibb’s Free Energy
Needed to maintain healthy cell growth, division, etc.
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The change in free energy, ∆G during a biological processIs related directly to the
enthalpy change (∆H) and the change in entropy
∆H= total energy (usable + unusable energy)
∆S = change in entropyT = absolute temp (K)
∆G = ∆H – T∆S
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Cellular Respiration
& Metabolism
INPUT OF ENERGY
(ATP)…MORE ORDER!
WASTE AND HEAT
OUTPUT… MORE
DISORDER!!!
COMPACT/ STORED
ENERGY = ORDERED
INCREASE INENTHALPY
INCREASE INENTROPY
USED ENERGY = LESS ORDERED
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Why is ∆G helpful? It tells us if a chemical rxn will
occur spontaneously without input of energyNegative ∆G occurs
spontaneously (loses free energy)
+ or zero ∆G rxn never spontaneous
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Free Energy and Metabolism
• 2 types of Reactions in Metabolism
1.Exergonic (Exothermic)
2.Endergonic (Endothermic)
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Exergonic and Endergonic Reactions in Metabolism
An exergonic reaction (- ∆G )Proceeds with a net release of
free energy and IS spontaneous
Reactants
ProductsEnergy
Progress of the reaction
Amount ofenergyreleased (∆G <0)
Fre
e e
ner
gy
(a) Exergonic reaction: energy released
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Endergonic reactions (+ ∆G )absorbs free energy from its surroundings and is NOT
spontaneousStores free energy in molecules
Figure 8.6
Energy
Products
Amount ofenergyreleased (∆G>0)Reactants
Progress of the reaction
Fre
e e
ner
gy
(b) Endergonic reaction: energy required
Madnitude of GRepresents amt of energy
needed to drive rxn
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Real Life Examples… Exergonic (Exothermic)
Cellular Respiration Energy (ATP) is released when
glucose is broken down Endergonic (Endothermic)
Photosynthesis Energy (ATP) is NEEDED
(consumed) to put together glucose from CO2, H20 and sunlight
http://flightline.highline.edu/jbetzzall/BI100/animations/energy_changes.html
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Coupled Reactions
http://www.hippocampus.org/AP%20Biology%20IIWatch Central Catabolic Pathways (Metabolism)
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A cell does three main kinds of workMechanical = ex: movementTransport = ex: active cell
membrane transportChemical = ex: the pushing of
endergonic rxn’s
ATP powers cellular work by coupling exergonic rxns to
endergonic rxns
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The Structure and Hydrolysis of ATP
ATP (adenosine triphosphate) Is the cell’s energy shuttle (molecule) Provides energy for cellular functions It is renewable RNA nucleotide
O O O O CH2
H
OH OH
H
N
H H
O
NC
HC
N CC
N
NH2Adenine
Ribose3 Phosphate groups
O
O O
O
O
O
-- - -
CH
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Energy is released from ATP When the terminal phosphate bond is broken Exergonic rxn (G= -7.3 kcal/mol) PO4
-3 create instability
P
Adenosine triphosphate (ATP)
H2O
+ Free Energy given off
Inorganic phosphate + Adenosine diphosphate (ADP)
PP
P PP i
Sometimes referred to as “high energy”
phosphate bonds
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ATP an “energy currency”
Example of Energy Coupling
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ATP hydrolysis (splitting of ATP) Can be coupled to other reactions
Endergonic reaction: ∆G is positive, reaction is not spontaneous
∆G = +3.4 kcal/molGlu Glu
∆G = + 7.3 kcal/molATP H2O+
+ NH3
ADP +
NH2
Glutamicacid
Ammonia Glutamine
Exergonic reaction: ∆ G is negative, reaction is spontaneous
P
Coupled reactions: Overall ∆G is negative; together, reactions are spontaneous ∆G = –3.9 kcal/mol
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How ATP Performs Work ATP drives endergonic reactions
By phosphorylation, which is transferring a phosphate (PO4
3-) to other molecules (reactant becomes “phosphorylated”)More reactive (less stable) with PO4
3- on it acts as an intermediate in many rxns