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Proteins Continued Amino Acid Chemistry Tertiary & Quaternary Structure
Biological Thermodynamics Metabolic/Anabolic/Catabolic Energy & Thermodynamics
1st & 2nd Laws applied to biological processes Free Energy ATP
Proteins – Tertiary Structure
Interactions amongst side (R) groups Interactions include:
hydrogen bonds ionic bonds hydrophobic interactions van der Waals interactions
Strong covalent bonds called disulfide bridges may reinforce the protein’s structure
Hydrogenbond
Polypeptidebackbone
Proteins – Tertiary Structure
Usually form between COOH and HO on different residues
Can form between N and H on different residues
Figure 5.20f
Disulfidebridge
Polypeptidebackbone
Proteins – Tertiary Structure
Disulfide bridge Covalent bond
between sulfhydryl groups on two neighboring cysteine residues
Figure 5.20f
Hydrogenbond
Polypeptidebackbone
Ionic bond
Proteins – Tertiary Structure
Hydrophobic interactions side-chains aggregate create pockets within
proteins that effectively exclude water
ionic bond interactions between
positively and negatively charged residues
occur deep in the protein, away from water
Proteins – Tertiary Structure
Other factors influencing folding pH Location of secondary structures The chemical make-up of the solution it’s in Temperature
Proteins Quaternary Structure Multiple polypeptide subunits Subunits may be loosely or tightly bound
together Many enzymes
Proteins Structure
Shape of the protein is critical for it’s function Location of the active site Orientation/interaction with other
molecules Loss of the proper shape can destroy
function DNA mutations Temperature Denaturation
Proteins - Review
Made out of 20 amino acids Form follows function
Four structural levels Important Functions
Enzymes Structural Support (collagen/keratin) Storage ( Hormones Transport Cellular communications Movement Defense against foreign substances
Metabolism
The totality of an organism’s chemical reactions
Metabolic Pathway begins with a specific molecule and ends with a product Each step is catalyzed by a specific enzyme
Metabolic PathwayFigure 8.UN01
Enzyme 1 Enzyme 2 Enzyme 3
Reaction 1 Reaction 2 Reaction 3ProductStarting
molecule
A B C D
Catabolic pathways
Release energy Complex Simple Example: Cellular respiration, the
breakdown of glucose in the presence of oxygen
Energy
The capacity to cause change Forms of Energy:
Kinetic energy: energy associated with motion Heat (thermal energy): kinetic energy associated
with random movement of atoms or molecules Potential energy: energy that matter possesses
because of its location or structure Chemical energy: potential energy available for
release in a chemical reaction
Energy can be converted from one form to another
Thermodynamics
The study of energy transformations Isolated system: closed or isolated
from surroundings. Liquid in thermos
Open system: energy and matter can be transferred between the system and its surroundings Organisms are open systems
First Law of Thermodynamics The energy of the universe is constant
Energy can be transferred and transformed, but it cannot be created or destroyed
Also called the principle of conservation of energy
Second Law of Thermodynamics
During every energy transfer or transformation, some energy is unusable Unusable energy is often lost as heat
The Second law of thermodynamics Every energy transfer or transformation
increases the entropy (disorder) of the universe
1st & 2nd Laws Applied
Chemical Energy (food)
CO2 & H2O
Heat
Cells unavoidably convert organized forms of energy to heat
Spontaneous Processes
Occur without energy input; they can happen quickly or slowly Examples:
A drop of food coloring will spread in a glass of water. Methane (CH4) burns in O2 gas. Ice melts in your hand. Ammonium chloride dissolves in a test tube with
water, making the test tube colder
For a process to occur without energy input, it must increase the entropy of the universe
Biological Order/Disorder
Cells create ordered structures from less ordered materials
Does the evolution of more complex organisms violate the second law of thermodynamics?
Biological Order/Disorder
Entropy (disorder) may decrease in an organism, but the universe’s total entropy increases
Organisms also replace ordered forms of matter and energy with less ordered forms
Energy flows into an ecosystem in the form of light and exits in the form of heat
Free-energy
The free-energy change of a reaction tells us whether or not the reaction occurs spontaneously.
Free-energy - The energy that can do work when temperature and pressure are uniform The energy that cells can use to do work
G
Change in free energy (∆G)
The change in free energy (∆G) during a process is related to the change in enthalpy, or change in total energy (∆H), change in entropy (∆S), and temperature in Kelvin (T)
∆G = ∆H – T∆S Only processes with a negative ∆G are
spontaneous Spontaneous processes can be harnessed
to perform work
Free Energy, Stability & Equilibrium
Free energy is a measure of a system’s instability, its tendency to change to a more stable state
During a spontaneous change, free energy decreases and the stability of a system increases
Equilibrium is a state of maximum stability A process is spontaneous and can perform
work only when it is moving toward equilibrium
Figure 8.5a
• More free energy (higher G)• Less stable• Greater work capacity
In a spontaneous change• The free energy of the system decreases (G 0)• The system becomes more stable• The released free energy can be harnessed to do work
• Less free energy (lower G)• More stable• Less work capacity
Free Energy and Metabolism
The concept of free energy can be applied to the chemistry of life’s processes
Exergonic reaction
Proceeds with a net release of free energy and is spontaneous (DG is less than 0)
Endergonic Reaction
Absorbs free energy from its surroundings and is nonspontaneous (DG is greater than 0).
Figure 8.6a
(a) Exergonic reaction: energy released, spontaneous
Reactants
EnergyProducts
Progress of the reaction
Amount of energy
released(G 0)
Fre
e e
nerg
y
Figure 8.6b
(b) Endergonic reaction: energy required, nonspontaneous
ReactantsEnergy
Products
Amount of energy
required(G 0)
Progress of the reaction
Fre
e e
nerg
y
Metabolism and Equilibrium
Reactions in a closed system eventually reach equilibrium and then do no work
Cells are not in equilibrium; they are open systems experiencing a constant flow of materials
A defining feature of life is that metabolism is never at equilibrium
A catabolic pathway in a cell releases free energy in a series of reactions
Exergonic & Endergonic reactions in the cell – ATP
A cell does three main kinds of work Chemical Transport Mechanical
To do work, cells manage energy resources by energy coupling, the use of an exergonic process to drive an endergonic one
Most energy coupling in cells is mediated by ATP
Phosphate groups
Adenine
Ribose
ATP (adenosine triphosphate) The cell’s energy shuttle Composed of:
ribose (a sugar) adenine (a nitrogenous base) three phosphate groups
Figure 8.8a
Hydrolysis of ATP = ADP + Energy
The bonds between the phosphate groups of ATP’s tail can be broken by hydrolysis
Energy is released from ATP when the terminal phosphate bond is broken
This release of energy comes from the chemical change to a state of lower free energy, not from the phosphate bonds themselves
Figure 8.8b
Adenosine triphosphate (ATP)
Energy
Inorganicphosphate
Adenosine diphosphate (ADP)
The hydrolysis of ATP
Hydrolysis of ATP
Mechanical, transport, and chemical work are powered by the hydrolysis of ATP
The energy from the exergonic reaction of ATP hydrolysis can be used to drive an endergonic reaction
Overall, the coupled reactions are exergonic
ATP phosphorylated intermediates
ATP drives endergonic reactions by phosphorylation ATP can transfer a phosphate group to
some other molecule, such as a reactant Called a phosphorylated intermediate
ATP ADP
PO43- H2O
Figure 8.9
Glutamicacid
Ammonia Glutamine
(b)Conversionreactioncoupledwith ATPhydrolysis
Glutamic acidconversionto glutamine
(a)
(c)Free-energychange forcoupledreaction
Glutamicacid
GlutaminePhosphorylatedintermediate
GluNH3 NH2
Glu GGlu = +3.4 kcal/mol
ATP ADP ADP
NH3
Glu Glu
PP i
P iADP
GluNH2
GGlu = +3.4 kcal/mol
Glu GluNH3 NH2ATP
GATP = 7.3 kcal/molGGlu = +3.4 kcal/mol
+ GATP = 7.3 kcal/mol
Net G = 3.9 kcal/mol
1 2
Chemical Work
Figure 8.10 Transport protein Solute
ATP
P P i
P iADP
P iADPATP
ATP
Solute transported
Vesicle Cytoskeletal track
Motor protein Protein andvesicle moved
(b) Mechanical work: ATP binds noncovalently to motor proteins and then is hydrolyzed.
(a) Transport work: ATP phosphorylates transport proteins.
Energy fromcatabolism (exergonic,energy-releasingprocesses)
Energy for cellularwork (endergonic,energy-consumingprocesses)
ATP
ADP P i
H2O
Regeneration of ATP
ATP is renewable regenerated by adding a phosphate group to
adenosine diphosphate (ADP). The energy to phosphorylate ADP comes
from catabolic reactions in the cell.
Figure 8.11