LECTURE - 5

Biological Thermodynamics

Outline

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

Figure 5.20f

Hydrogenbond

Disulfidebridge

Polypeptidebackbone

Ionic bond

Hydrophobicinteractions

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

Anabolic pathways

Consume energy Simple Complex Example: Synthesis of a protein from amino

acids

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

Energy

Potential Energy

Kinetic EnergyHeat Energy

Chemical Energy

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

Spontanious Processes

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

Figure 8.7a

(a) An isolated hydroelectric system

G 0 G 0

Figure 8.7b

(b) An open hydroelectric system

G 0

Figure 8.7c

(c) A multistep open hydroelectric system

G 0

G 0

G 0

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

ENZYMES

Enzymes speed up metabolic reactions by lowering energy barriers