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Chemical Foundations
Aulanni’amBiochemistry LaboratoryChemistry Departement
Brawijaya University
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The Chemicals of Life
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The Chemicals of Life
Macromolecules
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Covalent bonds Formed when two different atoms share electrons in the
outer atomic orbitals
Each atom can make a characteristic number of bonds (e.g., carbon is able to form 4 covalent bonds)
Covalent bonds in biological systems are typically single (one shared electron pair) or double (two shared electron pairs) bonds
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The making or breaking of covalent bonds involves large energy changes
In comparison, thermal energy at 25ºC is < 1 kcal/mol
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Covalent bonds have characteristic geometries
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Covalent double bonds cause all atoms to lie in the same plane
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Electrons are shared unequally in polar covalent bonds
Atoms with higher electronegativity values have a greater attraction for electrons
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water molecule has a net dipole moment caused by unequal sharing of electrons
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Asymmetric carbon atoms are present in most biological molecules
Carbon atoms that are bound to four different atoms or groups are said to be asymmetric
The bonds formed by an asymmetric carbon can be arranged in two different mirror images (stereoisomers) of each other
Stereoisomers are either right-handed or left-handed and typically have completely different biological activities
Asymmetric carbons are key features of amino acids and carbohydrates
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Stereoisomers of the amino acid alanine
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Different monosaccharides have different arrangements around asymmetric carbons
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and glycosidic bonds link monosaccharides
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Noncovalent bonds Several types: hydrogen bonds, ionic bonds, van
der Waals interactions, hydrophobic bonds Noncovalent bonds require less energy to break
than covalent bonds The energy required to break noncovalent bonds is
only slightly greater than the average kinetic energy of molecules at room temperature
Noncovalent bonds are required for maintaining the three-dimensional structure of many macromolecules and for stabilizing specific associations between macromolecules
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Multiple weak bonds stabilize large molecule interactions
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The hydrogen bond underlies water’s chemical and biological properties
Molecules with polar bonds that form hydrogen bonds with water can dissolve in water and are termed hydrophilic
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Hydrogen bonds within proteins
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Ionic bonds
Ionic bonds result from the attraction of a positively charged ion (cation) for a negatively charged ion (anion)
The atoms that form the bond have very different electronegativity values and the electron is completely transferred to the more electronegative atom
Ions in aqueous solutions are surrounded by water molecules, which interact via the end of the water dipole carrying the opposite charge of the ion
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Ions in aqueous solutions are surrounded by water molecules
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van der Waals interactions are caused by transient dipoles
When any two atoms approach each other closely, a weak nonspecific attractive force (the van der Waals force) is created due to momentary random fluctuations that produce a transient electric dipole
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Hydrophobic bonds cause nonpolar molecules to adhere to one another
Nonpolar molecules (e.g., hydrocarbons) are insoluble in water and are termed hydrophobic
Since these molecules cannot form hydrogen bonds with water, it is energetically favorable for such molecules to interact with other hydrophobic molecules
This force that causes hydrophobic molecules to interact is termed a hydrophobic bond
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Multiple noncovalent bonds can confer binding specificity
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Phospholipids are amphipathic molecules
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Phospholipids spontaneously assemble via multiple noncovalent interactions to form different structures in aqueous solutions
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Chemical equilibrium
The extent to which a reaction can proceed and the rate at which the reaction takes place determines which reactions occur in a cell
Reactions in which the rates of the forward and backward reactions are equal, so that the concentrations of reactants and products stop changing, are said to be in chemical equilibrium
At equilibrium, the ratio of products to reactants is a fixed value termed the equilibrium constant (Keq) and is independent of reaction rate
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Equilibrium constants reflect the extent of a chemical reaction
Keq depends on the nature of the reactants and products, the temperature, and the pressure
The Keq is always the same for a reaction, whether a catalyst is present or not
Keq equals the ratio of the forward and reverse rate constants (Keq = kf/kr)
The concentrations of complexes can be estimated from equilibrium constants for binding reactions
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Biological fluids have characteristic pH values
All aqueous solutions, including those in and around cells, contain some concentration of H+ and OH- ions, the dissociation products of water
In pure water, [H+] = [OH-] = 10-7 M The concentration of H+ in a solution is expressed as pH
pH = -log [H+] So for pure water, pH = 7.0 On the pH scale, 7.0 is neutral, pH < 7.0 is acidic, and pH >
7.0 is basic The cytosol of most cells has a pH of 7.2
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The pH Scale
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Hydrogen ions are released by acids and taken up by bases
When acid is added to a solution, [H+] increases and [OH-] decreases
When base is added to a solution, [H+] decreases and [OH-] increases
The degree to which an acid releases H+ or a base takes up H+ depends on the pH
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The Henderson-Hasselbalch equation relates the pH and Keq of an acid-base system
The pKa of any acid is equal to the pH at which half the molecules are dissociated and half are neutral (undissociated)
It is possible to calculate the degree of dissociation if both the pH and the pKa are known
The Henderson-Hasselbalch equation
pH = pKa + log —[A-]
[HA]
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Cells have a reservoir of weak bases and weak acids, called buffers, which ensure that the cell’s pH remains relatively constant
The titration curve for phosphoric acid (H3PO4), a physiologically important buffer
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Biochemical energetics
Living systems use a variety of interconvertible energy forms Energy may be kinetic (the energy of movement) or potential
(energy stored in chemical bonds or ion gradients)
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The change in free energy determines the direction of a chemical reaction
Living systems are usually held at constant temperature and pressure, so one may predict the direction of a chemical reaction by using a measure of potential energy termed free energy (G)
The free-energy change (G) of a reaction is given byG = Gproducts – Greactants
If G < 0, the forward reaction will tend to occur spontaneously
If G > 0, the reverse reaction will tend to occur If G = 0, both reactions will occur at equal rates
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The G of a reaction depends on changes in enthalpy (bond energy) and entropy
The G of a reaction is determined by the change in bond energy (enthalpy, or H) between reactants and products and the change in the randomness (entropy, or S) of the system
G = H - T S In exothermic reactions (H < 0), the products contain less
bond energy than the reactants and the liberated energy is converted to heat
In endothermic reactions (H > 0), the products contain more bond energy than the reactants and heat is absorbed
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Entropy
Entropy is a measure of the degree of randomness or disorder of a system
Entropy increases as the system becomes more disordered and decreases as it becomes more structured
Many biological reactions lead to an increase in order and thus a decrease in entropy (S < 0)
Exothermic reactions (H < 0) that increase entropy (S > 0) occur spontaneously (G < 0)
Endothermic reactions (H > 0) may occur spontaneously if S increases enough so that T S offsets the positive H
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Many cellular processes involve oxidation-reduction reactions
Many chemical reactions result in the transfer of electrons without the formation of a new chemical bond
The loss of electrons from an atom or molecule is termed oxidation and the gain of electrons is termed reduction
If one atom or molecule is oxidized during a chemical reaction then another molecule must be reduced
Many biological oxidation-reduction reactions involve the removal or addition of H atoms (protons plus electrons) rather than the transfer of isolated electrons
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The oxidation of succinate to fumarate
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An unfavorable chemical reaction can proceed if it is coupled to an energetically favorable reaction
Many chemical reactions are energetically unfavorable (G > 0) and will not proceed spontaneously
Cells can carry out such a reaction by coupling it to a reaction that has a negative G of larger magnitude
Energetically unfavorable reactions in cells are often coupled to the hydrolysis of adenosine triphosphate (ATP), which has a Gº = -7.3 kcal/mol
The useful free energy in an ATP molecule is contained is phosphoanhydride bonds
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The phosphoanhydride bonds of ATP
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ATP is used to fuel many cell processes
The ATP cycle
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Activation energy and reaction rate
Many chemical reactions that exhibit a negative G°´ do not proceed unaided at a measurable rate
Chemical reactions proceed through high energy transition states. The free energy of these intermediates is greater than either the reactants or products
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Example changes in the conversion of a reactant to a product in the presence and absence of a catalyst
Enzymes accelerate biochemical reactions by reducing transition-state free energy
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