aulanni’am biochemistry laboratory chemistry departement brawijaya university

Aulani " Biokimia" Presentasi1

Chemical Foundations

Aulanni’amBiochemistry LaboratoryChemistry Departement

Brawijaya University


The Chemicals of Life


The Chemicals of Life

Macromolecules


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


The making or breaking of covalent bonds involves large energy changes

In comparison, thermal energy at 25ºC is < 1 kcal/mol


Covalent bonds have characteristic geometries


Covalent double bonds cause all atoms to lie in the same plane


Electrons are shared unequally in polar covalent bonds

Atoms with higher electronegativity values have a greater attraction for electrons


water molecule has a net dipole moment caused by unequal sharing of electrons


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


Stereoisomers of the amino acid alanine


Different monosaccharides have different arrangements around asymmetric carbons


and glycosidic bonds link monosaccharides


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


Multiple weak bonds stabilize large molecule interactions


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


Hydrogen bonds within proteins


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


Ions in aqueous solutions are surrounded by water molecules


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


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


Multiple noncovalent bonds can confer binding specificity


Phospholipids are amphipathic molecules


Phospholipids spontaneously assemble via multiple noncovalent interactions to form different structures in aqueous solutions


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


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


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


The pH Scale


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


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]


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


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)


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


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


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


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


The oxidation of succinate to fumarate


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


The phosphoanhydride bonds of ATP


ATP is used to fuel many cell processes

The ATP cycle


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


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

aulanni’am biochemistry laboratory chemistry departement brawijaya university

Documents

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covalent bondscovalent

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