Bioquímica I- Química Biológica I

Biomoléculas

• La actividad de las moléculas que constituyen las células está regida por los principios básicos de química

• El agua, los iones inorgánicos y las pequenas moléculas orgánicas constituyen 75-80% del peso celular

• Macromoléculas (proteínas, polisacárides, DNA) constituyen el resto del peso celular

The Chemicals of Life

Figure 2-1a

2.0 The Chemicals of Life

Figure 2-1b

(b) Macromolecules (23%)

macromolécules

The plasma membrane separates the cell from the environment

Figure 1-6

• The fundamental structure of all cell membranes is the lipid bilayer

• Various membrane proteins present in the different cell membranes give each membrane a specific function

Componentes celulares

Prokaryotic cells

• Single cell organisms• Two main types: bacteria and archaea• Relatively simple structure

Figure 1-7a

Eukaryotic cells

• Single cell or multicellular organisms• Plants and animals• Structurally more complex: organelles, cytoskeleton

Each chromosome is a single linear DNA molecule associated with proteins

The total DNA in the chromosomes of an organism is its genome

Eukaryotic DNA is packaged into chromosomes

Cells associate to form tissues

• Tissues are composed of cells and extracellular matrix• Tissues may form organs• Rudimentary tissues and an overall body plan form early in

development due to a defined pattern of gene expression and the ability of cells to interact with other cells

• Many animals share the same basic pattern of development, which reflects commonalities in molecular and cellular mechanisms controlling development

Evolución Molecular

• La evolución es un proceso histórico que dicta la forma y la estructura de la vida

• La evolución depende de las alteraciones en la estructura y organización de los genes y de sus productos

• Aspectos fundamentales de la vida celular se dan en muy diversos organismos y dependen de genes relacionadoss

• cambios pequenos en ciertos genes permiten a los organismos adaptarse a diferentes entornos

1.3 Lineage tree of life on earth

Figure 1-5

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

Covalent bonds have characteristic geometries

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

The making or breaking of covalent bonds involves large energy changes

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

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

electrons

Figure 2-5

Ions in aqueous solutions are surrounded by water molecules

Figure 2-14

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

Figure 2-6

Different monosaccharides have different arrangements around asymmetric

carbons

Figure 2-8

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

The hydrogen bond underlies water’s chemical and biological properties

Figure 2-12

Molecules with polar bonds that form hydrogen bonds with water can dissolve in water and are termed hydrophilic

Hydrogen bonds within proteins

Figure 2-13

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

Hydrophobic bonds cause nonpolar molecules to adhere to one another

Figure 2-16

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

2.2 Phospholipids are amphipathic molecules

Figure 2-19

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

Figure 2-20

van der Waals interactions are caused by transient dipoles

Figure 2-15

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

Multiple weak bonds stabilize large molecule interactions

Figure 2-11

Multiple noncovalent bonds can confer binding specificity

Figure 2-17

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

2.3 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]

2.3 Cells have a reservoir of weak bases and weak acids, called buffers, which ensure that

the cell’s pH remains relatively constant

Figure 2-22

The titration curve forphosphoric 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 by

G = 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

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

Figure 2-24

ATP is used to fuel many cell processes

Figure 2-25

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

Figure 2-27

Enzymes accelerate biochemical reactions by reducing transition-state free energy