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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
(b) Macromolecules (23%)
Figure 2-1b
macromolécules
The plasma membrane separates the cell
from the environment
• 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
Figure 1-6
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
Eukaryotic DNA is packaged into chromosomes
Each chromosome is a single linear
DNA molecule associated with proteins
The total DNA in the chromosomes of
an organism is its genome
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 threedimensional structure of many macromolecules and for
stabilizing specific associations between macromolecules
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
Figure 2-12
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
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
Figure 2-16
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
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
Figure 2-15
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
• The Henderson-Hasselbalch equation relates the pH and Keq
of an acid-base system
[A-]
pH = pKa + log —
[HA]
• 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
2.3 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
Figure 2-22
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
The ATP cycle
Figure 2-25
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