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Molecular Biology Book Summary
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Cellulaire biologieHoofdstuk 2- Cell chemistry and bioenerge9cs
p. 49-56 (Basischemie, bindingen en interac9es). HC1
Life depends on chemical reac1ons that take place in aqueous solu1on, and it’s based on carbon
compounds: organic chemistry. Most of the carbon atoms are incorporated into polymeric molecules:
macromolecules. Cell chemistry is extremely complex.
Living organisms are made of 4 elements: C, H, N & O. These elements are linked together by covalent
bonds to form molecules.
The O atom in water is nega1ve and the 2 H’s are posi1ve, because the O atom aIracts electrons
more strongly than the H atoms. Those bonds between the atoms are therefore polar. When one of
the H atoms comes near another O atom, they can form a bond called hydrogen bond. The donors
are the atoms who aIracts the electrons the most. The acceptors are the atoms that are more
posi1ve. A bond is the strongest when a straight line can be drawn between all the 3 involved
atoms.
Hydrophilic means the molecules are water-loving, such as sugars, DNA, RNA, and most proteins.
Hydrophobic means the molecules are water-fearing, such as hydrocarbons. They can’t form
hydrogen bonds.
4 types of noncovalent bonds: Hydrogen bonds, electrosta1c aIrac1on, Van der Waals bonds, and
hydrophobic force. Electrosta1c aIrac1ons are strongest when the atoms involved are fully charged or
ionized. But a weaker electrosta1c aIrac1on occurs between molecules that contain polar covalent bonds.
Van der Waals aIrac1ons, weak nonspecific interac1ons are due to fluctua1ons in the distribu1on of
electrons in every atom. The fourth, hydrophobic force is caused by a pushing of nonpolar surfaces out of
the hydrogen-bonded water network, where they would otherwise physically interfere with the highly
favorable interac1ons between water molecules.
When you put a highly polar covalent bond between a hydrogen and another
atom in water, it dissolves. The hydrogen atom has given up hiss electron tot
the companion atom, and so exists a posi1vely charged hydrogen nucleus: a
proton (H+). This proton can associate with the O of the water molecule,
genera1ng a hydronium ion (H3O+). Substances that release a proton when
they are dissolved in water are called acids. Acid: pH<7. Basic: pH>7. Strong
acids easily lose their protons. Most of the weak acids (hold 1ght to H+)
contain COOH. Any molecule capable of accep1ng a proton from a water
molecule is called a base(alkaline). Strong bases easily dissociate in aqueous
solu1on to form 2 new molecules, while weak bases do not accept a proton that easily from
water. Buffers: weak acids and bases that can release or take up protons near pH 7, keeping
the environment of the cell rela1vely constant under a variety of condi1ons.
The carbon compounds made by cells are called organic molecules. 4 major families of small
organic molecules: the sugars, the faIy acids, the nucleo1des and the amino acids.
Each polymer grows by the addi1on of a monomer onto the end of a growing chain in a condensa1on
reac1on, in which one molecule of water is lost with each subunit added.
,p. 57-63 (Energe9ca Algemeen). HC2,4
Small molecules are being used to construct an enormously
diverse range of proteins, nucleic acids and other
macromolecules. The control is exerted through specialized biological catalysts. These are almost always
protein called enzymes, although RNA catalyst also exist, called riboenzymes. Enzyme-catalyzed reac1ons
are connected in series, so that the product of one reac1on becomes the star1ng material, or substrate,
for the next one.
The catabolic pathways break down foodstuffs into smaller molecules, thereby genera1ng both a
useful form of energy for the cell and some of the small molecules that the cell needs as building
blocks. The anabolic or biosynthe1c, pathways use the small molecules plus the energy
harnessed by catabolism to drive the synthesis of the many molecules that form the cell.
Together these 2 sets of reac1ons cons1tute the metabolism of the cell.
The second law of thermodynamics states that in the
universe or in any isolated system, the degree of
disorder always increases. The movement toward disorder is a
spontaneous process, requiring a periodic effort to reverse it. The
amount of disorder in a system can be quan1fied and expressed
as the entropy of a system: the greater the disorder, the greater
the entropy. The first law of thermodynamics states that energy
can be converted from one form to another, but that it cannot be created or destroyed. It’s the 1ght
coupling of heat produc1on to an increase in order that dis1nguishes the metabolism of a cell from the
wasteful burning of fuel in a fire.
A cell is able to obtain energy from sugars or other organic molecules by
allowing their carbon and hydrogen atoms to combine with oxygen to produce
CO2 and H2O, a process called aerobic respira1on. Photosynthesis and
respira1on are complementary processes. This means that the transac1ons
between plants and animals are not all one way. Biosphere means all of the
living organisms on Earth.
Oxida1on refers to more that the addi1on of oxygen atoms; the term applies more generally to any
reac1on in which electrons are transferred from one atom to another. Oxida1on in this sense refers to the
removal of electrons and, reduc1on means the addi1on of electrons. Polar covalent bond means that one
atom has a slightly more nega1ve charge than the others. This
atom pulls harder on the electrons that the other (H2O à O
pulls harder). A + e- + H+ à AH, even though a proton plus an
electron is involved such hydrogena1on reac1on are reduc1ons,
and the reverse dehydrogena1on reac1ons are oxida1ons.
p. 63-65 (Enzymen, kine9ek en mechanismen). HC3,4
When you burn paper, no energy will be lost. There has been loss of free
energy, that is, of energy that can be
harnessed to do work or drive chemical
reac1ons. Where a ‘’downhill’’ reac1on is one
that is energe1cally favorable. A molecule
requires ac1va1on energy – a kick over the
barrier – before it can undergo a chemical
reac1on that leaves it in a more stable state.
The chemistry in a living cell is 1ghtly
controlled because the kick over energy
barriers is greatly aided by a specialized class
,of proteins: the enzymes. Each enzyme binds 1ghtly to one or more molecules, called substrate. The
substance that can lower the ac1va1on energy of a reac1on is termed a catalyst. Each enzyme selec1vely
lowers the ac1va1on energy of only one of the several possible reac1ons that its bound substrate
molecule could undergo. Each enzyme has a unique shape containing an ac1ve site into which only
par1cular substrates will fit.
p. 65-79 (Thermodynamica). HC2
The molecular mo1ons can be classified into 3 kinds: 1) the movement of a
molecule from one place to another - transla1onal mo1on. 2) The rapid
back-and-forth movement of covalently linked atoms with respect to one
another - vibra1on. 3) Rota1ons. Molecules are also in constant transla1onal
mo1on, which causes the, to explore the space inside the cell very efficient
by wandering through it, a process called diffusion. Molecules move in a random walk, if you take the
square root of the 1me in seconds, you get the distance in micrometer. In general, the stronger the
binding of the enzyme and substrate, the slower their rate of dissocia1on.
The disorder of the universe can be expressed most conveniently in terms of free energy, G. Free energy is
an expression of the energy available to do work. The value of G is of interest only when a system
undergoes change. The free energy change, ∆G, is a direct measure of disorder created. Energe1cally
favorable reac1ons are those that decrease free energy; they have a nega1ve ∆G and disorder the
universe. When ∆G is lower that 0, the reac1on can happen spontaneously. When you have the reac1on Y
à X, and the concentra1on of Y increases ∆G becomes more nega1ve for Y à X. ∆Go, standard free-
energy change is the change in free energy under a standard condi1on, where all the concentra1on are 1
mole/liter. ∆G = ∆Go + R × T × ln([X]/[Y]), R is the gas constant, T is the absolute temperature, and X and Y
are the concentra1ons. When ∆G = 0, a chemical equilibrium will be aIained. A equilibrium constant K: K
= [X] / [Y]. ∆Go = - R × T × ln(K).
A + B à C + D : K = ([C][D]) / ([A][B]).
In most cases, energy is stored as chemical-bond energy in
a small set of ac1vated ‘’carrier molecules’’, which contain
1 or more energy-rich covalent bonds. The ac1vated
carriers, coenzymes, store energy in an easily exchangeable
form as a readily transferable chemical group or as
electrons held at a high energy level. The most important
ones are ATP, NADH & NADPH. A coupled reac1on, an
energe1cally favorable chemical reac1on by which one reac1on follows the other:
ATP is formed out of ADP and a phosphate group that is added to the ADP. ATP gives up
its energy packet through its energe1cally favorable hydrolysis to ADP and inorganic
phosphate. ATP à ADP ∆Go < 0.
Condensa1on reac1on: B-H + A-OH à A-B + H2O. Hereby is ATP used to bind A to
phosphate and then to bind with B.
The most important electron carrier is NAD+ and the closely related molecule NADP+.
With a H+ they can reduce to the form NADH and NADPH. Acetyl CoA is used to add 2 carbon units in the
biosynthesis of larger molecules. FADH2 is used like NADH in electron and proton transfer.
, p. 80-93 (Moleculaire Netwerken, Glycolyse en Citroenzuurcyclus). HC4
Sugars are par1cularly important fuel molecules, and they are oxidized in
small, controlled steps to carbon dioxide and water.
The major process for oxidizing sugars is the sequence of reac1ons known as
glycolysis, which produces ATP without involvement of molecular oxygen.
During glycolysis, a glucose molecule with 6 carbon atoms is converted into 2
molecules of pyruvate. For each glucose molecule, 2 molecules of ATP are
hydrolyzed to provide energy to drive the early
step, but 4 molecules of ATP are produced in later
steps. The sugar oxida1on occurs when electrons
are removed by NAD+ from some of the carbons
derived from the glucose molecules. Some of the
energy released by this oxida1on drives the direct
synthesis of ATP molecules from ADP and
phosphate, and some remains with the electrons
in the ac1vated electron carrier NADH.
The chemical reac1ons are precisely guided by 2
enzymes to which the sugar intermediates are
1ghtly bound. The first enzyme forms a covalent
bond to the sugar aldehyde group through a
reac1ve -SH group on the enzyme and then
catalyzes the oxida1on of the aldehyde group to a
carboxylic acid. The intermediate then binds to
the second enzyme, which catalyzes an
energe1cally favorable transfer of 1s high-energy
phosphate to ADP, forming ATP and comple1ng
the process of oxidizing a sugar aldehyde to a
carboxylic acid. Energy-yielding pathways like these are called fermenta1ons.
To compensate for long periods of
fas1ng, animals store faIy acids as fat
droplets composed of water-insoluble
triaglycerol. For short-term storage,
sugar is stored as glucose subunits in
the large branched polysaccharide
glycogen, which is present as small
granules in the cytoplasm. Fat is far
more important than glycogen as an
energy store for animals, because it provides for more efficient storage. During
periods of excess photosynthesis capacity during the day, chloroplasts convert some
of the sugars that they make into fats and starch.
Low glucose levels in the blood trigger the breakdown of fats for energy produc1on.
Notably, the brain must rely on circula1ng glucose – or ketone bodies when
available – because faIy acids are poorly u1lized by the brain. Consump1on of a
diet very low in carbohydrate (a ketogenic diet) leads to the produc1on of ketone
bodies and can enable weight loss in most individuals.
The faIy acids imported from the bloodstream are moved into
mitochondria, where all of their oxida1on takes place. Each molecule
of faIy acid (as the ac1vated molecule faIy acyl CoA) is broken down
completely by a cycle of ATP. In mitochondria the large amount of
energy stored in electrons of NADH and FADH2 is u1lized for ATP
produc1on through the process of oxida1ve phosphoryla1on, which is the only step in the oxida1ve
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