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Summary Biochemistry from Lehninger, Principles of Biochemistry (Chapters 2,3,4,5,6,8,10,11,13,14,15,16,17,18,19,24,25,26 and 27)
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BiochemistryChapter 2
2.1
The nonpolar molecules tend to cluster together in polar solvents. Hydrogen bonds, ionic bonds,
hydrophobic and van der Waals interactions make the three-dimensional structure of the proteins,
nucleic acids, etc.
In water the oxygen molecules have a partial negative charge and the hydrogens a partial positive charge.
As result the oxygen gets a negative charge of 2 and there will be an electrostatic attraction between an
oxygen atom and of one molecule and a hydrogen of the other molecule, this is called a hydrogen bond.
These bonds are relatively weak. These in liquid water have a dissociation energy (the energy required to
break a bond) of about 23 kJ/mol. An covalent bond between OH is about 470 kJ/mol.
When one hydrogen bond breaks, another is formed. The hydrogen bonds switch very vast between the
molecules. This happens in continues motion, so that each molecule forms about 3.4 hydrogen bonds
with other molecules. In ice the chaos is smaller, so the molecules can form 4 hydrogen bonds. This is
much stronger. The power to get more randomness is called free-energy change:
∆ G=∆ H−T ∆ S
When the ΔG is negative, the process occurs spontaneously.
Compounds that dissolve easily in water are hydrophilic and nonpolar molecules (that do not dissolve in
water) are hydrophobic.
When you have two different components how cannot dissolve there will form two layers. What also can
happen is that the water molecules surround the hydrophobic molecules. The water molecules are not as
highly oriented as those in clathrates, crystalline compounds of nonpolar solutions and water. The
entropy will reduces.
Amphipathic compounds contain regions that are polar and nonpolar. If these compounds are mixed
with water micelles will be formed. These have in the inside hydrophobic interactions and the outside
are the hydrophilic parts.
The two dipoles weakly attract each other bringing the two nuclei closer, this is called the van der Waals
interaction. Each atom has its van der Waals radius, a measure of how close that atom will allow another
to approach.
2.2
Water has the tendency to undergo a reversible ionization. H20 H+ + OH-
The H+, free protons do not exist in a solution, in water it will form
hydronium ions (H3O+). With electricity this molecule goes to the cathode
and the OH- to the anode, this because of proton hopping.
How much there are in a solution of the different atoms is given by the
equilibrium constant, Keq. (is for the reaction A+B↔C+D) Then the Keq can
[ C ] eq [ D ] eq
be defined as (these are in concentrations). The
[ A ] eq [ B ] eq
equilibrium constant of water at 25°C is (55.5 M)(K eq), the ion product of
water (Kw). If the concentrations of H+ and OH- are equal, there is a neural
pH.
, H +¿
¿
H +¿
¿
The Kw is the basis for the pH scale, the term pH is defined by: ¿
¿
1
¿
pH=log ¿
The pH of 7 is a neutral environment. The concentrations higher than 7, have more OH-, are more basic.
The lower concentrations are more acidic and have more H3O+.
In the bloodstream the pH is about 7.4, when is will go beneath it, it is called acidosis. If the pH is higher
than normal, it is called alkalosis.
The acids are proton donors and bases are proton acceptors. A proton
donor and its corresponding proton acceptor make up a conjugate acid-
base pair.
The ionization constants or acid dissociation constants, Ka, is the
equilibrium constant for the ionization reactions. The pKa is analogous to pH
1
and defined as: pKa=log =−log Ka . If the pKa is low, the stronger
Ka
the acid, so the stronger the tendency to lose a proton.
With titrations, the pH can be determined. The plot of that is called a titration curve.
2.3
Buffers are aqueous systems that tend to resist changes in pH when a small amount of acid or base are
added. The flat zone in the titration curve is the buffer region, the buffer holds here the pH constant,
between midpoint and ±1 pH unit of the midpoint.
All titration curves has nearly the same shapes. The shape can be explained by the Henderson-
A−¿
¿
Hasselbalch equation: ¿ (where A is the acid molecule).
¿
pH = pKa+ log ¿
Chapter 3
3.1
Proteins are polymers of amino acids, with each amino acid
residue joined to its neighbor. All the amino acids are build up
the same way (see picture). The side chains, R-groups vary in
structure, size and electric charge. For all common amino acids
except glycine the α carbon is bonded to four different groups,
therefor the α-carbon is a chiral center, this means that the
molecules have two stereoisomers. They are nonsuperposible
mirror images of each other, a class called enantiomers. Because it has a chiral center, they are optical
active (rotate plane polarized light). To specify the absolute configuration of the four substituents, the
D,L system is developed. You leave the H out of the atom, then look if the side groups are shaped in a L or
a D. There is also a RS system, which can name organic compounds with more than one chiral center.
The different amino acids can be divided in five main groups, based on the properties of the side chains:
, - Nonpolar aliphatic R groups
o These are nonpolar and hydrophobic, tend to cluster together and form hydrophobic
interactions
Alanine, valine, leucine, isoleucine, glycine, methionine and proline.
- Aromatic R groups
o Relatively nonpolar, can participate with hydrophobic interactions, can absorb light
Phenylalanine, tyrosine, tryptophan.
- Polar, uncharged groups
o Soluble in water
Serine, threonine, cysteine, asparagine, glutamine and cysteine (which can form
disulfide bonds).
- Positively charged (basic) R groups
o Positively charged at pH 7
Lysine, arginine, histidine
- Negatively charged (acidic) groups
o Net negative charged at pH 7
Aspartate and glutamine.
There are also uncommon amino acids how are very important, namely 4-
hydroxyproline (derivative of proline), 5-hydroxylysine (from lysine), 6-N-
Methyllysine, γ-carboxylglutamine, demosine, selenocystecine, ornithine and
cirtulline.
Amino acids are dipolar ions, or zwitterions, which can act either as acid or
base. Substances how have this dual nature are amphoteric.
In the titration curve of an amino acid you see that there are more than one
pKa’s. In the middle, when the net charge of the molecule is 0, is the isoelectric
point or isoelectric pH indicated as pI. Most of the groups have very similar pKa
values, namely those from the groups –COOH at pH 1.8 till 2.4 and the group
–NH3+ around 8.8 till 11.0. The differences are in the R groups.
3.2
The polymers of amino acids are polypeptides and proteins. Two amino acids how are covalently bond
with an amide linkage have a peptide bond. This can be made by the removal of water (dehydration)
from the α-carboxyl group of one amino acid and the α-amino group from the other. When a few amino
acids are joined this way, it is called an oligopeptide. When there are many, it is called a polypeptide
(generally have a molecular weight below 10,000). The end of these molecules are on the one side a free
α-amine group, amino-terminal and on the other side a free α-carboxyl group, carboxyl-terminal.
Different polypeptides can have a single chain or more than one chain, called multisubunit. If the at least
two are identical the protein is oligomeric. Then the identical units are called protomers.
3.3
How to separate proteins in the cell?
The first step to all protein purifications is to break the cells open and release the proteins into the
solution, called the crude extract. Then the proteins can be separated into different fractions, based on a
property such as size or charge, a process called fractionation. There are different types of fractionating:
- Dialysis
o Separates on the proteins by using a semipermeable membrane, every molecule can go
through except the proteins.
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