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A summary of biochemistry for MIB10306
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Summary biochemistryBy Emma Burgwal, wur
Chapter 1
1.1 The biological world is diverse. The microscope, however, showed unifying features of all species.
All organisms consist of cells. Biochemistry is the study of the chemistry of life processes. These
processes entail the interplay of biological macromolecules and metabolites. All cellular
organisms store genetic information in DNA and proteins are built from the same set of amino
acids. Many metabolic processes are also common to many organisms. This suggest that alle
living organisms have a common ancestor. This resulted in three fundamental groups, domains;
eukaryotes (with nucleus), archaea and bacteria. Evolution occurs with the adapting of existing
macromolecules.
1.2 The proposal of the 3D-structure of DNA set the stage for many advances of biochemistry. It
shows the relation between structure and function (storing genetic information). DNA is a linear
polymer made up of four different monomers (A,C, T and G). The fixed backbone connects
variable substituents, bases. The backbones has phosphate and sugar groups. Most DNA occurs
in a double helix (two strands) with the bases inside and the backbone outside. The bases form
specific base pairs connected with hydrogen bonds (weaker than covalent bonds). The structure
is compatible with any sequence of bases. The sequence of one strand determines the sequence
along the other.
1.3 When two sequences are mixed, a double helix forms spontaneously, how? Atoms interact with
each other through chemical bonds. Covalent bonds are the strongest and hold atoms together
(by sharing of electron pair). These bonds can be altered in several ways, resulting in resonance.
Noncovalent bonds are weaker, but are crucial. There are four types. Charged groups on
molecules can interact with other charged groups; ionic interaction. E=kq 1∗q 2/ Dr
Hydrogen bonds are a type of ionic interactions. The hydrogen donor is more tightly linked than
the acceptor. It occurs with electronegativity. The strongest hydrogen bonds are when the
acceptor and the donor are on the same line. The distribution of charge around an atom
changes; van der Waals interactions. This asymmetry attracts other atoms.
Water is polar, with asymmetric charge distribution. It is also highly cohesive (hydrogen bonds).
This is apparent in the structure of ice. The properties of water result in a final interaction, the
hydrophobic effect. Water molecules form cages around nonpolar molecules. Two nonpolar
molecules will cluster together more favourably.
There are unfavourable ionic interactions between phosphate in DNA. It opposes the formation
of the double helix. Hydrogen bonds do not contribute substantially to the overall process
(breakage and linkage), but contribute to specificity. Base stacking is due to van der Waals
interactions and is nearly optimal. The hydrophobic effect is also favourable.
A system is matter with a defined region of space. The surroundings is the rest of the universe.
First law of thermodynamics: the total energy of system and surrounding is constant, energy
can’t be destroyed nor created, but it can take different forms. The entropy is a measure of the
degree of randomness or disorder in a system.
Second law: the total entropy of system and surroundings always increases. Enthalpy is the heat
content. So: ΔSsurroundings=−ΔHsystem / T . The free energy can also be calculated:
, ΔG=ΔHsystem−TΔSsystem . Free energy must be negative for spontaneous processes. The
formation of the double helix releases heat, so the second law is correct.
1.4 Some human disease have been linked to changes in the genomic sequence. One single base
change can already cause diseases (but often leads to predisposition of the disease). One
genome can serve as a reference for other genomes. The average genome difference between
two individuals within one ethnic group is greater than the difference between the averages of
two different ethnic groups. Each human contains 10 times more microbial cells than own human
cells. These microbiomes differ from one person to another. Due to analysis, it occurred that
human species originated in Africa. This also gave insight in unity of organisms. Factors in a
person’s environment are also important (like vitamins and trace elements). Food provides
calories in the form of substances that can be broken down to release energy for biological
processes.
The most fundamental role of DNA is to encode the sequences of proteins. The 20 types of
amino acids enables proteins to perform a wide range of functions. Proteins can also fold
spontaneously, like DNA. A codon, a set of three bases along the strand, determines the identity
of a amino acid. The genetic code is the set of rules that links the DNA sequence to the encoded
protein sequence. These regions only encounter 3% of the human’s genome. The rest can
contain information for regulating expression of genes and physiological conditions.
Chapter 2
2.1 Amino acids are the building blocks of proteins. It consists of a carbon atom, an amino group, a
carboxylic group, a hydrogen atom and a R group (side chain). The carbon atom is therefore chiral.
The L isomer occurs more often than the S isomer. In neutral pH, amino acids exist as dipolar ions
(zwitterions) with a protonated amino and a deprotonated carboxylic group. pH can change this.
Side chains differ in size, shape, charge, hydrogen bonding capacity, hydrophobic character and
chemical reactivity. These can be classified in four groups:
1. Hydrophobic and nonpolar side chains: aliphatic side chains tend to cluster together. Side
chains here can also be cyclic or aromatic.
2. Polar with neutral side chains (but charge not evenly distributed): three amino acids contain
OH-groups (more hydrophilic an reactive), two contain a carboxamide and one a sulfhydryl
(thiol, SH).
3. Positively charged: at neutral pH. Histidine has an aromatic ring.
4. Negatively charged: two amino acids with acidic side chains.
Amino acids are often designated by either a three-letter abbreviation or a one-letter symbol. Amino
acids were probably available before the origin of life.
2.2 Proteins are linear polymers formed by linking the carboxyl group to the amino group (peptide
bond/amide bond). This is accompanied by the loss of water. The equilibrium lies on the side of
hydrolysis. Peptide bonds are kinetically stable (but needs an input of free energy). Each amino acid
in a polypeptide chain is called a residue. A chain has a N-terminal and a C-terminal. It consists of a
regular part, the backbone (hydrogen bond rich), and a variable part, side chains. Polypeptides of a
small amount of amino acids are called oligopeptides or peptides. The linear polypeptide chain can
be cross-linked with disulfide bonds (cysteine). The resulting of two cysteine linked is cystine. Each
protein has a unique, precisely defined amino acid sequence (the primary structure). This is
determined by the nucleotide sequences of genes (DNA-RNA-protein). Knowing the sequence of a
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