Analysis of Biological System. Despite of all their complexity, an understanding of biological system can be simplified by analyzing the system at several different levels: the cell level: microbiology, cell biology; the molecular level: biochemistry, molecular biology ;
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Despite of all their complexity, an understanding of biological system can be simplified by analyzing the system at several different levels:
Introduction of the biological system at molecule level.
This section is devoted mainly to the structure and functions of biological molecules.
Understand the basic definitions, characteristics and functions of these biochemicals.
Proteins are the most abundant molecules in living cells, constituting 40% - 70% of their dry weight. Proteins are built from
Amino acid is any molecule that contains both
Where "R" represents a side chain specific to each amino acid.
Amino acids are usually classified by properties of the side chain into
acidic, basic, hydrophilic (polar), and hydrophobic (nonpolar).
α-amino acid are amino acid in which the amino and carboxylate
functionalities are attached to the same carbon, the so-called α–carbon.
They are the building blacks of proteins.
Zwitterion is an amino acid having positively and negatively
charged groups, a dipolar molecule.
Isoelectric point (IEP) is the pH value at which amino acids
IEP varies depending on the R group of amino acids.
At IEP, an amino acid does not migrate under the influence of an electric field.
pH effect on the charge of amino acids
We can arbitrarily control the pH of an aqueous solution containing amino acids by adding base or acid. The equilibrium reactions for the simple amino acid (HA) are
HAH+ = H++AH(1)
HA = H++A- (2)
pH effect on the charge of amino acids
The proton dissociation constants are K1, K2
Taking the logs of equations 3 and 4, yields,
[ ] represents concentration in dilute solution.
where pH=-log(H+), pK1=-log(K1), and pK2=-log(K2).
Standard amino acids: there are 20 standard amino acids that are commonly found in proteins.
Essential amino acids: An essential amino acid for an organism is an amino acid that cannot be synthesized by the organism from other available resources, and therefore must be supplied as part of its diet.
Most of the plants and microorganism cells are able to use inorganic compounds to make amino acids necessary for the normal growth.
Eight amino acids are generally regarded as essential for humans: tryptophan, lysine, methionine, phenylalanine, threonine, valine, leucine, isoleucine.
Two others, histidine and arginine are essential only in children. A good memonic device for remembering these is "Private Tim Hall", abbreviated as:
PVT TIM HALL:
Phenylalanine, Valine, Tryptophan
Threonine, Isoleucine, Methionine
Histidine, Arginine, Lysine, Leucine
limiting amino acid content: the essential amino acid found in the smallest quantity in the foodstuff.
Protein sourceLimiting amino acid
Ricelysine and threonine
Maizelysine and tryptophan
Beefmethionine and cysteine
Peptides (from the Greek πεπτος, "digestible"), are formed through condensation of amino acids through peptide bonds.
: basic unit
: amino acid chain, containing 2 or more AA.
: containing less than 50 AA.
: > 50 AA.
Peptide bond: a chemical bond formed between two AA
This is a condensation (also called dehydration synthesis) reaction.
Dalton is a unit of mass equivalent to a hydrogen atom,
1 dalton = 1.66053886 × 10−27 kg.
Conjugated protein: hemoglobin
Prosthetic group: heme in green
Amino acid units in red and yellow
Proteins are essential to the structure and function of all living cells and viruses. They can be classified into:
- : antibodies
Proteins are amino acid chains that fold into unique 3-dimensional structures.
The shape into which a protein naturally folds is known as its native state,
which is determined by its sequence of amino acids and interaction of groups.
The three-dimensional structure can be described at four distinct levels:
Primary structure: .
Secondary structure: highly patterned sub-structures
α-helix and β-pleated sheet
Secondary structure: α-helix
- Formed within the same protein chain.
- Hydrogen bonding can occur between
- the α-carboxyl group of one residue and
- the –NH group of its neighbor four units down the same chain.
- The helical structure can be easily disturbed since hydrogen bond is unstable.
Secondary structure: β-pleated sheet
Tertiary structure: the overall shape of a single protein molecule
Quaternary structure: the shape or structure that results from the union of more than protein molecule, which function as part of the larger assembly or protein complex.
Protein Denaturation: A protein that is not in its native state and their shape which allows for optimal activity.
Irreversible egg protein denaturation and loss of solubility,
caused by the high temperature (while cooking it)
Summary of Amino Acids and Proteins
- Primary structure: the sequence of amino acids.
- Secondary structure: a way that the polypeptide chain is extended. α-helix and β-pleated sheet formed by hydrogen bond.
- Tertiary structure: the overall shape of a protein molecule and the result of interaction between R groups mainly through hydrophobic interaction.
- Quaternary: the interaction between different polypeptide chains of protein. This structure is important to the active function of protein especially enzyme.