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;

• the population level: microbiology, ecology;

• the production level: bioprocess.

 Biochemistry
Introduction of the biological system at
molecule level.

This section is devoted mainly to the structure

and functions of biological molecules.
Outline of Biochemistry Section
Contents-Cell construction
• Protein and amino acids
• Carbohydrates
• Lipids, fats and steroids
• Nucleic acids, RNA and DNA

Requirements:
Understand the basic definitions, characteristics
and functions of these biochemicals.
 Amino Acids and Proteins

Proteins are the most abundant molecules

in living cells, constituting 40% - 70% of
their dry weight. Proteins are built from
monomers.

Amino acid is any molecule that contains

both
functional groups.
 Amino Acids
H

α
H2N C COOH

Where "R" represents a side chain specific to each amino acid.

Amino acids are usually classified by properties of the side chain into
four groups:
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.
 Amino Acids
Zwitterion is an amino acid having positively and negatively
charged groups, a dipolar molecule.

H H H
-H+ -H+
H3N+ C COOH H3 N+ C COO- H2N C COO-
+H+ +H+
R R R
Zwitterion
 Amino Acids
Isoelectric point (IEP) is the pH value at which amino acids
have .
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)
 Amino Acids

pH effect on the charge of amino acids

The proton dissociation constants are K1, K2

[ HA][ H ]  [ A ][ H  ]
K1  (3) K2  (4)
[ HAH  ] [ HA]
Taking the logs of equations 3 and 4, yields,

[ HA] [ A ]
pH  pK1  log (5) pH  pK 2  log (6)
[ HAH  ] [ HA]
[ ] 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.
 Amino Acids
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 source Limiting amino acid

Wheat lysine
Rice lysine and threonine

Maize lysine and tryptophan

Pulses methionine
Beef methionine and cysteine

Whey none
Milk none
 Use of Amino Acids
• Aspartame (aspartyl-phenylalanine-1-methyl ester) is an
artificial sweetener.

• 5-HTP (5-hydroxytryptophan) has been used to treat

neurological problems associated with PKU
(phenylketonuria), as well as depression.

• L-DOPA (L-dihydroxyphenylalanine) is a drug used to

treat Parkinsonism.

• Monosodium glutamate is a food additive to enhance

flavor.
 Amino Acid (AA)-Protein
: basic unit

: amino acid chain, containing 2 or more AA.

: containing less than 50 AA.

: > 50 AA.

Peptides (from the Greek πεπτος, "digestible"), are formed through

condensation of amino acids through peptide bonds.
Peptide bond: a chemical bond formed between two AA
- the of one amino acid reacts with

- the of the other amino acid,

- releasing a molecule of .
This is a condensation (also called dehydration synthesis)
reaction.
 Proteins
• Proteins are the polymers built through the
condensation of amino acids.
(protein recovery)
• Protein constitutes 40-70% dry weight of cell. Its
molecular weight is from 6000 to several hundred
thousand daltons.
Dalton is a unit of mass equivalent to a hydrogen atom,
1 dalton = 1.66053886 × 10−27 kg.

• prosthetic groups: organic or inorganic components

other than amino acids contained in many proteins.
• conjugated proteins: the proteins contain prosthetic
groups.
Conjugated protein: hemoglobin Heme group
Prosthetic group: heme in green
Amino acid units in red and yellow
 Proteins
Proteins are essential to the structure and
function of all living cells and viruses. They
can be classified into:
- : glycoprotein
- : enzymes
- : hemoglobin
- : hormones (insulin, growth hormone)

- : antibodies
 Protein 3-D Structure

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.
 Protein Structure
The three-dimensional structure can be described at four
distinct levels:

Primary structure: .

- It is held together by covalent peptide bonds

- Each protein has not only a definite amino acids

composition, but also a unique sequence.

- The amino acid sequence has profound effect on the

resulting three-dimensional structure and on the function
of protein.
 Protein Structure
Secondary structure: highly patterned sub-structures
α-helix and β-pleated sheet

• It is the way that the polypeptide chain is extended and

is a result of between protein residues.

• Secondary structures are locally defined, meaning that

there can be many different secondary motifs present in
one single protein molecule.

• Two major types of secondary structure are α-helix and

β-pleated sheet.
 Protein Structure
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.
 Protein Structure
Secondary structure: β-pleated sheet

- within the same protein molecule

- consists of two or more amino acid sequences that are arranged
adjacently and in parallel, but with alternating orientation
-Hydrogen bonds can form between the two strands.
-Hydrogen bonds established between the N-H groups in the backbone of one strand
with the C=O groups in the backbone of the adjacent, parallel strand(s).
- The sheet's stability and structural rigidity and integrity are the result of
multiple such hydrogen bonds arranged in this way.
 Protein Structure
Tertiary structure: the overall shape of a single protein molecule

• The tertiary structure is a result of interaction between

widely separated along the chain. The folding or bending of an
amino acids chain induced by interaction of R groups determines
the tertiary structure.

• It is held together primarily by but hydrogen

bonds, ionic interactions, and disulfide bonds are usually involved
too.

• The tertiary structure has a profound effect on its function.

 Protein Structure
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.

• Only protein with more than one polypeptide chain has quaternary
structure. This structure has an important role in the control of their
catalytic activity.

• These tertiary or quaternary structures are usually referred to as

"conformations," or “folding” and transitions between them are
called conformational changes.
• The mechanism of protein folding is not entirely understood.
 Protein Denaturation
Protein Denaturation: A protein that is not in its native state and their
shape which allows for optimal activity.

• Proteins denature when they lose their three-dimensional structure -

their chemical conformation and thus their characteristic folded
structure.

• Proteins may be denatured at

structural levels, but not at the structural level.

• This change is usually caused by heat, acids, bases, detergents,

alcohols, heavy metal salts, reducing agents or certain chemicals
such as urea.

• The proteins can regain their native state when the denaturing
influence is removed. Such denature is reversible. Some other
denature is irreversible.- direct purification processes.
Irreversible egg protein denaturation and loss of solubility,
caused by the high temperature (while cooking it)
 Summary of Amino Acids and Proteins
• Amino acids are basic building blocks of
proteins.
• They contain acid carboxyl group and base
amino group as well as side group R.
• They can be neutral, positively or negatively
charged.
• They are 20 standard amino acid and 10
essential amino acids for human being.
Summary of Amino Acids and Proteins

• Proteins are amino acid chain linked through

peptide bond.
• They can be classified into structural protein,
catalytic protein, transport protein , regulatory
and protective proteins in either globular or
fibrous forms.
 Summary of Amino Acids and Proteins
• Protein has three-dimensional structure at four level.
- 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.
• Protein can be denatured at its three dimensional
structure. Protein denature could be reversible or
irreversible.