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

C

R

H

COOHH2N

α-amino acid are amino acid in which the amino and carboxylatefunctionalities are attached to the same carbon, the so-called α–carbon. They are the building blacks of proteins.

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

Zwitterion is an amino acid having positively and negatively charged groups, a dipolar molecule.

C

R

H

COO-H3N+ C

R

H

COO-H2NC

R

H

COOHH3N+

+H+

-H+

+H+

-H+

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.

Amino Acids

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

][

]][[2 HA

HAK

(3)][

]][[1

HAH

HHAK (4)

[ ] represents concentration in dilute solution.

Amino Acids

Taking the logs of equations 3 and 4, yields,

][

][log1

HAH

HApKpH (5)

][

][log2 HA

ApKpH

(6)

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 AcidsEssential 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, TryptophanThreonine, Isoleucine, MethionineHistidine, 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

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

- 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 Prosthetic group: heme in greenAmino acid units in red and yellow

Heme group

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.

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

Protein StructureQuaternary 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 DenaturationProtein 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)

• 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.

Summary of Amino Acids and Proteins