ORGANIC CHEMISTRY

Module 6. Proteins

Lesson 18B
PRIMARY, SECONDARY, TERTIARY AND QUATERNARY STRUCTURE OF PROTEINS

18.B.1 Introduction

• Three important conformations of proteins- helical structure (α-helix), extended chain structure (β-structure) and folded (globular) structure
1. Helical structure (α-helix)

• Obtained by winding the peptide chain around an imaginary cylinder to form one turn to the next
• The winding - in such a way that –CONH- groups faces each other at a suitable distance
• First proposed by Pouling and Corey. (Fig. 18.14)

18.B.1.1 Important characteristics

a) Peptide bonds are planner
b) Right handed helix – most stable conformation of polypeptide chain
c) ‘R’ groups- protruded outward- therefore tight helix formation
d) Number of amino acids per turn of the helix- 3.6
e) Distance travelled per turn – 5.4°A (0.54 nm)
f) The helix – stabilized by hydrogen bonds H atom attached to peptide N and O attached to peptide C-bond length 2.8°A
g) Generally present in globular proteins
h) Certain amino acids disrupt the α-helix formation e.g.

• proline and hydroxyproline –α-N is in rigid ring structure—therefore no free rotation (turning)- therefore causes sharp bending of polypeptide.
• if charge groups (-COO^-, NH₃⁺, etc) in R-are cultured – cause electrostatic repulsion – disrupt the α-helix formation.

2. Extended chain: (β-structure)

• In this structure- peptide chains are essentially linear and tend to lie side by side
• The structure is maintained by multiple hydrogen bonding between the peptide chains (Fig. 18.15)

• Two adjacent polypeptide chains run in antiparallel direction- one chain run from N-terminal to C- terminal while the other run from C- terminal to N-terminal
• Each of the chain also form hydrogen bond with still another polypeptide chain and so on – therefore large protein aggregate
• The structure- formed only if R groups are relatively small- so that the chains held sufficiently near to form hydrogen bonds – e.g. amino acids glycine , alanine, serine etc
• Found in structural proteins – i.e. fibrous proteins

18.B.2 Properties of Proteins

1. Each protein has its own isoelectric point pH (casein 4.6)
2. Amphoteric in nature- reacts both with acid and alkali
3. Can bind both anion and cation- some ions form insoluble salt – causes precipitation of protein – used for isolation
4. Solubility depends on pH and ionic composition
5. May interact with aqueous solution and swell – gel structure
6. Have optical activity - because activity of amino acids
7. Absorb in UV light at 280 nm because of aromatic ring of aromatic amino acids – used for estimation of proteins
8. Many proteins can be obtained in crystalline form.

18.B.3 Native State of Proteins

• Highly ordered conformation in which biological activity is manifested
• Have three dimensional configuration
• Native – as such or unchanged- as occurring in nature

18.B.4 Denaturation Of Proteins

• Any change caused in native state of protein
• Fundamentally a disorganization of molecular configuration
• Does not include cleavage of peptide bond- primary structure of protein is not affected.
• Secondary, tertiary and quaternary structure of proteins are affected- forces responsible for these structures are destroyed partially or completely

18.B.5 Effect Of Denaturation On Proteins

1. Decreased solubility and loss of biological value e.g. enzymes
2. Soluble globular protein changed to insoluble – fibrous
3. Increased reactivity – reactive groups- exposed- because unfolding
4. Loss of crystallizability
5. Marked increase in viscosity of solution
6. Increased susceptibility to enzymatic hydrolysis- therefore better digestibility- therefore food is cooked
7. Change in sedimentation pattern

18.B.5.1 Denaturing agents

Certain reagents and conditions

1. Physical treatments- heat, UV-light, violent agitation
2. Chemical reagents

• Organic solvents- alcohol, acetone etc – breaks H bonds
• Acids and alkalies- break ionic bonds and slat bridges
• Salts of heavy metals- AgNO₃, HgNO₃ – cation binds with –COO^- - precipitation
• Alkloidal reagents- tannic acid, picric acid, phosphotungestic acid
• Urea- used for fractionation of casein (α, β, κ, γ)
• Detergent- Lauryl sulphate- ionic bonds
• Oxidising and reducing agents= -S-S- bond – for hair style change
• Dyes- microscopic examination of micro organisms after staining, determination of protein

18.B.6 Colloidal Behaviour of Proteins

• Most of the proteins form colloidal solution – of emulsoid type- solid dispersed in liquid medium
• Both hydrophobic and hydrophilic interaction present in protein – therefore colloidal state forms.
• Stability of colloidal particle rests on – charge and hydration

18.B.6.1 Charges

• Because ionized groups on the surface = -COO^-, PO₄^-3, NH₃⁺, etc in case of proteins
• Equal and similar charge on all the particles
• Similar charge – electrostatic repulsion- keeps the particle away from each other

18.B.6.2 Hydration

• Water binding capacity= because hydrophilic groups such as –OH , side chain R of amino acids , serine and threonine
• Forms a covering layer around the particle and prevents intimate contact between the particles
• Charge and water of hydration- removed= coagulation of protein (Fig. 18.16)

• Charge and water of hydration- vary from protein to protein= because variation in amino acids make-up = qualitative and quantitative

18.B.7 Note

* Isoelectric point

Like amino acids, there exists for each protein a certain pH, known as the isoelectric point, at which its ionization is minimum and it is least soluble. For example casein, the major milk protein, has an isoelectric point of 4.6. This character of protein is often made use of in their isolation.