Covalent bond : electron pairs are shared between atoms.

Non – Covalent bonds :

1)    Ionic bonds : result from the electrostatic attraction between two ionized groups of opposite charge.

2)    Hydrogen bounding : is an attraction between hydrogen atom covalently bounded to highly electronegative atom on a second electronegative atom

3)    Vander Waals Forces : are short range attractive forces. Vander Waals forces are weaker than ionic and hydrogen bonding.

Intermolecular force : is an attraction. The net attraction is the sum of pair of      interactions between the molecules.

4)    Hydrophobic Interactions : Molecules such as proteins have polar and nonpolar groups.

polar groups : have tendency to be solvated in water.

nonpolar groups : do not have tendency to contact with water.

Amino Acids : are the building blocks of proteins.

>>>        >>>

R Groups:

         1) Nonpolar or Hydrophobic R groups

         2) Unchanged , neutral R groups

         3) Polar negatively charged R groups

         4) Polar positive charged R groups

Properties of Amino Acids :

1)    They are white crystillane substances.

2)    They are much soluble in water than nonpolar ( organic ) solvent.

3)    Net charge , solubility , reactivity in chemical rxn and  acception behaviour of amino acids is related to the chemical nature of R groups. The solubility of proteins in water is related to essentially  to the distribution of the polar and nonpolar groups of the side chain

4)    Crystalline amino acids have relatively high melting points ( above 200 ). Ionic compounds exhibith high melting points because all the strong ionic attraction between the ionized groups.

5)    Aminoacids in neutral aqeous solutions have both positive and negative charges.

A dipolar ion of any amino acid act as an acid ( proton donor ) as a base ( proton accepter )

Any molecule containing both groups and being able to act as an acid or a base is called an amphoteric molecule.

PEPTIDE: small # of AA linked in defined sequence.

In proteins , the – carboxyl groups of one AA is joined to the -amino group of other amino acid by peptide bond.

Disulfide Bond :

-SH ( sulfydryl group ) is highly reactive.

interchain bond

Properties of Peptides :

1)    Usually high melting points

2)    – carboxyl groups and -amino groups in the peptide linkages can not ionize in the ph zone from 0 to 14

3)    Acid – Base properties of peptides are determined by free -amino group of the N-terminal residue , the free  -carboxyl group of C-terminal residue and those R groups of the residues which can ionize.

4)    Give the avarage elemental composition of proteins basis of the percent C,N,H,O …

Conformation of Polypeptide Chains:

         1) Primary Structure: involves the sequenced amino acids. Zig-zag shape with R groups protruding in opposite directions. NH group does not protonate between pH 0 to 14. The C-N link is not able to rotate freely ( very stable ).

CO-NH atoms involved in the peptide bond and two -C atoms are in the sample plane. A series of rigid planes are seperated by HCR groups.

The primary structured proteins are determined by breaking the peptide bond by hydrolysis reactions under the catalytic activity of enzymes or by acid hydrolysis.

2) Secondary Structure : H bonding between O and H of  amino group.

·         – helix

·         -plated sheet parallel , anti-parallel

–helix structure : is governed by intramolecular H – bonding. -helix structure

is an ordered particularly stable structure. Side chains are located outside of the helix. Each peptide bond is engaged in the formation of H – bond , the helixal structure has hight stability and this structure resricts the H bonding with other molecules esp with water.

-plated sheet : a rises from the intermolecular H bonding. The side chains are located above and beneath the plane of the sheets , and their charges and long R groups have a little effect on the structure.

         3) Tertiary Structure : non-covalent interactions  if chains

·         electrostatic interactions

·         hydrogen bonding

·         vander waals interaction

·         interactional non-polar side chains

·         disulfide bonds

4) Quaternary Structure : non-covalent associate ion of polypeptide. chain subunits >> identical subunits , different subunits.

         Denaturation Of Proteins : ( change in the protein conformation ) Acid , alkali , concentrated soline  solutions , heat , radiation.

Protein denaturation is modification of secondary , tertiary or quaternary structure not accompained by the rupture of peptide bonds involved in the primary structure.

Pysical Agents :

·   Heat

·   Cold

·   Mechanical Treatment

·   Heigh pressure

·   Interfaces : adsorption at the interface >> irreversible denaturation

·   Irradiation

o   electromagnetic radiation

o   ultraviolet radiation is observed by aromatic a.a residues.

Chemical Agents :

·   Acid and alkalies

·   Metals

·   Organic solvents

·   Aq. solutions of organic compounds urea , Quanidine salt

·   Quanidine Hydrochloride and Ures  are widely used denaturating agents used for the preparation of partially unfolded proteins.

Determination of Sequence of Amino Acids:

1. Break All Cys-S-S-Cys disulfide bonds :  mercaptoethonol urea used to cleaves all S-S bond

2. Determine the amino acid composition : 6N HCI for abouth 20-24 hrs at 100 C all peptide bonds are broken down. Aminoacids >> molar ratios are determined by aminoacids analysis. Ninhydrin and fluorescomine are used for detection of a.a

3. Identıfy N-terminal and C-terminal a.a :

• Identification of N terminal a.a : Edman degradation and Sanger’s methot used.Edman reagent is Pheynlisothiocyanate and sanger’s method reagent is fluorodinitrobenzene.

• Identification of C terminal a.a : Carboxypeptidase and hydrazine are used to determine C – terminal a.a because both enzymes do not react.

1. Break polypeptides into fragments , determine the a.a composition of each fragment

2. Determine a.a sequence of each fragment and determine sequence of polypeptide.

3. Lorate S-S bond

Protein – Water Interactions: The amount water located inside the protein or strongly absorbed to specific surface sites  >>> 0.3 g /g dry protein.

The amount of water that occupies the first layer adjacent to protein >> 0.3g/g dry protein. Water interacts with protein through :

–       Their peptide bonds ( H – bonding , dipole-dipole )

–       Their a.a side chains ( ionized group , polar )

Water Solubility of Proteins :

·   Influence of pH: PI = isoelectric point

                                       At PI  # of negative = # of positive charges

                                       Net charge of protein is min. At pH value higher or lower than the isometric point >> protein carries a negative or positive electric charge  >> water molecules may interact with those charges so solubility of protein increases. (). Protein chains carrying the same electric charge have a tendency to repel each other to dissociate or unfold >> more groups capable interacting with water so solubility increases. () At PI there is minimum repulsion and no interactions with solvent , protein molecules interact with each other >>> precipitation . Hydrophobic interaction >>> aggregates >>> precipitation

·   Influence of İonic Strenght :  .At 0.5 -1.0 M >> solubility of protein increases >> salting in .  The ions react with charge of proteins and decrease the electrostatic attraction between the opposite charge of neigbouring molecules.

Conc. of salts > 1.0 M >>> solubility of proteins decreases >>> salting out. Mostly the water molecules interact with ions . Not enough water molecule is avaible for the interaction with protein so the protein –protein interaction occurs >>> aggregation >>> precipitation.

·   Influence of Temperature : ( at constant  and pH ) . Solubility of protein with T  in 0 – 40 -50 C . The molecular motion becomes sufficent to distrupt the bonds involved the 2 dary 3 ery structures >>> partial denaturation >>> solubility . Above  40 – 50 C , the complete denaturation of protein can occur. Through hydrohobic interaction between the protein molecules >>> aggregation >> precipitation >>> decrease solubility.

·   Influence of Nonaqueous Solvents: The electrostatic forces of repulsion among protein molecules >>> contributes to the aggregation.

General Information:

Complex macromolecules  %50 more of dry  weight of living organisms.

>>> Homoproteins composed of all a.a

>>>Heteroproteins : a.a + prosthetic groups such as nucleoproteins , lipoproteins , phospoproteins , hemoproteins

According to the conformatios : fibrous proteins and globular proteins.

According to their functions : Structure proteins protein with biological activity , food proteins >>> are those that are palatable , digestible , nontoxic and available economically for humans, essentiall a.a such as isoleurine , leucine , lysine , methionine

Surface Tension :

Liquids have tendency to have the minimum surface to maintain minimum free energy.Surface tension is the energy or work required to increase the surface area of a liquid by unit amount . As the temperature –and hence the intensity of molecular motion increases , intermolecular forces become less effective. Less work is required to extend the surface of a liquid surface tension decreases with increase temperature.

1.    Cohesive Forces : intermolecular forces between like molecules.

2.    Adhesive Forces : intermolecular forces between unlike molecules.

Substances that reduce surface tensioned water and allow it to spread more easiyl are known as wetting agents

Ex: water >> have concave meniscus  because adhesive forces > cohesive forces

mercury >> have convey meniscus because adhesive forces < cohesive forces

air – water >>> surface tension  ,  oil – water >>> interfacial tension

The interfacial tension of a binary system lies between the surface tensions of the two pure liquid at the same temperature.

The presence of interface between two liquid phases indicates that the intermolecular forces between the molecule in the liquids are not balanced.

Adsorption from solution :

Adsorption is the phenomenon whereby dissolved molecules accumulate at the surface in greater concentrations than conc. which obtained when the molecules are randomly distributed through out the system.

Two types of surface active materials :

·         small  molecule surfactant  ( are considered  to adsorp reversibly )

·         macromolecules such as protein  ( are considered  to adsorp irreversibly )

Gibbs adsorption equation :

Materials that adsorp strongly at the interface and cause substantial lowering of the surface tension at low conc. are called surfactant ( small molecules + protein )

Surface properties of proteins:

·   a soluble protein

·   diffusion towards interface

·   adsorption >>> once a portion of protein contacts the interface than the nonpolar a.a residues orient toward the nonaqueous phase.

·   rearrangement >> the remainder of the protein adsorbs spontenously

Absorption and unfolding in achieved easily in a short time by flexible proteins >>> good emulsifiers . Globular proteins need a long time for unfolding after adsorption even adsorption might be slow with globular proteins.