BIOCHEM PROTEIN (Part nga nakaila taka #01)

Nagmamahal: Khalid 02

PROTEINS
-a highly complex substance that is present in all living organisms.
-they account for about 15% of a cells overall mass.
HISTORY
Gerardus Johannes Mulder
-Dutch chemist found that EGG and MILK can be coagulated on heating and were NITROGENOUS substances.
JJ Berzelius
-Suggested to Mulder that these substances should be called PROTEINS.
-from Greek word “proteios” which means “primary”, or “holding first place” or “preeminent”
-Proteins are fundamental structural components of the body: nitrogenous macromolecules composed of
many amino acids

PROTEIN SUBUNITS
-the proteins in the body are made up of some combination of 20 different subunits called AMINO ACIDS.
-Functional groups present in the molecules amino acids are: Amino, Hydrogen, R-group, and Carboxyl

AMINO ACID
-building blocks of proteins
-an organic compound that contains both an amino (-NH2) group and a carboxyl (COOH) group
-ALPHA AMINO ACIDS are always found in proteins
-alpha amino acid is an amino acid in which he amino group and the carboxyl group are attached to the alpha
carbon
-all amino acids isolated from proteins, with the exception of PROLINE, have the same general structure
-side chains vary in size, shape, charge, acidity, functional group present, hydrogen-bonding ability, and
chemical reactivity
-the carboxyl group attach to the alpha carbon can be either be UNPROTONATED (COO-) which has -1 net
charge or NEUTRAL (COOH) with 0 charge
-the amino group attach to attach to alpha carbon can either be PROTONATED (NH3+) which has +1 net
charge or NEUTRAL (NH2) which has 0 charge

THE 20 IMPORTANT AMINO ACID

Neutral-nonpolar amino acids
 Glycine (Gly, G)
 Alanine (Ala, A)
 Valine (Val, A)
 Isoleucine (Ile, I)
 Tryptophan (Trp, W)
 Phenylalanine (Phe, F)
 Proline ( Pro, P)
 Methionine (Met, M)
 Leucine (Leu, L)
Neutral-polar amino acids
 Serine (Ser, S)
 Threonine (Thr, T)
 Tyrosine (Tyr, T)
 Asparagine (Asn, A)
 Glutamine (Gln, Q)
 Cysteine (Cys, C)
Acidic amino acids
 Aspartic acid (Asp, D)
 Glutamic acid (Glu, E)
Basic amino acids
 Lysine (Lys, K)
 Arginine (Arg, R)
 Histidine (His, H)
Zwitterion
-any neutral molecule with equal number of positive and negative charges
-Dipolar ions
-Amino acids in the presence of water becomes Zwitter ions

CLASSES OF AMINO ACIDS

Non Polar Groups
-These group of amino acid prefer to contact with one another rather than water and are said to be
“hydrophobic amino acids”—water fearing
-they are usually found buried in the interior of proteins, where they can associate with one another and
remain isolated from water
Polar Group
-they are attracted to polar water molecules, they are said to be “hydrophilic amino acids”—water loving
-the hydrophilic side chains are found on the surface of the proteins

3 CLASSES OF POLAR AMINO GROUP

>Polar, neutral amino acids
-They have R-groups that have high affinity for water but that are not ionic pH7
-most of these amino acids associate with one another by hydrogen bonding: but CYSTEINE molecules form
disulfide bonds with one another.

>Negatively charge Amino acids

-have ionized carboxyl groups in their side chains. At pH7 these amino acids have a net charge of -1
-they are acidic amino acids because ionization of the carboxylic acid releases a proton

>Positively charged Amino acids

-at pH7 these amino acids have a net positive charge because their side chains contain positive groups
-these amino groups are basic because the side chain reacts with water, picking up proton and releasing a
hydroxide anion
PROPERTIES OF AMINO ACIDS
1.SOLUBILITY
-amino group exhibits a wide range of solubilities. In general, amino acids are minimally soluble at their
ISOELECTRIC POINT
-those amino acids with longer aliphatic side chains are less soluble than those with shorter chain polar groups
such as carboxyl and hydroxyl, tend increase solubility
2.MELTING POINT
-amino acids possess high melting points, usually above 200 degrees celcius
3.TASTES OF AMINO ACIDS
-amino acids are usually sweet (Gly, Ala, Val, Ser), tasteless (Leu), or bitter (Iso)
4.APPEARANCE
-the amino acids are white crystalline substance; the crystal from being characteristic for each one
5.ULTRAVIOLET ABSORPTION SPECTRUM OF AROMATIC AMINO ACIDS
-the aromatic amino acids W, Y, and F absorb ultraviolet light. Most of the UV absorption of proteins is due to
their W content
6.OPTICAL PROPERTIES OF AMINO ACID
-the alpha carbon of all amino acids except glycine are asymmetric, so they show optical activity. The rotation
of the amino acid vary according to the pH of the solution, which determines the ionic state of the amino acid
7.ACID-BASE PROPERTIES OF AMINO ACIDS
-amino acids in aqueous solution are ionized and can act as acid or bases
-amino acid having single amino and carboxyl group crystallize from neutral aqueous solutions in a fully
ionized species called dipolar ion or zwitter ion

AMPHOTERIC NATURE AND ISOELECTRIC pH

-NH2 and COOH groups are ionizable, charged polar side chain of amino acids
-depending on the pH of the solution, these groups act as a PROTON DONOR (ACIDS), or PROTON ACCEPTORS
(BASES). This property is called AMPHOTERIC and therefor amino acids are called AMPHOLYTES
-at a specific pH, amino acid carries both the charges in equal number and exists a dipolar or zwitterion. At this
point, the net charge is zero (+ and – charge on the protein amino acid molecule equalizes)
-pl or isoelectric pH—the pH at which it occurs without any charge on it. On the acidic side of its pl, amino acid
exist as cation by accepting a proton and on alkaline side as anion by donating a proton.

FUNCTIONS OF AMINO ACIDS

-Monomeric constituents of proteins and peptides
-some amino acids are converted to carbohydrates and are called GLUCOGENIC AMINO ACIDS
-specific amino acids give rise to specialized products e.g. tyrosine forms hormones such as thyroid hormones
(T3, T4), epinephrine and norepinephrine and a pigment called melanin
-Tryptophan can synthesize a vitamin called niacin
-Glycine, arginine, and methionine synthesize creatinine
-Glycine and cysteine helps synthesize of bile salts
-Glutamate, cysteine, and glycine synthesize glutathione
-Histidine changes to histamine
-In addition to tripeptide formation, glycine is used for the synthesize of heme
-Pyrimidines and purines use several amino acid for their synthesis such as aspartate and glutamine for
pyrimidines and glycine, aspartic acid, glutamine and serine for purine synthesis.
-some amino acids such as glycine and cysteine, are used as detoxicants of specific substances.
-Methionine acts as “active” methionine (S-adenosylmethionine) transfer methyl group to various substances
by transmethylation.
-Cystine and methionine are sources of sulfur

SPECIAL AMINO ACIDS PRESENT IN SOME PROTEINS

Hydroxyproline and hydroxylysine- found in collagen of connective tissue
N-Methyllysine- found in myosin, a muscle protein functioning in contraction
Gamma-carboxyglutamic acid- found in the blood-clotting protein prothrombin
Desmosine- a derivative of lysine, found only in the fibrous protein elastin

ESSENTIALS OF AMINO ACIDS

Essential amino acids: not synthesized by the body and must be taken in the diet (valine, leucine, isoleucine,
phenylalanine, threonine, tryptophan, histidine, arginine, methionine and lysine)
Non-essential amino acids: these can be synthesized by the body and may not be the requisite components of
the diet
Semi-essential amino acids: these are growth promoting factors since they are not synthesized insufficient
quantity during growth. They include arginine and histidine 9 (for infants only and not for adults). They
become essential in growing children, pregnancy, and lactating woman.
Conditional amino acids: are usually not essential, except in times of illness and stress

STEREOISOMERS OF AMINO ACIDS

The configuration of alpha-amino acids isolated from proteins is in L configuration, in which the amino group
attach in alpha carbon is on the left side.

CHEMICAL REACTIONS OF AMINO ACIDS

3 important components which give the different amino acids their characteristic reactivities:
 The amino or NH2 group
 The carboxyl or COOH group
 The various R group

IMPORTANT CHEMICAL REACTION USE IN AMINO ACID

A.Ninhydrin reaction
-when alpha amino acid boiled with ninhydrin, a powerful oxidizing agent forming a purple product
(Ruhemann’s purple)
-Proline and hydroxyproline will give a yellow color.
-Use as quantitative and qualitative test for protein

B.Reaction with Sanger’s reagent

-Sanger’s reagent is 1-fluoro-2,4-dinitrobenzene (FDNM).
-It is useful in the identification of individual amino acids
-Give colored bright yellow
-Important in determining the amino acid sequence of peptides

THE PEPTIDE BOND

-Proteins are linear polymers of L-a-amino acids in which the carboxyl group of one amino acid is linked to the
amino group of another amino acid.
-The peptide bond is an amide bond formed between the -COO- group of one amino acid and a-N+H3 group of
another amino acids.
-The molecules formed by condensing 2 amino acids is called DIPEPTIDE.

PEPTIDES WITH BIOLOGICAL ACTIVITY

Insulin- a hormone secreted by B cells of pancreas which stimulates the capacity of cells to use glucose as a
metabolic fuel.
Oxytocin- a hormone with 9 amino acid residue secreted by the posterior pituitary gland which stimulates
uterine contractions
Bradykin-a substance that inhibits inflammation of tissues
Enkephalins- a short peptide formed in the central nervous system: it binds to specific receptors in certain
cells of the brain and induces analgesia, deadening of pain sensations.
Corticotropin- a hormone of the pituitary gland stimulates the adrenal cortex

PROTEINS CAN BE ALSO CLASSIFIED ON THE BASIS OF THEIR SHAPE:

1.Globular proteins
-peptide chain is tightly folded into compact, spherical or globular shape.
-usually soluble in aqueous systems and diffuse readily
-nearly all enzymes are globular proteins, as are blood transport proteins, antibodies and nutrients storage
proteins
2.Fibrous proteins
-Consist of polypeptide chains arrange in a parallel fashion along a single axis, to yield long fibers or sheets
-Physically tough and are soluble in water or dilute salt solutions.
-The basic structural elements in connective tissue of higher animals.
EX.Keratin of hair, skin and nails