PROTEIN

Organic Chemistry Practice Task

Lecturer: Dr. Ismono, M.S.

Name : Era Melania

Class : PKU 2018
Regist. Number : 18030194085

Chemistry Departement
Faculty of Mathematics and Natural Sciences
Surabaya State University
2020
A. Definition of Protein
The word protein comes from protos or porotes which means first
or foremost. Protein is an important component or main component of
animal or human cells. Because cells are the shape of our body, the
proteins contained in food function as the main substances in the
formation and growth of the body (Poedjiadi, 1994).
Proteins are long polymers composed of amino acids, often
referred to as "residues" (especially during protein degradation to ensure
its amino acid sequences) that are covalently bonded by peptide bonds.
Naturally, there are twenty different types of amino acids in proteins. All
amino acids that are perfectly biologically ionized, except prolin, have a
general structure as shown in Figure 1. The α-car is the central atom in
which an amino group (NH3+) and an attached carboxyl (COO-) group. As
the pH rises above neutrality (pH 7), an increasingly alkaline environment
tends to neutralize the acidic carboxyl groups of proteins, and as pH
decreases below neutrality, the increasingly acidic environment tends to
neutralize the basic amino groups (Elrod and Stansfield, 2007).
Proteins are large biomolecules, or macrmolecules, consisting of
one or more long chains of amino acid residues. Proteins perform a vast
array of function within living organisms, including catalyzing metabolic
reactions, DNA replication, responding to stimuli, and transporting
molecules from one location to another. Protein differ from one another
primarily in their sequence of amino acids, which is dictated by the
nucletide sequence of their genes, and which usually results in protein
folding into a specific three-dimensional structure that determines its
activity.
B. Protein Structure
There are four kinds of protein structure that is primary, secondary,
tertiary and quarterner structure. (Mastjeh, S., dkk, 1994)
a. Primary structure
It is the basic structure of the protein chain. The
polypeptide chain can be illustrated as follows:
 Peptide bonding
ikatan peptida
O
N C
n-2

Ikatanbonding
Peptide peptida

This chain lies in a plane. The structure as mentioned above

is called the primary structure. The primary structure only describes
the arrangement of amino acids in the peptide chain by not
considering the possible interaction between the amino acids in the
polypeptides. The primary structure of proteins is formed by
peptide bonds. The determination of the amino acid structure in the
primary structure is essentially the same as the determination of
amino acids on the peptide (Mastjeh, S., dkk, 1994).
b. Secondary Structure
If the interaction between the amino acids in the
polypeptide is concerned, the polyptide chain is predicted by
helical (spiral) or multiple sheets. The resulting structure is called
the secondary structure of the protein. The bond responsible for the
formation of the structure is the hydrogen bond. The arrangement
of amino acids on the peptide chain in such a way leads to the
occurrence of hydrogen bonds between the oxygen atoms of the
carbonyl (CO) group of one amine acid with the hydrogen atom in
the amino group (NH) of the other amino acid. The formation of
helical or folded sheets depends on the position and type of amino
acids making up the protein chain (Mastjeh, S., dkk, 1994).
c. Tertiary Structure
Tertiary structures refer to the folding of secondary
structures to form three dimensions. One example of tertiary
structures is the folding of spiral-protein proteins resulting in the
form of globular proteins. The tertiary structure is by the
interaction between side chain (R) groups of amino acids (Mastjeh,
S., dkk, 1994).
d. Quarterner Structure
 Protein molecules can consist of more than one polypeptide
chain. So, in addition to various interactions in the chain that
produce secondary and tertiary structures, we must also consider
the interactions between the chains. The overall arrangement of the
polypeptide chain is called the quaternary structure (Chang, 2008).
The fourth structure called quarterner structure is formed
because of the association of two or more protein molecules. An
example is the hemoglobin structure that occurs because of the
globin association. Globins are the four protein molecules that
make up a unity (Mastjeh, S., dkk, 1994).
C. Protein Classification
Proteins Based on Biological Function.
 Enzyme Proteins, This group of proteins plays a role in
biocatalysts and generally has a globular shape.
 Carrier Proteins have the ability to carry certain ions or
molecules from one organ to another through the bloodstream.
 Structural Proteins. The role of structural proteins is as a
structural forming of tissue cells and gives strength to tissues.
 Hormone Protein Is a hormone produced by endocrine glands
that helps regulate metabolic activity in the body.
 Protein Protector This protein is generally present in the blood,
protecting the organism by resisting the attack of foreign
substances that enter the body.
 Contractile Proteins This group plays a role in the process of
movement, giving the ability of cells to contract or change
shape.
 Reserved Proteins Reserved proteins or stored proteins are
proteins that are stored and stored for several metabolic
processes.
Proteins Based on Molecular Structure.
 Fibriler / Skleroprotein Protein This protein is in the form of
fibers, insoluble in dilute solvents, both saline, acidic, basic, or
 alcoholic solutions. Its large molecular weight cannot be
determined with certainty and is difficult to purify.
 Globular Protein / Spheroid Protein This protein is spherical,
abundant in food such as milk, eggs and meat.
Protein Based on Components of Compilation.
 Simple Protein This protein is composed of amino acids only,
therefore in hydrolysis only the constituent amino acids are
obtained.
 Compound Protein This protein is composed of simple proteins
and other substances that are not proteins.
Protein Based on the Source.
 Animal Protein is a protein in food derived from animals, such
as meat, fish, chicken, eggs, and milk protein.
 Vegetable Protein is a protein derived from plant food
ingredients, such as corn protein, long beans, wheat, soybeans,
and vegetables.
D. The Properties of Protein
a. Physical Properties of Protein
 Proteins are colorless and tasteless
 They are homogeneous and crystalline.
 Proteins vary in shape, proteins can form from simple crystalloid
structures to long fibrilar structures.
 The structure of proteins consists of two different patterns -
globular proteins and fibrilar proteins.
 Globular proteins that are round and are present in plants. Fibillar
proteins are like threads, they are generally present in animals.
 Proteins generally have large molecular weights ranging from 5 x
103 and 1 x 106. because of their large size proteins have many
colloidal properties
 The level of protein diffusion is very slow
 Protein shows tyndall effect
  Protein solubility depends on pH. The lowest solubility is seen at
the isoelectric point. Solubility increases with increasing acidity
or alkalinity
 All proteins show a polarized plane of light to the left, namely
laevorotatory
b. Chemical Properties of Protein
 Protein when hydrolyzed with alkali causes hydrolysis of certain
amino acids such as ariginie, cysteine, sterin, etc. also the optical
activity of the amino acids lost
 Proteins reacted with alcohol give the corresponding esters. This
process is known as esterification
 Amino acids react with amines to form amides
 When free amino acids or proteins are said to react with mineral
acids such as HCl, acid salts will form
 When amino acids in an alkaline medium react with a lot of
hydrochloric acid, the acylation reaction takes place
 Sanger reaction is a protein reacting with FDNB reagents to
produce yellow derivatives, DNB amino acids.
 Folin test is a specific test for amino acid trosin, where blue
develops with phosphomolybdotungstic acid in an alkaline
solution due to the presence of phenol groups
E. The Reaction of Protein
Reaction of Protein
1. Xantoprotein Reaction
Concentrated citric acid is added to a protein solution,
forming a white precipitate, when heated turns yellowish.

2. Sakaguchi’s Reaction
 Sakaguci's reaction is carried out using naphol and sodium
hypobromite reagents. Basically this reaction can give positive
results if there is a guanidine group. So arginine or protein
containing arginine can produce red color.
3. The reaction that occurs in the ninhydrin test. Ninhydrin added
amino acids to produce the salt of dico-hydrihalide-dico-hydramine
which causes a purple color.

4. Biuret Reaction
This test is for amino acids that have more than one peptide
bond, by reaction:

5. Hopkin Cole Reaction

This reaction is based on condensation of 2 diol nuclei from
tryptophan with aldehydes. A positive reaction is indicated by the
occurrence of a purple ring in the upper plane.
F. The Synthesis of Protein
Proteins are synthesized stepwise by the polymerization of amino
acids in a unidirectional manner. In general, the process of protein
synthesis is divided into 3 stages as follows:
1. DNA Replication Stage
 In every cell found in living things, of course, will
experience cell division, which is usually the division of cells can be
divided based on multiples, for example here is the division of 4
cells into 8 cells. Replication is the process of synthesizing new
DNA that occurs in the cell's nucleus. In the process of DNA
replication, this requires the assistance of the helicase enzyme whose
job is to release the bases and hydrogen bonds contained in the DNA
sequence. When the replication process takes place, the parent DNA
will form a DNA child that has the same shape as the parent, thus it
can be concluded that the parent DNA has the task of forming new
DNA.
2. Transcription Phase
Transcription stage is the stage where DNA will form RNA
by deciphering the genetic code derived from DNA. This process is
called transcription because the mRNA is like a transcript, or copy,
of the gene’s DNA code. At this stage will produce 3 types of RNA,
namely: mRNA, tRNA, rRNA. This stage can take place in the
cytoplasm by starting the process of opening the double chains
owned by DNA with the help of the RNA polymerase enzyme.
During transcription, a strand of mRNA is made to complement a
strand of DNA. At this stage there is a single chain that acts as a
chain of sense, while other chains that originate from DNA pairs are
called anti-sense chains. After the mRNA is processed, it carries the
instructions to a ribosome in the cytoplasm.
The transcription stage itself is divided into 3 stages,
namely the initiation, elongation and termination stages.
a. Initiation : is the beginning of transcription. It occurs when
the enzyme RNA polymerase binds to a region of a gene called
the promoter (a particular sequence of nucleotides). This signals
the DNA to unwind so the enzyme can “read” the bases in one of
the DNA strands. The enzyme is ready to make a strand of
mRNA with a complementary sequence of bases.
 b. Elongation : the addition of nucleotides to the mRNA strand.
Transcription starts when RNA polymerase unwinds the DNA
segment. One strand, referred to as the coding strand, becomes the
template with the genes to be coded. The polymerase then aligns
the correct nucleic acid (A, C, G, or U) with its complementary
base on the coding strand of DNA. RNA polymerase is an
enzyme that adds new nucleotides to a growing strand of RNA.
c. Termination : the ending of transcription. When the polymerase
has reached the end of the gene, one of three specific triplets
(UAA, UAG, or UGA) codes a “stop” signal, which triggers the
enzymes to terminate transcription and release the mRNA
transcript.
The new mRNA is not yet ready for translation. It is called
pre-mRNA, and it must go through more processing. The processing
may include splicing, editing, and polyadenylation.
a. Slicing : removes introns (regions that do not code for the protein)
from mRNA. The remaining mRNA consists only of regions
called exons that do code for the protein
b. Editing : changes some of the nucleotides in mRNA
c. Polyadenylation : adds a “tail” to the mRNA. The tail consists of
a string of As (adenine bases). It signals the end of mRNA. It is
also involved in exporting mRNA from the nucleus, and it
protects mRNA from enzymes that might break it down.
3. Translation Phase
Translation is the process of translating codon codes
derived from RNA m to become amino acids called polypetide
which will form proteins. Each sequence of different nitrogen bases
will later be translated into different amino acids. After mRNA
leaves the nucleus, it moves to a ribosome, which consists of rRNA
and proteins. An example here is the amino acid phenylalanine
which is a translation of the UUU codon (3 bases of uracil), amino
 acid glycine (CGC), amino acid serine (UCA) and amino acid
tryptophan (UGG).
At this stage there are at least 20 types of amino acids
needed to be able to form proteins derived from the translation of the
mRNA codon. Furthermore, some of these amino acids will produce
specific polypeptide chains and later will form specific proteins. The
translation process itself is divided into 3 stages:
a. Initiation : the binding of a ribosome to an mRNA transcript
b. Elongation : the recognition of a tRNA anticodon with the next
mRNA codon in the sequence. Once the anticodon and codon
sequences are bound, the tRNA presents its amino acid cargo and the
growing polypeptide strand is attached to this next amino acid. The
tRNA molecule then releases the mRNA strand, the mRNA strand
shifts one codon over in the ribosome, and the next appropriate
tRNA arrives with its matching anticodon.
c. Termination : the final codon on the mRNA is reached which
provides a “stop” message that signals termination of translation and
triggers the release of the complete, newly synthesized protein.
G. The Uses of Protein
1. Improvement and growth
Protein is often called the foundation / substance of development in the
human body. Because protein plays an active role in the maintenance of
body tissues, ranging from hair, skin, muscles, eyes, and so forth.
2. As an antibody or immune forming
This protein will help the antibody cells in the body to identify and
surround the antigens (viruses or bacteria) to remain confined until
eventually eradicated by white blood cells.
3. As a source of energy
Protein can also be used as a source of energy in the human body.
Eating foods that contain high protein, can help humans themselves to
treat tissues and other bodily functions. In addition, excess protein in
 the body will be converted to fat and become a source of energy
reserves for the body.
4. Helps the body's metabolism
One of the functions of protein is to help regulate metabolism in the
body. Protein is used to balance the fluids in the body with acidic bases
so that it will create a stable PH of the fluid in the body.
5. Facilitating chemical reactions
Protein is able to bind to hemoglobin and carry oxygen from the blood.
The process that usually occurs is that hemoglobin initially takes
oxygen from the lungs, then red blood cells move around the body.
Hemoglobin also then releases oxygen to human body tissue cells.
H. References
Chang, R. 2008. General Chemistry: The Essential Concept. New York:
Mc. Graw Hill
Elrod, S., and Stansfield, W. 2007. Schaum's Outlines: Genetika (4 ed.).
Jakarta: Erlangga
Mastjeh, S., dkk. 1994. Kimia Organik II. Yogyakarta: Universitas Gadjah
Mada
Poedjiadi, Anna. 1994. Dasar-Dasar Biokimia. Jakarta: Universitas
Indonesia