AMINO ACID & PROTEIN

Ulivina Pratini127795086

Science Education Post Graduate Program

The State University Of Surabaya

Learning objectives

1. Understanding the meaning of protein and amino acids as well as its function

2. Explain review the outline of the decomposition of proteins for the body

3. Describes several types of metabolic reactions of amino acids

4. Describes the urea cycle5. Understanding the biosynthesis of proteins

Introduction of Protein

The proteins in the cells of the body is formed by amino acids.The Structure Of Amino Acids

in other words, amino acids are the monomers (units of Shaper) protein

The Structure Of Amino Acids

From this general formula can be seen that the α-carbon atom is an asymmetric carbon atom.

consisting of an amine group, a carboxyl group, and a group of -R (side chain ) that are bound to the same carbon atom.

The Fischer projection formulas

D-gliseraldehid

Due to the asymmetric carbon, then the amino acid molecule has two configurations D and L. it can be compared to the molecular configuration of monosaccharides.

• D (destrorotatory )configuration when the position of the -NH2 group on the right of the α-carbon atom

• L (levorotatory) configuration when the position of the -NH2 group on the Left of the α-carbon atom

These amino acids found in proteins generally have configuration L

Properties of Amino AcidsWhen the amino acid is soluble in water, a carboxylic group will release H+ ions, whereas amine groups will receive the H+ ions, as written below.

By the presence of both the Group of amino acids in aqueous solution can form a positively charged ions and negatively charged ions (zwitterionic) or an amphoteric substance.

The State of this ion strongly depends on the pH of the solution.

In a State of bases, amino acids will form as shown below:

because of the concentration of OH- are high which is able to bind H + ions that are present in the – NH3

+ groups

In a State of Acid, amino acids will form as shown below:

Because the concentration of H + ion is high, it is able to bind with ion – COO-, Thus was formed –COOH groups

ClassificationBased on the formation of amino acids can be divided into two classes:1. Essential amino acids (which cannot be produced by the body)2. Non-essential amino acids (which can be made in the body)

In addition these amino acids can also be grouped according to the structure of the side chains i.e.

1. the carbon-chain aliphatic2. Contain hydroxyl groups3. Contain sulfur atoms4. Containing acid groups or amida groups5. Contain a base groups6. Contain aromatic rings7. form a bond with the amino group on the N atom

1. Amino Acids which have the carbon-chain aliphatic

2. Contain hydroxyl groups

3. Contain sulfur atoms

4. Containing acid groups or amida groups

5. Contain a base groups

6. Contain Aromatic Rings

7. Form a bond with the amino group on the N atom

Peptide

Some amino acid molecules can bind to one another to form a compound called peptide.

When the amount of amino acids that are formed more than ten then it is called polypeptide

Protein is a polypeptide comprising more than a hundred amino acids

Nomenclature of Peptide Compounds

acyl

Basically a peptide is an acyl-amino acids

Example

The name of the peptide is given based on the type of amino acid that formed it.

Amino acids which the carboxyl group react with the NH2 group – given the suffix “il” in their names,

while the order of naming is based on amino acid sequence, starting from the ends of the amino acid which still have the -NH2 group.

or it can be abbreviated as follows : gly-ala-OH

Protein Protein is a polypeptide has a molecular weights vary widely, from 5000 to over one million. In addition to different molecular weight proteins have different properties.

Protein Structure

There are four levels of the basic structure of the protein, i.e., -primary structure, -secondary, -tertiary, and -kuartener.

Primary Structure

The primary structure of the enzyme Ribonuclease

Primary structure indicate the number, types and order of amino acids in protein molecules.

Secondary Structure

The structure of a polypeptide Alpha Helix

Polypeptide chains composed of many >C=O and >N-H groups.

Both of these groups can remain bound to each other due to the formation of hydrogen bonds between the oxygen atoms of the > C = O with a hydrogen atom from the >N-H group.

When these hydrogen bonds formed between the cluster-cluster which is contained in a single polypeptide chain, will form the structure of the Helix.

as it looks on the picture beside:

These hydrogen bonds can also occur between two or more polypeptide

chains and will form a configuration of α is not a form of parallel helical

winding but chains and called pleated sheet structure

There are two forms of pleated sheet structure, i.e. parallel and anti parallel

Parallel forms occur when the

polypeptide chains bonded

through hydrogen bonding that is

parallel and in the same direction,

Pleated sheet structure parallel

Secondary Structure

The non-parallel form occurs if

monomers bound in a position

parallel but opposite in

direction.

Pleated sheet structure non parallel

Secondary Structure

Tertiary StructureTertiary structure shows a tendency to form the polypeptide folds or rolls, and thus form a more complex structure. The structure is established by the existence of multiple bonds between R group of amino acids that make up proteins.

Some types of bonds are for example:(a) electrostatic bonding,(b) hydrogen bonding,(c) the interaction between the hydrophobic side chains of non polar,(d) the interaction of Dipole-Dipole and(e) bonds of disulfide which is a covalent bond

Kuartener StructureThree-dimensional Model appears as in Figure 1.6 indicates the degree of participation of units of protein. Most of the globular proteins consist of several separate polypeptide chains.

This polypeptide chains interacting to form Alliance, The Figure 1.7 shows a model of the structure of kuartener which consists of two globular protein units

Figure 1.6.Globular protein complex folds

Figure 1.7. The structure of the globular protein complex kuartener

Classification of proteinsReview of the structure of proteins can be divided into major groups, namely the simple proteins and combined protein

1. Simple proteins are proteins made up of amino acid molecules

Simple Proteins can be divided in two parts according to the shape of the molecule, namely protein fiber and protein globular. Protein fiber has long molecular shape as fiber or protein fibers, whereas globular round.

2. Combined protein is a protein consisting of protein and non protein group. This group is called prosthetic group and consists of carbohydrates, lipids, or nucleic acids. Such as: Mukoprotein, glycoproteins, lipoproteins, nukleoprotein

Figur 1.8. The triple helix structure

METABOLISM OF PROTEINS AND AMINO ACIDS

The proteins in our bodies undergoes certain changes with different speeds for each protein. Daily, 1.2 grams the average of protein per kilogram of body weight is converted into other compounds.

There are three possible mechanisms of conversion of the protein that is:

1. Dead cells, then its components undergoes decomposition or catabolism and formed new cells

2. Each protein undergoes the process of decomposition and occur a new protein synthesis, without any cells that die.

3. Protein secreted from the cell is replaced with a new protein synthesis

The Decomposition of Proteins in the Body

Digestion Of Proteins

1. Protein digestion starts in the stomach with the help of pepsin, proteolytic enzymes that hydrolyze peptide bonds on the phenylalanine residues of amino, tyrosine and tryptophan

2. The resulting short polypeptide then enters into the small intestine where digestion of protein is continued by trypsin, chymotrypsin, aminopeptidase, and carboxy-peptidase that produced amino acids.

3. The resulting amino acid is then transported through the membrane of the small intestine into the bloodstream.

4. Blood distributes amino acids to peripheral tissues for synthesis of proteins and to the liver to untangle.

Metabolism of Amino Acid

The early stages of the reaction of amino acid metabolism involves: 1. Release of the amino group, and then 2. Changes to a new framework on carbon molecules of amino acids.

1. Two core processes of Release the amino group i.e. Transamination and deamination will be discussed as follows:

1.a. Transamination is the process of catabolism of amino acids that involves the transfer of amino acids from one amino acid to another amino acid.

In this transamination reaction of the amino group of an amino acid is transferred to one of three keto compound, namely pyruvic acid, Alpha ketoglutarate or oksaloasetat, so this keto compound converted into amino acids, whereas the original amino acid is converted into an acid keto.

TransaminationThere are two important enzyme in reactions of transaminasi i.e. alanin transaminase reactions and glutamate transaminase reactions that works as a catalyst in the following reaction:

This reaction occurs in the mitochondria or in liquid cytoplasm

Oxidative Deamination

In this process the amino group of glutamic acid release in the form of NH4

+, in addition to NAD+ glutamate dehidrogenasi can also use NADP+ as an electron acceptor. Because glutamate is the end result of the process of transamination, then the glutamate dehydrogenase is an enzyme which is essential in the metabolism of amino acids.

2. Changes to a new framework on carbon of amino acids molecules.

The picture shows the carbon chains of amino acid metabolism associated with the citric acid cycle

The Formation Of Acetyl Coenzyme A

In Figure looks that Acetyl Coenzyme A is connector compounds between the amino acid metabolism and the citric acid cycle.

There are two metabolic pathways that lead to the formation of Acetyl Coenzyme A, i.e. -through the pyruvic acid and -through acetoacetate acid

Amino acids that undergoes metabolic pathways through the pyruvic acid is alanin, cysteine, glycine, serine, and threonine.

Alanin produces pyruvic acid by direct reaction with transaminasi α ketoglutarate.

Serin undergoes dehydration and deamination by the enzyme of serine α dehidratase.

Threonine is converted to glycine and asetaldehid by the enzyme of threonine aldolase.

Glycine is then converted into Acetyl Coenzyme A via the serine formation with the addition of one atom of carbon, such as methyl hydroxyl and formyl. Coenzyme that works here is tetrahidrofolat.

Glycin

Enzymes: glycine oxidase

Oxidative deamination reaction

5-formyltetrahydrofolate as a donor the formyl group to glycine

AlanineTransamination process:

These reaction is reversible

Pyruvic acid is a compound that is formed on the carbohydrate metabolism. Thus the metabolic reaction alanin is the relationship between metabolism of proteins with carbohydrate metabolism

ValinThrough a few stages of the reaction, valin can be converted into suksinil KoA which then enter into the citric acid cycle

isobutril KoA

suksinil KoA

Leucine transamination-oxidative reaction

citric acid cycle

Urea cycle

Reaction 1. Synthesis of Karbamil Phosphate

In reaction to the formation of karbamil phosphate, one mole of ammonia reacts with one mole of carbon dioxide with the help of the enzyme karbamilfosfat synthetases. This reaction requires energy, so this reaction involves two moles of ATP is converted into ADP

In addition as a cofactor required Mg ++ and N-acetyl-glutamate.

Reaction 2. The formation of sitrulin

Karbamil phosphate formed reacts with ornitin to form sitrulin. In this reaction the karbamil join ornitin and separate the phosphate groups. As a catalyst to the formation of sitrulin is ornitin transkarbamilase found in the mitochondria of liver cells.

Reaction 3. The formation of arginosuksinate acid.

Sitrulin reacts with aspartic acid forming argininosuksinat acid. This reaction takes place with the help of the enzyme argininosuksinat synthetases.

In the reaction of ATP is a source of energy by way of releasing the phosphate group and turned into AMP

Reaction 4. Decomposition of Argininosuksinat acid.

Argininosuksinat acid in this reaction is outlined to be arginine and fumaric acid. This reaction takes place with the help of the enzyme argininosuksinase, an enzyme in the liver and kidneys.

Reaction 5. Decipherment of arginine

This last reaction phase complete reaction of the urea cycle. In this reaction the arginine outlined being urea and ornitin. An enzyme that works as a catalyst in the reaction of this decomposition is arginase in liver.

Ornitin formed in the reaction of this hydrolysis react again with karbamilphosphete to form sitrulin (In reaction 2)

This reaction take place repeatedly form a cycle. As for urea removed from the body through the urine.

The overall reaction of Urea cycle is as follows:

Chemical process in urea cycle occurs in the liver because of the enzymes work as catalysts are primarily found in the mitochondria of liver cells

Biosynthesis of Protein

In the process of protein biosynthesis, DNA molecule serves as a mold for the formation of RNA, and RNA molecule then directs the sequence of amino acids in the formation of protein molecules, which occurs in Ribosomes.

Thus the flow of genetic information in cells is as follows:

DNA (Deoxyribo Nucleic Acid)The DNA molecule is a chain of polinukleotida which has some kind of purin base and primidin, and the form is double helix.

Among one chains with the partner in the double helix there are hydrogen bonds, i.e. bonds that occurs between adenine with thymine (A-T) and between guanine and cytosine (G-C)

In the process of protein biosynthesis, DNA molecule serves as a mold for the formation of RNA

RNA (Ribo Nucleic Acid)

Kinds of RNA

1. rRNA (ribosomal RNA) together with proteins are components that form Ribosomes in the cell.

even though it is the main component of the rRNA Ribosome, however his role in protein synthesis takes place in the Ribosomes is not yet known

2. mRNA (massanger RNA)

3. tRNA (transfer RNA)

2. mRNA (massanger RNA) is produced within the cell nucleus and RNA is the least amount, i.e. approximately 5% of all RNA within the cell.

formation of mRNA in the cell nucleus uses a DNA molecule as a molecule of mold and order of bases on the mRNA complement is one of a chain of DNA molecules.

Thus the sequence of bases purin and primidin one of the chains of the DNA molecule, where the base thymine (T) is replaced by uracil (U).

mRNA that has been formed in the cell nucleus and then out of the cell nucleus and into the cytoplasm and are bound to Ribosomes

3. tRNA (Transfer RNA)The primary function of tRNA is to bring the amino acid in translation process of mRNA codon into a sequence of amino acids that form a protein

1. Stem of the amino acids.

2. The stem and loop UH2 or

dihydro uridin

3. Stem and loop of antikodon

4. Extra Stem

5. Stem and loop the U or

pseudoridin.

Genetic code

Two Process in the synthesis of proteins is:

1. Transcriptiontranscription is the formation of RNA molecules according to the messages given by DNA. At this stage of genetic information was given to the RNA molecule that is formed as an intermediate in the synthesis of proteins

2. TranslationNA molecules translate genetic information into protein formation process

Transcription

Translation