AMINO ACIDS & PROTEINS Ulivina Pratini 127795086 Science Education Post Graduate ProgramThe State University Of Surabaya
Learning objectives1. Understanding the meaning of protein and amino acids as well as its function2. Explain review the outline of the decomposition of proteins for the body3. Describes several types of metabolic reactions of amino acids4. Describes the urea cycle5. Understanding the biosynthesis of proteins
Introduction of ProteinsThe proteins in the cells of the body is formed by aminoacids.The Structure Of Amino Acidsin other words, amino acids are the monomers (units ofShaper) protein
The Structure Of Amino AcidsFrom 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 agroup of -R (side chain ) that are bound to the samecarbon atom.
The Fischerprojection formulas D-gliseraldehidDue to the asymmetric carbon, then the amino acid molecule has twoconfigurations D and L. it can be compared to the molecular configurationof 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 atomThese 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 canform a positively charged ions and negatively charged ions (zwitterionic)or an amphoteric substance.
The State of this ion strongly depends on the pHof the solution.In a State of bases, amino acids will form asshown below: because of the concentration of OH- are high which is able to bind H + ions that are present in the – NH3 + groupsIn a State of Acid, amino acids will form as shown below:Because the concentration of H + ion ishigh, it is able to bind with ion – COO-,Thus was formed –COOH groups
ClassificationBased on the formation of amino acids can be divided into twoclasses: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 tothe structure of the side chains i.e. 1. 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
1. Amino Acids which have the carbon-chain aliphatic
7. Form a bond with the amino group on the N atom
PeptideSome amino acid molecules can bind to one another to form a compoundcalled peptide.When the amount of amino acids that are formed more than ten then it iscalled polypeptideProtein is a polypeptide comprising more than a hundred amino acids
Nomenclature of Peptide CompoundsBasically a peptide is an acyl-amino acids acyl
ExampleThe name of the peptide is given based on the type ofamino acid that formed it.Amino acids which the carboxyl group react with the NH2group – given the suffix “il” in their names,while the order of naming is based on amino acidsequence, starting from the ends of the amino acid whichstill have the -NH2 group.or it can be abbreviated as follows : gly-ala-OH
ProteinProtein is a polypeptide has a molecular weights varywidely, from 5000 to over one million. In addition todifferent molecular weight proteins have differentproperties.Protein StructureThere are four levels of the basic structure of theprotein, i.e.,-primary structure,-secondary,-tertiary, and-kuartener.
PrimaryStructure Primary structure indicate the number, types and order of amino acids in protein molecules. The primary structure of the enzyme Ribonuclease
Secondary StructurePolypeptide chains composed of many>C=O and >N-H groups.Both of these groups can remain bound toeach other due to the formation ofhydrogen bonds between the oxygen atomsof the > C = O with a hydrogen atom fromthe >N-H group.When these hydrogen bonds formedbetween the cluster-cluster which iscontained in a single polypeptide chain, willform the structure of the Helix.as it looks on the picture beside: The structure of a polypeptide Alpha Helix
Secondary Structure 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 StructurePleated sheet structure non parallel The non-parallel form occurs if monomers bound in a position parallel but opposite in direction.
Tertiary Structure Tertiary 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 ofparticipation of units of protein. Most of the globular proteins consist ofseveral 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, namelythe simple proteins and combined protein1. Simple proteins are proteins made up of amino acid moleculesSimple Proteins can be divided in two parts according to the shape of themolecule, namely protein fiber and protein globular. Protein fiber has longmolecular shape as fiber or protein fibers, whereas globular round. Figur 1.8. The triple helix structure2. Combined protein is a protein consisting of protein and non protein group.This group is called prosthetic group and consists of carbohydrates, lipids, ornucleic acids. Such as: Mukoprotein, glycoproteins, lipoproteins,nukleoprotein
METABOLISM OF PROTEINS AND AMINO ACIDSThe proteins in our bodies undergoes certain changes with different speeds foreach protein. Daily, 1.2 grams the average of protein per kilogram of bodyweight 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
Digestion Of Proteins1. Protein digestion starts in thestomach with the help of pepsin,proteolytic enzymes that hydrolyzepeptide bonds on the phenylalanineresidues of amino, tyrosine andtryptophan2. The resulting short polypeptidethen enters into the small intestinewhere digestion of protein iscontinued by trypsin, chymotrypsin,aminopeptidase, and carboxy-peptidase that produced amino acids.3. The resulting amino acid is thentransported through the membraneof the small intestine into thebloodstream.4. Blood distributes amino acids to peripheral tissues for synthesis of proteins and to theliver to untangle.
Metabolism of Amino AcidThe early stages of the reaction of amino acid metabolism involves:1. Release of the amino group, and then2. Changes to a new framework on carbon molecules of amino acids.1. Two core processes of Release the amino group i.e. Transamination anddeamination will be discussed as follows:1.a. Transamination is the process of catabolism of amino acids thatinvolves the transfer of amino acids from one amino acid to another aminoacid.In this transamination reaction of the amino group of an amino acid istransferred to one of three keto compound, namely pyruvic acid, Alphaketoglutarate or oksaloasetat, so this keto compound converted into aminoacids, whereas the original amino acid is converted into an acid keto.
TransaminationThere are two important enzyme in reactions oftransaminasi i.e. alanin transaminase reactions andglutamate transaminase reactions that works as a catalystin the following reaction:This reaction occurs in the mitochondria or in liquid cytoplasm
Oxidative DeaminationIn this process the amino group of glutamic acid release inthe form of NH4+, in addition to NAD+ glutamatedehidrogenasi can also use NADP+ as an electron acceptor.Because glutamate is the end result of the process oftransamination, then the glutamate dehydrogenase is anenzyme which is essential in the metabolism of aminoacids.
2. Changes to a new framework on carbon of amino acids molecules.The picture shows the carbon chains of amino acid metabolism associatedwith the citric acid cycle
The Formation Of Acetyl Coenzyme AIn Figure looks that AcetylCoenzyme A is connectorcompounds between theamino acid metabolism andthe citric acid cycle.There are two metabolicpathways that lead to theformation of Acetyl CoenzymeA, i.e.-through the pyruvic acid and-through acetoacetate acid
Amino acids that undergoes metabolic pathways through thepyruvic acid is alanin, cysteine, glycine, serine, and threonine.Alanin produces pyruvic acid by directreaction with transaminasi αketoglutarate.Serin undergoes dehydration anddeamination by the enzyme of serine αdehidratase.Threonine is converted to glycine andasetaldehid by the enzyme of threoninealdolase.Glycine is then converted into Acetyl Coenzyme A via the serine formation withthe addition of one atom of carbon, such as methyl hydroxyl and formyl.Coenzyme that works here is tetrahidrofolat.
GlycinOxidative deamination reactionEnzymes: glycine oxidase5-formyltetrahydrofolate as a donor the formyl group to glycine
Alanine Transamination 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 convertedinto suksinil KoA which then enter into the citric acid cycle isobutril KoA suksinil KoA
Reaction 1. Synthesis of Karbamil PhosphateIn reaction to the formation of karbamil phosphate, one moleof ammonia reacts with one mole of carbon dioxide with thehelp of the enzyme karbamilfosfat synthetases. This reactionrequires energy, so this reaction involves two moles of ATP isconverted into ADP In addition as a cofactor required Mg ++ and N-acetyl- glutamate.
Reaction 2. The formation of sitrulinKarbamil phosphate formed reacts with ornitin to formsitrulin. In this reaction the karbamil join ornitin and separatethe phosphate groups. As a catalyst to the formation of sitrulinis ornitin transkarbamilase found in the mitochondria of livercells.
Reaction 3. The formation of arginosuksinate acid.Sitrulin reacts with aspartic acid forming argininosuksinat acid.This reaction takes place with the help of the enzymeargininosuksinat synthetases.In the reaction of ATP is a source of energy by way of releasingthe phosphate group and turned into AMP
Reaction 4. Decomposition of Argininosuksinat acid.Argininosuksinat acid in this reaction is outlined to be arginine andfumaric acid. This reaction takes place with the help of the enzymeargininosuksinase, an enzyme in the liver and kidneys.
Reaction 5. Decipherment of arginineThis last reaction phase complete reaction of the urea cycle. Inthis reaction the arginine outlined being urea and ornitin. Anenzyme that works as a catalyst in the reaction of thisdecomposition is arginase in liver.Ornitin formed in the reaction of this hydrolysis react again withkarbamilphosphete to form sitrulin (In reaction 2)This reaction take place repeatedly form a cycle. As for urea removed from thebody 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 ProteinIn the process of protein biosynthesis, DNA molecule servesas a mold for the formation of RNA, and RNA molecule thendirects the sequence of amino acids in the formation ofprotein 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 somekind of purin base and primidin, and the form is double helix.Among one chains with thepartner in the double helix thereare hydrogen bonds, i.e. bondsthat occurs between adenine withthymine (A-T) and betweenguanine and cytosine (G-C)In the process of protein biosynthesis, DNAmolecule serves as a mold for the formation ofRNA
Kinds of RNA1. rRNA (ribosomal RNA) together with proteins arecomponents that form Ribosomes in the cell.even though it is the main component of the rRNARibosome, however his role in protein synthesis takesplace in the Ribosomes is not yet known2. mRNA (massanger RNA)3. tRNA (transfer RNA)
2. mRNA (massanger RNA) is produced within the cell nucleusand RNA is the least amount, i.e. approximately 5% of all RNAwithin the cell.formation of mRNA in the cell nucleus uses a DNA molecule as amolecule of mold and order of bases on the mRNA complementis one of a chain of DNA molecules.Thus the sequence of bases purinand primidin one of the chains ofthe DNA molecule, where the basethymine (T) is replaced by uracil(U).mRNA that has been formed in thecell nucleus and then out of thecell nucleus and into the cytoplasmand are bound to Ribosomes
3. tRNA (Transfer RNA)The primary function of tRNA is to bring the amino acid intranslation process of mRNA codon into a sequence of aminoacids 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.
Two Process in the synthesis of proteins is:1. Transcription transcription 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 proteins2. Translation NA molecules translate genetic information into protein formation process