LECTERE 5LECTERE 5

Lecturer: Yevheniya B. Dmukhalska

THEME: THEME: AMINO ACIDS, PEPTIDES AND AMINO ACIDS, PEPTIDES AND PROTEINSPROTEINS..

PLANPLAN Biological role of amino acidsBiological role of amino acids and proteinsand proteins Classification of amino acids.Classification of amino acids. Structure of amino acids. Structure of amino acids. Chemical properties of amino acids.Chemical properties of amino acids. Peptides.Peptides. Proteins: levels of structure of proteins. Proteins: levels of structure of proteins.  Compound proteins.Compound proteins.

А А proteinprotein is in polymer in which the is in polymer in which the monomer units are aminoacids. Thus the monomer units are aminoacids. Thus the starting point for а discussion of proteins starting point for а discussion of proteins is an understanding of the structures and is an understanding of the structures and chemical properties of aminoacids.chemical properties of aminoacids.

The word The word proteinprotein comes from the Greek comes from the Greek proteiosproteios, which means "of first , which means "of first importance." This derivation alludes to importance." This derivation alludes to the key role that proteins play in life the key role that proteins play in life processes. processes.

PROTEIN

Proteins are the most abundant substances in Proteins are the most abundant substances in most cells - from 10% to 20% of the cell’s mass. most cells - from 10% to 20% of the cell’s mass.

More than 70-80 % of dry weight of muscles, More than 70-80 % of dry weight of muscles, lungs, kidneys, spleen; 57 % of dry weight of lungs, kidneys, spleen; 57 % of dry weight of liver, 45 % of dry weight of brain are proteins. liver, 45 % of dry weight of brain are proteins. The lowest proteins constituting in bones and The lowest proteins constituting in bones and teeth (20 and 18 % responding). teeth (20 and 18 % responding).

Contents of chemical elements in proteins: Contents of chemical elements in proteins: carboncarbon is is 51-55 51-55 %%, oxygen, oxygen is is 21-28 21-28 %%, nitrogen , nitrogen is is 15-18 %, hydrogen 15-18 %, hydrogen is is 6-7 %, sulfur6-7 %, sulfur is is 0.3-2.5 0.3-2.5 %. Some proteins contain phosphorus iron, zinc, %. Some proteins contain phosphorus iron, zinc, copper and other elements copper and other elements - - (0.2-2%).(0.2-2%).

AMINO ACIDSAMINO ACIDS An An amino acidamino acid is an organic compound that is an organic compound that

contains both an amino (–NНcontains both an amino (–NН33) group and a ) group and a

carboxyl (-СООН) group. The amino acids carboxyl (-СООН) group. The amino acids found in proteins are always α-amino acids.found in proteins are always α-amino acids.

Classification of amino acidsClassification of amino acids Nonpolar amino acidsNonpolar amino acids contain one amino group, contain one amino group,

one carboxyl group, and a nonpolar side chain.one carboxyl group, and a nonpolar side chain. Polar neutral amino acidsPolar neutral amino acids contain one amino contain one amino

group, one carboxyl group, and а side chain that is group, one carboxyl group, and а side chain that is polar but neutral. polar but neutral.

Polar acidic amino acidsPolar acidic amino acids contain one amino group contain one amino group and two carboxyl groups, the second carboxyl group and two carboxyl groups, the second carboxyl group being part of the side chain. There are two polar being part of the side chain. There are two polar acidic amino acids: aspartic acid and glutamic acid.acidic amino acids: aspartic acid and glutamic acid.

Polar basic amino acidsPolar basic amino acids contain two amino groups contain two amino groups and one carboxyl group, the second amino group and one carboxyl group, the second amino group being part of the side chain. There are three polar being part of the side chain. There are three polar basic amino acids: lysine, arginine, and histidine.basic amino acids: lysine, arginine, and histidine.

The most important aminoacidsThe most important aminoacids

Glycine

Alanine

Valine

Leucine

Isoleucine

Monoaminomonocarboxylic aminoacids

The most important aminoacidsThe most important aminoacids

Ornytine Lysine

Threonine

Diaminomonocarboxylic aminoacids

Mnoaminodicarboxylic aminoacids

Glutamic acod Aspartic acid

Serine

Hydroxylaminoacids

Tyrosine Phenyalanine

Methionine

Cystine

Cysteine

The most important aminoacidsThe most important aminoacidsSulphorcontain aminoacids

Aromatic aminoacids

The most important aminoacidsThe most important aminoacidsHeterocyclic aminoacids

TryptophaneTryptophane Proline Hydroxiproline Histidine

Aminoacids with amide group

Arginine

Essential and non-essential amino acidsEssential and non-essential amino acids All of the 20 amino acids are necessary constituents of All of the 20 amino acids are necessary constituents of

human protein. Adequate amounts of 11 of the 20 amino human protein. Adequate amounts of 11 of the 20 amino acids can be synthesized from carbohydrates and lipids in acids can be synthesized from carbohydrates and lipids in the body if а source of nitrogen is also available. Because the body if а source of nitrogen is also available. Because the human body is incapable of producing 9 of these 20 the human body is incapable of producing 9 of these 20 acids, these 9 amino acids, called essential amino acids, acids, these 9 amino acids, called essential amino acids, must be obtained from food. The human body can must be obtained from food. The human body can synthesize small amounts of some of the essential amino synthesize small amounts of some of the essential amino acids, but not enough to meet its needs, especially in the acids, but not enough to meet its needs, especially in the case of growing children.case of growing children.

The 9 essential amino acids for adults are The 9 essential amino acids for adults are histidine, histidine, isoleucine, leucine, lysine, methionine, phenylalanine, isoleucine, leucine, lysine, methionine, phenylalanine, threonine, tryptophan, and valinethreonine, tryptophan, and valine. (In addition, arginine is . (In addition, arginine is essential for children).essential for children).

AcidityAcidity Both an acidic group (-СООН) and а basic group (-NНBoth an acidic group (-СООН) and а basic group (-NН22) are ) are

present on the same carbon in an α-amino acid.present on the same carbon in an α-amino acid.

The net result is that in neutral solution, amino acid molecules The net result is that in neutral solution, amino acid molecules have the structure:have the structure:

А А zwitterion zwitterion is а molecule that has а positive charge on one is а molecule that has а positive charge on one atom and а negative charge on another atom. atom and а negative charge on another atom.

Reaction of amino acidsReaction of amino acids Reaction with alcohols – esters formation:Reaction with alcohols – esters formation:

Reaction with ammonia – amides formation:Reaction with ammonia – amides formation:

Decarboxylation:Decarboxylation:

Salts are formed:Salts are formed:

DeaminationDeamination oxidation deaminationoxidation deamination::

hydrolitic deaminationhydrolitic deamination::

intramolecular deaminationintramolecular deamination: :

redaction deaminationredaction deamination::

Peptide formationPeptide formation Two amino acids can react in а similar way - the Two amino acids can react in а similar way - the

carboxyl group of one amino acid reacts with the carboxyl group of one amino acid reacts with the amino group of the other amino acid. The products amino group of the other amino acid. The products are а molecule of water and а molecule containing are а molecule of water and а molecule containing the two amino acids linked by an amide bond.the two amino acids linked by an amide bond.

Ninhydrin test. The ninhydrin colour reaction is the most commonly test used for the detection of alpha-amino acids. This is an extremely delicate test, to which proteins, their hydrolytic products, and α-amino acids react. When ninhydrin is added to а protein solution and the mixture is heated to boil, blue to violet colour appears on cooling. The colour is due to the formation of а complex compound.

React React αα-aminoacids with ninhydrin -aminoacids with ninhydrin

OH

OH

O

O

+ H3N-CH-COO-

R

+

O

O

N-CH-COOH+H2O

R

Ninhydrin

O

O

N-CH-C

R

H

O

O

N=C-C

R

H2OH

NH2

O

O

2-aminoindandion

O

OHO

OH

H

H2N

O

O

OH

OH

O

O

+

O

O

N

H

O

O

O

O

N

O

O

H+

Âlue - violet dye-stuff

Qualitative tests for amino acids and protein.amino acids and protein.

XANTHOPROTEIC TEST. On treatment with concentrated nitric acid, certain proteins give yellow colour. This yellow colour is the same that is formed on the skin when the latter comes in contact with the concentrated nitric acid. The test is given only by the proteins having at least one mole of aromatic amino acid, such as tryptophan, phenylalanine, and tyrosine which are actually nitrated during treatment with concentrated nitric acid.

FOLL REACTION. FOLL REACTION. This reaction reveals the sulfur This reaction reveals the sulfur containing amino acids (cysteine, cystine). containing amino acids (cysteine, cystine). Treatment of Treatment of the sulfur containing amino acids with salt of lead and the sulfur containing amino acids with salt of lead and alkali yields a black sediment. alkali yields a black sediment.

ADAMKEVICH REACTION. ADAMKEVICH REACTION. This reaction detects the This reaction detects the amino acid tryptophan containing indol ring. amino acid tryptophan containing indol ring. The The addition of the concentrated acetic and sulfuric acids to addition of the concentrated acetic and sulfuric acids to the solution of tryptophan results in the formation of the solution of tryptophan results in the formation of red-violet ring appearing on the boundary of different red-violet ring appearing on the boundary of different liquids. liquids.

PeptidesPeptides Short to medium-sized chains of amino acids are Short to medium-sized chains of amino acids are

known as peptides. А known as peptides. А peptidepeptide is а sequence of is а sequence of amino acids, of up to 50 units, in which the amino acids, of up to 50 units, in which the amino acids are joined together through amide amino acids are joined together through amide (peptide) bonds. А compound containing two (peptide) bonds. А compound containing two amino acids joined by а peptide bond is amino acids joined by а peptide bond is specifically called а dipeptide; three amino acids specifically called а dipeptide; three amino acids in а chain constitute а tripeptide; and so on. The in а chain constitute а tripeptide; and so on. The name oligopeptide is loosely used to refer to name oligopeptide is loosely used to refer to peptides with 10 to 20 amino acid residues and peptides with 10 to 20 amino acid residues and polypeptide to larger peptides.polypeptide to larger peptides.

ProteinsProteins Proteins Proteins are polypeptides that contain more are polypeptides that contain more

than 50 amino acid units. The dividing line than 50 amino acid units. The dividing line between between аа polypeptide and polypeptide and аа protein is protein is arbitrary. The important point is that proteins arbitrary. The important point is that proteins are polymers containing are polymers containing аа large number of large number of amino acid units linked by peptide bonds. amino acid units linked by peptide bonds. Polypeptides are shorter chains of amino acids. Polypeptides are shorter chains of amino acids. Some proteins have molecular masses in the Some proteins have molecular masses in the millions. Some proteins also contain more than millions. Some proteins also contain more than one polypeptide chain.one polypeptide chain.

Function of proteinsFunction of proteinsCatalysis. EnzymesCatalysis. Enzymes, the proteins that direct and accelerate thousands of , the proteins that direct and accelerate thousands of biochemical reactionsbiochemical reactionsStructure.Structure. Some proteins function as structural materials that provide Some proteins function as structural materials that provide protection and support. protection and support. Movement.Movement. Proteins are involved in all types of cell movement. For example, Proteins are involved in all types of cell movement. For example, actin, tubulinactin, tubulin, and а variety of other proteins comprise the cytoskeleton. , and а variety of other proteins comprise the cytoskeleton. Defense.Defense. А wide variety of proteins have а protective role. Examples found in А wide variety of proteins have а protective role. Examples found in vertebrates include vertebrates include keratin,keratin, the protein found in skin cells that aids in protecting the protein found in skin cells that aids in protecting the organism against mechanical and chemical injury. The blood-clotting proteins the organism against mechanical and chemical injury. The blood-clotting proteins fibrinogen fibrinogen and and thrombinthrombin prevent blood loss when blood vessels are damaged. prevent blood loss when blood vessels are damaged. The The immuno-globulins immuno-globulins (or antibodies) are produced by lymphocytes in (or antibodies) are produced by lymphocytes in response to the invasion of foreign organisms such as bacteria. response to the invasion of foreign organisms such as bacteria. Regulation.Regulation. The binding of The binding of аа hormone molecule to its target cell results in hormone molecule to its target cell results in specific changes in cellular function. Examples of peptide hormones include specific changes in cellular function. Examples of peptide hormones include insulininsulin and and glucagonglucagon, which regulate blood glucose levels. , which regulate blood glucose levels. Growth hormoneGrowth hormone stimulates cell growth and division.stimulates cell growth and division.Transport.Transport. Many proteins function as carriers of molecules or ions across Many proteins function as carriers of molecules or ions across membranes or between cells. Examples of membrane proteins include the membranes or between cells. Examples of membrane proteins include the NaNa++--КК+ + ATPase ATPase and the and the glucose transporterglucose transporter. Other transport proteins include . Other transport proteins include hemoglobinhemoglobin, which carries O, which carries O22 to the tissues from the lungs, and the to the tissues from the lungs, and the lipoproteinslipoproteins, which transport lipids from the liver and intestines to other organs, which transport lipids from the liver and intestines to other organs

PPrimary structure of а proteinrimary structure of а protein

The The primary structure of а proteinprimary structure of а protein is the sequence of is the sequence of amino acids present in its peptide chain or chainsamino acids present in its peptide chain or chains. .

The end with the free HThe end with the free H33NN++ group is called the group is called the N-N-

terminal endterminal end, and the end with the free СОО, and the end with the free СОО-- group is group is called the called the С-terminal endС-terminal end. .

SecondarySecondary structure of а protein structure of а protein The The secondary structure of а proteinsecondary structure of а protein is the arrangement in is the arrangement in

space of the atoms in the backbone of the protein. Three space of the atoms in the backbone of the protein. Three major types of protein secondary structure are known; the major types of protein secondary structure are known; the alpha helix, the beta pleated sheet, and the triple helix. The alpha helix, the beta pleated sheet, and the triple helix. The major force responsible for all three types of secondary major force responsible for all three types of secondary structure is hydrogen bonding between а carbonyl oxygen structure is hydrogen bonding between а carbonyl oxygen atom of а peptide linkage and the hydrogen atom of an amino atom of а peptide linkage and the hydrogen atom of an amino group (-NH) of another peptide linkage farther along the group (-NH) of another peptide linkage farther along the backbone. backbone.

Alpha HelixAlpha Helix The The Alpha HelixAlpha Helix The alpha helix (α-helix) structure The alpha helix (α-helix) structure

resembles а coiled helical spring, with the coil configuration resembles а coiled helical spring, with the coil configuration maintained by hydrogen bonds between N – Н and С= О maintained by hydrogen bonds between N – Н and С= О groups of every fourth amino acidgroups of every fourth amino acid

 

Beta pleated sheetBeta pleated sheet The The beta pleated sheetbeta pleated sheet (β-pleated sheet) secondary (β-pleated sheet) secondary

structure involves amino acid chains that are almost structure involves amino acid chains that are almost completely extended. completely extended.

 

Tertiary structureTertiary structure The The tertiary structure of а proteintertiary structure of а protein is is

the overall three-dimensional shape that the overall three-dimensional shape that results from the attractive forces results from the attractive forces between amino acid side chains (R between amino acid side chains (R groups) that are widely separated from groups) that are widely separated from each other within the chain.each other within the chain.

hydrogen bonds; hydrophobic attractions;

Interactions responsible for tertiary Interactions responsible for tertiary structurestructure

covalent disulfide bonds;electrostatic attractions (salt bridges);

Electrostatic attractions (salt bridges), Hydrogen bonds,Electrostatic attractions (salt bridges), Hydrogen bonds,

Quaternary structureQuaternary structure Quaternary structureQuaternary structure is the highest level of is the highest level of

protein organization. It is found only in proteins protein organization. It is found only in proteins that have structures involving two or more that have structures involving two or more polypeptide chains that are independent of polypeptide chains that are independent of each other — that is, are not covalently bonded each other — that is, are not covalently bonded to each other. These multichain proteins are to each other. These multichain proteins are often called oligomeric proteins. The often called oligomeric proteins. The quaternary structure of а protein involves the quaternary structure of а protein involves the associations among the separate chains in an associations among the separate chains in an oligomeric protein.oligomeric protein.

The function of hemoglobin in an organism is to transport oxygen.1 g of hemoglobin absorbs 1.35 ml of oxygen at STP, corresponding to exactly one molecule of О2 per iron.

HemoglobinHemoglobin

Globular and fibrous proteinsGlobular and fibrous proteins On the basis of structural shape, proteins can be classified On the basis of structural shape, proteins can be classified

into two major types: fibrous proteins and globular proteins. into two major types: fibrous proteins and globular proteins. А fibrous protein is а protein that has а long, thin, fibrous А fibrous protein is а protein that has а long, thin, fibrous

shape. Such proteins are made up of long rod-shaped or shape. Such proteins are made up of long rod-shaped or string-like molecules that can intertwine with one another string-like molecules that can intertwine with one another and form strong fibers. They are water-insoluble and and form strong fibers. They are water-insoluble and generally have structural functions within the human body. generally have structural functions within the human body.

А globular protein is а protein whose overall shape is А globular protein is а protein whose overall shape is roughly spherical or globular. Globular proteins either roughly spherical or globular. Globular proteins either dissolve in water or form stable suspensions in water, dissolve in water or form stable suspensions in water, which allows them to travel through the blood and other which allows them to travel through the blood and other body fluids to sites where their activity is needed. body fluids to sites where their activity is needed.

Simple and Conjugated ProteinsSimple and Conjugated Proteins Proteins are classified as either simple Proteins are classified as either simple

proteins or conjugated proteins. proteins or conjugated proteins. А А SIMPLE PROTEINSIMPLE PROTEIN is made up entirely is made up entirely

of amino acid residues. of amino acid residues. А А COMPOUND PROTEINCOMPOUND PROTEIN has other has other

chemical components in addition to amino chemical components in addition to amino acids. These additional components, acids. These additional components, which may be organic or inorganic, are which may be organic or inorganic, are called called prosthetic groups.prosthetic groups.

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