AMINO ACIDS ARE ORGANIC COMPOUNDS MADE OUT OF CARBON HYDROGEN OXYGEN NITROGEN SULPHUR (IN A FEW CASES)
carbon atom that is bonded to an amino group (-NH2), carboxyl group (-COOH), hydrogen atom (H) R group or the side chain differs from one amino acid to another R group can vary widely and is responsible for the differences in the chemical properties
R H2NaC COOH H
In chemistry, chirality refers to how a molecule's components are arranged, in space, about a central atom (or atoms). Chiral molecules lack symmetry and therefore cannot be superimposed on their mirror images
This chiral center allows for stereoisomerism. For example, take a look at the stereo representations and Fischer projection formulas of the enantiomers of serine
All amino acids found in proteins occur in the L-configuration about the chiral carbon atom. D-amino acids are not naturally found in proteins and are not involved in the metabolic pathways of eukaryotic organisms, D-amino acids are important in the structure and metabolism of bacteria. For example, Dglutamic acid and D-alanine are structural components of certain bacterial cell walls. D-amino acids are in polypeptide anitbiotics.
CHIRALITY
POLARIMETRY
a method to analyze chiral substances. The magnitude and direction of rotation of the plane of polarized light by a chiral compound is a specific physical property of the compound that can be used to characterize it Most biomolecules are chiral and hence rotate polarized light. Angle of rotation is depends on Concentration of the solution Path length of the solution Wave length of the light Chemical configuration of the substance
LIGHT WAVES
POLARIMETER
EACH AMINO ACID DIFFERS FROM ONE ANOTHER, DUE TO THE NATURE OF R
IMINO ACIDS
PROLINE
AMINO ACID CLASSIFICATIONS There are two broad classes of amino acids based upon whether the R-group is
hydrophobic hydrophilic.
HYDROPHOBIC
The hydrophobic amino acids tend to repel the aqueous environment reside predominantly in the interior of proteins. does not ionize nor participate in the formation of H-bonds.
HYDROPHILC
The hydrophilic amino acids tend to interact with the aqueous environment,
Side chains which have pure hydrocarbon alkyl groups (alkane branches) or aromatic (benzene rings) are nonpolar. Examples include valine, alanine, leucine, isoleucine, phenylalanine.
The number of alkyl groups also influences the polarity. The more alkyl groups present, the more non-polar the amino acid will be. This effect makes valine more nonpolar than alanine leucine is more non-polar than valine.
Neutral Side Chains both an amine and acid group which have been neutralized in the zwitterion, the amino acid is neutral unless there is an extra acid or base on the side chain. If neither is present then the whole amino acid is neutral.
Neutral Side Chains Amino acids with an amide on the side chain do not produce basic solutions i.e. asparagine and glutamine. You need to look at the functional groups carefully because an amide starts out looking like an amine, but has the carbon double bond oxygen which changes the property. Amides are not basic. Even though tryptophan has an amine group as part of a five member ring, the electron withdrawing effects of the two ring systems do not allow nitrogen to act as a base by attracting hydrogen ions.
If the side chain contains an amine functional group, the amino acid produces a basic solution because the extra amine group is not neutralized by the acid group. Amino acids which have basic side chains include: lysine, arginine, and histidine. Amino acids with an amide on the side chain do not produce basic solutions i.e. asparagine and glutamine.
POLAR POSITIVE
Side chains which have various functional groups such as acids, amides, alcohols, and amines will impart a more polar character to the amino acid. The ranking of polarity will depend on the relative ranking of polarity for various functional groups as determined in functional groups. In addition, the number of carbon-hydrogens in the alkane or aromatic portion of the side chain should be considered along with the functional group.
Example: Aspartic acid is more polar than serine because an acid functional group is more polar than an alcohol group. Example: Serine is more polar than threonine since threonine has one more methyl group than serine. The methyl group gives a little more non-polar character to threonine. Example: Serine is more polar than tyrosine, since tyrosine has the hydrocarbon benzene ring.
If the side chain contains an acid functional group, the whole amino acid produces an acidic solution. Normally, an amino acid produces a nearly neutral solution since the acid group and the basic amine group on the root amino acid neutralize each other in the zwitterion. If the amino acid structure contains two acid groups and one amine group, there is a net acid producing effect. The two acidic amino acids are aspartic and glutamic.
POLAR NEGATIVE
POLAR NEGATIVE
SWITTERION FORMATION
. PH DEPENDENCY
Since amino acids, as well as peptides and proteins, incorporate both acidic and basic functional groups, the predominant molecular species present in an aqueous solution will depend on the pH of the solution. In order to determine the nature of the molecular and ionic species that are present in aqueous solutions at different pH's, we make use of the Henderson-Hasselbach Equation,
PKA REPRESENTS THE ACIDITY OF A SPECIFIC CONJUGATE ACID FUNCTION (HA). WHEN THE PH OF THE SOLUTION EQUALS PKA, THE CONCENTRATIONS OF HA AND A(-) MUST BE EQUAL (LOG 1 = 0).
pKR: The pK of the side arm R of the amino acid. Only the specified AA's have ionizable side chains.
NINHYDRIN REACTION
specific
for amino acids a bluish purple coloured complex is formed with Ninhydrin. widely used in paper and ionexchange chromatography to visualize the separated amino acids.
This Rpurple colored imino derivative, which provides as a useful color test for these amino acids, most of which are colorless
CHROMATOGRAPHY
The ratio of the distance a compound moves from the baseline to the distance of the solvent front from the baseline is defined as the retardation (or retention) factor Rf. Different amino acids usually have different Rf's under suitable conditions.
CHROMATOGRAPHY
COMPOSITION OF PROTEINS
There are 20 -amino acids that are relevant to the make-up of mammalian proteins Several other amino acids are found in the body free or in combined states (i.e. not associated with peptides or proteins). These non-protein associated amino acids perform specialized functions. Several of the amino acids found in proteins also serve functions distinct from the formation of peptides and proteins, e.g., tyrosine in the formation of thyroid hormones. glutamate acting as a neurotransmitter
5. Cystine
6. Glutamic acid 7. Glutamine* 8. Glycine 9. Proline 10. Serine 11. Tyrosine
Peptide bond formation is a condensation reaction leading to the polymerization of amino acids into peptides and proteins. Peptides are small consisting of few amino acids. A number of hormones and neurotransmitters are peptides. Additionally, several antibiotics and antitumor agents are peptides. Proteins are polypeptides of greatly divergent length.
The simplest peptide, a dipeptide, contains a single peptide bond formed by the condensation of the carboxyl group of one amino acid with the amino group of the second with the concomitant elimination of water. The presence of the carbonyl group in a peptide bond allows electron resonance stabilization to occur such that the peptide bond exhibits rigidity not unlike the typical C=C double bond. The peptide bond is, therefore, said to have partial double-bond character.
R1 H2N C COOH H
-H2O
R2 H N C COOH H H
H2N C CO H
R1
R2 HN C COOH H
OLIGOPEPTIDES
NH2 CC - NH COOH COOH NH2 NH CH2 (CH2)2 (CH2)4 (CH2)3 H2N CCONHCCON CCONHCCOOH H H H H Aspartic glutamic lysine Arginine
**
BIURET REACTION
Peptides and proteins (long-chain polypeptides) react with Cu2+ in alkalinity to create a blue-violet colored chelate complex with an absorbance maximum at 540 nm. The peptide must have three peptide bonds at least.
BIURET REACTION
The method consists of heating a substance with sulfuric acid, which decomposes the organic substance by oxidation to liberate the reduced nitrogen as ammonium sulfate. In this step potassium sulfate is added in order to increase the boiling point of the medium (from 337F to 373F / 169C to 189C). Chemical decomposition of the sample is complete when the medium has become clear and colorless (initially very dark).
KJELDAHL METHOD
The solution is then distilled with sodium hydroxide (added in small quantities) which converts the ammonium salt to ammonia. The amount of ammonia present (hence the amount of nitrogen present in the sample) is determined by back titration. The end of the condenser is dipped into a solution of boric acid. The ammonia reacts with the acid and the remainder of the acid is then titrated with a sodium carbonate solution with a methyl orange pH indicator.
Degradation: Protein + H2SO4 (NH4)2SO4(aq) + CO2(g) + SO2(g) + H2O(g) Liberation of ammonia: (NH4)2SO4(aq) + 2NaOH Na2SO4(aq) + 2H2O(l) + 2NH3(g) Capture of ammonia: B(OH)3 + H2O + NH3 NH4+ + B(OH)4 Back-titration: B(OH)3 + H2O + Na2CO3 NaHCO3(aq) + NaB(OH)4(aq) + CO2(g) + H2O
Nowadays, the Kjeldahl method is largely automated and makes use of specific catalysts (mercury oxide or copper sulfate) to speed up the decomposition.
KJELDAHL METHOD
The interferecnces of Kjeldhahl method Nitrogen containing substances such as Melamine and urea
Melamine
THE BACKBONE OF THE AMINO-ACID SEQUENCE LEU-ALA-GLU IS SHOWN IN PURPLE, AND THE SIDE CHAINS ARE SHOWN IN GREEN
PRIMARY STRUCTURE
Primary Structure refers to the linear sequence of amino acids that make up the polypeptide chain. This sequence is determined by the genetic code, the sequence of nucleotide bases in the DNA. The bond between two amino acids is a peptide bond. The sequence of amino acids determines the positioning of the different R groups relative to each other. This positioning therefore determines the way that the protein folds and the final structure of the molecule
ANOTHER COMMON REPRESENTATION FOR PROTEINS AND PEPTIDES IS THE RIBBON, WHICH TRACES THE BACKBONE OF A PROTEIN OR PEPTIDE. THIS REPRESENTATION DOES NOT INCLUDE THE ATOMS IN THE SIDE CHAINS OF THE RESIDUES AND IS OFTEN USED TO REPRESENT THE THREE DIMENSIONAL STRUCTURE NOTICE THE BUNDLE OF HELICAL, OR COILED, PARTS OF THE BACKBONE
alpha-helix in a peptide chain of ferritin. The helical shape is held by hydrogen bonds between the -NH and CO functional groups in the backbone. the ribbon representation (showing only the trace of the backbone) is superimposed on a ball-and-stick representation, in which the non-hydrogen atoms are shown as spheres and the bonds are shown as sticks
HYDROGEN BONDING
Polypeptides contain numerous proton donors and acceptors both in their backbone and in the R-groups of the amino acids. The environment in which proteins are found also contains the ample H-bond donors and acceptors of the water molecule. H-bonding, therefore, occurs not only within and between polypeptide chains but with the surrounding aqueous medium.
HYDROGEN BOND
HYDROGEN BOND
IN AN -HELIX AND A -SHEET, ALL OF THE POSSIBLE HBONDS INVOLVING THE PEPTIDE BOND'S DONOR AND ACCEPTOR GROUPS ARE FORMED. THIS STABILIZES THE STRUCTURE.
IN AN -HELIX , THE R-GROUPS POINT OUTWARD FROM THE LONG AXIS OF THE HELIX
SECONDARY PROTEIN STRUCTURE SEQUENCE OF AMINO ACIDS ARE LINKED BY HYDROGEN BONDS
SECONDARY STRUCTURE
Tertiary structure refers to the three dimensional globular structure formed by bending and twisting of the polypeptide chain. This process often means that the linear sequence of amino acids is folded into a compact globular structure. The folding of the polypeptide chain is stabilized by multiple weak, noncovalent interactions. These interactions include:
Hydrogen bonds that form when a Hydrogen atom is shared by two other atoms. Electrostatic interactions that occur between charged amino acid side chains. Electrostatic interactions are attractions between positive and negative sites on macromolecules. Hydrophobic interactions: During folding of the polypeptide chain, amino acids with a polar (water soluble) side chain are often found on the surface of the molecule while amino acids with non polar (water insoluble) side chain are buried in the interior. This means that the folded protein is soluble in water or aqueous solutions.
If two cysteine side chains end up next to each other because of folding in the peptide chain, they can react to form a sulphur bridge. This is another covalent link. sometimes this link can be considered as part of the primary structure of the protein.
DISULFIDE BOND
Sulfur groups on cysteines may undergo oxidation to form disulfide bonds that are not normally present. Extra disulfide bonds can form when proteins are removed from their normal environment. Reducing agents such as dithiothreitol or mercaptoethanol are often added to prevent undesirable disulfiate bond formation
IONIC INTERACTIONS
Some amino acids (such as aspartic acid and glutamic acid) contain an extra -COOH group. Some amino acids (such as lysine) contain an extra -NH2 group. can transfer a hydrogen ion from the -COOH to the -NH2 group to form zwitterions just as in simple amino acids. can obviously get an ionic bond between the negative and the positive group if the chains folded in such a way that they were close to each other.
IONIC BONDS
Several amino acids have quite large hydrocarbon groups in their side chains. A few examples are shown below.
Temporary
fluctuating dipoles in one of these groups could induce opposite dipoles in another group on a nearby folded chain. The dispersion forces set up would be enough to hold the folded structure together
TERTIARY PROTEIN STRUCTURE CERTAIN ATTRACTIONS ARE PRESENT BETWEEN ALPHA HELICES AND PLEATED SHEETS
TERTIARY STRUCTURE
IN -SHEETS, THE H-BONDS BETWEEN THE PEPTIDE BOND DONOR AND ACCEPTOR GROUPS ARE MADE BETWEEN EITHER PARALLEL OR ANTI-PARALLEL POLYPEPTIDE CHAINS. THESE ARE ANTI-PARALLEL -SHEETS THE R-GROUPS POINT OUT OF AND INTO THE PLANE OF THE SHEET.
QUATERNARY STRUCTURE PROTEIN CONSISTING OF MORE THAN ONE AMINO ACID CHAIN
QUATERNARY STRUCTURE
PROLINE PEPTIDE BONDS ARE FOUND IN THE CIS CONFIGURATION ~100 TIMES AS OFTEN AS THOSE BETWEEN OTHER AMINO ACIDS. THERE IS NO H-BOND DONOR IN THE PROLINE PEPTIDE BOND AND THE PRESENCE OF PROLINE LEADS TO A BEND OR KINK IN THE POLYPEPTIDE CHAIN.
HAEMOGLOBIN
comprised of four polypeptide subunits, two with alpha helix secondary structure and two with beta pleated sheet form. All four components carry a heme group that can bind to oxygen, and all four components must be present to form haemoglobin. The shape of the haemaglobin affects its ability to carry oxygen, and travel freely throughout the circulatory system.
HAEMOGLOBIN
A condition that is a result of a malformed haemoglobin unit is sickle-cell anemia. position glutamic acid is replaced by a valine, (This is the result of a single base pair change at the DNA level.) an ionic cross-link is not formed resulting in a severe change of shape of the tertiary structure of the haemoglobin. The resultant shape is a crescent or sickle which reduces the oxygen carrying capacity of the red blood cell. Sickle cells are removed from circulation faster than normal cells resulting in anemia. They can also clump together causing blockages, pain and organ damage
HAEMOGLOBIN
CLASSIFICATION OF PROTEINS
Proteins are the most abundant organic macromolecules found in the cells and body fluids.
Molecular weight of proteins range from 68,000 (eg: haemoglobin) to 5.2 million (eg: b-lipoproteins). Proteins are of importance in all biological processes.
CLASSIFICATION OF PROTEINS
Classification system based on salient features of proteins * solubility * shape * function * physical properties * three dimensional structure
SOLUBILITY
Classification of globulins Pseudoglobulins freely water soluble Euglobulins insoluble in salt free water
SHAPE
Based on axial ratio (ratio of length to breadth of the molecule. Globular proteins axial ratio less than 10. Fibrous proteins grater than 10 eg polypeptide chains or group of chains coiled in spiral or helix, cross linked by hydrogen and disulfide links. Eg. keratin, myosin
SHAPE OF PROTEINS
The shape of proteins is critical to their function, the shape is largely a result of the bonds that form between the side chains of amino acids that make the protein. primary purpose of the side chains in amino acids is to give proteins their shape, which dictates their function.
FUNCTIONS OF PROTEINS
AS HORMONES
Some hormones are structurally proteins eg * thyroid stimulating hormones (TSH) * growth hormones (GH)
FUNCTIONS OF PROTEINS
Nutrition Metabolism of proteins released amino acids to the pool. used for synthesis of new proteins / nitrogenous compounds. deaminated to give CO2 and water (catabolize).
FUNCTIONS OF PROTEINS
Transport of small molecules
Small molecules are transported in the plasma combined with proteins, specially albumin.. Hormone, cortisol combines with protein, transcortin Iron transferrin nucleic acid nucleoproteins pigments such as Bilirubin conjugate with albumin thyroxin hormone combines with Thyroxin Binding Globulin (TBG) Toxic substances covert non toxic by binding to proteins
FUNCTIONS OF PROTEINS
Control of body water distribution Maintenance of oncotic pressure Albumin, mainly acts to maintain the oncotic pressure in body fluids prevent, accumulation of fluids in the body tissues to prevent oedema. Oncotic pressure osmotic pressure exerted due to the presence of albumin
Functions of proteins
Functions of proteins
BLOOD COAGULATION
RECEPTORS
glycoprotein structures * * Cytoplasm (oestriol receptors) surface of the cell membranes (insulin receptors).
ENZYMES ARE PROTEINS, SMALL AMOUNTS SPEEDS UP THE RATE OF A BIOLOGICAL REACTION, WITHOUT BEING USED UP.
FUNCTIONS OF PROTEINS
BUFFERING ACTION
Proteins act as buffers in the body, Proteins are negatively charged at body pH and act as bases accepting hydrogen ions.
SIMPLE PROTEINS
these on hydrolysis give only amino acids Hydrolysis is the chemical reaction, in which proteins reacts with water to produce amino acids
CONJUGATED PROTEINS
Some proteins are conjugated with nonprotein molecules. conjugated with
Carbohydrate glycoproteins lipids lipoproteins nucleic acid nucleoproteins pigments such as Bilirubin conjugate with albumin
Proteins can be broadly classified into three groups, based on their shape and solubility.
Fibrous proteins: these proteins have a rod like structure. They are not soluble in water collagen is an example of a fibrous protein. Globular proteins: these proteins more or less spherical in nature. Due to their distribution of amino acids (hydrophobic inside, hydrophillic outside) they are very soluble in aqueous solution. Myoglobin is an example of a globular protein.
Membrane proteins: these are protein which are in association with lipid membranes. Those membrane proteins that are embedded in the lipid bilayer have extensive hydrophobic amino acids that interact with the non-polar environment of the bilayer interior. Membrane proteins are not soluble in aqueous solution. Rhodopsin is an example of a membrane protein. Note that rhodopsin is an integral membrane protein and is embedded in the bilayer.
FUNCTIONAL SIGNIFICANCE OF AMINO ACID R-GROUPS In solution it is the nature of the amino acid R-groups that dictate structure-function relationships of peptides and proteins. The hydrophobic amino acids will generally be encountered in the interior of proteins shielded from direct contact with water. Conversely, the hydrophilic amino acids are generally found on the exterior of proteins as well as in the active centers of enzymatically active proteins. Indeed, it is the very nature of certain amino acid R-groups that allow enzyme reactions to occur.
The imidazole ring of histidine allows it to act as either a proton donor or acceptor at physiological pH. Hence, it is frequently found in the reactive center of enzymes. ability of histidines in hemoglobin to buffer the H+ ions from carbonic acid ionization in red blood cells. It is this property of hemoglobin that allows it to exchange O2 and CO2 at the tissues or lungs, respectively.
DENATURATION OF PROTEINS
The natural or native structures of proteins may be altered, and their biological activity changed or destroyed by treatment that does not disrupt the primary structure. This denaturation is often done deliberately in the course of separating and purifying proteins. For example, many soluble globular proteins precipitate if the pH of the solution is set at the pI of the protein.
DENATURATION OF PROTEINS
Also, addition of trichloroacetic acid or the bisamide urea (NH2CONH2) is commonly used to effect protein precipitation. Following denaturation, some proteins will return to their native structures under proper conditions; but extreme conditions, such as strong heating, usually cause irreversible change.
DENATURATION. THE POLYPEPTIDE CHAIN HAS LOST ITS HIGHER ORDER STRUCTURE AND IS NOW A RANDOM COIL.
DENATURATION OF PROTEINS
Some treatments known to denature proteins are. Denaturing Action-Mechanism of Operation Heat - hydrogen bonds are broken by increased translational and vibrational energy.(coagulation of egg white albumin on frying.)
DENATURATION OF PROTEINS
Urea Solution competition for hydrogen bonds. (precipitation of soluble proteins.) Some Organic Solvents (e.g. ethanol & acetone)change in dielectric constant and hydration of ionic groups. (disinfectant action and precipitation of protein.) Agitation - shearing of hydrogen bonds. (beating egg white albumin into a meringue.)
PROTEOLYSIS
Proteins can also be broken apart by enzymes, called proteases, that digest the covalent peptide bonds between amino acids that are responsible for the primary structure. This process is called proteolysis and is irreversible. Cells contain proteases that are found in lysosomes, membrane bound organelles inside the cell. When cells are disrupted, lysosomes break and release these proteases, which can damage the other proteins in the cell.
PROTEOLYSIS
In the laboratory, it is therefore necessary to minimize the activities of cellular proteases to protect proteins from proteolysis. Methods used to minimize proteolysis include working at lower temperatures (4C), and adding chemicals that inhibit protease activity.
ADSORB TO SURFACE
Proteins readily adsorb (stick to) surfaces, thereby reducing their available activity. To prevent significant loss, do not store dilute solutions of proteins for prolonged periods of time. Always dilute them right before use.
hemoglobin electrophoresis
LANES 1 AND 5 ARE HEMOGLOBIN STANDARDS. LANE 2 IS A NORMAL ADULT. LANE 3 IS A NORMAL NEONATE. LANE 4 IS A HOMOZYGOUS HBS INDIVIDUAL. LANES 6 AND 8 ARE HETEROZYGOUS SICKLE INDIVIDUALS. LANE 7 IS A SC DISEASE INDIVIDUAL.
SYLLABUS
Amino acids and protein Chemical nature of amino acids, classification, optical properties, functional properties of Rgroups, acid -base properties of proteins, characteristics of the peptide bond, classification of proteins-primary, secondary, tertiary and quaternary structure of proteins, forces controlling the protein structures, denaturation of protein.Practical (3hrs)
THE END
THANK YOU!
the oxygen carrying protein in the blood, is also a tetramer but it is composed of two polypeptide chains of one type (141 amino acids) and two of a different type (146 amino acids). In chemical shorthand, this is referred to as a22 . For some proteins, quaternary structure is required for full activity (function) of the protein
Hydrophobic Forces Proteins are composed of amino acids that contain either hydrophilic or hydrophobic R-groups. It is the nature of the interaction of the different R-groups with the aqueous environment that plays the major role in shaping protein structure. The spontaneous folded state of globular proteins is a reflection of a balance between the opposing energetics of H-bonding between hydrophilic R-groups and the aqueous environment and the repulsion from the aqueous environment by the hydrophobic R-groups. The hydrophobicity of certain amino acid R-groups tends to drive them away from the exterior of proteins and into the interior. This driving force restricts the available conformations into which a protein may fold.
Electrostatic Forces Electrostatic forces are mainly of three types; chargecharge, charge-dipole and dipole-dipole. Typical chargecharge interactions that favor protein folding are those between oppositely charged R-groups such as K or R and D or E. A substantial component of the energy involved in protein folding is charge-dipole interactions. This refers to the interaction of ionized R-groups of amino acids with the dipole of the water molecule. The slight dipole moment that exist in the polar R-groups of amino acid also influences their interaction with water. It is, therefore, understandable that the majority of the amino acids found on the exterior surfaces of globular proteins contain charged or polar Rgroups.
There are both attractive and repulsive van der Waals forces that control protein folding. Attractive van der Waals forces involve the interactions among induced dipoles that arise from fluctuations in the charge densities that occur between adjacent uncharged nonbonded atoms. Repulsive van der Waals forces involve the interactions that occur when uncharged non-bonded atoms come very close together but do not induce dipoles. The repulsion is the result of the electronelectron repulsion that occurs as two clouds of electrons begin to overlap. Although van der Waals forces are extremely weak, relative to other forces governing conformation, it is the huge number of such interactions that occur in large protein molecules that make them significant to the folding of proteins.
The key factor that determines the specific details of polypeptide folding is the interaction between R-groups, not only with one another but with water and dissolved ions. In a water soluble polypeptide, most but not necessarily all of the surface R-groups will by hydrophilic. Hydrophobic groups will tend to be buried in the polypeptide's interior. Some polypeptides are inserted into membranes. In these polypeptides, hydrophobic R-groups on the surface of the folded polypeptide will interact with the hydrophobic interior of the lipid bilayer.
IN ADDITION there are other amino acids in proteins: Naturally occuring chemical modifications of the 20 genetically encoded amino acids, eg. Hydroxylation of proline and lysine Phosphorylation of Serine & Tyrosine R-group methylation of lysine, histidine and arginine. R-group acetylation of lysine. N-terminal methylation of alanine. N-terminal acetylation of serine. N-terminal formylation of methionine. Addition of carbohydrates (at Asparagine and Serine). Addition of Lipids (at Cysteine, N-terminal glycine and C-terminal via carbohydrate linker group) Covalent attachment of cofactors (eg. pyridoxal-5-phosphate attached at lysine; hemes attached at cysteines).
In solution it is the nature of the amino acid R-groups that dictate structure-function relationships of peptides and proteins. The hydrophobic amino acids will generally be encountered in the interior of proteins shielded from direct contact with water. Conversely, the hydrophilic amino acids are generally found on the exterior of proteins as well as in the active centers of enzymatically active proteins. Indeed, it is the very nature of certain amino acid R-groups that allow enzyme reactions to occur. The imidazole ring of histidine allows it to act as either a proton donor or acceptor at physiological pH. Hence, it is frequently found in the reactive center of enzymes. Equally important is the ability of histidines in hemoglobin to buffer the H+ ions from carbonic acid ionization in red blood cells. It is this property of hemoglobin that allows it to exchange O2 and CO2 at the tissues or lungs, respectively.
The primary alcohol of serine and threonine as well as the thiol (SH) of cysteine allow these amino acids to act as nucleophiles during enzymatic catalysis. Additionally, the thiol of cysteine is able to form a disulfide bond with other cysteines: Cysteine-SH + HS-Cysteine <> Cysteine-S-S-Cysteine This simple disulfide is identified as cystine. The formation of disulfide bonds between cysteines present within proteins is important to the formation of active structural domains in a large number of proteins. Disulfide bonding between cysteines in different polypeptide chains of oligomeric proteins plays a crucial role in ordering the structure of complex proteins, e.g. the insulin receptor. back to the top