Amino Acids“Amino Acid”Amino Acids are the building units of proteins. Proteins arepolymers of amino acids linked together by what is called “Peptide bond” (see latter). There are about 300 amino acids occur in nature. Only 20 ofthem occur in proteins.Structure of amino acids:Each amino acid has 4 different groups attached to α- carbon( which is C-atom next to COOH). These 4 groups are : aminogroup, COOH gp,Hydrogen atom and sideChain (R) R
• At physiological PH (7.4), -COOH gp is dissociated forming a negatively charged carboxylate ion (COO-) and amino gp is protonated forming positively charged ion (NH3+) forming Zwitter ion• N.B. Proline is an imino acid not amino acid (see latter) Classification of amino acidsI- Chemical classification: According to number of COOH and NH2 groups i.e. according to net charge on amino acid.A- Monobasic, monocarboxylic amino acids i.e. neutral or uncharged: R
(Lecture 2):B- Basic amino acids: Contain two or more NH2 groups or nitrogen atoms that act as base i.e. can bind proton.At physiological pH, basic amino acids will be positively charged.e.g.a- Lysineb- Arginine: contains guanido groupc- Histidine: is an example on basic heterocyclic amino acids
C- Acidic Amino acids: at physiological pH will carry negative charge.e.g. Aspartic acid (aspartate) and Glutamic acid (glutamate). seestructures in hand out.Aspargine and Glutamine: They are amide forms of aspartate andglutamate in which side chain COOH groups are amidated.They are classified as neutral amino acids.
II- Classification according to polarity of side chain (R):A- Polar amino acids: in which R contains polar hydrophilic group socan forms hydrogen bond with H2O. In those amino acids, R maycontain: 1- OH group : as in serine, threonine and tyrosine 2- SH group : as in cysteine 3- amide group: as in glutamine and aspargine 4- NH2 group or nitrogen act as a base (basic amino acids ): as lysine,arginine and histidine 5- COOH group ( acidic amino acids): as aspartic and glutamic .B- Non polar amino acids:R is alkyl hydrophobic group which can’t enter in hydrogen bonfformation. 9 amino acids are non polar ( glycine, alanine, valine, leucine,isoleucine, phenyl alanine, tryptophan, proline and methionine)
IV- Metabolic classification: according to metabolic or degradationproducts of amino acids they may be:1- Ketogenic amino acids: which give ketone bodies . Lysine andLeucine are the only pure ketogenic amino acids.2- Mixed ketogenic and glucogenic amino acids: which give bothketonbodies and glucose.These are: isoleucine, phenyl alanine,tyrosine and tryptophan.3- Glucogenic amino acids: Which give glucose. They include therest of amino acids. These amino acids by catabolism yields productsthat enter in glycogen and glucose formation.
Amphoteric properties of amino acids: that is they have both basicand acidic groups and so can act as base or acid.Neutral amino acids (monobasic, monocarboxylic) exist in aqueoussolution as “ Zwitter ion” i.e. contain both positive and negativecharge. Zwitter ion is electrically neutral and can’t migrate into electricfield. Isoelectric point (IEP) = is the pH at which the zwitter ion is formed.e.g IEP of alanine is 6Chemical properties of amino acids:1- Reactions due to COOH group:-Salt formation with alkalis, ester formation with alcohols, amideformation with amines and decarboxylation-2- Reactions due toNH2 group: deamination and reaction withninhydrin reagent.-Ninhydrin reagent reacts with amino group of amino acid yieldingblue colored product. The intensity of blue color indicates quantity ofamino acids present.
Ninhydrine can react with imino acids as proline and hydroxyproline but gives yellow color.3- Reactions due to side chain (R):1- Millon reaction: for tyrosine gives red colored mass2- Rosenheim reaction: for tryptophan and gives violet ring.3- Pauly reaction: for imidazole ring of histidine: gives yellow toreddish product4- Sakagushi test: for guanido group of arginine andgives redcolor.5- Lead sulfide test (sulfur test): for sulfur containing aminoacids as cysteine give brown color.
These nonessential nutrients -- some prefer the term "dispensable" -- can be manufactured from other amino acids or from simpler compounds already present in your body. alanine glutamic serine acid asparagine glutamine tyrosine aspartic glycine arginine acid cysteine proline
Are obtained from dietary sources. Although you do not have to consume these amino acids on a daily basis -- they are recycled, to some extent -- you cannot remain healthy if you are deprived of them for very long.
Ques:Name the dipeptides below using the two letter aminoacid abbreviations separated by hyphen. Ο O || ||H₂N―CH―C―NH―CH―C―OH | | CH₂ CH₂ | | CH₂ OH | C=O | OH
Proteins –is a naturally occuring ,unbranched polymer in which the monomer units are amino acids. -is a peptide in which atleast amino acid residues are present.Proteins are classified as monomeric or multimeric.
Monomeric Multimeric protein protein -is a protein on -is a protein in which more than one peptide chain is which only one present. peptide chain is present.
-a protein inwhich only amino -is a protein that has one oracid residues are more non-amino acidpresent. residues are present.
• is the order in • Is the which amino arrangemen acids are linked t in together in a spaceadopt protein. edby the backbone portion of a protein.
The alpha helix Beta pleated sheet -is a protein -is a protein secondary structure secondary structure in which a single in which two fully protein chain adopts extended protein a shape that chain segment in the resembles a coiled same or different spring(helix)with the molecules are held coil configuration together by maintained by hydrogen bonds. hydrogen bond.
Question: Draw the secondary structure of a-helix and b-pleated sheet.
Is the overall three dimensionalshape of a protein that results fromthe interactions between amino acidside chains (R group ) that are widelyseparated from each other within apeptide chain.
Interactions responsible for tertiary structure”Four types of attractive interactions contribute to the tertiary structure of a protein:1. Covalent disulfide bonds2. Electrostatic attraction(salt bridges)3. Hydrogen bonds4. Hydrophobic bonds
The strongest of the tertiary –structure interactions ,result from Also called salt the –SH groups of two bridges,always involve cysteine residues the interaction between reacting with each other acidic side chain (R to form a covalent group )and a basic side disulfide bond. chain (R Group) Cysteine-is the only amino acid that contains a sulfhydryl group (-SH)
INTERACTIONS RESPONSIBLE FOR TERTIARY STRUCTURE
Questions : What is the only a-amino acid thatcontains sulfhydryl group?
Questions: Identify the following and name itsstructure:(a.) (b.)(c.) (d.)
Protein classification based on function Catalytic proteins Defense proteins Transport proteins Messenger proteins
Globular Proteins - consist of polypeptides folded into the shape of a ball. - are soluble in water or form colloidal dispersions and active globulins. - ex. Hemoglobin, albumin, and the globulins.
- consist of parallel polypeptide chainsthat are coiled and stretch out.- are insoluble in water.- ex. Collagen, fibrin, and myosin.
Colloidal Nature - proteins form colloidal dispersions in water. - proteins present in the bloodstream and cannot pass through membranes. -the presence of protein in the urine indicates damage to the membranes in the kidneys.
- A protein refers to the unfolding and rearrangement of the secondary and tertiary structures of a protein without breaking the peptide bonds.- A protein that is denatured loses its biologic activity.