Lecture 1 Amino Acids PDF

Proteins & Amino acids  Amino Acids Amino acids are organic molecules with carboxyl and amino groups Amino acids are the building blocks of proteins. Contain a carboxylic acid group and an amino group on the alpha () carbon. Amino acids differ in their properties due to...

Proteins & Amino acids  Amino Acids Amino acids are organic molecules with carboxyl and amino groups Amino acids are the building blocks of proteins. Contain a carboxylic acid group and an amino group on the alpha () carbon. Amino acids differ in their properties due to differing side chains, called R groups  -Carbon a side chain Amino Carboxyl group group Asymmetrical Carbon Atom ?= optical activities  Amino Acid Structure Amino acids may be characterized as α, β, or δ amino acids depending on the location of the amino group in the carbon chain.  α are on the carbon adjacent to the carboxyl group.  β are on the 2nd carbon  δ on the 3rd carbon from the carboxyl group  Amino Acids 20 standard amino acids are present in mammalian proteins All have amphoteric property (can act as both an acid and a base All have optical activity except ------------- are dipolar (have both charges) – +ve end (NH3+) – -ve end (COO-) Non-standard amino acids are found as a result of modifications of standard aa.  Amino acids stereoisomers All amino acids have chiral carbon except ---. Amino acids have stereoisomers. In biological systems, only L-amino acids – natural amino acids found in protein D-amino acids are found in antibiotics and in plant and bacterial cell walls Stereoisomers, Enantiomers, Optical Isomers Asymmetrical Carbon Atom ?= optical properties Rotate plane polarized light to give levorotatory & dextrorotatory forms  Proline imino acid: Has a secondary amino group  Each amino acid is given a three-letter abbreviation and a one- letter symbol. They often use the first three letter and the first letter. When there is confusion, an alternative is used. These must be remembered.  Amino Acid Functions 1. Amino acids are the building blocks of proteins 2. Some amino acids and their derivatives function as neurotransmitters and other regulators Examples Include L-dopamine Epinephrine Thyroxine Histamin  Nonpolar The 20 amino acids of proteins Glycine Alanine Valine Leucine Isoleucine (Gly or G) (Ala or A) (Val or V) (Leu or L) (Ile or I) Methionine Phenylalanine Trypotphan Proline (Met or M) (Phe or F) (Trp or W) (Pro or P) Polar Serine Threonine Cysteine Tyrosine Asparagine Glutamine (Ser or S) (Thr or T) (Cys or C) (Tyr or Y) (Asn or N) (Gln or Q) Electrically charged Acidic Basic Aspartic acid Glutamic acid Lysine Arginine Histidine (Asp or D) (Glu or E) (Lys or K) (Arg or R) (His or H)  Classification of amino acids 1. Essential or Non-essential,(? Semi-essential ) 2. Glucogenic , ketogenic, or Glucogenic & ketogenic 3. Neutral , acidic and basic 4. According to the side chain properties  Essential & Non-Essential Amino Acids Group of amino acids not synthesized by human body Must obtain from the diet All in diary products Proteins in diet comes from both animal and vegetable sources. Most animal sources (meat, milk, eggs) provide complete protein Vegetable sources usually low on or missing some essential aa. Some aa are classified as Semi-essential or conditionally aa(arginine, cysteine, glutamine, glycine, proline)  Essential Amino Acids Essential amino acids Non-Essential amino acids Arginine Alanine Asparagine (from aspartic acid) Histidine Aspartic Acid Isoleucine Cysteine Glutamic Acid Leucine Glutamine (from glutamic acid) Lysine Glycine Proline Methionine Serine Phenylalanine Tyrosine (from phenylalanine) Threonine Tryptophan Valine  Essential Amino Acids Complete protein Incomplete protein Lack one of more of the Contains all 10 essential amino acids essential amino acids Most vegetable proteins Proteins derived from are incomplete proteins animal sources are Beans are an exception complete proteins to this generalizations Beans contain some complete protein as well Glucogenic Or ketogenic Amino Acids Classification according to the side chain properties Non-polar (Hydrophobic) AA – Side chain does not bind or give off protons – Promote hydrophobic interaction – In aqueous solution- clustered in the interior – Helps giving a 3-D shape for protein structure Non-polar (Hydrophobic), aliphatic amino acids Non-polar (Hydrophobic), aromatic amino acids Non-Polar (Hydrophobic) Uncharged Amino Acids Glycine Alanine Valine Leucine Isoleucine (Gly or G) (Ala or A) (Val or V) (Leu or L) (Ile or I) Proline Methionine Phenylalanine Tryptophan (Pro or P) (Met or M) (Phe or F) (Trp or W)  The 20 amino acids are usually grouped according to the polarity of their R groups  Six amino acids have nonpolar, aliphatic (hydrophobic) R groups.  They are Gly, Ala, Val, Leu, Ile, and Met.  Gly has a hydrogen as its R group, having minimal steric hindrance.  In protein structure Gly offers the most flexibility!  Ala, Val, Leu, Ile and Met have hydrocarbon R groups, often involved in hydrophobic interactions.  Aromatic amino acids Phe, Tyr, and Trp have aromatic R groups Phe and Tyr both have benzene rings. Tryptophan has an indole ring. Phe and Trp participate in hydrophobic interactions. The -OH group in Tyr make it polar molecule The -OH group in Tyr is an important functional group in proteins. (phosphorylation, hydrogen bond,) They are jointly responsible for the light absorption of proteins at 280 nm, a property used as a measure of the concentration of proteins.  Aromatic amino acids Phe, F,; Tyr, Y,; Trp, W,  Positively charged (basic) and negatively charged (acidic) R groups  The most hydrophilic R groups are those either + vely or - vely charged.  Asp and Glu have carboxyl gp in their R groups. They have net negative charge at pH 7.0, thus usually named as aspartate and glutamate  Arg, Lys, and His have positively charged R groups at pH 7.0. Their R groups contain guanidino, amino, imidazole groups respectively. The side chain of His can be positively or uncharged depending on the local environment near pH 7.0 Polar (Hydrophilic) Charged Amino Acids Polar, charged amino acid Negatively charged Positively charged  Six amino acids have polar, uncharged R groups.  They are: Ser, Thr, Asn, Gln, Cys, and Pro  The R groups are more hydrophilic, due to the presence of hydroxyl groups, sulfur atoms, or amide groups.  -SH group of two Cys in proteins can be oxidized to form a covalent disulfide bond.  Cys often participates in hydrophobic interactions.  Pro has an imino group, instead of an amino group, forming a five-membered ring structure, being rigid in conformation.  Pro is often found in the bends of folded protein chains and often present on the surface of proteins. It offers the least flexibility. Polar (Hydrophilic) uncharged amino acids Have zero net charge at neutral pH Polar, uncharged amino acid Serine Threonine Cysteine Tyrosine Asparagine Glutamine (Ser or S) (Thr or T) (Cys or C) (Tyr or Y) (Asn or N) (Gln or Q) Cystine is a dimer of cysteine Sickle Cell Disease It is a pathology that results from the substitution of polar glutamate by the non-polar valine in the B subunit of hemoglobin  Acidic & Basic Properties of Amino Acids pK Value It is the ability of an acid to donate a proton (dissociate) Also known as pKa or acid dissociation constant It is the pH at which 50% of the acid is dissociated The pK values of α-carboxylic group is in the range of 2.2 The pK values of an-amino group is in the range of 9.4 The smaller the pK value the stronger the acid, the larger the pK the weaker the acid  Zwitter ion Both the –NH2 and the –COOH groups in an amino acid undergo ionization in water. At physiological pH, most amino acids contain both positive and negative charges with a net charge of zero Zwitter ion = double ion – when both NH3+ and COO- are ionized COO- can accept a proton, NH3+ can accept electron, so can act as acid and base (amphoteric) At the isoelectric point (pI), the + and – charges in the zwitterion are equal. pI = pH at which the molecule is electrically neutral  Zwitterion (Dipolar ion form) pI = pH at which the molecule is electrically neutral  Amino Acids as Acids Or Base Amino Acids as Acids In solutions more basic than the pI, the —NH3+ in the amino acid donates a proton. + H3N—CH2—COO– OH– H2N—CH2—COO– Zwitter ion at pI Negative ion Amino Acids as Bases In solution more acidic than the pI, the COO- in the amino acid accepts a proton. + H+ + H3N—CH2—COO– H3N—CH2—COOH Zwitterion at pI Positive ion  pH and Ionization Acidic amino acids such as aspartic acid have a second carboxyl group that can donate and accept protons. The pI for aspartic acid occurs at a pH of 2.8.