Biochemistry: Proteins and Amino Acids PDF

1A BIOCHEMISTRY PROTEINS: AMINO ACIDS DR. JANDOC ...

1A BIOCHEMISTRY PROTEINS: AMINO ACIDS DR. JANDOC  At physiologic pH (7.4): carboxyl group (stronger acid) - OUTLINE exist almost entirely as R-COO (carboxylate ion) and amino + I. Overview groups (protonated) as R-NH3 II. Structure of Amino Acids o Zwitterions: molecules that contain an equal III. Classification of Amino Acid Side Chains number of positively- and negatively-charged A. Non-polar, Aliphatic Amino Acids groups bear no net charge B. Aromatic Amino Acids  Almost all carboxyl and amino groups are combined in C. Aliphatic, Polar, Uncharged Amino Acids peptide linkage – not available for chemical reaction D. Sulfur-Containing Amino Acids (except for hydrogen bond formation) E. Acidic and Basic Amino Acids  Side chains – dictate role of amino acids in proteins IV. Characteristics of Side Chains V. Optical Properties of Amino Acids VI. Modified Amino Acids VII. Acid-Base Properties of Amino Acids PROTEINS: AMINO ACIDS I. OVERVIEW PROTEINS - most abundant III. CLASSIFICATION OF AMINO ACID SIDE CHAINS - every life process depends on this class of molecules  According to polarity and structural features - common structural feature: linear polymers of amino acids A. NONPOLAR, ALIPHATIC AMINO ACIDS A. Functions 1. Glycine  Direct and regulate metabolism in the body - simplest amino acid o Hormones: carry signals from one group of cells - its side chain in only a hydrogen atom to another - small side chain → least amount of steric hindrance o Enzymes: increase rate of biochemical reactions in a protein (i.e., does not significantly impinge on the  Transporters of hydrophobic compounds in the blood (e.g. space occupied by other atoms or chemical groups) haemoglobin, plasma albumin) - often found in bends or in the tightly packed chains  Cell adhesion molecules of fibrous proteins  Ion channels – through lipid membranes  Movement (e.g. contractile proteins in muscles) 2. Alanine and Branched Chain Amino Acids (Valine,  Framework for deposition of calcium phosphate crystals Leucine, Isoleucine) (collagen in bone) - have bulky, nonpolar, aliphatic side chains  Protection (e.g. immunoglobulin) - high degree of hydrophobicity → within proteins, these amino acid side chains will cluster together to II. STRUCTURE OF AMINO ACIDS form hydrophobic cores - oily or lipid like → hydrophobic interactions ( tendency of nonpolar compounds to self- associate in an aqueous environment) - electrons shared equally between C and H atoms → cannot hydrogen bond with water - association is promoted by van der Waals forces between positively charged nucleus of one atom and the electron cloud of another → effective over short distances ( 2-4 Å) Trans 1 | ABACCO, ALDERITE, ASISTIN, BALANZA, BAYAS, BIANG 1 of 6  BIOCHEMISTRY PROTEINS: AMINO ACIDS 3. Tryptophan - more complex indole ring with a nitrogen that can engage in hydrogen bonds → more polar than phenylalanine 3. Proline - contains a rigid ring involving its α-carbon and α-amino group → imino group C. ALIPHATIC, POLAR, UNCHARGED AMINO ACIDS - causes a kink in the peptide backbone  Hydroxyl and Amide Groups in Side Chains - unique geometry contributes to the formation o Allow to form hydrogen bonds with: (a) water; of the fibrous structure of collagen (b) each other; (c) peptide backbone; (d) other - often interrupts the α-helices found in globular polar compounds in the binding sites of the proteins proteins o Hydrophilic → frequently found on the surface of water-soluble globular proteins B. AROMATIC AMINO ACIDS - side chains contain ring structures with similar properties 1. Asparagine (asn, N) - polarity differ - side chain aromatic ring is a six-membered carbon-hydrogen ring - side chain contain carbonyl and polar amide group with three conjugated double bonds (benzene ring or phenyl group) - amide of the amino acid aspartate - substituents in ring determine whether the amino acid side chain - amide group → site of attachment of oligosaccharide engages in polar or hydrophobic interactions chains in glycoproteins 1. Phenylalanine 2. Glutamine (gln, Q) - side chain ring contains no substituents - side chain contain carbonyl and polar amide group - electrons are shared equally between the carbons in - amide of the amino acid glutamate the ring → very nonpolar hydrophobic (rings can stack on each other 3. Serine (ser, S) - side chains contain a polar hydroxyl group → participate or serve as a site of attachment (ex: phosphate group) - side chain is an important component of the active site of many enzymes 2. Tyrosine 4. Threonine (thr, T) - side chains contain a polar hydroxyl group → - hydroxyl group on the phenyl ring participate or serve as a site of attachment (ex:  engage in hydrogen bonds → side chain is phosphate group) more polar and more hydrophilic - hydroxyl group → site of attachment of  participate or serve as a site of attachment oligosaccharide chains in glycoproteins (ex: phosphate group) - side chain can lose a proton at alkaline pH D. SULFUR-CONTAINING AMINO ACIDS 1. Methionine (met, M) - nonpolar - large, bulky side chain → hydrophobic - does not contain a sulfhydryl group - cannot form disulfide bonds -important and central role in metabolism is related to its ability to transfer the methyl group attached to the sulfur atom to other compounds S1T1 2 of 6  BIOCHEMISTRY PROTEINS: AMINO ACIDS 2. Cysteine (cys, C) - form ionic (electrostatic) bonds with - important component of the active site of many enzymes positively charged molecules (e.g., basic - side chains can lose a proton at alkaline pH a.a.) - side chains contain a sulfhydryl group (pKa ~ 8.4) → predominantly uncharged and undissociated at 2. Histidine (his, H) physiologic pH of 7.4 - side chain containing nitrogen - free cysteine molecule in solution can form a (nitrogen-containing imidazole ring) → covalent disulfide bond with another cysteine protonated and positively charged at physiologic and molecule through spontaneous (nonenzymatic) lower pH values oxidation of their sulfhydryl groups → cysteine (present in blood - weakly basic and tissues, not very water-soluble) - largely uncharged at physiologic pH - side chain can either be positively charged or neutral *Cystine Disulfide Bond depending on the ionic environment provided by the - plays an important role in holding two polypeptide chains (important in the function of polypeptide chains or two different regions of a myoglobin) chain together 3. Lysine (lys, K) - side chain:  containing nitrogen → protonated and positively charged at physiologic and lower pH values  often form ionic bonds with negatively charged compounds (e.g., phosphate groups in ATP)  at physiologic pH = fully ionized and positively charged th - primary amino group on the 6 or ε carbon 4. Arginine (arg, R) - side chain has the same characteristics with E. THE ACIDIC AND BASIC AMINO ACIDS lysine - participate in hydrogen bonding and the formation of salt bridges - has a guanidinium group +  Salt bridges: the binding of an inorganic ion such as Na between two partially or fully negatively charged groups IV. CHARACTERISTICS OF THE SIDE CHAINS o act over large distances → binding of A. pKa charged molecules and ions to proteins and B. Hydropathic Index nucleic acids - charges on these a.a. at physiologic pH is a function of their pK a for  Used to denote the hydrophobicity of the side chain o More positive = greater tendency to cluster with dissociation of protons from the: α-carboxylic acid groups; α-amino other nonpolar molecules (hydrophobic effect) groups; side chains [e.g., Isoleucine = 4.5] - charge on the a.a. at a particular pH → determined by the pK a of o More negative = more hydrophilic the side chain each group that has a dissociable proton (e.g., Arginine = -4.5) ACIDIC Summary of the 20 Fundamental Amino Acids Accdg. To Side  Aspartate Chains  Glutamate Aliphatic  Glycine Acidic  Aspartate BASIC Nonpolar  Alanine  Glutamate - positive charges → form ionic bonds with negatively charged  Valine groups (e.g., side chains of acidic a.a. or phosphate groups of  Leucine  Isoleucine coenzymes) Aromatic  Phenylalanine Amidic  Asparagine  Arginine  Tyrosine Amino  Glutamine  Lysine  Tryptophan Acids  Histidine OH-  Serine Basic  Lysine containing  Threonine  Arginine  Histidine 1. Aspartate (asp, D) & Glutamate (glu, E) Acidic  Aspartate Sulfur-  Cysteine - proton donor  Glutamate containing  Methionine - fully ionized side chains at neutral pH containing a negatively Imino Acid  Proline charged carboxylate group → aspartate or glutamate at physiologic pH S1T1 3 of 6  BIOCHEMISTRY PROTEINS: AMINO ACIDS Summary of the 20 Fundamental Amino Acids Accdg. To Side  The 2 forms in each pair are termed: stereoisomers, Chains optical isomers, enantiomers  ALL amino acids found in proteins are in L-configuration  D-amino acids → some antibiotics; bacterial cell walls VI. MODIFIED AMINO ACIDS  Not coded for in the DNA  Results of Modification o Serve a regulatory function o Target or anchor the protein in membranes o Enhance a protein’s association with other proteins o Target it for degradation  Post-translational Modification o When these reactions are enzyme-catalyzed A. GLYCOSYLATION  Oligosaccharides are bound to proteins by either N- linkages or O-linkages 1. N-linked oligosaccharides  Attached to cell surface proteins  Protect cell from proteolysis or an immune attack 2. O-glycosidic link  Common way to attach to serine or threonine hydroxyl groups secreted in proteins  Links glycogen to tyrosine B. FATTY ACYLATION OR PRENYLATION  Many membrane proteins contain a covalently attached lipid group that interacts hydrophobically with lipids in the membrane 1. Palmitoyl Groups (C16)  Often attached to plasma membrane proteins 2. Myristoyl Group (C14)  Often attached to proteins in the lipid membranes of intracellular vesicles 3. Farnesyl (C15) or Geranyl Group (C20) V. OPTICAL PROPERTIES OF AMINO ACIDS  Synthesized from the five-carbon isoprene unit (isopentenyl phyrophosphate) → isoprenoids A. α-Carbon  Attached in ether linkage to a specific cysteine residue of  Chiral Carbon certain membrane proteins → those involved in regulation o Optically active carbon o Attached to 4 different chemical groups C. REGULATORY MODIFICATIONS o Exception: GLYCINE  Change the activity of the protein  Α-carbon has 2 substituents → optically inactive 1. Phosphorylation  Transfer of phosphate group from ATP B. Mirror Images  Phosphorylation of OH group on  Amino acids that have assymetric center at the α-carbon o Serine → exists in 2 forms (D and L) o Threonine o Tyrosine S1T1 4 of 6  BIOCHEMISTRY PROTEINS: AMINO ACIDS  By protein kinase  At pH 7.4 = >99% of molecules are dissociated → negatively charged 2. Reversible acetylation  Occurs on lysine residues of histone proteins in the C. Amino acids with ionisable groups in side chains chromosome  Changes their interaction with the negatively charged 1. Acidic phosphate groups of DNA  Aspartate  Glutamate 3. ADP-ribosylation +  Transfer of an ADP-ribose from NAD to an arginine, 2. Basic glutamine, or a cysteine residue on a target protein in the  Histidine membrane (leukocytes, skeletal muscles, brain, and testes)  Lysine  Arginine D. OTHER AMINO ACID POSTRANSLATIONAL MODIFICATIONS D. Titration of an Amino Acid 1. Carboxylation of the γ Carbon of Glutamate (C4) 1. Dissociation of the Carboxyl Group (-COOH)  In certain blood clotting proteins  Alanine  Important for attaching the clot to a surface o Contains: α-amino group and α-carboxyl group o Calcium ions: mediate the attachment by binding to o Low pH: both groups are protonated the 2 negatively charged carboxyl groups of γ- o pH elevation glutamate and two additional negatively charged  -COOH dissociates losing a proton - groups provided by phospholipids in the cell  Form a carboxylate group (-COO ) membrane  Molecule assumes dipolar form (zwitterion or isoelectric) 2. Hydroxylation / Oxidation  Collagen 2. Application of the Henderson-Hasselbalch Equation o Fibrous extracellular protein o Contains hydroxyproline o Addition of OH group to the proline side chain  Extra group that can engage in H bonding between the polypeptide stands of the fibrous protein + E. SELENOCYSTEINE 3. Dissociation of the Amino Group (-NH3 )  Synthesis is not a  Much weaker acid than the –COOH group → smaller posttranslational modification dissociation constant  Modification to serine occurs while it is bound to a unique tRNA 4. pKs of Alanine  Each titrable group has a pKa that is numerically equal to the pH at which ½ of the protons have been removed from VII. ACID-BASE PROPERTIES OF AMINO ACIDS that group A. Amino acids are amphoteric molecules  Have both acidic and basic groups B. Amino acids in aqueous solutions at physiologic pH (7.4) 1. Amino group  pKa = 9.5 (8.8-11.)  At pH 7.4 = fully protonated and carry a positive charge 2. Carboxylic acid group  pKa (of primary carboxylic acid groups) = 2 (1.8-2.4) 5. Titration curve of Alanine  pH < pKa = all of the carboxylic acid groups are protonated  Buffer pairs  At pKa = 50% are dissociated into carboxylate anions and - o –COOH/-COO as buffer in the pH region around protons pK1 + o –NH3 /-NH2 as buffer in the region around pK2 S1T1 5 of 6  BIOCHEMISTRY PROTEINS: AMINO ACIDS  When pH=pK o pH = pK1 → forms I and II are equal in amount in the solution o pH = pK2 → forms II and III are equal in amount in the solution  Isoelectric point o Alanine at neutral pH  Exists predominantly as form II  Amino and carboxyl groups are ionized  Net charge is zero 6. Net charge of amino acids at physiologic (nearly neutral) pH  All amino acids have - o –COO + o –NH3  Amphoteric substances o Referred as amphocytes (amphoteric REFERENCE electrolytes) 1. Handout ni Doc Jandoc :D 7. Titration curve of histidine 8. Titrable Groups in Proteins  Only the amino acid side chains and the amino group at the amino terminal and carboxyl group at the carboxyl terminal have dissociable protons S1T1 6 of 6