Proteins: Biochemistry Module 4 PDF

Evolve. Adapt. Overcome. CEFI is now ready. PROTEINS CHEM 5: BIOCHEMISTRY CC 103: BIOCHEMISTRY FOR MLS HAZEL DOROTHY CESAR-VILAN, RCHE, MSC. College of Liber...

Evolve. Adapt. Overcome. CEFI is now ready. PROTEINS CHEM 5: BIOCHEMISTRY CC 103: BIOCHEMISTRY FOR MLS HAZEL DOROTHY CESAR-VILAN, RCHE, MSC. College of Liberal Arts, Sciences and Education  COLLEGE OF LIBERAL ARTS, SCIENCES & EDUCATION Calayan Educational Foundation, Inc. PROTEINS Greek: proteios (first of rank) Most abundant (~15%) biomolecule in the cell Coined by Gerard Johann Mulder, a Dutch chemist (1838) Most varied and most diverse in terms of structure and function Most versatile of the 4 biomolecules Protein function is determined by protein structure. No part of this material may be reproduced, stored in a retrieval system or transmitted in any form or by any means – electronic, mechanical, photocopying, recording or otherwise, without permission in writing from the author or lecturer.  COLLEGE OF LIBERAL ARTS, SCIENCES & EDUCATION Calayan Educational Foundation, Inc. No part of this material may be reproduced, stored in a retrieval system or transmitted in any form or by any means – electronic, mechanical, photocopying, recording or otherwise, without permission in writing from the author or lecturer.  COLLEGE OF LIBERAL ARTS, SCIENCES & EDUCATION Calayan Educational Foundation, Inc. AMINO ACIDS Group of organic compounds containing two functional groups: Amino (–NH2) – basic in nature Carboxyl (–COOH) – acidic in nature The amino acids are termed as α-amino acids, if both the carboxyl and amino groups are attached to the same C atom. No part of this material may be reproduced, stored in a retrieval system or transmitted in any form or by any means – electronic, mechanical, photocopying, recording or otherwise, without permission in writing from the author or lecturer.  COLLEGE OF LIBERAL ARTS, SCIENCES & EDUCATION Calayan Educational Foundation, Inc. AMINO ACIDS No part of this material may be reproduced, stored in a retrieval system or transmitted in any form or by any means – electronic, mechanical, photocopying, recording or otherwise, without permission in writing from the author or lecturer.  COLLEGE OF LIBERAL ARTS, SCIENCES & EDUCATION Calayan Educational Foundation, Inc. AMINO ACIDS 20 (+2) amino acids are commonly found in proteins Each amino acid is assigned a 3-letter or 1-letter symbol, commonly used to represent the amino acids in protein structure No part of this material may be reproduced, stored in a retrieval system or transmitted in any form or by any means – electronic, mechanical, photocopying, recording or otherwise, without permission in writing from the author or lecturer.  COLLEGE OF LIBERAL ARTS, SCIENCES & EDUCATION Calayan Educational Foundation, Inc. CLASSIFICATION No part of this material may be reproduced, stored in a retrieval system or transmitted in any form or by any means – electronic, mechanical, photocopying, recording or otherwise, without permission in writing from the author or lecturer.  COLLEGE OF LIBERAL ARTS, SCIENCES & EDUCATION Calayan Educational Foundation, Inc. CLASSIFICATION BASED ON STRUCTURE Sulfur- Acids + Alkyl Alcohols Bases Aromatic Imines containing Amides No part of this material may be reproduced, stored in a retrieval system or transmitted in any form or by any means – electronic, mechanical, photocopying, recording or otherwise, without permission in writing from the author or lecturer.  COLLEGE OF LIBERAL ARTS, SCIENCES & EDUCATION Calayan Educational Foundation, Inc. No part of this material may be reproduced, stored in a retrieval system or transmitted in any form or by any means – electronic, mechanical, photocopying, recording or otherwise, without permission in writing from the author or lecturer.  COLLEGE OF LIBERAL ARTS, SCIENCES & EDUCATION Calayan Educational Foundation, Inc. ALKYL / ALIPHATIC Glycine, Alanine, Valine, Leucine and Isoleucine Amino acids with aliphatic side chains Monoamino monocarboxylic acids Leu, Ile, Val –branched chain amino acids) No part of this material may be reproduced, stored in a retrieval system or transmitted in any form or by any means – electronic, mechanical, photocopying, recording or otherwise, without permission in writing from the author or lecturer.  COLLEGE OF LIBERAL ARTS, SCIENCES & EDUCATION Calayan Educational Foundation, Inc. ALKYL / ALIPHATICS Glycine (Gly, G) Alanine (Ala, A) Valine (Val, V) Isoleucine (Ile, I) Leucine (Leu, L) No part of this material may be reproduced, stored in a retrieval system or transmitted in any form or by any means – electronic, mechanical, photocopying, recording or otherwise, without permission in writing from the author or lecturer.  COLLEGE OF LIBERAL ARTS, SCIENCES & EDUCATION Calayan Educational Foundation, Inc. ALCOHOLS Serine, Threonine and Tyrosine Amino acids with hydroxyl group Monoamino monocarboxylic acids Tyr – usually considered under aromatic amino acids No part of this material may be reproduced, stored in a retrieval system or transmitted in any form or by any means – electronic, mechanical, photocopying, recording or otherwise, without permission in writing from the author or lecturer.  COLLEGE OF LIBERAL ARTS, SCIENCES & EDUCATION Calayan Educational Foundation, Inc. ALCOHOLS Serine (Ser, S) Threonine (Thr, T) No part of this material may be reproduced, stored in a retrieval system or transmitted in any form or by any means – electronic, mechanical, photocopying, recording or otherwise, without permission in writing from the author or lecturer.  COLLEGE OF LIBERAL ARTS, SCIENCES & EDUCATION Calayan Educational Foundation, Inc. SULFUR-CONTAINING Cysteine, Methionine Cys – with sulfhydryl group Met – with thioether group Cystine – formed by the condensation of two molecules of cysteine No part of this material may be reproduced, stored in a retrieval system or transmitted in any form or by any means – electronic, mechanical, photocopying, recording or otherwise, without permission in writing from the author or lecturer.  COLLEGE OF LIBERAL ARTS, SCIENCES & EDUCATION Calayan Educational Foundation, Inc. SULFUR-CONTAINING Cysteine (Cys, C) Methionine (Met, M) No part of this material may be reproduced, stored in a retrieval system or transmitted in any form or by any means – electronic, mechanical, photocopying, recording or otherwise, without permission in writing from the author or lecturer.  COLLEGE OF LIBERAL ARTS, SCIENCES & EDUCATION Calayan Educational Foundation, Inc. ACIDS AND THEIR AMIDES ACIDS: Aspartic Acid and Glutamic Acid Dicarboxylic monoamino acids AMIDES: Asparagine and Glutamine Derivatives of the acids No part of this material may be reproduced, stored in a retrieval system or transmitted in any form or by any means – electronic, mechanical, photocopying, recording or otherwise, without permission in writing from the author or lecturer.  COLLEGE OF LIBERAL ARTS, SCIENCES & EDUCATION Calayan Educational Foundation, Inc. ACIDS AND THEIR AMIDES Aspartic Acid (Asp, D) Glutamic Acid (Glu, E) Asparagine (Asn, N) Glutamine (Gln, Q) No part of this material may be reproduced, stored in a retrieval system or transmitted in any form or by any means – electronic, mechanical, photocopying, recording or otherwise, without permission in writing from the author or lecturer.  COLLEGE OF LIBERAL ARTS, SCIENCES & EDUCATION Calayan Educational Foundation, Inc. BASES Lysine, Arginine and Histidine Dibasic monocarboxylic acids Highly basic in character Arg – with guanidine group His – with imidazole ring No part of this material may be reproduced, stored in a retrieval system or transmitted in any form or by any means – electronic, mechanical, photocopying, recording or otherwise, without permission in writing from the author or lecturer.  COLLEGE OF LIBERAL ARTS, SCIENCES & EDUCATION Calayan Educational Foundation, Inc. BASES Lysine (Lys, K) Arginine (Arg, R) Histidine (His, H) No part of this material may be reproduced, stored in a retrieval system or transmitted in any form or by any means – electronic, mechanical, photocopying, recording or otherwise, without permission in writing from the author or lecturer.  COLLEGE OF LIBERAL ARTS, SCIENCES & EDUCATION Calayan Educational Foundation, Inc. AROMATICS Phenylalanine, Tyrosine and Tryptophan Trp – with indole ring His – may also be considered under this category No part of this material may be reproduced, stored in a retrieval system or transmitted in any form or by any means – electronic, mechanical, photocopying, recording or otherwise, without permission in writing from the author or lecturer.  COLLEGE OF LIBERAL ARTS, SCIENCES & EDUCATION Calayan Educational Foundation, Inc. AROMATICS Phenylalanine (Phe, F) Tyrosine (Tyr, Y) Tryptophan (Trp, W) No part of this material may be reproduced, stored in a retrieval system or transmitted in any form or by any means – electronic, mechanical, photocopying, recording or otherwise, without permission in writing from the author or lecturer.  COLLEGE OF LIBERAL ARTS, SCIENCES & EDUCATION Calayan Educational Foundation, Inc. IMINE Proline Pro – with pyrrolidine ring An α-imino acid: contains an imino group (-NH), instead of an amino group (-NH2) found in other amino acids His, Trp, and Pro are heterocyclic amino acids No part of this material may be reproduced, stored in a retrieval system or transmitted in any form or by any means – electronic, mechanical, photocopying, recording or otherwise, without permission in writing from the author or lecturer.  COLLEGE OF LIBERAL ARTS, SCIENCES & EDUCATION Calayan Educational Foundation, Inc. IMINE Proline (Pro, P) No part of this material may be reproduced, stored in a retrieval system or transmitted in any form or by any means – electronic, mechanical, photocopying, recording or otherwise, without permission in writing from the author or lecturer.  COLLEGE OF LIBERAL ARTS, SCIENCES & EDUCATION Calayan Educational Foundation, Inc. CLASSIFICATION BASED ON POLARITY Polar with no Polar with + ‘R’ Polar with – ‘R’ Non-polar charge on ‘R’ group group group No part of this material may be reproduced, stored in a retrieval system or transmitted in any form or by any means – electronic, mechanical, photocopying, recording or otherwise, without permission in writing from the author or lecturer.  COLLEGE OF LIBERAL ARTS, SCIENCES & EDUCATION Calayan Educational Foundation, Inc. NON-POLAR Aliphatic Residues Alanine, Leucine, Isoleucine, Valine, Methionine, Phenylalanine, Tryptophan Sulfur- and Proline containing Also referred to as hydrophobic or water- hating Have no charge on the ‘R’ group Aromatics With Aromatic Residues No part of this material may be reproduced, stored in a retrieval system or transmitted in any form or by any means – electronic, mechanical, photocopying, recording or otherwise, without permission in writing from the author or lecturer.  COLLEGE OF LIBERAL ARTS, SCIENCES & EDUCATION Calayan Educational Foundation, Inc. POLAR WITH NO CHARGE ON ‘R’ GROUP Alcohols Glycine, Serine, Threonine, Cysteine, Glutamine, Asparagine and Tyrosine Carry no charge on the ‘R’ group but have Thiols groups such as hydroxyl, sulfydryl and amide and participate in H bonding of protein structure Phenols Amides No part of this material may be reproduced, stored in a retrieval system or transmitted in any form or by any means – electronic, mechanical, photocopying, recording or otherwise, without permission in writing from the author or lecturer.  COLLEGE OF LIBERAL ARTS, SCIENCES & EDUCATION Calayan Educational Foundation, Inc. POLAR WITH + CHARGE ON ‘R’ GROUP Lysine, Arginine and Histidine Have basic –NH2 side chains No part of this material may be reproduced, stored in a retrieval system or transmitted in any form or by any means – electronic, mechanical, photocopying, recording or otherwise, without permission in writing from the author or lecturer.  COLLEGE OF LIBERAL ARTS, SCIENCES & EDUCATION Calayan Educational Foundation, Inc. CLASSIFICATION BASED ON NUTRITION Essential / Non-essential / Indispensable Dispensable No part of this material may be reproduced, stored in a retrieval system or transmitted in any form or by any means – electronic, mechanical, photocopying, recording or otherwise, without permission in writing from the author or lecturer.  COLLEGE OF LIBERAL ARTS, SCIENCES & EDUCATION Calayan Educational Foundation, Inc. NON-ESSENTIAL Glycine, Alanine, Serine, Cysteine, Aspartate, Asparagine, Glutamate, Glutamine, Tyrosine and Proline Dispensable amino acids Can be synthesized by the body – need not be consumed in the diet No part of this material may be reproduced, stored in a retrieval system or transmitted in any form or by any means – electronic, mechanical, photocopying, recording or otherwise, without permission in writing from the author or lecturer.  COLLEGE OF LIBERAL ARTS, SCIENCES & EDUCATION Calayan Educational Foundation, Inc. ESSENTIAL Arginine, Valine, Histidine, Isoleucine, Leucine, Lysine, Methionine, Phenylalanine, Threonine and Tryptophan Indispensable amino acids Cannot be synthesized in the body – need to be supplied through the diet Required for proper growth and maintenance of an individual Semi-essential amino acids: Arg and His – can be synthesized by adults but not by growing children No part of this material may be reproduced, stored in a retrieval system or transmitted in any form or by any means – electronic, mechanical, photocopying, recording or otherwise, without permission in writing from the author or lecturer.  COLLEGE OF LIBERAL ARTS, SCIENCES & EDUCATION Calayan Educational Foundation, Inc. PHYSICAL PROPERTIES Appearance: crystalline solid Solubility: usually soluble in water Melting Points: generally melt at higher temperatures, often above 200°C Taste: may be sweet (Gly, Ala, Val), tasteless (Leu) or bitter (Arg, Ile) Ampholytes: contain both acidic (–COOH) and basic (–NH2) components can donate a proton or accept a proton No part of this material may be reproduced, stored in a retrieval system or transmitted in any form or by any means – electronic, mechanical, photocopying, recording or otherwise, without permission in writing from the author or lecturer.  COLLEGE OF LIBERAL ARTS, SCIENCES & EDUCATION Calayan Educational Foundation, Inc. PHYSICAL PROPERTIES Chiral molecules: Have an asymmetric carbon (except for Gly) Optically active glycine alanine Optical properties: all except Gly possess optical isomers due to the presence of asymmetric carbon atom (L- and D- amino acids) Predominantly occurs as a Zwitterion or dipolar ion No part of this material may be reproduced, stored in a retrieval system or transmitted in any form or by any means – electronic, mechanical, photocopying, recording or otherwise, without permission in writing from the author or lecturer.  COLLEGE OF LIBERAL ARTS, SCIENCES & EDUCATION Calayan Educational Foundation, Inc. ZWITTERION German: zwitter (hybrid) Aka dipolar ion, a hybrid molecule containing positive and negative ionic groups The amino acids rarely exist in neutral form with free carboxylic and free amino groups. In strongly acidic pH (low), the amino acid is positively charged (cation), while in strongly alkaline pH (high), it is negatively charged (anion). Each amino acid has a characteristic pH at which it carries both positive and negative charges and exists as zwitterion. No part of this material may be reproduced, stored in a retrieval system or transmitted in any form or by any means – electronic, mechanical, photocopying, recording or otherwise, without permission in writing from the author or lecturer.  COLLEGE OF LIBERAL ARTS, SCIENCES & EDUCATION Calayan Educational Foundation, Inc. ZWITTERION No part of this material may be reproduced, stored in a retrieval system or transmitted in any form or by any means – electronic, mechanical, photocopying, recording or otherwise, without permission in writing from the author or lecturer.  COLLEGE OF LIBERAL ARTS, SCIENCES & EDUCATION Calayan Educational Foundation, Inc. pKa tells you what the pH needs to be in order for a chemical species to donate or accept a proton. These values are true for a 25°C environment with 1 atm. Values for amino acids may be slightly different depending on the environment. No part of this material may be reproduced, stored in a retrieval system or transmitted in any form or by any means – electronic, mechanical, photocopying, recording or otherwise, without permission in writing from the author or lecturer.  COLLEGE OF LIBERAL ARTS, SCIENCES & EDUCATION Calayan Educational Foundation, Inc. No part of this material may be reproduced, stored in a retrieval system or transmitted in any form or by any means – electronic, mechanical, photocopying, recording or otherwise, without permission in writing from the author or lecturer.  COLLEGE OF LIBERAL ARTS, SCIENCES & EDUCATION Calayan Educational Foundation, Inc. ISOELECTRIC POINT / PH (pI or IpH) The pH at which a molecule exists as a zwitterion or dipolar ion and carries no net charge The molecule is electrically neutral Can be calculated by taking the average pKa values corresponding to the ionizable groups No part of this material may be reproduced, stored in a retrieval system or transmitted in any form or by any means – electronic, mechanical, photocopying, recording or otherwise, without permission in writing from the author or lecturer.  COLLEGE OF LIBERAL ARTS, SCIENCES & EDUCATION Calayan Educational Foundation, Inc. Net Point pH Predominant Forms Charge Almost all monopositive 1 pH < pKaC +1 form Half monopositive, half 2 pH = pKaC +0.5 isoelectric pH = ½ (pKac 3 All isoelectric form 0 + pKan) Half isoelectric, half 4 pH = pKaN -0.5 mononegative 5 pH > pKaN Almost all mononegative -1 No part of this material may be reproduced, stored in a retrieval system or transmitted in any form or by any means – electronic, mechanical, photocopying, recording or otherwise, without permission in writing from the author or lecturer.  COLLEGE OF LIBERAL ARTS, SCIENCES & EDUCATION pKa Calayan Educational Foundation, Inc. pKa pKa Amino Acids (protonated α- (α-carboxyl) (side chain) amino) Glycine 2.34 9.60 ISOELECTRIC PH (pI or IpH) Alanine Valine 2.34 2.32 9.69 9.62 Leucine 2.36 9.60 " % Isoleucine 2.36 9.68 𝒑𝑲𝟏 𝑪𝑶𝑶 %𝒑𝑲𝟐(𝑵𝑯𝟑 ) IpH = Proline 1.99 10.96 𝟐 Phenylalanine 1.83 9.13 Tyrosine 2.20 9.11 10.07 Tryptophan 2.38 9.39 ,../ %0.12 IpH = , Serine Threonine 2.21 2.11 9.15 9.62 Cysteine 1.96 8.18 10.28 Methionine 2.28 9.21 IpH = 5.97 Asparagine Glutamine 2.02 2.17 8.80 9.13 Aspartate 1.88 9.60 3.65 Glutamate 2.19 9.67 4.25 Lysine 2.18 8.95 10.53 Arginine 2.17 9.04 12.48 No part of this material may be reproduced, stored in a retrieval system or transmitted in any form or by any Histidine 1.82 means – electronic, mechanical, 9.17 recording or photocopying, 6.00 otherwise, without permission in writing from the author or lecturer.  COLLEGE OF LIBERAL ARTS, SCIENCES & EDUCATION Calayan Educational Foundation, Inc. AT LOW PH RELEASING PROTON At very low pH, the predominant ionic The third stage of the titration species of Glycine is the fully protonated corresponds to the removal of a proton form, +H3N-CH2-COOH. For Glycine, the from the –NH3+ group of Glycine. The pH at the midpoint is 2.34, thus it’s pH at the midpoint of this stage is 9.60, Carboxyl group (–COOH) has pKa of 2.34. equal to the pKa for the –NH3+ group. REACHING MIDDLE PH As the titration proceeds, another important point is reached at pH 5.97. Here there is another point of infection, at which removal of the first proton is essentially complete and removal of the second proton has just begun. No part of this material may be reproduced, stored in a retrieval system or transmitted in any form or by any means – electronic, mechanical, photocopying, recording or otherwise, without permission in writing from the author or lecturer.  COLLEGE OF LIBERAL ARTS, SCIENCES & EDUCATION Calayan Educational Foundation, Inc. EXAMPLE: ALANINE pKa pKa pKa Amino Acids (protonated α- (α-carboxyl) (side chain) amino) Alanine 2.34 9.69 No part of this material may be reproduced, stored in a retrieval system or transmitted in any form or by any means – electronic, mechanical, photocopying, recording or otherwise, without permission in writing from the author or lecturer.  COLLEGE OF LIBERAL ARTS, SCIENCES & EDUCATION Calayan Educational Foundation, Inc. EXAMPLE: ALANINE pKa pKa pKa Amino Acids (protonated α- (α-carboxyl) (side chain) amino) Alanine 2.34 9.69 No part of this material may be reproduced, stored in a retrieval system or transmitted in any form or by any means – electronic, mechanical, photocopying, recording or otherwise, without permission in writing from the author or lecturer.  COLLEGE OF LIBERAL ARTS, SCIENCES & EDUCATION Calayan Educational Foundation, Inc. EXAMPLE: ASPARTIC ACID pKa pKa pKa Amino Acids (protonated α- (α-carboxyl) (side chain) amino) Aspartate 2.1 9.8 3.9 No part of this material may be reproduced, stored in a retrieval system or transmitted in any form or by any means – electronic, mechanical, photocopying, recording or otherwise, without permission in writing from the author or lecturer.  COLLEGE OF LIBERAL ARTS, SCIENCES & EDUCATION Calayan Educational Foundation, Inc. EXAMPLE: ASPARTIC ACID pKa pKa pKa Amino Acids (protonated α- (α-carboxyl) (side chain) amino) Aspartate 1.88 9.60 3.65 No part of this material may be reproduced, stored in a retrieval system or transmitted in any form or by any means – electronic, mechanical, photocopying, recording or otherwise, without permission in writing from the author or lecturer.  COLLEGE OF LIBERAL ARTS, SCIENCES & EDUCATION Calayan Educational Foundation, Inc. EXAMPLE: ARGININE pKa pKa pKa Amino Acids (protonated α- (α-carboxyl) (side chain) amino) Lysine 2.18 8.95 10.53 No part of this material may be reproduced, stored in a retrieval system or transmitted in any form or by any means – electronic, mechanical, photocopying, recording or otherwise, without permission in writing from the author or lecturer.  COLLEGE OF LIBERAL ARTS, SCIENCES & EDUCATION Calayan Educational Foundation, Inc. EXAMPLE: ARGININE pKa pKa pKa Amino Acids (protonated α- (α-carboxyl) (side chain) amino) Lysine 2.17 9.04 12.48 No part of this material may be reproduced, stored in a retrieval system or transmitted in any form or by any means – electronic, mechanical, photocopying, recording or otherwise, without permission in writing from the author or lecturer.  COLLEGE OF LIBERAL ARTS, SCIENCES & EDUCATION Calayan Educational Foundation, Inc. PROTEINS No part of this material may be reproduced, stored in a retrieval system or transmitted in any form or by any means – electronic, mechanical, photocopying, recording or otherwise, without permission in writing from the author or lecturer.  COLLEGE OF LIBERAL ARTS, SCIENCES & EDUCATION Calayan Educational Foundation, Inc. HIERARCHY OF PROTEIN STRUCTURE No part of this material may be reproduced, stored in a retrieval system or transmitted in any form or by any means – electronic, mechanical, photocopying, recording or otherwise, without permission in writing from the author or lecturer.  COLLEGE OF LIBERAL ARTS, SCIENCES & EDUCATION Calayan Educational Foundation, Inc. HIERARCHY OF PROTEIN STRUCTURE No part of this material may be reproduced, stored in a retrieval system or transmitted in any form or by any means – electronic, mechanical, photocopying, recording or otherwise, without permission in writing from the author or lecturer.  COLLEGE OF LIBERAL ARTS, SCIENCES & EDUCATION Calayan Educational Foundation, Inc. PRIMARY STRUCTURE the linear sequence of amino acids forming the backbone of proteins (polypeptides) peptide bond No part of this material may be reproduced, stored in a retrieval system or transmitted in any form or by any means – electronic, mechanical, photocopying, recording or otherwise, without permission in writing from the author or lecturer.  COLLEGE OF LIBERAL ARTS, SCIENCES & EDUCATION Calayan Educational Foundation, Inc. PEPTIDE BOND The amino acids are held together in a protein by covalent peptide bonds or linkages. These bonds are rather strong and serve as the “cementing material” between the individual amino acids. peptide bond No part of this material may be reproduced, stored in a retrieval system or transmitted in any form or by any means – electronic, mechanical, photocopying, recording or otherwise, without permission in writing from the author or lecturer.  COLLEGE OF LIBERAL ARTS, SCIENCES & EDUCATION Calayan Educational Foundation, Inc. PEPTIDE BOND Formation of a peptide bond: Amino group of an amino acid combines with the carboxyl group of another amino acid Dipeptide = 2 amino acids, 1 peptide bond Conventional writing of peptide structures: Free amino end (N-terminal residue) at the left, and the free carboxyl end (C-terminal residue) at peptide bond the right No part of this material may be reproduced, stored in a retrieval system or transmitted in any form or by any means – electronic, mechanical, photocopying, recording or otherwise, without permission in writing from the author or lecturer.  COLLEGE OF LIBERAL ARTS, SCIENCES & EDUCATION Calayan Educational Foundation, Inc. PRIMARY STRUCTURE Chemical shorthand to write proteins: Represented by the 3-letter or one-letter abbreviation Peptide naming: No part of this material may be reproduced, stored in a retrieval system or transmitted in any form or by any means – electronic, mechanical, photocopying, recording or otherwise, without permission in writing from the author or lecturer.  COLLEGE OF LIBERAL ARTS, SCIENCES & EDUCATION Calayan Educational Foundation, Inc. No part of this material may be reproduced, stored in a retrieval system or transmitted in any form or by any means – electronic, mechanical, photocopying, recording or otherwise, without permission in writing from the author or lecturer.  COLLEGE OF LIBERAL ARTS, SCIENCES & EDUCATION Calayan Educational Foundation, Inc. No part of this material may be reproduced, stored in a retrieval system or transmitted in any form or by any means – electronic, mechanical, photocopying, recording or otherwise, without permission in writing from the author or lecturer.  COLLEGE OF LIBERAL ARTS, SCIENCES & EDUCATION Calayan Educational Foundation, Inc. No part of this material may be reproduced, stored in a retrieval system or transmitted in any form or by any means – electronic, mechanical, photocopying, recording or otherwise, without permission in writing from the author or lecturer.  COLLEGE OF LIBERAL ARTS, SCIENCES & EDUCATION Calayan Educational Foundation, Inc. SECONDARY STRUCTURE the spatial arrangement of protein by twisting of the polypeptide chain No part of this material may be reproduced, stored in a retrieval system or transmitted in any form or by any means – electronic, mechanical, photocopying, recording or otherwise, without permission in writing from the author or lecturer.  COLLEGE OF LIBERAL ARTS, SCIENCES & EDUCATION Calayan Educational Foundation, Inc. α-HELIX Proposed by Pauling and Corey (1951) Most common spiral structure of protein Has a rigid arrangement of polypeptide chain No part of this material may be reproduced, stored in a retrieval system or transmitted in any form or by any means – electronic, mechanical, photocopying, recording or otherwise, without permission in writing from the author or lecturer.  COLLEGE OF LIBERAL ARTS, SCIENCES & EDUCATION Calayan Educational Foundation, Inc. α-HELIX Tightly packed coiled structure with Each turn of α-helix amino acid side chains extending contains 3.6 amino outward from the central axis acids and travels a distance of 0.54 nm. Stabilized by extensive H-bonding The spacing of each formed between H atom attached to amino acid is 0.15 nm. peptide N, and O atom attached to peptide C α-Helix is a stable conformation formed All peptide bonds, except the first and spontaneously with last in a polypeptide chain, the lowest energy. participate in H-bonding No part of this material may be reproduced, stored in a retrieval system or transmitted in any form or by any means – electronic, mechanical, photocopying, recording or otherwise, without permission in writing from the author or lecturer.  COLLEGE OF LIBERAL ARTS, SCIENCES & EDUCATION Calayan Educational Foundation, Inc. β-PLEATED SHEET Proposed by Pauling and Corey β-Pleated sheets (β-sheets) are composed of two or more segments of fully extended peptide chains H-bonds are formed between the neighboring segments of polypeptide chains May be parallel or anti-parallel No part of this material may be reproduced, stored in a retrieval system or transmitted in any form or by any means – electronic, mechanical, photocopying, recording or otherwise, without permission in writing from the author or lecturer.  COLLEGE OF LIBERAL ARTS, SCIENCES & EDUCATION Calayan Educational Foundation, Inc. SECONDARY STRUCTURE No part of this material may be reproduced, stored in a retrieval system or transmitted in any form or by any means – electronic, mechanical, photocopying, recording or otherwise, without permission in writing from the author or lecturer.  COLLEGE OF LIBERAL ARTS, SCIENCES & EDUCATION Calayan Educational Foundation, Inc. TERTIARY STRUCTURE the three-dimensional structure of a functional protein No part of this material may be reproduced, stored in a retrieval system or transmitted in any form or by any means – electronic, mechanical, photocopying, recording or otherwise, without permission in writing from the author or lecturer.  COLLEGE OF LIBERAL ARTS, SCIENCES & EDUCATION Calayan Educational Foundation, Inc. TERTIARY STRUCTURE No part of this material may be reproduced, stored in a retrieval system or transmitted in any form or by any means – electronic, mechanical, photocopying, recording or otherwise, without permission in writing from the author or lecturer.  COLLEGE OF LIBERAL ARTS, SCIENCES & EDUCATION Calayan Educational Foundation, Inc. QUATERNARY STRUCTURE Some of the proteins are composed of two or more polypeptide chains referred to as subunits. No part of this material may be reproduced, stored in a retrieval system or transmitted in any form or by any means – electronic, mechanical, photocopying, recording or otherwise, without permission in writing from the author or lecturer.  COLLEGE OF LIBERAL ARTS, SCIENCES & EDUCATION Calayan Educational Foundation, Inc. QUATERNARY STRUCTURE Hemoglobin Lactate Aspartate dehydrogenase No part of this material may be reproduced, stored in a retrieval systemtranscarbomylase or transmitted in any form or by any means – electronic, mechanical, photocopying, recording or otherwise, without permission in writing from the author or lecturer.  COLLEGE OF LIBERAL ARTS, SCIENCES & EDUCATION Calayan Educational Foundation, Inc. HIERARCHY OF PROTEIN STRUCTURE No part of this material may be reproduced, stored in a retrieval system or transmitted in any form or by any means – electronic, mechanical, photocopying, recording or otherwise, without permission in writing from the author or lecturer.  COLLEGE OF LIBERAL ARTS, SCIENCES & EDUCATION Calayan Educational Foundation, Inc. CLASSIFICATION OF PROTEINS Based on function Based on chemical nature and solubility Based on nutrition No part of this material may be reproduced, stored in a retrieval system or transmitted in any form or by any means – electronic, mechanical, photocopying, recording or otherwise, without permission in writing from the author or lecturer.  COLLEGE OF LIBERAL ARTS, SCIENCES & EDUCATION Calayan Educational Foundation, Inc. BASED ON FUNCTION Structural Enzymes or Genetic Catalytic Storage Transport Contractile Hormonal No part of this material may be reproduced, stored in a retrieval system or transmitted in any form or by any means – electronic, mechanical, photocopying, recording or otherwise, without permission in writing from the author or lecturer.  COLLEGE OF LIBERAL ARTS, SCIENCES & EDUCATION Calayan Educational Foundation, Inc. BASED ON CHEMICAL NATURE AND SOLUBILITY No part of this material may be reproduced, stored in a retrieval system or transmitted in any form or by any means – electronic, mechanical, photocopying, recording or otherwise, without permission in writing from the author or lecturer.  COLLEGE OF LIBERAL ARTS, SCIENCES & EDUCATION Calayan Educational Foundation, Inc. S I M P L E P R O T E I N S Subclasses Solubility Other properties and functions Examples Albumins Soluble in water and in dilute aqueous Coagulated by heat and usually Egg albumin, myogen of muscle, serum solution deficient in glycine albumin of blood, leucosin of wheat, lactalbumin of milk and legumelin of peas Globulins Soluble in dilute salt solutions but are Coagulated by heat and generally Ovoglobulin of egg yolk, serum globulin of insoluble (euglobulins) or sparingly soluble contain glycine blood, myosin of muscle, edestin of hemp (pseudoglobulins) in water seed, phaseolin of beans, legumin of peas, excelsin of brazil nuts, arachin of peanuts and amandin of almonds Glutelins Insoluble in neutral solvents but are Occur only in plants Glutenin of wheat and oryzenin of rice soluble in dilute solutions of acids and bases Prolamins Insoluble in most ordinary solvents like Entirely animal proteins and are chief Keratins of hair, hoofs, horn, nails; elastin water, salt solutions, dilute acids, alkalies constituents of exoskeletal structures, of connective tissue and ligaments; and alcohols supporting and connecting fibrous collagen of bones, cartilage and tendons; tissues and organic materials of fibroin and sericin of silk cartilage and bones Scleroproteins Soluble in 70-80% alcohol (others in 50- Generally yield much proline upon Zein of corn, hordein of barley, gliadin of or Albuminoids 90%); insoluble in water, neutral solvents hydrolysis but are deficient in lysine; wheat and kafirin of kafir corn or may No part of this material absolute alcoholstored in a retrieval system or transmitted be reproduced, plant protein found in any form or by principally in any means – electronic, mechanical, photocopying, recording or otherwise, without permission in writing from the author or lecturer. seeds  COLLEGE OF LIBERAL ARTS, SCIENCES & EDUCATION Calayan Educational Foundation, Inc. CONJ UGATED PROTEI NS Subclasses Occurrence Prosthetic group Examples Nucleoproteins Most abundant in both plant and animal tissues Nucleic acids Nucleohistone and that have a large proportion of nuclear materials nucleoprotamine such as yeasts, asparagus tips, thymus and sperm Glycoproteins Many membrane proteins and most proteins Carbohydrates Immunoglobulin G secreted by eukaryotic cells like antibodies Lipoproteins Phospholipid protein complexes (also called Lipids β1-Lipoprotein of blood lecithoproteins) are widely found in animals and plants. Materials such as milk, blood, cell nuclei, egg yolk, cell membrane and chloroplasts; also found in bacterial antigen and viruses Phosphoproteins Phosphate groups Casein from milk and vitellin from egg yolk Hemoproteins Heme (Iron porphyrin) Hemoglobins, cytochromes, catalase, peroxidase Flavoproteins Flavin nucleotides Succinate dehydrogenase Metalloproteins Metal No part of this material may be reproduced, stored in a retrieval system or transmitted in any form ions, or by any iron, means coppermechanical, photocopying, – electronic, Ferritin, plastocyanin recording or otherwise, without permission in writing from the author or lecturer.  COLLEGE OF LIBERAL ARTS, SCIENCES & EDUCATION Calayan Educational Foundation, Inc. BASED ON NUTRITION Complete proteins Partially Incomplete incomplete proteins proteins No part of this material may be reproduced, stored in a retrieval system or transmitted in any form or by any means – electronic, mechanical, photocopying, recording or otherwise, without permission in writing from the author or lecturer.  COLLEGE OF LIBERAL ARTS, SCIENCES & EDUCATION Calayan Educational Foundation, Inc. DENATURATION No part of this material may be reproduced, stored in a retrieval system or transmitted in any form or by any means – electronic, mechanical, photocopying, recording or otherwise, without permission in writing from the author or lecturer.  COLLEGE OF LIBERAL ARTS, SCIENCES & EDUCATION Calayan Educational Foundation, Inc. NATIVE STRUCTURE – certain identifying properties of a protein (biological, enzymatic, solubility, ionic, reactivity of side group, MW and size) Any change in the native structure results in DENATURATION, brought about by disruption of forces that stabilize the secondary, tertiary and quaternary structures. No part of this material may be reproduced, stored in a retrieval system or transmitted in any form or by any means – electronic, mechanical, photocopying, recording or otherwise, without permission in writing from the author or lecturer. Evolve. Adapt. Overcome. CEFI is now ready. Thank you for listening!