Amino acids are the building blocks of proteins. They contain an alpha carbon atom bonded to an amino group, a carboxyl group, and a side chain specific to each amino acid. There are 20 standard amino acids, of which 9 are essential and must be obtained through diet. Amino acids can be classified based on properties like polarity, acid-base behavior, and capacity to interact with water. They play important roles in enzymatic reactions and protein structure due to these varying properties. As zwitterions, amino acids have buffering effects and undergo changes in charge depending on environmental pH.
This document discusses the acid-base properties of amino acids and their behavior during titration. It explains that amino acids contain both a carboxylic acid group and an amine group, making them amphoteric. Depending on the pH:
1. At low pH, amino acids exist as cations with two protons.
2. At intermediate pH, they exist as zwitterions with one proton.
3. At high pH, they exist as anions with no protons.
The isoelectric point is the pH at which the net charge is zero. Amino acids can also act as buffers near the pKa values of their carboxyl and amine groups.
Amino acids are organic compounds that contain an amine group, a carboxyl group, and a side chain specific to each amino acid. They are made up of carbon, hydrogen, oxygen, and nitrogen. Amino acids can exist as zwitterions that have both positive and negative charges at their isoelectric pH point, making them electrically neutral. Their physical properties, such as solubility, melting point, taste, and optical activity, depend on their specific structure and side chain.
This document discusses aromatic amines and their properties and synthesis. It defines aromatic amines as those where nitrogen is attached directly to an aromatic ring. It notes that aromatic amines are less basic than aliphatic amines due to resonance stabilization of the aromatic ring. Several methods for synthesizing aromatic amines are described, including reduction of nitrobenzene, reductive amination of carbonyl groups, and reduction of nitriles. The Hofmann rearrangement, which converts a primary amide to a primary amine, is also summarized.
This document provides an overview of acid-base theories and properties. It covers the Bronsted-Lowry and Lewis theories of acids and bases. It defines strong and weak acids and bases, and how their strength affects properties like conductivity and reaction rate. It also introduces the pH scale and explains how pH is determined by the concentration of hydrogen ions in solution.
An aliphatic amine has no aromatic ring attached directly to the nitrogen atom. Aromatic amines have the nitrogen atom connected to an aromatic ring as in the various anilines. The aromatic ring decreases the alkalinity of the amine, depending on its substituents. The presence of an amine group strongly increases the reactivity of the aromatic ring, due to an electron-donating effect.
Amines are organized into four subcategories:
Primary amines—Primary amines arise when one of three hydrogen atoms in ammonia is replaced by an alkyl or aromatic. Important primary alkyl amines include, methylamine, most amino acids, and the buffering agent tris, while primary aromatic amines include aniline.
Secondary amines—Secondary amines have two organic substituents (alkyl, aryl or both) bound to the nitrogen together with one hydrogen. Important representatives include dimethylamine, while an example of an aromatic amine would be diphenylamine.
Tertiary amines—In tertiary amines, nitrogen has three organic substituents. Examples include trimethylamine, which has a distinctively fishy smell, and EDTA.
Cyclic amines—Cyclic amines are either secondary or tertiary amines. Examples of cyclic amines include the 3-membered ring aziridine and the six-membered ring piperidine. N-methylpiperidine and N-phenylpiperidine are examples of cyclic tertiary amines.
It is also possible to have four organic substituents on the nitrogen. These species are not amines but are quaternary ammonium cations and have a charged nitrogen center. Quaternary ammonium salts exist with many kinds of anions.
The document provides an overview of key topics in biochemistry including energy from food, proteins, carbohydrates, lipids, and nucleic acids. Specifically, it discusses how calorimetry can be used to determine the energy content of foods, the structures and functions of amino acids, proteins, carbohydrates like glucose and starch, and lipid molecules like triglycerides. It also briefly outlines analysis techniques for proteins like chromatography and electrophoresis. The document serves as an introductory guide to understanding the basic building blocks and energy sources in living organisms.
Relative strengths of acids and bases, pH scale, pH of weak acids and bases, degree of hydrolysis and hydrolysis constant, buffer equation, buffer capacity, buffer in pharmaceutical and biological systems, buffered isotonic solutions, methods of adjusting tonicity and pH, application of pH, buffer and salt hydrolysis in pharmacy.
This document discusses acid-base homeostasis and balance. It explains that acid-base homeostasis involves chemical and physiological processes that maintain the acidity of body fluids at levels that allow optimal body function. These processes include extracellular and intracellular buffers as the first line of defense against acid or base loads, as well as changes in cellular metabolism and excretion of acids by the lungs and kidneys. Derangements in hydrogen and bicarbonate ion concentrations are common in disease and acid-base balance is primarily concerned with regulating these two ions to maintain pH within a narrow normal range.
This document discusses the acid-base properties of amino acids and their behavior during titration. It explains that amino acids contain both a carboxylic acid group and an amine group, making them amphoteric. Depending on the pH:
1. At low pH, amino acids exist as cations with two protons.
2. At intermediate pH, they exist as zwitterions with one proton.
3. At high pH, they exist as anions with no protons.
The isoelectric point is the pH at which the net charge is zero. Amino acids can also act as buffers near the pKa values of their carboxyl and amine groups.
Amino acids are organic compounds that contain an amine group, a carboxyl group, and a side chain specific to each amino acid. They are made up of carbon, hydrogen, oxygen, and nitrogen. Amino acids can exist as zwitterions that have both positive and negative charges at their isoelectric pH point, making them electrically neutral. Their physical properties, such as solubility, melting point, taste, and optical activity, depend on their specific structure and side chain.
This document discusses aromatic amines and their properties and synthesis. It defines aromatic amines as those where nitrogen is attached directly to an aromatic ring. It notes that aromatic amines are less basic than aliphatic amines due to resonance stabilization of the aromatic ring. Several methods for synthesizing aromatic amines are described, including reduction of nitrobenzene, reductive amination of carbonyl groups, and reduction of nitriles. The Hofmann rearrangement, which converts a primary amide to a primary amine, is also summarized.
This document provides an overview of acid-base theories and properties. It covers the Bronsted-Lowry and Lewis theories of acids and bases. It defines strong and weak acids and bases, and how their strength affects properties like conductivity and reaction rate. It also introduces the pH scale and explains how pH is determined by the concentration of hydrogen ions in solution.
An aliphatic amine has no aromatic ring attached directly to the nitrogen atom. Aromatic amines have the nitrogen atom connected to an aromatic ring as in the various anilines. The aromatic ring decreases the alkalinity of the amine, depending on its substituents. The presence of an amine group strongly increases the reactivity of the aromatic ring, due to an electron-donating effect.
Amines are organized into four subcategories:
Primary amines—Primary amines arise when one of three hydrogen atoms in ammonia is replaced by an alkyl or aromatic. Important primary alkyl amines include, methylamine, most amino acids, and the buffering agent tris, while primary aromatic amines include aniline.
Secondary amines—Secondary amines have two organic substituents (alkyl, aryl or both) bound to the nitrogen together with one hydrogen. Important representatives include dimethylamine, while an example of an aromatic amine would be diphenylamine.
Tertiary amines—In tertiary amines, nitrogen has three organic substituents. Examples include trimethylamine, which has a distinctively fishy smell, and EDTA.
Cyclic amines—Cyclic amines are either secondary or tertiary amines. Examples of cyclic amines include the 3-membered ring aziridine and the six-membered ring piperidine. N-methylpiperidine and N-phenylpiperidine are examples of cyclic tertiary amines.
It is also possible to have four organic substituents on the nitrogen. These species are not amines but are quaternary ammonium cations and have a charged nitrogen center. Quaternary ammonium salts exist with many kinds of anions.
The document provides an overview of key topics in biochemistry including energy from food, proteins, carbohydrates, lipids, and nucleic acids. Specifically, it discusses how calorimetry can be used to determine the energy content of foods, the structures and functions of amino acids, proteins, carbohydrates like glucose and starch, and lipid molecules like triglycerides. It also briefly outlines analysis techniques for proteins like chromatography and electrophoresis. The document serves as an introductory guide to understanding the basic building blocks and energy sources in living organisms.
Relative strengths of acids and bases, pH scale, pH of weak acids and bases, degree of hydrolysis and hydrolysis constant, buffer equation, buffer capacity, buffer in pharmaceutical and biological systems, buffered isotonic solutions, methods of adjusting tonicity and pH, application of pH, buffer and salt hydrolysis in pharmacy.
This document discusses acid-base homeostasis and balance. It explains that acid-base homeostasis involves chemical and physiological processes that maintain the acidity of body fluids at levels that allow optimal body function. These processes include extracellular and intracellular buffers as the first line of defense against acid or base loads, as well as changes in cellular metabolism and excretion of acids by the lungs and kidneys. Derangements in hydrogen and bicarbonate ion concentrations are common in disease and acid-base balance is primarily concerned with regulating these two ions to maintain pH within a narrow normal range.
The document summarizes key concepts in aromatic substitution reactions. It describes the electrophilic aromatic substitution mechanism where an electrophile such as the nitronium ion attacks the aromatic ring. It outlines different electrophiles used such as halogens, acyl groups, and alkyl groups. It discusses the effects of different substituents on the ring in terms of their electronic properties as either activating or deactivating groups, and whether they are ortho/para or meta directors. Examples of industrially important aromatic compounds formed by substitution reactions are also mentioned, such as TNT.
This document discusses weak bases and how they react with water to form the conjugate acid and hydroxide ions. It defines the base dissociation constant Kb and explains how it refers to the equilibrium of a base reacting with water. It provides examples of calculating the concentration of hydroxide ions produced from a weak base solution and calculating Kb or Ka values for conjugate acid-base pairs using known constants. The document also discusses how the properties of salt solutions are determined by the constituent ions and how buffers resist changes in pH upon addition of acids or bases.
This document discusses alcohols, phenols, and ethers. It defines these compounds and describes their structures. Alcohols contain a hydroxyl group bonded to carbon, while phenols have a hydroxyl group bonded to an aromatic carbon. Ethers have an alkoxy or aryloxy group in place of a hydrogen. The document classifies these compounds based on the number and position of functional groups. It also discusses their naming conventions, physical properties, bonding, and methods of synthesis.
This document discusses amines, including their classification, preparation methods, physical and chemical properties, and reactions. Amines are derivatives of ammonia where hydrogen atoms are replaced by alkyl groups. They are prepared through reduction of nitro compounds, ammonolysis of alkyl halides, reduction of nitriles or amides, and other methods. Amines are basic due to the lone pair on the nitrogen. Primary and secondary amines are more basic than tertiary amines due to solvation effects. Aromatic amines are less basic than alkyl amines. Amines undergo reactions such as acylation, carbylamine formation, and electrophilic aromatic substitution.
1. Carboxyl derivatives such as acid chlorides, anhydrides, esters, amides, and nitriles undergo nucleophilic acyl substitution or hydrolysis reactions depending on conditions.
2. Acid chlorides undergo substitution readily due to the good leaving ability of the chloride ion. Esters hydrolyze slowly in water but more readily with acid or base via addition-elimination mechanisms.
3. Amides hydrolyze in acidic conditions through a resonance-stabilized cation intermediate or in basic conditions via a dianion intermediate to give carboxylic acids. Nitriles hydrolyze to carboxylic acids or amides.
The NO2 group attached with organic chain is called as nitro functional group. All the compounds containing the nitro functional group are called as organic nitro compounds.
This document discusses various methods for preparing carboxylic acids, including the oxidation of primary alcohols, hydrolysis of nitriles, reaction of Grignard reagents with carbon dioxide, hydrolysis of esters, and the malonic ester synthesis. The malonic ester synthesis involves treating malonic ester with sodium ethoxide to form its salt, then reacting the salt with an alkyl halide to form a dialkyl malonic ester which decarboxylates to form a substituted acetic acid. Important carboxylic acids like acetic and benzoic acid are prepared industrially using these oxidation, nitrile hydrolysis, and substitution reactions.
Chemistry of aromatic amines, Classification of amines, Preparation, reactions of amines, synthetic uses of aromatic amines, basicity of aromatic amines and factor affecting basicity amine.
1. This chapter discusses five classes of organic compounds derived from carboxylic acids: acid chlorides, acid anhydrides, esters, amides, and nitriles.
2. These derivatives are formed by replacing functional groups on the carboxyl group of carboxylic acids, such as replacing the hydroxyl group with a chlorine in acid chlorides or a double bonded oxygen in anhydrides.
3. The compounds are named based on the parent carboxylic acid and the functional group replacing the hydroxyl group, such as naming benzoic anhydride from benzoic acid or ethyl ethanoate from ethanoic acid.
PHENOL INTRODUCTION, REACTIVITY, ACIDITY, FACTOR AFFECTING ON ACIDITY, PREPARATION, REACTION,COMPARISON OF ACIDITY WITH ALCOHOL AND ACID, USES OF PHENOL, CRESOL, RESORCINOL, NAPTHOL
The document discusses the classification, nomenclature, properties, preparation, and reactions of amines. Amines are classified as primary, secondary, or tertiary depending on the number of alkyl or aryl groups bonded to the nitrogen atom. They are further divided into aliphatic, aromatic, and heterocyclic amines. Amines are named according to IUPAC nomenclature rules. They are weak bases due to resonance stabilization of the conjugate acid. Common methods for preparing amines include reduction of nitriles, amides, imines, and nitro compounds. Amines react with acids to form water-soluble salts and with nitrous acid to undergo proton-transfer and electrophilic aromatic substitution reactions.
This document discusses phenols, including their:
- Classification into simple phenols, monohydric phenols, dihydric phenols, and trihydric phenols
- Nomenclature and physico-chemical properties such as acidity, hydrogen bonding, and effect of substituents on acidity
- Preparation methods like hydrolysis of diazonium salts, alkali fusion of sulfonates
- Reactions including acidity/salt formation, ester formation, ring substitution, and reactions with formaldehyde
- Qualitative tests for phenols using ferric chloride and Libermann reaction
- Uses of phenol, o-cresol, resorcinol, and
This document discusses the properties and reactions of amines. It defines amines as organic derivatives of ammonia with one or more alkyl or aryl groups bonded to the nitrogen atom. Amines are classified as primary, secondary, or tertiary depending on the number of alkyl or aryl groups attached to the nitrogen. The document discusses nomenclature, physical properties, basicity, reactions including salt formation and reactions with acids, and uses of amines such as in the synthesis of nylon and azo dyes.
This document discusses the classification, nomenclature, physical properties, synthesis, and reactions of alcohols. Alcohols are classified based on the carbon chain containing the hydroxyl group as primary, secondary, or tertiary. They can be synthesized by hydrolysis of alkyl halides, fermentation of sugars, or oxidation of aldehydes or alkenes. Common reactions include forming esters, undergoing halogenation with HX, and being oxidized to carbonyl compounds.
Lithium aluminium hydride (LAH) is a strong reducing agent that is commonly used to reduce carbonyl groups, esters, amides, nitriles, epoxides, lactones, and haloalkanes/haloarenes. LAH is prepared through the reaction of lithium hydride with aluminum chloride. It is a white solid that reacts violently with water, producing hydrogen gas, so reactions must be performed under anhydrous conditions. The mechanism of LAH involves nucleophilic hydride attack on the carbonyl carbon to form an intermediate tetrahedral structure.
1) Amines act as bases according to both Lewis and Bronsted-Lowry theories due to their ability to donate a lone pair of electrons or accept a proton.
2) The basicity of amines depends on factors such as the stability of the conjugate acid formed, inductive effects, and hydrogen bonding capabilities. In general, aliphatic amines are stronger bases than aromatic amines.
3) Within aliphatic amines, the order of basicity from strongest to weakest is typically tertiary > secondary > primary > ammonia in the gas phase. In aqueous solution, primary amines are stronger bases due to hydrogen bonding of the conjugate acid form.
The document summarizes various chemical reactions of alcohols and phenols. It discusses alcohols and phenols acting as acids and undergoing reactions like esterification, reactions involving cleavage of C-O and O-H bonds, dehydration, oxidation, and reactions of phenols including electrophilic aromatic substitution, halogenation, nitration, and reduction/oxidation reactions. Phenols undergo similar reactions to alcohols but are more acidic due to resonance and substitution effects of the benzene ring.
Ionic equilibrium chapter 3(12th HSC Maharashtra state board)Freya Cardozo
The document discusses ionic equilibrium and acid-base theories. It provides examples of different types of salts based on the strength of acids and bases involved:
1) Salts of strong acids and bases, like NaCl, are neutral as they do not undergo hydrolysis.
2) Salts of strong acids and weak bases, like CuSO4, are acidic due to hydrolysis of the metal cation.
3) Salts of weak acids and strong bases, like CH3COONa, are basic due to hydrolysis of the anion.
4) Salts of weak acids and weak bases can be acidic, basic or neutral depending on whether the Ka or Kb is greater and the extent of hydro
The document contains information about 5 students' matric numbers and a passage discussing alkyl halides. It defines alkyl halides and describes their classification, nomenclature, physical properties, synthesis from alcohols and alkenes, and reactions including nucleophilic substitution and elimination. Examples are provided to illustrate key concepts and reaction mechanisms.
The document discusses several techniques for automated protein classification including ProtoMap and PRODISTIN. ProtoMap clusters proteins based on sequence similarity scores, while PRODISTIN clusters based on protein-protein interaction data. Both techniques have limitations as biological networks, such as protein and domain interaction networks, have been found to have scale-free topologies. Any improved protein classification algorithm needs to account for this scale-free network structure.
1) The study analyzed insertions of accessory domains in the haloalkanoic dehalogenase superfamily (HADSF) to understand the effects on the core Rossmann fold structure.
2) Structural similarity networks revealed that sequences with the same inserted domain type shared greater core structure similarity compared to different domain types.
3) Variation in the core structure occurred in alpha helices flanking the central beta sheet, rather than at the core-domain interface, suggesting independent divergence of core and inserted domains during evolution.
The document summarizes key concepts in aromatic substitution reactions. It describes the electrophilic aromatic substitution mechanism where an electrophile such as the nitronium ion attacks the aromatic ring. It outlines different electrophiles used such as halogens, acyl groups, and alkyl groups. It discusses the effects of different substituents on the ring in terms of their electronic properties as either activating or deactivating groups, and whether they are ortho/para or meta directors. Examples of industrially important aromatic compounds formed by substitution reactions are also mentioned, such as TNT.
This document discusses weak bases and how they react with water to form the conjugate acid and hydroxide ions. It defines the base dissociation constant Kb and explains how it refers to the equilibrium of a base reacting with water. It provides examples of calculating the concentration of hydroxide ions produced from a weak base solution and calculating Kb or Ka values for conjugate acid-base pairs using known constants. The document also discusses how the properties of salt solutions are determined by the constituent ions and how buffers resist changes in pH upon addition of acids or bases.
This document discusses alcohols, phenols, and ethers. It defines these compounds and describes their structures. Alcohols contain a hydroxyl group bonded to carbon, while phenols have a hydroxyl group bonded to an aromatic carbon. Ethers have an alkoxy or aryloxy group in place of a hydrogen. The document classifies these compounds based on the number and position of functional groups. It also discusses their naming conventions, physical properties, bonding, and methods of synthesis.
This document discusses amines, including their classification, preparation methods, physical and chemical properties, and reactions. Amines are derivatives of ammonia where hydrogen atoms are replaced by alkyl groups. They are prepared through reduction of nitro compounds, ammonolysis of alkyl halides, reduction of nitriles or amides, and other methods. Amines are basic due to the lone pair on the nitrogen. Primary and secondary amines are more basic than tertiary amines due to solvation effects. Aromatic amines are less basic than alkyl amines. Amines undergo reactions such as acylation, carbylamine formation, and electrophilic aromatic substitution.
1. Carboxyl derivatives such as acid chlorides, anhydrides, esters, amides, and nitriles undergo nucleophilic acyl substitution or hydrolysis reactions depending on conditions.
2. Acid chlorides undergo substitution readily due to the good leaving ability of the chloride ion. Esters hydrolyze slowly in water but more readily with acid or base via addition-elimination mechanisms.
3. Amides hydrolyze in acidic conditions through a resonance-stabilized cation intermediate or in basic conditions via a dianion intermediate to give carboxylic acids. Nitriles hydrolyze to carboxylic acids or amides.
The NO2 group attached with organic chain is called as nitro functional group. All the compounds containing the nitro functional group are called as organic nitro compounds.
This document discusses various methods for preparing carboxylic acids, including the oxidation of primary alcohols, hydrolysis of nitriles, reaction of Grignard reagents with carbon dioxide, hydrolysis of esters, and the malonic ester synthesis. The malonic ester synthesis involves treating malonic ester with sodium ethoxide to form its salt, then reacting the salt with an alkyl halide to form a dialkyl malonic ester which decarboxylates to form a substituted acetic acid. Important carboxylic acids like acetic and benzoic acid are prepared industrially using these oxidation, nitrile hydrolysis, and substitution reactions.
Chemistry of aromatic amines, Classification of amines, Preparation, reactions of amines, synthetic uses of aromatic amines, basicity of aromatic amines and factor affecting basicity amine.
1. This chapter discusses five classes of organic compounds derived from carboxylic acids: acid chlorides, acid anhydrides, esters, amides, and nitriles.
2. These derivatives are formed by replacing functional groups on the carboxyl group of carboxylic acids, such as replacing the hydroxyl group with a chlorine in acid chlorides or a double bonded oxygen in anhydrides.
3. The compounds are named based on the parent carboxylic acid and the functional group replacing the hydroxyl group, such as naming benzoic anhydride from benzoic acid or ethyl ethanoate from ethanoic acid.
PHENOL INTRODUCTION, REACTIVITY, ACIDITY, FACTOR AFFECTING ON ACIDITY, PREPARATION, REACTION,COMPARISON OF ACIDITY WITH ALCOHOL AND ACID, USES OF PHENOL, CRESOL, RESORCINOL, NAPTHOL
The document discusses the classification, nomenclature, properties, preparation, and reactions of amines. Amines are classified as primary, secondary, or tertiary depending on the number of alkyl or aryl groups bonded to the nitrogen atom. They are further divided into aliphatic, aromatic, and heterocyclic amines. Amines are named according to IUPAC nomenclature rules. They are weak bases due to resonance stabilization of the conjugate acid. Common methods for preparing amines include reduction of nitriles, amides, imines, and nitro compounds. Amines react with acids to form water-soluble salts and with nitrous acid to undergo proton-transfer and electrophilic aromatic substitution reactions.
This document discusses phenols, including their:
- Classification into simple phenols, monohydric phenols, dihydric phenols, and trihydric phenols
- Nomenclature and physico-chemical properties such as acidity, hydrogen bonding, and effect of substituents on acidity
- Preparation methods like hydrolysis of diazonium salts, alkali fusion of sulfonates
- Reactions including acidity/salt formation, ester formation, ring substitution, and reactions with formaldehyde
- Qualitative tests for phenols using ferric chloride and Libermann reaction
- Uses of phenol, o-cresol, resorcinol, and
This document discusses the properties and reactions of amines. It defines amines as organic derivatives of ammonia with one or more alkyl or aryl groups bonded to the nitrogen atom. Amines are classified as primary, secondary, or tertiary depending on the number of alkyl or aryl groups attached to the nitrogen. The document discusses nomenclature, physical properties, basicity, reactions including salt formation and reactions with acids, and uses of amines such as in the synthesis of nylon and azo dyes.
This document discusses the classification, nomenclature, physical properties, synthesis, and reactions of alcohols. Alcohols are classified based on the carbon chain containing the hydroxyl group as primary, secondary, or tertiary. They can be synthesized by hydrolysis of alkyl halides, fermentation of sugars, or oxidation of aldehydes or alkenes. Common reactions include forming esters, undergoing halogenation with HX, and being oxidized to carbonyl compounds.
Lithium aluminium hydride (LAH) is a strong reducing agent that is commonly used to reduce carbonyl groups, esters, amides, nitriles, epoxides, lactones, and haloalkanes/haloarenes. LAH is prepared through the reaction of lithium hydride with aluminum chloride. It is a white solid that reacts violently with water, producing hydrogen gas, so reactions must be performed under anhydrous conditions. The mechanism of LAH involves nucleophilic hydride attack on the carbonyl carbon to form an intermediate tetrahedral structure.
1) Amines act as bases according to both Lewis and Bronsted-Lowry theories due to their ability to donate a lone pair of electrons or accept a proton.
2) The basicity of amines depends on factors such as the stability of the conjugate acid formed, inductive effects, and hydrogen bonding capabilities. In general, aliphatic amines are stronger bases than aromatic amines.
3) Within aliphatic amines, the order of basicity from strongest to weakest is typically tertiary > secondary > primary > ammonia in the gas phase. In aqueous solution, primary amines are stronger bases due to hydrogen bonding of the conjugate acid form.
The document summarizes various chemical reactions of alcohols and phenols. It discusses alcohols and phenols acting as acids and undergoing reactions like esterification, reactions involving cleavage of C-O and O-H bonds, dehydration, oxidation, and reactions of phenols including electrophilic aromatic substitution, halogenation, nitration, and reduction/oxidation reactions. Phenols undergo similar reactions to alcohols but are more acidic due to resonance and substitution effects of the benzene ring.
Ionic equilibrium chapter 3(12th HSC Maharashtra state board)Freya Cardozo
The document discusses ionic equilibrium and acid-base theories. It provides examples of different types of salts based on the strength of acids and bases involved:
1) Salts of strong acids and bases, like NaCl, are neutral as they do not undergo hydrolysis.
2) Salts of strong acids and weak bases, like CuSO4, are acidic due to hydrolysis of the metal cation.
3) Salts of weak acids and strong bases, like CH3COONa, are basic due to hydrolysis of the anion.
4) Salts of weak acids and weak bases can be acidic, basic or neutral depending on whether the Ka or Kb is greater and the extent of hydro
The document contains information about 5 students' matric numbers and a passage discussing alkyl halides. It defines alkyl halides and describes their classification, nomenclature, physical properties, synthesis from alcohols and alkenes, and reactions including nucleophilic substitution and elimination. Examples are provided to illustrate key concepts and reaction mechanisms.
The document discusses several techniques for automated protein classification including ProtoMap and PRODISTIN. ProtoMap clusters proteins based on sequence similarity scores, while PRODISTIN clusters based on protein-protein interaction data. Both techniques have limitations as biological networks, such as protein and domain interaction networks, have been found to have scale-free topologies. Any improved protein classification algorithm needs to account for this scale-free network structure.
1) The study analyzed insertions of accessory domains in the haloalkanoic dehalogenase superfamily (HADSF) to understand the effects on the core Rossmann fold structure.
2) Structural similarity networks revealed that sequences with the same inserted domain type shared greater core structure similarity compared to different domain types.
3) Variation in the core structure occurred in alpha helices flanking the central beta sheet, rather than at the core-domain interface, suggesting independent divergence of core and inserted domains during evolution.
The document discusses several techniques for automated protein classification including ProtoMap and PRODISTIN. ProtoMap clusters proteins based on sequence similarity scores, while PRODISTIN clusters based on protein interaction data. Both have limitations as protein and domain interaction networks have been found to have scale-free topologies, violating assumptions of random network structures. Future protein classification algorithms need to account for this scale-free property to more accurately cluster proteins by function.
Generic approach for predicting unannotated protein pair function using proteinIAEME Publication
This document discusses several approaches for predicting protein function, including methods that use amino acid sequences, protein structures, genomic sequences, phylogenetic data, microarray expression data, and protein interaction networks. It provides details on each type of data source and summarizes common computational techniques used for protein function prediction, such as homology-based approaches, clustering-based approaches, and classification-based approaches.
This document contains an agenda for bioinformatics lessons covering various topics like biological databases, sequence similarity, sequence alignments, database searching, phylogenetics, protein structure, gene prediction, and bioinformatics applications in drug discovery. It also discusses ongoing bioinformatics research projects and ambitions to publish peer-reviewed work. Finally, it provides background on protein structure, levels of protein structure from primary to tertiary, and experimental methods like X-ray crystallography used to determine protein structures.
This document provides an overview of a lecture on membrane structure and ligand-gated ion channels. The first part of the lecture will discuss the lipid composition and forces that contribute to the stability of the lipid bilayer membrane environment that ion channels reside in. The second part will present ion channels that are gated by intracellular molecules like ATP and G proteins, as well as those gated by extracellular molecules like acetylcholine and glutamate. Learning objectives cover topics like lipid structure, membrane dynamics, protein-membrane interactions, and specific ion channel activation mechanisms.
Evolutionary relationship between diverse protein with similar domainjj_zein
This document discusses protein domains and their evolutionary relationship between diverse proteins. Protein domains are conserved parts of a protein sequence that determine structure and function. Domains act as compact, independently folding modules that provide specific catalytic and binding sites and serve as building blocks for large protein assemblies. Domains are found across different proteins and have been adapted through evolution, with some folds favored over others as they represent stable arrangements. Bioinformatics approaches like the Protein Data Bank and CATH classify protein structures into families and domains to better understand evolutionary relationships and comparisons between proteins.
The document discusses various topics in bioinformatics and protein structure. It provides an overview of ongoing thesis topics at Biobix including biomarker prediction, methylation, metabolomics, peptidomics, and more. It also discusses the rationale for understanding protein structure and function, levels of protein structure from primary to quaternary, methods for determining structure like X-ray crystallography, and approaches to secondary structure prediction including Chou-Fasman.
The document discusses amino acids and peptides. It provides information on:
1. The structure and properties of the 20 common amino acids found in proteins, including their ionization states and isoelectric points.
2. How amino acids can act as acids or bases depending on pH due to ionization of their carboxyl and amino groups.
3. The formation of peptide bonds between amino acids and how this leads to the creation of polypeptides and proteins of physiological significance.
Proteins are the most abundant organic molecules in living systems and are made up of polymers of amino acids. There are 20 standard amino acids that are commonly found in proteins across different life forms. Amino acids contain an amine group, a carboxyl group, and a variable R group that gives each amino acid its unique properties. Proteins perform important structural and functional roles in the body as enzymes, hormones, and structural components. They are made through the linking of amino acids through peptide bonds and can have various properties and classifications depending on the R groups present in each amino acid.
Principle of protein structure and functionAsheesh Pandey
The document discusses principles of protein structure, including primary, secondary, and tertiary structure. It covers amino acids and their properties, peptide bonds, and common structural elements like the alpha helix. Specifically, it defines primary structure as the amino acid sequence, discusses the 20 common amino acids and their characteristics like chirality. It also covers dihedral angles, Ramachandran plots, common secondary structures like the alpha helix and their properties, including hydrogen bonding patterns and characteristic phi and psi angles.
Proteins are composed of amino acids linked by peptide bonds. They have four levels of structure - primary, secondary, tertiary, and quaternary. The primary structure is the amino acid sequence. Secondary structures include alpha helices and beta sheets formed by hydrogen bonding. Tertiary structure is the overall 3D shape formed by interactions between secondary structures. Quaternary structure refers to the arrangement of multiple polypeptide subunits in a protein.
The document discusses amino acids, which are the building blocks of proteins. It describes that amino acids contain both an amino group and a carboxyl group and exist in different ionized forms depending on pH. There are 20 standard amino acids that make up proteins in humans. Amino acids can undergo various chemical reactions due to these functional groups and are also classified based on the polarity of their side chains.
The document discusses amino acids, which are the building blocks of proteins. It describes that amino acids contain both an amino group and a carboxyl group and exist in different ionized forms depending on pH. There are 20 standard amino acids that make up proteins in humans. Amino acids can undergo various chemical reactions due to these functional groups and are also classified based on the polarity of their side chains.
The document discusses amino acids, which are the building blocks of proteins. It describes that amino acids contain both an amino group and a carboxyl group and exist in different ionized forms depending on pH. There are 20 standard amino acids that make up proteins in humans. Amino acids can undergo various chemical reactions due to these functional groups and are also classified based on the polarity of their side chains.
Amino acids are organic compounds that contain amino and carboxyl groups. They are the building blocks of proteins. There are 20 standard amino acids that make up proteins. Amino acids can be classified based on their structure, including whether they are nonpolar, polar, or have other functional groups. The classification determines each amino acid's properties and role in protein structure and function. Some amino acids are essential to obtain through diet, while others can be synthesized in the body. Amino acids have optical activity, acid-base properties, and can absorb ultraviolet light depending on their structure. They generally exist as zwitterions at physiological pH.
Proteins are composed of amino acids linked by peptide bonds. There are four levels of protein structure: primary, secondary, tertiary, and quaternary. The primary structure is the linear sequence of amino acids. Secondary structures form based on hydrogen bonding patterns between amino acids. The two main secondary structures are the alpha helix, where amino acids coil into a helical shape, and the beta sheet, where amino acids align into beta strands connected by hydrogen bonds.
Proteins are composed of amino acids linked by peptide bonds. There are four levels of protein structure - primary, secondary, tertiary, and quaternary. The primary structure is the linear sequence of amino acids. The two most common types of secondary structure are the alpha helix and beta sheet. In an alpha helix, amino acid residues form a coil stabilized by hydrogen bonds between residues four places apart in the sequence. In a beta sheet, residues form extended zigzag patterns stabilized by hydrogen bonds between residues on adjacent strands running in parallel or anti-parallel directions.
Proteins are composed of amino acids linked by peptide bonds. They have four levels of structure - primary, secondary, tertiary, and quaternary. The primary structure is the amino acid sequence. Common secondary structures are alpha helices and beta sheets formed by hydrogen bonding between amino acids. Tertiary structure refers to the overall 3D structure formed from secondary structures. Quaternary structure involves interactions between multiple polypeptide subunits.
Detailed Amino acid structure, Zwitter ions, acid base properties of Amino acids, Chirality, L and D forms of amino acids,standard and non standard amino acids, Essential and non essential amino acids,Learn all amino acids, their properties in detail,methods to quantify amino acids
[Biochemistry 1] amphoteric properties of proteinsAtikah Jr.
Amino acids contain ionizable amino and carboxyl groups that allow them to act as both acids and bases depending on the pH of their environment, giving them amphoteric properties. As the pH changes, the amino acids exist in equilibrium between cationic and anionic states, sometimes simultaneously possessing both positive and negative charges within the same molecule, making them zwitterions. Their ability to donate or accept protons is responsible for amino acids functioning as acids or bases in biological systems.
There are 20 common amino acids that serve as the building blocks of proteins. Amino acids contain an amino group, a carboxyl group, and a variable side chain. They join together through peptide bonds to form polypeptides and proteins. Ten of the 20 amino acids are considered essential and must be obtained through diet as humans cannot synthesize them. Proteins perform a wide variety of important functions in the body.
Proteins are made up of amino acids and perform important functions in the body. They can act as enzymes, hormones, antibodies, and structures. Amino acids are the building blocks of proteins, containing an amino group, a carboxyl group, and an R group that determines their properties. Amino acids can be classified based on their R group, charge, and essential/nonessential status. Key amino acid properties include acid-base behavior, isoelectric point, and ability to form zwitterions. Common reactions used to identify amino acids include ninhydrin, FDNB, Dansyl, and Edman reactions.
amino acid structure and classification.pptAyman Abdo
This presentation the chemical structure of natural amino acids. It also classifies amino acids according to several criteria e.g., structure (aliphatic, aromatic, and heterocyclic amino acids), reaction (Neutral, acidic and basic amino acids), polarity (polar and nonpolar amino acids), and metabolic fate ( glucogenic, ketogenic and glucoketogenic amino acids)
This document discusses amino acids, which are organic compounds that contain amino and carboxyl groups and form proteins by binding together via peptide bonds. Amino acids are classified based on their structure, polarity, and nutritional requirements. There are essential and non-essential amino acids. Amino acids can undergo reactions like decarboxylation, amide formation, transamination, and oxidative deamination. They have amphoteric properties due to acidic and basic groups and exist as zwitterions at their isoelectric pH. Peptide bonds between amino acids are planar and rigid.
Amino acids are the units of proteins, and understanding its chemistry and the the properties assists in understanding the functions of proteins. This gives in an idea to why a certain protein behaves in a certain way.
Amino acids are the building blocks of proteins. They join together through peptide bonds to form polypeptide chains. There are over 300 amino acids but only 20 are commonly found in mammalian proteins. Amino acids have various roles like forming enzymes, hormones, antibodies and being precursors for other important molecules. They are amphoteric due to possessing both amino and carboxyl groups. Amino acids differ in their physical and chemical properties like color, solubility, isomerism and reactions.
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2. Protein are polymers of α-amino acids
•The amino acids used to make proteins are
2-aminocarboxylic acids.
•The α (alpha) carbon is the carbon to which a
functional group is attached.
3. Properties of amino acids:
•structure and chemical functionality
•chirality
•acid-base properties
•capacity to polymerize
4. Proteins in the Diet
9 of the 20 amino acids must be obtained from the
diet. These are referred to as the essential amino
acids.
– Histidine
– Isoleucine
– Leucine
– Lysine
– Methionine
– Phenylalanine
– Threonine
– Tryptophan
– Valine
Proteins are also the major source of nitrogen in the
diet
5.
6. Properties of amino acids:
•Aliphatic chains: Gly, Ala, Val, Leu, and Ile
Hydrophibicity
•Hydroxyl or sulfur side chains: Ser, Thr, Cys, Met
•Aromatic: Phe, Trp, Tyr
•Basic: His, Lys, Arg
•Acidic and their amides: Asp, Asn, Glu, Gln
7. Amino acids
• Classified according to their capacity to interact with
water
• 4 classes: NON POLAR, POLAR, ACIDIC AND BASIC
• Non polar amino acids contain hydrocarbon R groups
• R groups do not have (+) or (-) charges and interact
poorly with water
• 2 types of hydrocarbon chains: aliphatic and aromatic
8. • Non-Polar Side Chains:
• Side chains which have pure hydrocarbon alkyl groups
(alkane branches) or aromatic (benzene rings) are
non-polar. 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 non-polar than alanine; leucine is more
non-polar than valine.
9. Polar Side Chains:
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
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.
10. >
Example: Aspartic acid is more polar than serine because an
acid functional group is more polar than an alcohol group.
11. >
Example: Serine is more polar than tyrosine, since tyrosine
has the hydrocarbon benzene ring.
12. Acid - Base Properties of Amino Acids:
• Acidic Side Chains:
• 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
13. • Basic Side Chains:
• 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.
15. Hydrophobic Amino Acids (aromatic)
• all very
hydrophobic
•Some contain
aromatic group
•Absorb UV at
280 nm
16. Sulfur Containing Amino Acids
•Methionine (Met, M) – “start”
amino acid, very hydrophobic
•Cysteine (Cys,C) – sulfur in
form of sulfhydroyl, important
in disulfide linkages, weak acid,
can form hydrogen bonds.
17. Charged Amino Acids
• Asp and Glu are acidic amino
acids
•Contain carboxyl groups
Negatively charged at
physiological pH, present as
conjugatebases
•Hydrophillic nitrogenous bases
• Carboxyl groups function as
•Positively charged at
nucleophiles in some enzymatic
physiological pH
reactions
•Histidine – imidazole ring
protonated/ionized, only amino
acid that functions as buffer in
physiol range.
•Lysine - diamino acid,
protonated at pH 7.0
•Arginine - guianidinium ion
always protonated, most basic
amino acid
20. Classification of Amino Acids by Polarity
POLAR Acidic Neutral Basic
Asp Asn Ser Arg
Tyr Cys His
Glu Gln Thr Lys
Gly
POLAR
Ala Ile Phe Trp
NON-
Val Leu Met Pro
Polar or non-polar, it is the bases of the amino acid properties.
Juang RH (2003) Biochemistry
21. Functional significance
•Hydrophobic amino acids: encountered in the interior
of proteins shielded from direct contact with water
•Hydrophillic amino acids: generally found on the
exterior of proteins as well as in the active centers of
enzymes
•Imidazole group: act as either proton donor or
acceptor at physiological pH
– Reactive centers of enzymes
•Primary alcohol and thiol groups: act as nucleophiles
during enzymatic catalysis
– Disulfide bonds
22. Stereochemistry
• Note that the R group means that the α-carbon is a
chiral center. All natural amino acids are L-amino
acids.
23. L-Form Amino Acid Structure
Carboxylic group -
COO
Amino group
+
H3 N α H
H = Glycine
R group
CH3 = Alanine
Juang RH (2004) BCbasics
24. Mirror Images of Amino Acid
α Mirror
image
α
Same chemical properties
Stereo isomers
Juang RH (2004) BCbasics
25. THE ACID-BASE BEHAVIOUR OF AMINO ACIDS
• Amino acids are zwitterions:
• An amino acid has both a basic amine group
and an acidic carboxylic acid group.
26. • There is an internal transfer of a hydrogen ion
from the -COOH group to the -NH2 group to
leave an ion with both a negative charge and a
positive charge.
• This is called a zwitterion.
27. Adding an alkali to an amino acid solution
• increase the pH of a solution of an amino acid
by adding hydroxide ions, the hydrogen ion is
removed from the -NH3+ group
• The amino acid would be found to travel towards
the anode (the positive electrode).
28. Adding an acid to an amino acid solution
• decrease the pH by adding an acid to a
solution of an amino acid, the -COO- part of
the zwitterion picks up a hydrogen ion.
• the amino acid would move towards the
cathode (the negative electrode).
29. Shifting the pH from one extreme to the other
• Suppose you start with the ion we've just
produced under acidic conditions and slowly
add alkali to it.
• That ion contains two acidic hydrogens - the
one in the -COOH group and the one in the
-NH3+ group.
• The more acidic of these is the one in the
-COOH group, and so that is removed first -
and you get back to the zwitterion.
30. • So when you have added just the right amount
of alkali, the amino acid no longer has a net
positive or negative charge. That means that it
wouldn't move towards either the cathode or
anode during electrophoresis.
• The pH at which this lack of movement during
electrophoresis happens is known as the
isoelectric point of the amino acid. This pH
varies from amino acid to amino acid.
31. • If you go on adding hydroxide ions, you will
get the reaction we've already seen, in which
a hydrogen ion is removed from the -NH3+
group.
32. • You can, of course, reverse the whole process
by adding an acid to the ion we've just finished
up with.
• That ion contains two basic groups - the -NH 2
group and the -COO- group. The -NH2 group is
the stronger base, and so picks up hydrogen
ions first. That leads you back to the zwitterion
again.
33. • . . . and, of course, you can keep going by then
adding a hydrogen ion to the -COO- group.
34. Proton Is Adsorbed or Desorbed
Proton : abundant and small, affects the charge of a molecule
lone pair High Low
electrons pKa
H+
Amino N H H+ N H
H H
Low pKa High
O H O
Carboxylic C C H+
O O
Ampholyte contains both positive and negative groups on its molecule
Juang RH (2004) BCbasics
38. Buffer pH
Environment pH vs Protein Charge
10
9
8
7
Isoelectric point,
pI 6
5
4
3
+ 0 - -
Net Charge of a Protein
Juang RH (2004) BCbasics
39. H first Aspartic acid
HOOC-CH2-C-COOH +1
NH3+ Isoelectric point is the average
pK1 = 2.1 of the two pKa flanking the
zero net-charged form
second H 2.1 + 3.9
HOOC-CH2-C-COO- 0 2
= 3.0
NH3+
Isoelectric point
pK2 = 3.9
H -2
-
OOC-CH2-C-COO- -1 pK3
NH3+ third -1
pK2
pK3 = 9.8 0
H pK1
+1
-
OOC-CH2-C-COO- -2 [OH]
NH2
Juang RH (2004) BCbasics
40. Peptide bond formation:
• Polypeptides are linear polymers composed of amino
acids linked together by peptide bonds
• Peptide bonds are amide linkages formed when
unshared electron pair of α-carboxyl of another
amino acid
• When 2 amino acids reacted with one another, the
product is called a dipeptide.
• Therefore tripeptide contain 3 amino acid residues,
tetrapeptide 4 and so forth
41. Formation of Peptide Bonds by Dehydration
Amino acids are connected head to tail
NH2 1 COOH NH2 2 COOH
Carbodiimide Dehydration
-H2O
O
NH2 1 C N 2 COOH
H
Juang RH (2004) BCbasics
42.
43. • By convention, amino acid residue with free –NH2 group is
called N –terminal residue and is written to the left
• Free –COOH on C-terminal is written on the right. Peptides
are named by using their amino acid sequences beginning
from N-terminal residues,
• E.g:
H2N----Tyr----Ala----Cys----Gly----COOH
Above is a tetratpeptide named tyrosylalanylcysteinylglycine
44. Polypeptide backbone:
• Polypeptides are polymers composed of amino acids linked
together by peptide/amide bonds
• Order of amino acids in polypeptide is called amino acid
sequence
• Disulphide bridges formed by oxidation of Cys residues are an
important structural element in polypeptides and proteins
45. Peptides:
• Less complex than larger protein molecules have significant
biological activities
• E.g: Glutathione, Oxytocin, Vasopressin, substance P and
bradykinin
• Peptides are found in almost all organisms, involved in many
important biological processes:
-protein DNA synthesis
-Drug and environment toxin metabolism
-amino acid transport
-reducing agent (-SH group of cys) protects cells from
destructuve effects of oxidation by reacting with substances
such as peroxidase
46. Disulphide bond
• 2 cysteine - cystine ; 2 R-SH- R-S-S-R (+2H)
(Oxidation reaction)
- Intracellular conditions are maintained sufficiently reducing to
inhibit formation of most disulfide bonds
- Extracellular conditions (as well as those found in some
organelles) are more oxidizing, favouring disulphide formation
- Thus, extracellular proteins containing cysteines often have
disulfides, while intracellular (cytosolic) proteins rarely have
disulfides.
47. Detection, identificationand quantificaton
of amino acids and proteins
• Reaction between the thiol group of cysteine
and Ellman’s reagent
• Produce nitrothiobenzoate anion and since
this product adsorbs light at 410nm it provides
a route for quantifying protein concentration.
• Other reagents for estimating protein
concentration are: ninhydrin, fluorescamine,
dansyl chloride, nitrophenols and
fluorodinitrobenzene (all react with functional
groups)
48. Protein quantitation:
Quick and simple way of estimating protein cncentration
1. Spectrophotometric method at 280 nm using quartz
cuvettes, absorption mainly due to Trp and Tyr
2. Biuret reaction
3. Bradford method: widely used
4. BCA (Bichinchoninic acid)
5. Modified lowry assay
6. fluorescamine protein assay
Note: to understand the principle behind the reaction
used to determine protein concentration, also
sensitivity of method used (eg: detection limits of
protein assay)
Extracts containing protein should be treated with care
49. 1. Absorbance at 280 nm:
Principle:
• Proteins in solution absorb ultraviolet light with
absorbance maxima at 280 and 200 nm.
• Amino acids with aromatic rings are the primary
reason for the absorbance peak at 280 nm.
• Peptide bonds are primarily responsible for the peak
at 200 nm.
• Secondary, tertiary, and quaternary structure all
affect absorbance, therefore factors such as pH,
ionic strength, etc. can alter the absorbance
spectrum.
• Advantage: Quick estimation, protein not consumed,
no additional reagent,incubation needed, no protein
standard needed
50. • Historically use biuret reaction:
solutionofcopper(II) sulphate in alkaline
tartarate solution reacts with peptide bonds
to form purple complex absorbing light at540
nm
51. • Disadvantage: considerable error due to varying
absoprtion characteristics of protein samples
2. Bradford method:
Principle:
• The assay is based on the observation that the
absorbance maximum for an acidic solution of
Coomassie Brilliant Blue G-250 shifts from 465 nm to
595 nm when binding to protein occurs.
• Both hydrophobic and ionic interactions stabilize the
anionic form of the dye, causing a visible color
change.
• Advantage: relatively fast, fairly accurate
52. • Disadvantage:
-The dye reagent reacts primarily with arginine
residues and less so with histidine, lysine, tyrosine,
tryptophan, and phenylalanine residues. Obviously, the
assay is less accurate for basic or acidic proteins.
-The Bradford assay is rather sensitive to bovine
serum albumin, more so than "average" proteins, by
about a factor of two.
53. 3. BCA
Principle:
• BCA serves the purpose of the Folin reagent in
the Lowry assay, namely to react with complexes
between copper ions and peptide bonds to produce a
purple end product.
• The advantage of BCA is that the reagent is fairly
stable under alkaline conditions, and can be included
in the copper solution to allow a one step procedure.
A molybdenum/tungsten blue product is produced as
with the Lowry
• Disadvantage: greater variability among proteins and
the assay is less sensitive
54. 4. Modified lowry assay
Principle:
• Under alkaline conditions the divalent copper ion forms a
complex with peptide bonds in which it is reduced to a
monovalent ion.
• Monovalent copper ion and the radical groups of
tyrosine, tryptophan, and cysteine react with Folin
reagent to produce an unstable product that becomes
reduced to molybdenum/tungsten blue
• Advantage: fairly accurate
• Disadvantage: proteins are consumed and proteins with
an abnormally high or low percentage of tyrosine,
tryptophan, or cysteine residues will give high or low
errors, respectively.
55.
56. 5. Fluorescamine protein assay:
Principle:
• Fluorescamine react with amino acids containing primary
amines such as lysine and n-terminal amino acid to yield a
highly fluorescent product. Fluoresence measure using a
standard fluorometer with the excitation wavelenght at 390
nm and emission at 475nm
• Advantage: sensitive (nano gram range), fast, reaction is
instantaneous
• Disadvantage: reagents hydrolyzed very rapidly therefore
rapid mixing is required to produce reproducible results as
fluorescamine react with primary amine, primary amine buffer
eg: tris and glycine cant be used
57. Secondary stucture:
• Secondary structure of polypeptides consists of several
repeating structures most common types: α-helix and β-
pleated sheet
• α-helix and β-pleated sheet stabilize by H bonds between
carbonyl and NH groups (interactions with other amino acids
in close proximity) in polypeptide backbone
• α-helix : rigid, rodlike structure that forms when a
polypeptide chain twists into right-handed or left-handed
helical conformation.
58. Nonstandard amino acids
chemically modified after they have been incorporated into a
protein (termed a “posttranslational modification”)
- γ-carboxyglutamic acid, a calcium-binding amino acid residue
found in the blood-clotting protein prothrombin (as well as in
other proteins that bind calcium as part of their biological
function).
- collagen: Significant proportions of the amino acids in
collagen are modified forms of proline and lysine: 4-
hydroxyproline and 5-hydroxylysine.
- Phosphate molecule to the hydroxyl portion of the R groups of
serine, threonine, and tyrosine. This event is known as
phosphorylation and is used to regulate the activity of proteins
in the cell. Serine is the most common in proteins, threonine is
second, and tyrosine is third.
59. - Glycoproteins are widely distributed in nature and provide
the spectrum of functions already discussed for unmodified
proteins. The sugar groups in glycoproteins are attached to
amino acids through either oxygen (O-linked sugars) or
nitrogen atoms (N-linked sugars) in the amino acid residues.
- Selenocysteine: Although it is part of only a few known
proteins, there is a sound scientific reason to consider this the
21st amino acid because it is in fact introduced during protein
biosynthesis rather than created by a posttranslational
modification. Selenocysteine is actually derived from the
amino acid serine (in a very complicated fashion), and it
contains selenium instead of the sulfur of cysteine.
60.
61. A helix has the following features:
•every 3.6 residues make one turn,
•the distance between two turns is 0.54 nm,
•the C=O (or N-H) of one turn is hydrogen bonded to N-H (or
C=O) of the neighboring turn.
•Hydrogen bonds play a role in stabilizing the a helix
conformation. However, the size and charges of sidechains
are also important factors. Alanine has a greater propensity
to form a helices than proline.
62. The hydrogen bonds that stabilize the helix are parallel to the long axis of the helix.
63. Beta strand
In a beta strand, the torsion angle of N-Ca-C-N in the
backbone is about 120 degrees. The following figure shows
the conformation of an ideal b strand. Note that the
sidechains of two neighboring residues project in the
opposite direction from the backbone
64. Beta sheet
A beta sheet consists of two or more hydrogen bonded b
strands. The two neighboring b strands may be parallel if
they are aligned in the same direction from one terminus (N
or C) to the other, or anti-parallel if they are aligned in the
opposite direction.
65.
66.
67. Structural motif (supersecondary structure):
a structural motif is a three-dimensional structural
element or fold within the chain, which appears also
in a variety of other molecules. In the context of
proteins, the term is sometimes used
interchangeably with "structural domain," although a
domain need not be a motif nor, if it contains a
motif, need not be made up of only one.
70. What are domains of proteins?
• A domain is a basic structural unit of a protein structure-
distinct from those that make up the conformation
• Part of protein that can fold into a stable structure
independently
• different domains can impart different functions to proteins
•Proteins can have one too many domains depending on
protein size
•In an unbranched chain-like biological molecule, such as a
protein or RNA, a structural motif is the three dimensional
structural element within the chain, which appears also ina
variety of other molecules.
72. Tertiary structure:
• 3D conformation as a result of interactions betweeen side
chains in their primary structure
• Hydrophobic intercations: as polypeptide folds, R groups are
brought into close proximity
• Electrostatic interactions: strongest electrostatic interaction
between ionic groups of opposite charge
• H bonds: significant number of H bonds forms within interior
of protein, polar amino acids interact with water or with
polypeptide backbone
• Covalent bonds: most important, covalent bonds in tertiary
structure are disulfide bridges found in many extracellular
proteins
73. Quaternary structure:
• Proteins esp high M.W composed of several polypeptide
chains
• Each polypeptide is called a subunit
• Subunits in a protein complex may be identical or quite
different
• Multisubunit proteins in which some or all subunits are
identical are called oligomers
• Polypeptide units assemble and held together by noncovalent
interactions such as
-hydrophobic interactions
-electrostatic interactions
-H bonds
-covalent cross links
74. Hydrophobic interactions play an important role in protein
folding as well as covalent crosslinks help stabilize
multisubunit proteins
Eg: disulfide bridges in immunoglobulins, the desmosine and
lysinonorleucine linkages in certain connective tissues
Eg: desmosine cross links connects 4 polypepide chains in the
rubberlike connective tissue called elastin
Lysinonorleucine: crosslink structure found in elastin and
collagen
Interactions between subunit are also affected by binding of
ligands
75. In allostery, control of protei fundtion through ligand binding to
specific site in protein triggers conformational change that
alters its affinity for other ligands
Ligand induced corformational changes in such proteins are
called allosteric transitions, ligands which trigger them are
called effectors or modulators
Loss of protein structure:
• Protein sensitive to environmental factors
• Disruption of native conformation is called denaturation
• Factors: physical and chemical
Denaturing agents:
1. Strong acids or base
2. Organic solvents
77. 3. Detergents
4. Reducing agents
5. Salt concentrations
6. Heavy metal ions
7. Temperature changes
8. Mechanical stress
78. Antibody family:
• A family of proteins that can be created to bind almost any
molecule
• Ntibodies (imminoglobulin) are made in response to a foreign
molecule i.e: bacteria, virus, pollen..callled and antigen
• Bind together tightly and therefore inactivates the antigen or
marks it for destruction
79. Protein folding:
• The peptide bond allows for rotation around it and therefore
the protein can fold and orient the R groups in favourable
positions
• Weak non covalent interactions will hold the protein in its
functional shape-these are weak and will take many to hold the
shape.
• H bonds form between 1) atoms involved in the peptide bonds
2) peptide bond atoms and R groups, 3) R groups
Protein folding:
• Protein shape is determined by the sequence of the amino
acids
• The final shape is called the conformation and has the lowest
free energy possible
80. 3 main classes of protein folding accessory proteins:
Allow protein to fold within few minutes in cell (in vivo)
a) Protein disulfide isomerases
b) Peptidyl prolyl ci-trans isomerases
c) Molecular chaperones
• Denatured proteins may renature or refold if chemical
compound that causes denaturation can be removed
• Molecular chaperons are small proteins that help guide the
folding and help keep the new protein from associating with
the wrong partner
81.
82. Useful protein:
• There are many diferent combinations of amino acids that
can make up proteins and that would increase if each one had
multiple shape
• Proteins usually have one useful conformation because
otherwise it would not be efficient use of energy available to
the system
• Natural selection has elimited proteins that donot perform a
specific function in the cell
• Have similarities in amino acid sequence and 3d structure
• Have similar functions such as breakdown proteins but do it
differently
83. Proteins –multiple peptides
• non covalent bonds can form interactions between
individual polypeptide chains
• binding site-where proteins interact with one another
•Subunit-each polypeptide chain of large protein
• dimer –protein made of 2 subunits
84. Oxygen binding protein:
• Hemoglobin:
Carry O2 in blood from lungs to other tisues in body; function
is to supply O2 to cells for oxidative phosphorylation
• Myoglobin
stores O2 in tissues of body, available when cells reuire it;
highest concentration of myoglobin in skeletal and cardiac
muscle which require large amounts of energy
Myoglobin: small protein, 17.8 Kda, made up of 153 amino acids
in a single polypeptide
85. • Globular protein have a highly folded compact structure with
most of the hydrophobic residues found in the interior while
polar residues on surfaces
• Structure of hemoglobin determined by Max Perutz was the
first protein structure determined via x-ray crystallography
• Secondary structure: α-helix, 8 α-helices, heme prosthetic
group is found in hydrophobic crevice formed by folding of
polypeptide chains
• Hemoglobin made up of 4 polypeptide chains
• Each have similar 3D of single polypeptide chain in myoglobin
even though aino acid sequences differ at 83 % of residues
• This highlight relatively common theme in protein structure:
different primary sequence can specify very similar 3D
structures
86. • Major tyoe of hemoglobin found in adults (HbA):
• Made of 2 diferent polypeptide chains:
- α-chain: 141 amino acid
-β-chain: 146 amino acid
• Each chain has 8 α-helices, each containing heme prosthetic
group; therfore hemoglobin can bind 4 molecules of O2
• 4 polypeptide chains are α2β2, consists of 2α and 2β packed
tightly together ina tetrahedral array to form spherical
shaped molecule held together by multiple noncovalent
interactions
87.
88.
89. Important fibrous proteins:
• Intermediate filaments of the cytoskeleton
-structural scaffold inside the cells
-keratin in hair, horns and nails
• Extracellular matrix
-binds cells together to make tissues
-secreted from cells and assemble in long fibers
-collagen: fiber with a glycine every third amino acid in the
protein
-Elastin: unstructured fibers that give tissues an elastic
characteristic
90. Fibrous proteins:
• Typically contain high proportion of regular secondary
structures such as α-helices and β-pleated sheets
• E.g: alpha-keratin, collagen, silk fibroin
alpha-keratin:bundles of helical polypeptides twisted
together into large bundles
• Alpha-keratin found in hair wool, skins, horns, fingernails are
alpha-helical polypeptides.
91.
92. Globular protein:
Stabilization of cross linkages
• Cross linkages can be between 2 parts of a protein or
between 2 subunits
• Disulphide bonds (-S-S-) form between adjacent –SH groups
on the amino acid cystein
93. Proteins at work:
• Conformation of a protein gives it a unigque function
• To work proteins must interact with other molecules, usually 1
or a few molecules from the thousands .
• Ligand: the molecule that a protein can bind
• Binding site
-part of a protein that interacts with the ligand
-consists of a cavity formed by a specific arrangment of amino
acids
• The binding site forms when amino acids from within the
protein come together
• The remaining sequence may play a role in regulating the
protein’s activity
94.
95. Chemical characteristic of proteins:
• Proteins have ionic and hydrophobic sites both internally
(within folds of tertiary structure) and on surfaces where
primary structures come in contact with the environment
• Ionic sites are provided by charged amino acids at physiological
pH and by covalentl attached modifying group (eg:
carbohydrates and phosphate)
• Net charge on protein contributed by free alpha-amino of N-
terminal residue, free alpha-carbonyl group of c terminal
residue, ionizable R groups and unique array of modifications
attached to proteins
• At isoelectric point (pI): no of (+) and (-) charges on protein are
equal. Protein is electrically neutral
• Protein has net (+) at pH values below its pI and (-) charge
above is pI
請注意 碳是不對稱的,因為它周圍的四個原子或基團都不相同;只有當 R 基團為氫原子時,是對稱的 碳 ( 因為接有兩個一樣的氫原子 ) ;也就是說只有 glycine 是對稱的胺基酸。 因此,除了 glycine 外,其它胺基酸都有其立體異構物,兩立體異構物間的化學式完全一樣,但互相成為鏡像,胺基酸的立體異構物以 L - 及 D -form 來表示之;地球上的生物大都採用 L -form 胺基酸。幾年前分析一顆外太空來的隕石,發現其中的 L -form 胺基酸的比例大於 D -form 者,令人推想地球上的生物使用 L -form 胺基酸可能有其原因。
質子 proton 是宇宙中的奇妙粒子,這是一顆光溜溜的粒子;當氫原子丟掉一個電子後,即可得到質子,因此寫作 H + 。 質子可以隨時附著到一個帶有電子密度的基團 ( 如胺基 ) ,使該基團多帶 了一個正電。質子也很容易由某一個基團脫出 ( 如羧基 ) ,而使該基團成為帶負電。 胺基酸同時帶有上面兩種基團,因此可同時帶有正電及負電,稱為雙性離子 ampholyte 。若胺基酸同時帶有一個正電及一個負電,則其淨電荷為零,特稱之為 zwitterion 。 請注意上述基團的解離與否,受環境 pH 影響甚鉅;當環境的 pH 大於此基團的 p Ka 時,此基團將帶負電;反之則帶正電。因此,一個基團的 p Ka 越小 ( 我們說越酸性的物質 ) ,就越容易帶負電,因為其質子很容易跑掉,剩下的分子就呈負電荷。 再舉一例, glycine 上有胺基及羧基各一,其 p Ka 分別為 9.6 及 2.3 ,則在中性 pH 下,其胺基將帶正電如上圖 ( 因為環境 pH < 胺基的 p Ka ) ;反之羧基則帶負電如上圖。在中性溶液中, glycine 因此同時帶有正電及負電各一,是一個 zwitterion 。
胺基酸 非常特別,同一個分子上同時帶有一個弱酸及弱鹼;因此可以用胺基酸來作為酸性或鹼性的緩衝液。例如,某胺基酸的酸基 p K 1 = 2 ,胺基的 p K 2 = 9 ,則此胺基酸在 pH 為 2 或 9 附近,都有緩衝作用。 在胺基酸質子的解離過程中,在某個 pH 條件下,同時帶有一個正電及負電 ( 上圖中央 ) ,其淨電荷恰好為零,這種形式稱為 zwitterion ,這個 pH 則稱為此胺基酸的等電點 (pI) ;處於等電點的胺基酸並非不帶電,而是正、負電荷的數目剛好相等。 等電點的算法很簡單,只要把等電點上下的兩個 p K 值平均即得;如上例中 (2 + 9) ÷ 2 = 5.5 。
由 上面胺基酸的滴定曲線看來,當環境的 [OH - ] 逐漸增加時,在其兩個 p K 處的 pH 變化最小,具有緩衝作用;而在其 pI 處,幾乎完全沒有緩衝作用。為何處於等電點的分子,完全不具緩衝作用? 而其分子上有一個 H + ,看來可以作為供應質子者;也有一個 – COO - 可以作為接受質子者,非常完美。 原因是這個 H + 無法放出,因為攜帶 H + 的基團是 – NH 3 + ,要到 pH = 9 才會放出 ( 因為其 p K = 9) ;相似的理由,這個 – COO - 也無法接受質子,成為 – COOH ,要到 3 以下才行。因此,你可以得到一個概念,分子上的這些基團能否收放質子,都決定於其自身的 p K 。回過來想一想, p K 到底是什麼? p K 就是描述一個基團釋出或吸收質子的能力或程度, p K 越大的基團,就越不容易釋出;反之, p K 越小的基團,也就越不容易吸入質子。
通常 一個蛋白質分子上都帶有電荷,有正電荷、也有副電荷,這些正、負電荷的淨值,即為此蛋白質所帶的 淨電荷 ;蛋白質的淨電荷可能為正、也可能為負,在某 pH 下蛋白質的淨電荷可能為零,則此 pH 稱為此蛋白質的『 等電點 』 (isoelectric point, pI) ,一個蛋白質的 pI 通常不會變,除非其胺基酸的組成改變。 當環境的 pH 大於某蛋白質的的 pI ( 如上圖某蛋白質的 pI = 6 ,環境 pH = 9) ,則此蛋白質的淨電荷為負;反之則為正值。另外,環境的 pH 離其 pI 越遠,則其所帶的淨電荷數目將會越大;越接近 pI 時,所帶淨電荷變小,最後在其 pI 處淨電荷為零。因此,蛋白質溶液的 pH 要很小心選擇,以便使該蛋白質帶有我們所需要的淨電荷,或者不帶有淨電荷。
Aspartic acid 有三個官能基,如何求得其 pI ? 初次練習時,最好像上圖左邊一樣,把分子式寫出來,並且由酸性環境開始,把各官能基的解離狀況寫好,也就是說質子該解離的就解離,不該解離的就要把 H + 加上去。至於如何知道該不該解離,只要比較各基團的 p Ka 與環境的 pH ,即可得知。當環境的 pH 小於官能基的 p Ka 時,因為環境比較起來偏酸 (pH < p Ka ) ,則此官能基不便解離,應該加上質子;反之則減去質子。 如此,把每個基團的解離情形全部寫好。然後把每個不同 pH 下的淨電荷算出來,發現淨電荷變化由酸到鹼是 +1 → 0 → -1 → -2 ,可找到一個淨電荷為零的等電點,然後把等電點前後的兩個 p Ka 平均即是等電點的值。 有點麻煩? 在弄熟了原理之後,酸性胺基酸可以直接把靠酸性的那兩個 p Ka 平均即可,而鹼性胺基酸則把較大的那兩個 p Ka 平均。為何如此做的原理,也實在不難理解。