Amino Acids – Physical Properties, Structure, Classification, Functions

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What are Amino Acids?

  • Amino acids are fundamental organic compounds central to biochemistry, primarily known for their critical role as the building blocks of proteins. Structurally, each amino acid consists of a carboxylic acid group (-COOH) and an amino group (-NH2) attached to an alpha (α) carbon. This α-carbon is often chiral, giving many amino acids a specific stereochemistry, which contributes to the diverse functionality of proteins.
  • In the biosynthesis of proteins, 20 amino acids serve as the standard units, coded by genetic material. These amino acids, often called “proteinogenic,” are incorporated into proteins through a highly regulated process driven by genetic instructions. Although over 500 amino acids have been identified in nature, only 22 of them are utilized in genetic coding across living organisms. The remaining amino acids, often termed “non-protein” amino acids, either perform separate biochemical roles or exist in modified forms within proteins, thanks to post-translational modifications.
  • Amino acids can be categorized by structural features, including the location of their functional groups (such as alpha- (α-), beta- (β-), and gamma- (γ-) amino acids) and the nature of their side chains (which can be aliphatic, acyclic, aromatic, or polar). These classifications also help determine their chemical reactivity, polarity, and overall behavior in biological systems. Beyond proteins, amino acids participate in numerous physiological processes, such as neurotransmitter transport and synthesis, and play a crucial role in the development and functioning of muscle tissue, the second-largest component of human tissue after water.
  • The systematic nomenclature of amino acids, standardized by the IUPAC-IUBMB, provides each amino acid with a specific name based on its neutral structural form. For example, the amino acid alanine is named 2-aminopropanoic acid, referencing its chemical structure (CH3−CH(NH2)−COOH). This naming convention aids in distinguishing between amino acids and serves to maintain clarity within biochemical studies, even if these neutral forms do not represent their actual behavior under physiological conditions.

Definition of Amino Acids

Amino acids are organic compounds that serve as the building blocks of proteins. They consist of carbon, hydrogen, and nitrogen atoms and play essential roles in the proper functioning of living organisms.

List of 20 Amino acids with the chemical formula

AlanineC3H7NO2LeucineC6H13NO2
Aspartic AcidC4H7NO4LysineC6H14N2O2
AsparagineC4H8N2O3MethionineC5H11NO2S
ArginineC6H14N4O2ProlineC5H9NO2
CytosineC4H5N3OPhenylalanineC9H11NO2
CysteineC3H7NO2SSerineC3H7NO3
GlycineC2H5NO2TyrosineC9H11NO3
GlutamineC5H10N2O3ThreonineC4H9NO3
HistidineC6H9N3O2TryptophanC11H12N2O2
IsoleucineC6H13NO2ValineC5H11NO2

Properties of amino acids

Amino acids are organic compounds essential to various biological processes, particularly as the foundational building blocks of proteins. These compounds display a range of physical and chemical properties, making them unique among biomolecules.

  • Physical Properties
    • Color and Structure: Amino acids are colorless and exist in a crystalline solid form, underscoring their highly structured arrangement.
    • Melting Point: They exhibit high melting points, generally exceeding 200°C, a property indicative of their stable intermolecular forces.
    • Solubility: Most amino acids are readily soluble in water but only slightly soluble in alcohol. Solubility in methanol, ethanol, and propanol is limited and varies based on the R-group of the amino acid and the pH of the solvent.
    • Thermal Stability: When exposed to high temperatures, amino acids do not simply melt; instead, they decompose, which points to the strength of their bonds.
    • Optical Activity: All amino acids, except glycine, are optically active, meaning they can rotate polarized light. This property is due to their chiral center at the alpha-carbon.
    • Peptide Bond Formation: Amino acids can link through peptide bonds formed between the alpha-amino group of one amino acid and the alpha-carboxyl group of another. This bond (-CO-NH-) is covalent, planar, and partially ionic, contributing to the structural stability of proteins.
  • Chemical Properties
    • Zwitterionic Nature: In solution, amino acids exist primarily as zwitterions, molecules containing both positive and negative charges yet carrying a net neutral charge overall. This results from the basic amino (-NH2) group accepting a proton from the acidic carboxyl (-COOH) group, leaving a structure with -NH3+ and -COO- groups.
    • Amphoteric Behavior: Due to the presence of both amino and carboxylic groups, amino acids exhibit amphoteric properties, meaning they can function as either acids or bases, depending on the surrounding pH.
    • Ninhydrin Test: Amino acids can be identified by the Ninhydrin test, where heating with Ninhydrin solution produces a violet color, specifically indicating the presence of α-amino acids.
    • Xanthoproteic Test: This test is employed to detect aromatic amino acids like tyrosine, tryptophan, and phenylalanine. When reacted with nitric acid, these aromatic amino acids undergo nitration, producing a yellow color.
    • Reaction with Sanger’s Reagent: Sanger’s reagent (1-fluoro-2,4-dinitrobenzene) reacts with free amino groups in peptides under mildly alkaline and cold conditions. This reaction is particularly useful for identifying the amino groups within peptide chains.
    • Reaction with Nitrous Acid: Nitrous acid reacts with the amino group in amino acids, releasing nitrogen and forming a corresponding hydroxyl compound, a reaction that can aid in analytical and preparative biochemical applications.
Amino AcidCodeHydropathyChargepKa, NH2pKa, COOHpK(R)Solubility
ArginineRhydrophilic+9.092.1813.271.8
AsparagineNhydrophilicN8.82.02 2.4
AspartateDhydrophilic9.61.883.650.42
GlutamateEhydrophilic9.672.194.250.72
GlutamineQhydrophilicN9.132.17 2.6
LysineKhydrophilic+8.92.210.28 
SerineShydrophilicN9.152.21 36.2
ThreonineThydrophilicN9.122.15 freely
CysteineCmoderateN10.781.718.33freely
HistidineHmoderate+8.971.7864.19
MethionineMmoderateN9.212.28 5.14
AlanineAhydrophobicN9.872.35 15.8
ValineVhydrophobicN9.722.29 5.6
GlycineGhydrophobicN9.62.34 22.5
IsoleucineIhydrophobicN9.762.32 3.36
LeucineLhydrophobicN9.62.36 2.37
PhenylalanineFhydrophobicN9.242.58 2.7
ProlinePhydrophobicN10.61.99 1.54
TryptophanWhydrophobicN9.392.38 1.06
TyrosineYhydrophobicN9.112.210.10.038

Amino acid wheel

Amino acid wheel
Amino acid wheel

Structure of Amino acids

Structure of Amino acids
Structure of Amino acids

Amino acids are the foundational units of proteins, with each possessing a common structural framework that includes a central carbon atom, known as the α-carbon, to which specific functional groups are attached. This structure varies slightly across different amino acids, particularly in the nature of the side chain, or R group, attached to the α-carbon.

  • Core Structure:
    • Each amino acid is classified as an alpha-amino acid, with both an amino group (-NH2) and a carboxyl group (-COOH) connected to the same α-carbon atom.
    • The α-carbon also binds to a hydrogen atom, creating a common structural backbone across all amino acids. The variability among amino acids arises from the side chain, or R group, which differs in each type.
  • Side Chains (R Groups):
    • The R group is unique for each amino acid and is the component that influences properties like structure, shape, electric charge, and solubility.
    • Glycine, the simplest amino acid, has an R group consisting of just a hydrogen atom. This minimal side chain makes glycine the only amino acid without a chiral (asymmetric) α-carbon, rendering it neither optically active nor specific to D- or L-configuration.
    • Proline is an exception among amino acids, as its R group forms a ring that includes the nitrogen in the amino group, creating a distinctive structure. This ring structure limits the flexibility of proline in protein chains.
  • Optical Configuration:
    • Most amino acids, except glycine, have an asymmetric α-carbon, which allows them to exist in different optical forms (isomers). Naturally occurring amino acids are in the L-configuration, consistent across almost all protein-building amino acids.
Amino acid classification
Amino acid classification

Structure of 20 Amino acids with their chemical formula

Structure of 20 Amino acids with their chemical formula
Structure of 20 Amino acids with their chemical formula

Classification of Amino Acids

Amino acids can be classified in multiple ways, based on their structural characteristics, polarity, nutritional needs, and metabolic fate. Each classification highlights unique attributes and roles of amino acids in biological processes.

  • Classification by Structure:
    • Amino acids with aliphatic side chains: These have non-aromatic, straight or branched chains, like glycine, leucine, and valine.
    • Hydroxyl-containing amino acids: These amino acids include a hydroxyl (-OH) group, as seen in serine, threonine, and tyrosine.
    • Sulfur-containing amino acids: Cysteine and methionine contain sulfur atoms within their structure.
    • Acidic amino acids and their amides: Aspartic acid and glutamic acid are dicarboxylic monoacids, while asparagine and glutamine are their respective amide derivatives.
    • Basic amino acids: Lysine, arginine, and histidine have basic R groups, making them dibasic monocarboxylic acids.
    • Aromatic amino acids: Phenylalanine, tyrosine, and tryptophan possess aromatic rings, contributing to their hydrophobic nature.
    • Imino acids: Proline is an imino acid with a unique ring structure that incorporates the nitrogen atom, limiting its flexibility.
  • Classification by Polarity:
    • Non-polar amino acids: These are hydrophobic due to their non-polar R groups, such as methionine, proline, alanine, leucine, and valine.
    • Polar amino acids with no charge on R group: This group is hydrophilic and includes serine, glycine, threonine, and glutamine.
    • Polar amino acids with a positive charge: Amino acids like histidine, lysine, and arginine have positively charged R groups, making them basic.
    • Polar amino acids with a negative charge: Aspartic acid and glutamic acid are negatively charged, acidic amino acids.
  • Classification by Nutritional Requirements:
    • Essential amino acids: These cannot be synthesized by the body and must be obtained through diet. The essential amino acids include histidine, isoleucine, leucine, lysine, methionine, phenylalanine, threonine, tryptophan, and valine.
    • Non-essential amino acids: These amino acids can be synthesized by the body and do not necessarily need to be acquired through diet. They include glutamine, tyrosine, proline, glycine, alanine, serine, cysteine, aspartate, asparagine, and glutamate.
  • Classification by Metabolic Fate:
    • Glucogenic amino acids: These amino acids are precursors for gluconeogenesis and contribute to glucose formation. Examples include glycine, alanine, serine, aspartic acid, asparagine, glutamic acid, glutamine, proline, valine, methionine, cysteine, histidine, and arginine.
    • Ketogenic amino acids: Leucine and lysine break down to form ketone bodies, contributing to ketogenesis.
    • Both glucogenic and ketogenic amino acids: Isoleucine, phenylalanine, tryptophan, and tyrosine serve as precursors for both glucose and ketone body production.

Synthesis of amino acids

The synthesis of amino acids occurs through two primary pathways: chemical synthesis and biosynthesis. Both processes are vital for producing the numerous amino acids necessary for life. Understanding these mechanisms highlights the intricate relationship between amino acids and biological systems.

Amino acid biosynthesis overview.
Amino acid biosynthesis overview. (Image Source: Pillsmarch, CC BY 4.0, via Wikimedia Commons)
  • Chemical Synthesis
    • Commercial production of amino acids frequently employs mutant bacteria that are genetically modified to overproduce specific amino acids, utilizing glucose as a carbon source. This method efficiently yields large quantities of amino acids for various applications.
    • Some amino acids are produced through enzymatic conversions of synthetic intermediates. For instance, 2-aminothiazoline-4-carboxylic acid serves as an intermediate in the industrial synthesis of L-cysteine. Additionally, aspartic acid is synthesized by adding ammonia to fumarate, facilitated by the action of a lyase enzyme.
  • Biosynthesis
    • In plants, the process begins with the assimilation of nitrogen into organic compounds, primarily as glutamate. This transformation occurs in the mitochondria from alpha-ketoglutarate and ammonia. For the synthesis of other amino acids, plants utilize transaminases to transfer the amino group from glutamate to different alpha-keto acids. An example of this is aspartate aminotransferase, which converts glutamate and oxaloacetate into alpha-ketoglutarate and aspartate.
    • Other organisms also employ transaminases for amino acid synthesis, illustrating a common biochemical pathway across various life forms.
  • Formation of Nonstandard Amino Acids
    • Nonstandard amino acids generally arise through modifications of standard amino acids. For example, homocysteine is formed via the transsulfuration pathway or by demethylation of methionine through the intermediate metabolite S-adenosylmethionine. Hydroxyproline, another nonstandard amino acid, is created through post-translational modification of proline.
    • Microorganisms and plants have the capability to synthesize many uncommon amino acids. Certain microbes produce 2-aminoisobutyric acid and lanthionine, the latter being a sulfide-bridged derivative of alanine, both of which are components of peptidic lantibiotics like alamethicin. Additionally, plants synthesize 1-aminocyclopropane-1-carboxylic acid, which serves as an intermediate in the production of the plant hormone ethylene.
  • Primordial Synthesis
    • The origins of amino acids and peptides are believed to precede and potentially catalyze the emergence of life on Earth. Under various conditions, amino acids can form from simple precursors. Surface-based chemical processes may have contributed to the accumulation of amino acids, coenzymes, and small carbon molecules containing phosphate.
    • Historical experiments, such as the Urey-Miller experiment, demonstrated that passing an electric arc through a mixture of methane, hydrogen, and ammonia could generate a significant number of amino acids. This finding led to the exploration of multiple pathways for prebiotic formation and the chemical evolution of peptides, including mechanisms like condensing agents and self-replicating peptides.
    • The Strecker synthesis is another hypothesized pathway wherein hydrogen cyanide, simple aldehydes, ammonia, and water combine to yield amino acids. This synthesis underscores the relative ease of producing amino acids compared to nucleotides, suggesting that amino acids may have formed more readily under prebiotic conditions.
    • The concept of a ‘protein world’ or ‘polypeptide world’ has emerged, suggesting that these structures preceded the ‘RNA world’ and later the ‘DNA world’ in the evolution of life. Codon–amino acid mappings are proposed as a biological information system fundamental to the early development of life on Earth. While the synthesis of amino acids and simple peptides has been experimentally confirmed under various geochemical conditions, the transition from an abiotic environment to the first living organisms remains a largely unresolved area of study.

α-Ketoglutarates: glutamate, glutamine, proline, arginine

The synthesis of amino acids from α-ketoglutarates, specifically glutamate, glutamine, proline, and arginine, is a crucial biochemical process in various organisms. This synthesis occurs through a series of metabolic pathways that leverage α-ketoglutarate, an intermediate of the Citric Acid Cycle, as a key precursor. Understanding these pathways provides insights into how organisms produce essential components required for protein synthesis and overall metabolism.

This diagram shows the biosynthesis (analbolism) of amino acids glutamate, glutamine, proline, and arginine from the precursor alpha-ketoglutarate.
This diagram shows the biosynthesis (analbolism) of amino acids glutamate, glutamine, proline, and arginine from the precursor alpha-ketoglutarate. (Mplanine, CC0, via Wikimedia Commons)
  • Role of α-Ketoglutarate:
    • α-Ketoglutarate serves as a primary substrate in the synthesis of several amino acids.
    • It is formed in the Citric Acid Cycle and can be converted into glutamate via an amination reaction:
      • Reaction: α-ketoglutarate + NH₄⁺ ⇄ glutamate
    • Glutamate can subsequently act as an amino group donor in transamination reactions to form other amino acids:
      • Transamination: α-ketoacid + glutamate ⇄ amino acid + α-ketoglutarate
  • Synthesis of Glutamate:
    • The regulation of glutamate synthesis is intricately tied to the activity of the Citric Acid Cycle and the concentrations of various reactants.
    • The reversible nature of the transamination and glutamate dehydrogenase reactions allows for dynamic regulation depending on cellular conditions.
  • Conversion of Glutamate to Glutamine:
    • The enzyme glutamine synthetase (GS) catalyzes the conversion of glutamate to glutamine, a pivotal step in nitrogen metabolism.
    • Regulation of GS occurs through multiple mechanisms:
      • Repression linked to nitrogen availability.
      • Activation or inactivation based on the enzyme’s conformational states (taut and relaxed).
      • Cumulative feedback inhibition from metabolites such as L-tryptophan, L-histidine, and others.
      • Alterations via adenylation and deadenylation processes.
    • In conditions rich in nitrogen, GS levels decrease, while they increase significantly under nitrogen-limiting conditions. The activity of GS can be influenced by divalent cations, such as manganese, which impacts its conformation and functionality.
  • Proline Biosynthesis:
    • Proline synthesis is initiated from glutamate and regulated through feedback inhibition.
    • In E. coli, proline acts as an allosteric inhibitor of glutamate 5-kinase, which facilitates the conversion of L-glutamate to L-γ-Glutamyl phosphate, an unstable intermediate.
  • Arginine Synthesis:
    • Arginine is synthesized from glutamate and involves regulation through negative feedback and genetic repression.
    • The gene argR encodes an aporepressor that, in conjunction with arginine as a corepressor, modulates the operon responsible for arginine biosynthesis. The effectiveness of this repression is contingent upon the concentrations of both the repressor and corepressor.

Erythrose 4-phosphate and phosphoenolpyruvate: phenylalanine, tyrosine, and tryptophan

Erythrose 4-phosphate and phosphoenolpyruvate are vital precursors in the biosynthesis of the aromatic amino acids phenylalanine, tyrosine, and tryptophan. These amino acids originate from chorismate through a series of enzymatic reactions that are finely regulated to maintain cellular balance. Understanding the pathways and regulatory mechanisms involved in their synthesis is crucial for students and educators in the fields of biochemistry and molecular biology.

Erythrose 4-phosphate and phosphoenolpyruvate: phenylalanine, tyrosine, and tryptophan
Erythrose 4-phosphate and phosphoenolpyruvate: phenylalanine, tyrosine, and tryptophan (Mplanine, CC0, via Wikimedia Commons)
  • Aromatic Amino Acids Biosynthesis Overview:
    • Phenylalanine, tyrosine, and tryptophan are classified as aromatic amino acids, and their biosynthesis begins with chorismate.
    • The initial step in this biosynthetic pathway involves the condensation of 3-deoxy-D-arabino-heptulosonic acid 7-phosphate (DAHP) from phosphoenolpyruvate (PEP) and erythrose 4-phosphate (E4P).
    • This condensation is facilitated by three isoenzymes: AroF, AroG, and AroH, each regulated by the levels of phenylalanine, tyrosine, and tryptophan, respectively.
  • Conversion of DAHP to Chorismate:
    • Following the formation of DAHP, the subsequent enzymes leading to chorismate appear to be synthesized constitutively, with the notable exception of shikimate kinase.
    • Shikimate kinase is subject to linear mixed-type inhibition by shikimate, which provides a regulatory mechanism in the pathway.
  • Synthesis of Tyrosine and Phenylalanine:
    • Both tyrosine and phenylalanine are synthesized from prephenate, which is derived from chorismate.
    • This conversion is mediated by specific chorismate mutase-prephenate dehydrogenases, designated as PheA for phenylalanine and TyrA for tyrosine.
      • PheA converts prephenate to phenylpyruvate using a straightforward dehydrogenase.
      • TyrA, in contrast, utilizes a NAD-dependent dehydrogenase to produce 4-hydroxyphenylpyruvate.
    • Feedback inhibition regulates the activity of both PheA and TyrA, whereby the respective amino acids inhibit their own synthesis.
    • Additionally, the transcription of TyrA is inhibited by the TyrR repressor, which binds to specific TyrR boxes located on the operon near the promoter, preventing expression of the gene.
  • Biosynthesis of Tryptophan:
    • The synthesis of tryptophan involves the conversion of chorismate to anthranilate, catalyzed by anthranilate synthase.
    • This enzyme requires glutamine as the amino group donor or ammonia, highlighting its role in nitrogen metabolism.
    • Anthranilate synthase is composed of two subunits encoded by the genes trpE and trpG.
      • TrpE binds to chorismate and facilitates the transfer of the amino group, while TrpG aids in the transfer of the amino group from glutamine.
    • Feedback inhibition also plays a critical role in regulating tryptophan biosynthesis, where tryptophan acts as a co-repressor for the TrpR repressor, effectively controlling the operon.

Oxaloacetate/aspartate: lysine, asparagine, methionine, threonine, and isoleucine

The oxaloacetate/aspartate family of amino acids includes lysine, asparagine, methionine, threonine, and isoleucine. These amino acids are interconnected through various metabolic pathways, primarily stemming from the precursor aspartate, which itself is derived from oxaloacetate. The regulation of these biosynthetic pathways is complex, involving feedback inhibition and transcriptional control, ensuring a balanced production of amino acids essential for cellular functions.

Oxaloacetate/aspartate: lysine, asparagine, methionine, threonine, and isoleucine
Oxaloacetate/aspartate: lysine, asparagine, methionine, threonine, and isoleucine (Mplanine, CC0, via Wikimedia Commons)
  • Amino Acids Derived from Oxaloacetate:
    • The synthesis of lysine, asparagine, methionine, threonine, and isoleucine begins with oxaloacetate, which is converted into aspartate through transamination.
    • Aspartate serves as the central hub for producing these amino acids, highlighting its significance in amino acid metabolism.
    • The aspartate pathway utilizes L-aspartic acid as a precursor for the biosynthesis of several amino acids, constituting approximately one-fourth of the building block amino acids.
  • Aspartate Biosynthesis:
    • The conversion of oxaloacetate to aspartate is facilitated by transaminases, which transfer an amino group to oxaloacetate.
    • Aspartokinase is a key enzyme in this pathway, catalyzing the phosphorylation of aspartate and initiating its conversion into other amino acids.
      • There are three isozymes of aspartokinase: AK-I, AK-II, and AK-III.
      • AK-I is inhibited by threonine, while both AK-II and AK-III are inhibited by lysine, ensuring that the synthesis of these amino acids is tightly regulated based on their cellular concentrations.
  • Lysine Biosynthesis:
    • Lysine is synthesized from aspartate through the diaminopimelate (DAP) pathway, which is initiated by aspartokinase.
    • The initial steps of the DAP pathway involve aspartate semialdehyde dehydrogenase, which contributes to the formation of lysine.
    • Transcription of the genes encoding aspartokinase is regulated by the levels of lysine, threonine, and methionine; higher concentrations of these amino acids lead to reduced transcription.
    • Feedback inhibition plays a significant role in lysine biosynthesis, where high lysine concentrations inhibit the activity of key enzymes, including dihydrodipicolinate synthase (DHPS).
  • Asparagine Biosynthesis:
    • Asparagine is synthesized from aspartate through the action of asparagine synthetase, which utilizes glutamine as the amino group donor and ATP as a source of energy.
    • In this reaction, aspartate is activated to β-aspartyl-AMP, which then reacts with the ammonium group from glutamine to form asparagine.
    • There are two asparagine synthetases in bacteria, both known as AsnC, and their expression is regulated by asparagine itself, which provides a feedback mechanism to maintain amino acid levels.
  • Methionine Biosynthesis:
    • Methionine is synthesized via the transsulfuration pathway, beginning with aspartic acid.
    • Several enzymes are involved in this pathway, including aspartokinase and homoserine dehydrogenase.
    • Methionine biosynthesis is tightly regulated by the repressor protein MetJ, in conjunction with the corepressor S-adenosyl-methionine, which together inhibit the expression of methionine biosynthetic genes.
  • Threonine Biosynthesis:
    • Threonine is produced from aspartic acid through several intermediates, including α-aspartyl-semialdehyde and homoserine.
    • Homoserine kinase and threonine synthase are key enzymes in this biosynthetic pathway.
    • The synthesis of threonine is regulated by feedback mechanisms, where high levels of threonine inhibit the production of its precursor, homoserine, thus modulating the overall flux through the pathway.
  • Isoleucine Biosynthesis:
    • Isoleucine is synthesized from pyruvic acid and alpha-ketoglutarate, with several enzymes such as acetolactate synthase and valine aminotransferase participating in its biosynthesis.
    • Regulation of isoleucine biosynthesis is influenced by end-product inhibition, where elevated levels of isoleucine downregulate enzymes involved in its own synthesis as well as the biosynthesis of other related amino acids.

3-Phosphoglycerates: serine, glycine, cysteine

The 3-Phosphoglycerate family of amino acids consists of serine, glycine, and cysteine, which are interconnected through a series of biosynthetic pathways. The precursor 3-phosphoglycerate plays a pivotal role in the synthesis of these amino acids, highlighting its significance in metabolic processes. The regulation of these pathways is complex, involving various enzymes and regulatory proteins that ensure the proper balance and availability of each amino acid within the cell.

  • Serine Biosynthesis:
    • Serine is the first amino acid synthesized in this family, serving as a precursor for both glycine and cysteine.
    • The pathway for serine biosynthesis is as follows:
      • 3-phosphoglycerate → phosphohydroxyl-pyruvate → phosphoserine → serine
    • The enzyme phosphoglycerate dehydrogenase catalyzes the conversion of 3-phosphoglycerate to phosphohydroxyl-pyruvate.
      • This enzyme is crucial as it represents the key regulatory step in serine production.
    • The activity of phosphoglycerate dehydrogenase is modulated by the concentration of serine:
      • At high serine concentrations, the enzyme is inactive, halting serine production.
      • Conversely, at low serine levels, the enzyme is fully active, facilitating serine synthesis.
    • As serine is the first amino acid produced, its availability directly influences the production of glycine and cysteine.
  • Glycine Biosynthesis:
    • Glycine is synthesized from serine through the action of the enzyme serine hydroxymethyltransferase (SHMT), which replaces a hydroxymethyl group in serine with a hydrogen atom.
    • The gene coding for SHMT is glyA, and its regulation is multifaceted:
      • It is influenced by several metabolites, including serine, glycine, methionine, purines, thymine, and folates.
      • The regulatory protein MetR and the intermediate homocysteine are known to positively regulate glyA.
        • Homocysteine acts as a coactivator, working in conjunction with MetR to promote glyA expression.
      • In contrast, the protein PurR, involved in purine synthesis, along with S-adenosylmethionine, negatively regulates glyA.
        • PurR binds to the control region of glyA, inhibiting its expression and thereby reducing glycine synthesis.
  • Cysteine Biosynthesis:
    • Cysteine synthesis is governed by genes located within the cys regulon. The integration of sulfur into cysteine is positively regulated by the protein CysB.
      • Inducers for this regulon include N-acetyl-serine (NAS) and minimal amounts of reduced sulfur.
    • CysB functions by binding to specific DNA half sites on the cys regulon, which vary in quantity and arrangement based on the associated promoter.
      • A conserved half site lies just upstream of the -35 site of the promoter, critical for regulation.
      • In the absence of NAS, CysB binds to the DNA and blocks transcription by covering accessory half sites.
        • The presence of NAS prompts a conformational change in CysB, allowing it to bind effectively to all half sites, leading to the recruitment of RNA polymerase and subsequent transcription of the cys regulon.
    • Additional regulatory mechanisms exist within this pathway:
      • CysB can inhibit its own transcription by binding to its DNA sequence, blocking RNA polymerase action.
        • NAS prevents CysB from binding to its own sequence, thereby facilitating the transcription process.
      • The precursor O-acetylserine (OAS) is essential for NAS production; cysteine itself can inhibit the enzyme CysE, which synthesizes OAS.
      • Without adequate OAS, NAS synthesis is compromised, which in turn hinders cysteine production.
    • Two additional negative regulators, sulfide and thiosulfate, compete with NAS for binding to CysB, further modulating cysteine biosynthesis.

Pyruvate: alanine, valine, and leucine

Pyruvate, a key product of glycolysis, serves as a crucial precursor for the synthesis of several amino acids, notably alanine, valine, and leucine. The metabolic pathways leading from pyruvate to these amino acids highlight the interconnectedness of cellular processes, as well as the regulatory mechanisms that ensure balance within these biosynthetic routes. Understanding these pathways is essential for students and educators alike, as they illustrate fundamental principles of metabolism and regulation.

  • Alanine Biosynthesis:
    • Alanine is synthesized via transamination, which involves the transfer of an amino group from one molecule to another.
    • The synthesis occurs through two key steps:
      1. Conversion of glutamate to α-ketoglutarate: This step is facilitated by the enzyme glutamate-alanine transaminase.
      2. Conversion of valine to α-ketoisovalerate: This reaction is mediated by Transaminase C.
    • The regulation of alanine synthesis is not extensively characterized; however, it is known that the activity of Transaminase C can be repressed by the presence of either valine or leucine. This regulation is linked to the ilvEDA operon, which is significant in the context of amino acid regulation.
  • Valine Biosynthesis:
    • The pathway for valine production involves four enzymatic reactions:
      1. Condensation of pyruvate: Two equivalents of pyruvate are combined by the enzyme acetohydroxy acid synthase to yield α-acetolactate.
      2. Reduction of α-acetolactate: This step involves the NADPH+-dependent reduction of α-acetolactate, where methyl groups migrate to form α,β-dihydroxyisovalerate, catalyzed by acetohydroxy isomeroreductase.
      3. Dehydration of α,β-dihydroxyisovalerate: The third step is facilitated by dihydroxy acid dehydrase, leading to the formation of α-ketoisovalerate.
      4. Transamination of α-ketoisovalerate: The final step involves transamination, which can be catalyzed by either alanine-valine transaminase or glutamate-valine transaminase.
    • Valine biosynthesis is primarily regulated through feedback inhibition at the level of acetohydroxy acid synthase, ensuring that when valine concentrations are sufficient, further synthesis is halted.
  • Leucine Biosynthesis:
    • Leucine synthesis diverges from the valine pathway at the point of α-ketoisovalerate, and the following steps are involved:
      1. Condensation with acetyl CoA: The enzyme α-isopropylmalate synthase catalyzes this reaction to form α-isopropylmalate.
      2. Isomerization: The resulting compound is converted to β-isopropylmalate by an isomerase.
      3. NAD+-dependent oxidation: The β-isopropylmalate undergoes oxidation, facilitated by a dehydrogenase.
      4. Transamination of α-ketoisocaproate: The final reaction is catalyzed by glutamate-leucine transaminase, resulting in leucine synthesis.
    • Similar to valine, leucine regulates its own biosynthetic pathway by inhibiting the action of α-isopropylmalate synthase. Additionally, the feedback inhibition from valine also affects leucine production, reflecting the interdependence of these two pathways.
  • ilvEDA Operon:
    • The ilvEDA operon encodes several key enzymes involved in the biosynthesis of valine and leucine, including dihydroxy acid dehydrase and Transaminase E.
    • This operon is subject to regulation by the amino acids valine, leucine, and isoleucine. When these amino acids are abundant, they bind to the operon, effectively inhibiting its transcription.
      • In cases where one of these amino acids is limited, transcription of the gene furthest from the binding site can proceed, allowing for the synthesis of the necessary enzymes.
      • As additional amino acids become limiting, subsequent genes closer to the binding site are activated for transcription, thus illustrating a nuanced regulatory mechanism that responds to the cellular availability of these essential amino acids.

Physicochemical Properties of Amino Acids

1. Stereochemistry

  • Stereochemistry refers to the study of the three-dimensional arrangement of atoms within a molecule and how it affects the molecule’s properties and interactions. In the context of amino acids, stereochemistry plays a crucial role in their structure and function.
  • In the case of amino acids, they exist predominantly in the L-configuration, which was established by Emil Fischer. L-configuration refers to the spatial arrangement of the amino acid molecules as superimposable mirror images of each other. This configuration is significant because L-amino acids are the primary building blocks involved in protein synthesis during the translation process.
  • However, it is worth noting that there are rare instances where D-amino acids can be found in certain proteins. These D-amino acids have a different spatial arrangement and are mirror images of the L-amino acids.
  • The Fischer convention is a notation system used to describe the stereochemistry of molecules. It relates the configuration of a chiral center to the arrangement of groups around it in comparison to the structure of glyceraldehyde. For alpha-amino acids, the positioning of the amino, carboxyl, R, and H groups around the carbon atom is related to the arrangement of the hydroxyl, aldehyde, CH2OH, and H groups, respectively, in glyceraldehyde.
  • Understanding stereochemistry is crucial in biochemistry, as it influences the folding, structure, and function of proteins and other biomolecules. The spatial arrangement of atoms within a molecule can impact how molecules interact with each other, enzymes, receptors, and other biological systems, ultimately affecting their biological activity.
Stereochemistry
Stereochemistry

2. Peptide bond formation

  • Peptide bond formation is a crucial process in protein synthesis, determining the structure and function of proteins. It involves the covalent attachment of amino acids through a condensation reaction.
  • During peptide bond formation, the carboxyl group (-COOH) of one amino acid reacts with the amino group (-NH2) of another amino acid. This condensation reaction results in the release of a water molecule, and the formation of a peptide bond between the carbonyl carbon of one amino acid and the nitrogen of the other amino acid.
  • When fewer than 50 amino acids are linked together by peptide bonds, the resulting chain is called an oligopeptide. Chains of more than 50 amino acids are known as polypeptides, and proteins are formed by the combination of multiple polypeptides. In this context, individual amino acids are referred to as amino acid residues.
  • It is important to note that the acid-base properties of individual amino acids, such as the ability to donate or accept protons, are lost in proteins due to the involvement of the carboxyl group in peptide bond formation. Instead, the overall acidity or basicity of proteins is determined by the ionization characteristics of the individual R groups of the amino acid components. These R groups can be charged, polar, or nonpolar, contributing to the overall ionization behavior of proteins.
  • Overall, peptide bond formation is a critical process that links amino acids together, forming the backbone of proteins. The specific sequence and arrangement of amino acids in a protein chain determine its structure and function, playing a fundamental role in various biological processes.
Peptide bond formation between two amino acids with the release of a water molecule.
Peptide bond formation between two amino acids with the release of a water molecule.

3. Optical properties

  • Amino acids, with the exception of glycine, exhibit a property known as optical activity. This optical activity arises from the presence of chiral carbons in the amino acid molecules. Chiral carbons are carbons that have four different groups attached to them, resulting in a non-superimposable mirror image of the molecule.
  • The asymmetry created by these chiral carbons gives rise to enantiomers, which are molecules that are mirror images of each other but cannot be superimposed. Enantiomers have identical physical and chemical properties except for their interaction with plane-polarized light.
  • Glycine, however, does not possess a chiral carbon. It has two hydrogen atoms attached to its alpha-carbon, making it optically inactive.
  • When performing ordinary chemical synthesis, it is important to consider the concept of enantiomers. Chemical or physical processes generally do not have a stereochemical bias, which means that during the synthesis of chiral molecules, racemic mixtures are often produced. Racemic mixtures contain equal amounts of both the right-handed (D-enantiomer) and left-handed (L-enantiomer) forms of the molecule.
  • Understanding the optical properties and stereochemistry of amino acids and other molecules is essential in fields such as pharmaceuticals, biochemistry, and materials science, as it influences the behavior and interactions of these compounds in biological systems and chemical reactions.
Structure of alanine isomers.
Structure of alanine isomers.

4. Acid-base properties

  • Amino acids exhibit both acid and base properties, making them amphoteric molecules. The acidity or basicity of amino acids is determined by the charges on their carboxyl and amino groups.
  • The basic amino group in amino acids has a pKa value ranging from 9 to 10, indicating its strength as a base. On the other hand, the acidic carboxyl group has a pKa value close to 2, representing its strength as an acid. The pKa value is a measure of the acid dissociation constant (Ka) and is defined as the negative logarithm base 10 of Ka.
  • At physiological pH, amino acids exist as dipolar ions or zwitterions. This occurs when the concentration of protonated groups (positive charge) is equal to that of unprotonated groups (negative charge). The pH at which this balancing of charges occurs is called the isoelectric point (pI). It is important to note that at the isoelectric point, amino acids have a net-zero charge, but they are never considered to have an absolute zero charge. In an aqueous solution, amino acids do not exist in a completely neutral form.
  • Understanding the acid-base properties of amino acids is essential in various biochemical processes. The charges on amino acids influence their interactions with other molecules, such as enzymes or receptors, and their behavior within physiological systems. The isoelectric point and the balanced charge at physiological pH play important roles in protein folding, solubility, and other aspects of amino acid function in living organisms.
(1) General structure of amino acid, and (2) its zwitterionic form.
(1) General structure of amino acid, and (2) its zwitterionic form.

5. Chemical reactions

Amino acids undergo various chemical reactions involving their functional groups. Here are some important chemical reactions of amino acids:

  1. Deamination: Deamination involves the transfer of an amino group from an amino acid to another compound, resulting in the formation of a different amino acid. For instance, the transfer of an amino group to alpha-ketoglutarate leads to the formation of glutamate.
  2. Condensation Reaction: A condensation reaction occurs when two or more amino acids combine, forming a peptide bond and releasing a water molecule. This process links amino acids together, ultimately forming polypeptides and proteins.
  3. Cysteine Oxidation: Cysteine oxidation involves the oxidation of two cysteine molecules, resulting in the formation of cystine. Disulfide bonds are formed during this reaction, utilizing the high reactivity of the thiol group in cysteine. These disulfide bridges provide stability to proteins and are crucial for their structure and function.

These are just a few examples of the many chemical reactions that amino acids can undergo. These reactions play a significant role in protein synthesis, modification, and structure, influencing the diverse functions that proteins carry out in biological systems.

What are aliphatic amino acids?

Aliphatic amino acids are a group of amino acids characterized by having nonpolar, hydrophobic side chains. These amino acids are not soluble in water and tend to reside in the interior of proteins. The aliphatic amino acids include alanine (Ala), glycine (Gly), isoleucine (Ile), leucine (Leu), methionine (Met), and valine (Val). The side chains of these amino acids are composed of carbon and hydrogen atoms, except for methionine, which contains a sulfur atom in its side chain. The length of the side chains varies, with alanine having the shortest and valine having the longest.

Aliphatic amino acids play important roles in protein structure and function. They contribute to the stability of proteins by participating in hydrophobic interactions with other hydrophobic amino acids. They are also involved in protein folding processes. For instance, methionine is often found at the beginning of protein chains, where it aids in initiating protein folding.

Beyond their structural significance, aliphatic amino acids have various biological functions. For example, alanine serves as an energy source for cells, while methionine is involved in protein synthesis and the production of other molecules.

In summary, aliphatic amino acids possess hydrophobic properties and contribute to protein stability, folding, and function. Their presence in proteins is essential for maintaining proper structure and facilitating vital biological processes.

Amino acidSide chainNumber of carbon atomsHydrophobicity
Alanine-CH31High
Glycine-H1Low
Isoleucine-CH(CH3)CH33High
Leucine-CH2CH(CH3)24High
Methionine-CH2CH2S(CH3)5High
Valine-CH(CH3)23High

How to calculate pi of amino acid?

The isoelectric point (pI) of an amino acid can be calculated using the pKa values of its functional groups, specifically the amino group (-NH2) and the carboxyl group (-COOH). The pI is the pH at which the amino acid exists as a zwitterion, meaning it has no net charge.

Here’s a general approach to calculate the pI of an amino acid:

  1. Determine the pKa values of the amino and carboxyl groups. The pKa of the amino group is typically around 9-10, while the pKa of the carboxyl group is around 2.
  2. Find the average of the pKa values. Add the pKa of the amino group and the pKa of the carboxyl group, and then divide the sum by 2.
  3. If the side chain of the amino acid contains any additional functional groups with acidic or basic properties, consider their pKa values as well.
  4. The resulting average pKa value is the approximate pI of the amino acid.

It’s important to note that this method provides an estimation and the actual pI may vary due to factors such as temperature and pH conditions.

Additionally, there are online databases and software tools available that can calculate the pI of specific amino acids based on more precise algorithms and incorporating additional factors.

Deficiency of Amino acids

Amino acids serve as the fundamental building blocks of proteins, which are crucial for various biological processes in the body. The presence of all nine essential amino acids in the diet is necessary for maintaining optimal health and physiological function. A deficiency in amino acids can lead to a range of pathological disorders, impacting overall well-being.

  • Pathological Disorders Associated with Amino Acid Deficiency:
    • Edema: Insufficient amino acids can result in fluid retention, leading to swelling in different body parts.
    • Anemia: A lack of certain amino acids may impair hemoglobin production, resulting in reduced red blood cell count and subsequent anemia.
    • Insomnia: Amino acid deficiency can disrupt sleep patterns, contributing to difficulties in falling and staying asleep.
    • Diarrhea: Amino acids are involved in maintaining gut health; their deficiency may lead to gastrointestinal issues, including diarrhea.
    • Depression: The synthesis of neurotransmitters, which are vital for mood regulation, can be affected by insufficient amino acids, leading to depressive symptoms.
    • Hypoglycemia: Inadequate levels of amino acids can hinder gluconeogenesis, resulting in low blood sugar levels.
    • Loss of Appetite: Deficiency in amino acids may alter appetite-regulating mechanisms, leading to a reduced desire to eat.
    • Fat Deposit in the Liver: Insufficient amino acids can contribute to abnormal fat accumulation in the liver, potentially leading to liver dysfunction.
    • Skin and Hair-Related Problems: Amino acids are crucial for maintaining skin and hair health; their deficiency can lead to issues such as dryness, brittleness, and other dermatological conditions.
    • Headache, Weakness, Irritability, and Fatigue: A general deficiency can manifest as headaches, physical weakness, irritability, and fatigue due to impaired metabolic functions and energy production.

Functions of Amino acids

Amino acids play critical roles in various physiological functions, serving as the building blocks of proteins and participating in metabolic processes. They can be categorized into essential and non-essential amino acids, each contributing uniquely to health and well-being.

  • Functions of Essential Amino Acids:
    • Phenylalanine: Supports the nervous system and enhances memory.
    • Valine: Contributes significantly to muscle growth and repair.
    • Threonine: Plays a crucial role in bolstering the immune system’s functions.
    • Tryptophan: Involved in synthesizing vitamin B3 and serotonin, which regulates appetite, sleep, and mood.
    • Isoleucine: Essential for hemoglobin formation, stimulates insulin synthesis in the pancreas, and aids in oxygen transport from the lungs.
    • Methionine: Utilized in treating kidney stones, promotes healthy skin, and controls pathogenic bacterial growth.
    • Leucine: Encourages protein synthesis and stimulates the release of growth hormones.
    • Lysine: Vital for forming antibodies, hormones, and enzymes, and aids in calcium fixation in bones.
    • Histidine: Participates in enzymatic processes and is essential for synthesizing red blood cells (erythrocytes) and white blood cells (leukocytes).
  • Functions of Non-Essential Amino Acids:
    • Alanine: Assists in detoxifying the body and producing glucose and other amino acids.
    • Cysteine: Functions as an antioxidant, supports collagen production, and influences skin texture and elasticity.
    • Glutamine: Promotes brain health and is necessary for synthesizing nucleic acids, such as DNA and RNA.
    • Glycine: Important for proper cell growth, functioning, wound healing, and acts as a neurotransmitter.
    • Glutamic Acid: Functions as a neurotransmitter, crucial for brain development and function.
    • Arginine: Supports protein and hormone synthesis, detoxification in the kidneys, wound healing, and immune system health.
    • Tyrosine: Essential for producing thyroid hormones (T3 and T4), neurotransmitters, and melanin, which are natural pigments in the eyes, hair, and skin.
    • Serine: Promotes muscle growth and aids in synthesizing immune system proteins.
    • Asparagine: Involved in nitrogen transport into cells, purine and pyrimidine synthesis for DNA, nervous system development, and enhancing stamina.
    • Aspartic Acid: Plays a significant role in metabolism and the synthesis of other amino acids.
    • Proline: Critical for tissue repair, collagen formation, and preventing arterial thickening (arteriosclerosis), and aids in regenerating new skin.

Applications of Amino Acids

Amino acids find a wide range of applications in various industries. Here are some notable applications:

  1. Animal Feed Additives: Amino acids like lysine, methionine, threonine, and tryptophan are added to animal feed. These additives are chelated with metal cations to enhance mineral absorption, promoting better animal health.
  2. Artificial Sweetener: Aspartame, derived from aspartic acid and phenylalanine, is a widely used artificial sweetener in food and beverages.
  3. Flavor Enhancer: Glutamic acid, in the form of monosodium glutamate (MSG), is a popular flavor enhancer used in the food industry to improve the taste of various dishes.
  4. Mineral Absorption Supplements: Amino acids are utilized as supplements to enhance mineral absorption in the human body, particularly for individuals with mineral deficiencies.
  5. Pharmaceutical and Cosmetic Manufacturing: Amino acids are used in the production of drugs and cosmetic products due to their various properties and benefits for skin and hair health.
  6. Fertilizer Development: Amino acids are incorporated into fertilizers to improve mineral absorption in plants, preventing deficiencies and promoting healthy growth without compromising overall productivity.
  7. Biodegradable Polymers: Amino acids are utilized in the manufacturing of biodegradable polymers. These polymers are used to develop eco-friendly packaging materials, drug delivery carriers, and prosthetic implants.

FAQ

What are amino acids?

Amino acids are organic compounds that serve as the building blocks of proteins. They contain an amino group (-NH2), a carboxyl group (-COOH), and a side chain (R group) attached to a central carbon atom.

How many amino acids are there?

There are 20 standard amino acids that are commonly found in proteins. These are known as proteinogenic amino acids. However, there are also other non-standard and modified amino acids that have specific roles in certain biological processes.

What are essential amino acids?

Essential amino acids are amino acids that cannot be synthesized by the human body and must be obtained through the diet. There are nine essential amino acids: histidine, isoleucine, leucine, lysine, methionine, phenylalanine, threonine, tryptophan, and valine.

What are non-essential amino acids?

Non-essential amino acids are amino acids that can be synthesized by the human body from other sources. Although they are still important for various biological functions, they do not need to be obtained from the diet. Examples of non-essential amino acids include alanine, glutamine, glycine, and proline.

What is the role of amino acids in the body?

Amino acids have numerous roles in the body, including protein synthesis, enzyme production, hormone regulation, immune function, neurotransmitter synthesis, and energy production. They are essential for growth, repair, and maintenance of tissues and organs.

Can amino acids be used as dietary supplements?

Yes, amino acids are available as dietary supplements. They are often used by athletes and bodybuilders to support muscle growth, recovery, and overall performance. However, it is important to use supplements under the guidance of a healthcare professional to ensure proper dosage and safety.

Are amino acids only found in animal-based foods?

No, amino acids are found in both animal-based and plant-based foods. Animal sources such as meat, fish, eggs, and dairy products are considered complete proteins as they contain all essential amino acids. Plant sources like legumes, grains, nuts, and seeds can provide amino acids as well, but some plant proteins may lack certain essential amino acids.

Can amino acid deficiencies occur?

Yes, deficiencies in specific amino acids can occur, especially if the diet is imbalanced or lacks variety. Amino acid deficiencies can lead to various health problems, including impaired growth, muscle wasting, immune dysfunction, and neurological disorders.

Can amino acids have side effects?

While amino acids are generally safe when consumed through food, high doses of individual amino acid supplements may have side effects. Excessive intake of certain amino acids can disrupt the balance of other amino acids or interfere with metabolic processes. It is important to follow recommended dosages and consult a healthcare professional before taking amino acid supplements.

Can amino acids be obtained from vegetarian or vegan diets?

Yes, it is possible to obtain all essential amino acids from vegetarian or vegan diets by combining different plant-based protein sources. Consuming a variety of legumes, grains, nuts, seeds, and vegetables can provide adequate amounts of essential amino acids. It is important to plan meals carefully to ensure a balanced intake of amino acids for vegetarians and vegans.

Which part of an amino acid is always acidic?

The carboxyl group (-COOH) of an amino acid is always acidic. This group can release a proton (H+) in an aqueous solution, resulting in the formation of a negatively charged carboxylate ion (-COO-). The acidic nature of the carboxyl group is responsible for the acid-base properties of amino acids.

Which two functional groups are always found in amino acids?

The two functional groups that are always found in amino acids are the amino group (-NH2) and the carboxyl group (-COOH). These two groups are attached to a central carbon atom called the alpha carbon (-C-). The amino group acts as a base, capable of accepting a proton (H+) to form a positively charged amino group (-NH3+). The carboxyl group, on the other hand, acts as an acid, capable of donating a proton to form a negatively charged carboxylate group (-COO-). The presence of both the amino and carboxyl groups is what gives amino acids their unique properties and enables them to participate in peptide bond formation and protein synthesis.

What type of bonds link individual amino acids together?

Individual amino acids are linked together through peptide bonds. A peptide bond forms through a condensation reaction, also known as a dehydration reaction, between the carboxyl group (-COOH) of one amino acid and the amino group (-NH2) of another amino acid. During this process, a water molecule is released, and the carbon of the carboxyl group becomes covalently bonded to the nitrogen of the amino group, forming the peptide bond. This bond is crucial for the formation of polypeptides and proteins, as it connects the amino acids in a linear chain and determines the primary structure of the protein.

Which type of mutation results in abnormal amino acid sequence?

A type of mutation known as a missense mutation can result in an abnormal amino acid sequence. In a missense mutation, a single nucleotide change in the DNA sequence leads to the substitution of one amino acid for another during protein synthesis. This substitution can alter the structure and function of the resulting protein. The specific amino acid change introduced by the missense mutation may disrupt the protein’s normal folding, interactions, enzymatic activity, or stability, leading to a protein with abnormal properties. Missense mutations can have various effects, ranging from mild to severe, depending on the location of the mutation within the protein and the specific amino acid substitution that occurs.

a bunch of amino acids attached together is called a

A bunch of amino acids attached together is called a polypeptide. A polypeptide is a linear chain of amino acids that are linked together by peptide bonds. The length of a polypeptide can vary, ranging from just a few amino acids to hundreds or even thousands of amino acids. Polypeptides are the precursor molecules to proteins. They undergo further folding and modifications to form the three-dimensional structure of a functional protein, which performs specific biological functions in the body.

How many codons code for amino acids?

There are 64 possible codons, of which 61 code for amino acids. The genetic code is a set of rules that determines how the sequence of nucleotides in DNA or RNA is translated into the sequence of amino acids in a protein. Each codon consists of three nucleotides, and there are 4 different nucleotides (A, C, G, and U) that can occupy each position in a codon.
Out of the 64 possible codons, three of them are stop codons (UAA, UAG, and UGA) that signal the end of protein synthesis. The remaining 61 codons correspond to the 20 different amino acids that are used to build proteins. However, some amino acids are represented by multiple codons. For example, the amino acid leucine is coded by six different codons (CUU, CUC, CUA, CUG, UUA, and UUG), while others, like methionine and tryptophan, are coded by only one codon each.
It’s worth noting that the genetic code is nearly universal, with few exceptions across different organisms, allowing for the accurate translation of genetic information into proteins.

How many codons equal one amino acid?

Each amino acid is coded by one or more codons. There are 20 standard amino acids used in protein synthesis. However, the number of codons that code for a specific amino acid can vary. Some amino acids are represented by a single codon, while others are encoded by multiple codons. For example, methionine and tryptophan are each coded by a single codon (AUG and UGG, respectively). On the other hand, amino acids like leucine, serine, and arginine have multiple codons that specify them. Leucine, for instance, is coded by six different codons (CUU, CUC, CUA, CUG, UUA, and UUG). The precise number of codons per amino acid depends on the specific genetic code being considered.

Which pair of statements best describes an essential amino acid?
1 It is an amino acid that contains peptide bonds. An example is proline.
2 It is an amino acid that contains nitrogen. An example is aspartic acid.
3 It is an amino acid that cannot be made by the body. It must be obtained from eating certain foods.
4 It is an amino acid that can be produced by the body. Vitamin supplements maintain healthy levels.

The correct pair of statements that best describes an essential amino acid is:
It is an amino acid that cannot be made by the body. It must be obtained from eating certain foods.
Essential amino acids are those that the body cannot synthesize on its own and must be obtained from the diet. They are necessary for proper functioning and growth. Different foods contain essential amino acids, and a balanced diet is required to ensure an adequate intake of all essential amino acids.

What makes amino acids unique from one another?

Amino acids are differentiated from one another primarily by their side chains, also known as R groups. The side chain is a variable component of the amino acid structure that distinguishes one amino acid from another. The side chain can vary in size, shape, charge, and chemical properties, which imparts distinct characteristics to each amino acid.
The side chain can be simple, such as a single hydrogen atom in the case of glycine, or more complex with functional groups like hydroxyl, amino, carboxyl, methyl, aromatic rings, sulfur, and others. These side chains contribute to the amino acid’s unique chemical properties, such as polarity, hydrophobicity, acidity, basicity, and reactivity.
The differences in the side chains give amino acids their diverse characteristics, including their ability to interact with other molecules, participate in protein folding, enzymatic activity, and contribute to the overall structure and function of proteins.
The variations in side chains allow for a wide range of interactions and molecular recognition in biological systems. These unique properties of the side chains play a crucial role in determining the behavior, specificity, and functionality of amino acids and the proteins they form.

What is limiting amino acid?

A limiting amino acid refers to an essential amino acid that is present in the lowest quantity relative to the requirements for protein synthesis. When a diet lacks an adequate amount of a specific essential amino acid, that amino acid becomes the limiting factor in protein synthesis.
The availability of the limiting amino acid can restrict the rate of protein synthesis and limit the overall efficiency of protein production. Even if all other essential amino acids are present in sufficient amounts, protein synthesis will be hindered by the inadequate supply of the limiting amino acid.
The concept of limiting amino acids is often discussed in the context of formulating balanced diets, particularly for animals or individuals with specific nutritional needs. It involves identifying the amino acid(s) that are most deficient relative to the requirements for protein synthesis and ensuring that their intake is increased or supplemented.
By addressing the deficiency of the limiting amino acid(s), one can optimize protein synthesis and support proper growth, development, and overall health. It is important to note that the specific amino acid(s) that function as limiting factors can vary depending on the species or individual’s physiological requirements.

What is the amino acid pool?

The amino acid pool refers to the collective and readily available supply of amino acids in the body. It is a dynamic reservoir of amino acids that can be used for protein synthesis, energy production, and various metabolic processes.
The amino acid pool is maintained through a balance between dietary intake and the breakdown of proteins within the body. When dietary protein is consumed, the amino acids from the digested proteins are absorbed into the bloodstream and contribute to the amino acid pool. Additionally, the body can also break down its own proteins (such as those from muscle tissue) to release amino acids into the pool.
The amino acid pool serves as a crucial resource for protein synthesis, enabling the body to build and repair proteins as needed. It provides the necessary raw materials for the synthesis of enzymes, structural proteins, hormones, antibodies, and other vital molecules.
The amino acid pool also plays a role in energy metabolism. During periods of fasting or intense physical activity, amino acids can be used as an energy source through processes like gluconeogenesis, where amino acids are converted into glucose.
Maintaining a balanced amino acid pool is essential for overall health and proper functioning of various physiological processes. It requires an adequate intake of dietary protein and a healthy balance between protein breakdown and synthesis within the body.

what two functional groups are found in amino acids

The two functional groups that are found in amino acids are the amino group (-NH2) and the carboxyl group (-COOH). These functional groups are attached to the central carbon atom, known as the alpha carbon (-C-), of the amino acid structure.
The amino group is composed of a nitrogen atom bonded to two hydrogen atoms. It acts as a base, capable of accepting a proton (H+), and can become positively charged (NH3+) when protonated.
The carboxyl group consists of a carbon atom double-bonded to an oxygen atom and single-bonded to a hydroxyl group (-OH). It acts as an acid, capable of donating a proton, and can become negatively charged (-COO-) when deprotonated.
The combination of these two functional groups in amino acids makes them amphoteric, meaning they can act as both acids and bases depending on the pH conditions. This characteristic is essential for the role of amino acids in biochemical processes, such as protein synthesis and acid-base balance in the body.

how many nucleotides are needed to specify three amino acids

To specify three amino acids, a minimum of 9 nucleotides would be needed. Each amino acid is encoded by a codon, which consists of three nucleotides. Therefore, three amino acids would require three codons, and each codon consists of three nucleotides.
It’s important to note that while 9 nucleotides can specify three amino acids, the specific sequence of the nucleotides within the codons determines which amino acids are encoded. Different combinations of nucleotides can result in different amino acids being specified.

Reference
  1. Lehninger, A. L., Nelson, D. L., & Cox, M. M. (2000). Lehninger principles of biochemistry. New York: Worth Publishers.
  2. Reitzer, L. (2009). Amino Acid Synthesis. Encyclopedia of Microbiology, 1–17. doi:10.1016/b978-012373944-5.00063-8
  3. https://byjus.com/biology/amino-acids/
  4. https://biochemden.com/physio-chemical-properties-of-amino-acids/
  5. https://www.onlinebiologynotes.com/properties-of-amino-acids-physical-and-chemical/
  6. https://microbiologynotes.org/amino-acids-physical-chemical-properties-and-peptide-bond/
  7. https://www.thermofisher.com/in/en/home/life-science/protein-biology/protein-biology-learning-center/protein-biology-resource-library/pierce-protein-methods/amino-acid-physical-properties.html

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