BIOQUI - 28/03/2023

Understanding Amino Acids and Their Properties

Overview of Amino Acids

• The majority of amino acids in biology are alpha-amino acids, with some important gamma-amino acids like GABA (gamma-aminobutyric acid).

Structure of Amino Acids

• Each amino acid has a central carbon (alpha carbon), a carboxyl group (acid), an amino group, and a unique side chain or radical that identifies each amino acid.

Formation and Importance

• Amino acids are essential for life; they were among the first biological molecules formed. They combine to create peptides and proteins, which are vital for all living organisms.

Micromolecular Composition

• Amino acids consist of a carboxyl group, an amino group, and a side chain attached to the alpha carbon. Their structure can change based on pH levels.

Ionization States

• At physiological pH (around 7), amino acids exist as dipolar ions due to their dual charges: the carboxyl group loses hydrogen (negative charge), while the amino group gains hydrogen (positive charge).

Properties of Amino Acids

Ionization Behavior

• The ionization state of amino acids varies with pH: at acidic pH they act as cations, at neutral pH they are dipolar ions, and at basic pH they become anions.

Physical-Chemical Properties

• Key physical properties include high solubility in polar solvents and elevated melting points (>200°C). These properties arise from strong ionic attractions within their structures.

Isoelectric Point

Understanding Amino Acids and Their Properties

Isoelectric Point of Amino Acids

• The isoelectric point (pI) is the pH at which an amino acid has no net charge, indicating a balance between positive and negative charges.

• Each of the 20 standard amino acids has a unique isoelectric point, influenced by their specific dissociation constants (pKa).

Charge Variability with pH

• Histidine serves as a classic example; it can exhibit different charges depending on the pH, ranging from neutral to positively charged. At physiological pH, it typically carries no charge.

• The calculation of the isoelectric point involves averaging the pKa values of an amino acid's ionizable groups, resulting in a net charge of zero at that specific pH.

Classification of Amino Acids

• Amino acids can be categorized based on their side chains into acidic (e.g., aspartate and glutamate) and basic (e.g., arginine, lysine, histidine) groups. Basic amino acids carry a positive charge at physiological pH while acidic ones carry a negative charge.

• The classification also includes structural types such as aliphatic or cyclic amino acids, which influence their behavior in different environments due to varying charges across different pH levels.

Spatial Properties and Chirality

• Amino acids exist in two enantiomeric forms: L (left-handed) and D (right-handed), with L-amino acids being predominant in biological systems. This chirality affects their interactions within proteins.

• Most naturally occurring amino acids are L-amino acids; D-amino acids are rare but found in certain bacteria and antibiotics. The configuration impacts how these molecules function biologically.

Absorption Properties

• All amino acids absorb ultraviolet light at specific wavelengths; notably, they show maximum absorption around 280 nanometers, which correlates with concentration levels in solutions. This property aids in quantifying protein concentrations through spectrophotometry.

Understanding Amino Acids and Their Classification

Structure and Formation of Amino Acids

• Amino acids are micro-molecules composed of an acid group and a nitrogen group attached to a single carbon. When amino acids link together, they form peptides, which can further combine into polypeptides and ultimately proteins.

Essential vs. Non-Essential Amino Acids

• There are 20 proteinogenic amino acids; ten are essential (must be ingested through diet) while the other ten are non-essential (can be synthesized by the body).

• Essential amino acids cannot be formed by the human body and must be obtained from dietary sources. The classification is based on nutritional necessity rather than importance.

Non-Proteinogenic Amino Acids

• Over 300 non-proteinogenic amino acids exist, such as DOPA (a precursor to catecholamines), beta-alanine, and GABA (gamma-aminobutyric acid). These do not contribute to protein formation but have significant biological roles.

Mnemonics for Essential Amino Acids

• A mnemonic device called "Tim Hall" helps remember essential amino acids: histidine, arginine, lysine, leucine, proline (not essential), valine, threonine, phenylalanine, tryptophan, cysteine, and methionine.

Properties of Amino Acids

• Amino acids can carry positive or negative charges depending on pH levels. Polar amino acids interact with water while non-polar ones are hydrophobic.

• Six major groups classify all amino acids based on their side chains: aliphatic, aromatic, sulfur-containing, alcohol-containing, acidic/basic structures.

Structural Characteristics of Specific Amino Acids

• Hydrophobic amino acids like valine and leucine possess simple branched structures. Tyrosine has a phenolic group that becomes negatively charged at higher pH levels.

Bonding in Protein Structures

• Sulfur-containing amino acids like cysteine and methionine form disulfide bonds that stabilize tertiary and quaternary protein structures through strong covalent links.

Summary of Key Amino Acids

Classification and Characteristics of Amino Acids

Overview of Amino Acid Classification

• The classification of protein amino acids traditionally uses three-letter abbreviations, but a new system employs single-letter codes for modifications and sequencing.

• For practical purposes, students should remember amino acids by their three-letter codes; examples include histidine (His), arginine (Arg), and alanine (Ala).

Simple and Branched Amino Acids

• Glycine is noted as the simplest amino acid with only one hydrogen in its side chain, making it non-chiral.

• Alanine has a simple structure with a methyl group, while valine contains three aliphatic methyl groups. Leucine and isoleucine are larger branched-chain amino acids.

Nutritional Importance of Branched-Chain Amino Acids

• Branched-chain amino acids (BCAAs)—valine, leucine, and isoleucine—are significant in nutrition due to their rapid absorption from the intestine to the liver.

• BCAAs serve as nitrogen sources and contribute to various compounds beyond proteins, including creatinine and neurotransmitters.

Structural Variations Among Amino Acids

• Methionine contains sulfur; phenylalanine features a cyclic structure. Tryptophan is the largest amino acid with a double cyclic structure.

• Proline's unique ring structure allows for greater flexibility in protein folding compared to other amino acids.

Essential vs Non-Essential Amino Acids

• Essential amino acids must be obtained through diet; mnemonic "HILL PMT" helps recall essential ones like histidine, arginine, leucine, lysine, methionine, phenylalanine.

• The terminology around essentiality has shifted towards "indispensable" versus "non-indispensable," yet both terms remain relevant in discussions about dietary needs.

Understanding Single-Letter Codes

• Current practices often use single-letter codes for amino acids; for example, arginine is represented as 'R' instead of 'Arg'.

• Familiarity with these codes is crucial when interpreting sequences or structures presented in research literature.

Abundance and Molecular Weight of Amino Acids

• Commonly abundant amino acids include alanine and glutamate; glutamate also functions as a neurotransmitter.

• Average molecular weight varies among amino acids; tryptophan has the highest at 186 g/mol while glycine has the lowest at 57 g/mol.

Classification of Amino Acids

Overview of Amino Acid Classification

• Amino acids are classified based on their properties, including polarity and charge. Non-polar (hydrophobic) amino acids are typically found in the center of proteins, away from water.

• The classification includes non-polar aliphatic amino acids with open chains and non-polar aromatic amino acids with cyclic structures, such as phenylalanine and tryptophan.

Polar Amino Acids

• Polar amino acids are further divided into:

• Polar without charge: Examples include serine, threonine, tyrosine, and cysteine.

• Polar with negative charge: These are acidic amino acids like aspartic acid and glutamic acid.

• Polar with positive charge: Basic amino acids such as lysine, arginine, and histidine carry a positive charge.

Ionization of Amino Acids

• When acidic amino acids ionize, they lose the "acid" suffix; for example:

• Aspartic acid becomes aspartate.

• Glutamic acid becomes glutamate.

• Basic amino acids retain their names despite having a positive charge.

Importance of Polarity in Protein Structure

• Understanding the polarity of amino acids is crucial for analyzing protein structures (primary to quaternary levels) and their composition.

Discussion on Rare Proteins

Uncommon Proteinogenic Amino Acids

• Some rare proteinogenic amino acids derived from standard ones spark debate about whether to classify them among the twenty common ones or consider them separately.

• Examples include selenocysteine and hydroxylysine. Hydroxyproline is another derivative formed by hydroxylation at specific positions.

Controversy Over Classification

• There is significant discussion regarding whether these derivatives should be included in the count of standard amino acids. Some argue for a total count beyond twenty due to their prevalence in proteins like collagen.

Non-proteinogenic Amino Acids

Characteristics and Functions

• Non-proteinogenic amino acids do not form part of proteins but serve important roles as metabolic intermediates or structural components in various biological processes.

Key Non-proteinogenic Amino Acids

• GABA (gamma-Aminobutyric acid): A neurotransmitter derived from glutamate.

• Beta-alanine: Precursor to pantothenic acid (vitamin B5), which forms coenzyme A.

Biological Markers

• Homocysteine is highlighted as a biological marker indicating cardiovascular risk factors such as high cholesterol or diabetes. It derives from methionine metabolism.

Additional Important Non-proteinogenic Compounds

• Cystathionine: Formed from homocysteine; involved in various metabolic pathways.

• Citrulline: An intermediate in the urea cycle that plays roles in nitrogen metabolism.

Ciclo de la Urea y Funciones de los Aminoácidos

Derivados de Aminoácidos

• El ciclo de la urea y la síntesis de arginina producen compuestos derivados de aminoácidos, que son esenciales no solo para formar proteínas, sino también para otras funciones vitales en el organismo.

• Los aminoácidos son versátiles; pueden ser utilizados para formar glucosa, neurotransmisores y transportar grupos aminos, además de su función principal en la polimerización para formar proteínas.

Importancia de la Arginina

• La arginina es un aminoácido semiesencial; aunque puede ser sintetizada por el cuerpo, es crucial que los niños obtengan suficiente a través de su dieta.

• Participa en la formación de urea y compuestos llamados poliaminas (putrecina, espermidina y espermina), que son importantes factores de crecimiento y moduladores en la diferenciación celular.

Poliaminas y Su Función

• Las poliaminas derivadas de arginina estabilizan estructuras como ribosomas, virus y ADN, siendo fundamentales en procesos biológicos relacionados con el crecimiento celular.

Otros Aminoácidos Clave

• El ácido aspártico da lugar a pirimidinas; glicina forma creatinina (almacenamiento energético), sales biliares y está involucrada en antioxidantes como el glutatión.

• La histidina produce histamina, un vasodilatador importante relacionado con reacciones alérgicas. Se forma mediante descarboxilación por enzimas específicas.

Derivados Importantes: Tirosina

• La tirosina genera múltiples derivados significativos como adrenalina, noradrenalina (catecolaminas), melanina y hormonas como tiroxina.

• También se relaciona con drogas derivadas del opio (morfina, codeína). Su grupo R es un alcohol que deriva directamente de fenilalanina.

Catecolaminas y Enfermedades Neurológicas

• La tirosina se convierte en dopa; esta sustancia es crucial para producir dopamina. Dopa se utiliza clínicamente para tratar Parkinson debido a su capacidad para atravesar la barrera hematoencefálica.

• Dopamina es esencial para controlar movimientos; su deficiencia está relacionada con Parkinson mientras que su exceso puede causar esquizofrenia.

Hormonas Relacionadas con Estrés

Neurotransmitters and Their Functions in the Nervous System

Key Neurotransmitters in the Sympathetic Nervous System

• The primary neurotransmitter of the sympathetic nervous system is a catecholamine that plays a crucial role in responses to alert situations, such as increasing heart rate and bronchodilation.

• While adrenaline is more commonly used clinically, this neurotransmitter is essential for various functions and is produced in noradrenergic neurons located throughout the brain, intestines, and other tissues.

Natural Alkaloids and Their Effects

• Natural alkaloids like mescaline from cacti can induce hallucinations; thyroid hormones derived from tyrosine are involved in growth and metabolic rate regulation.

• Synthetic drugs such as amphetamines act as stimulants for the nervous system and suppress appetite. Tryptophan, an important amino acid, has significant derivatives.

Tryptophan: Structure and Derivatives

• Tryptophan is notable for its high molecular weight; it’s classified as an aromatic or cyclic amino acid due to its structure. It serves as a precursor to serotonin.

• Upon hydroxylation at carbon five, tryptophan forms serotonin (5-hydroxytryptamine), which regulates vascular dilation. Serotonin can also degrade into melatonin, which regulates circadian cycles.

Melatonin's Role in Sleep Regulation