Biomolecules and Amino Acids Flashcards L 2

Assessments

• Dates are believed to be correct. If there are any issues, let the instructor know well in advance.

• Standard format: online quiz, written work, online quiz, written work.

• There will be a workshop before the first online quiz.

Biomolecules, Enzymes, or Biochemistry

• Intermolecular interactions between biomolecules:

  • Electrostatic interactions (ion-ion, ion-dipole, dipole-dipole).

  • Hydrogen bonding.

  • Van der Waals forces.

  • Hydrophobic effect.

Amino Acids

• Amino acids contain an acid group (carboxylic acid group) and an amino group.

• The amino acids that are mostly talked about in nature are known as alpha amino acids.

• Generic structure:

  • NH_2 (amino group).

  • CO_2H (carboxylic acid group).

  • Alpha carbon in between with a possible substituent (R group).

• Other types of amino acids: beta, gamma (not naturally occurring, research for drug development).

• The substituent on the central carbon determines a lot of an amino acids feature in addition to the amine and the acid.

  • R group can be polar, nonpolar, basic, or acidic.

• There are 21 amino acids that we concerned with.

  • Amino acids all have a CO2H and the NH2 separated by a carbon.

  • Glycine has no R group.

  • Alanine has an R group of CH_3.

    • Other R groups: hydroxy, amide, amines, methylmalines, acid groups.

• A table of common amino acids will be provided in the exam.

• Amino acids are grouped according to aliphatic, aromatic, and their different side groups.

• Animals need amino acids, plants need amino acids, microorganisms need amino acids.

• Two types of amino acids:

  • Plants and microorganisms synthesize their amino acids from inorganic precursors (carbon dioxide, water, nitrogen sources).

  • Animals obtain essential amino acids from their diet.

• Essential amino acids: arginine, histidine, lysine, threonine, methionine, isoleucine, valine, phenylalanine, and tryptophan.

• If you get enough of these nine in your diet, your body will be able to synthesize all the other amino acids.

Amines

• Primary amines: one R group attached to the nitrogen.

• Secondary amines: two R groups attached to the nitrogen.

• Tertiary amines: three R groups attached to the nitrogen.

• Examples:

  • Methylamine (CH3NH2).

  • Dimethylamine ((CH3)2NH).

  • Methylethylamine (CH3(C2H_5)NH).

• Amines are bases.

• Pyridine is a commonly used organic base.

• The amine group is a nucleophile (likes a nucleus because the nucleus has a positive charge).

• Nucleophilic reaction:

  • Amine attacks a delta positive carbon on an acid chloride.

  • Formation of an amide.

  • R-NH_2 + R'-COCl \rightarrow R-NH-CO-R' + HCl

• The amines and amine groups will react with acids.

  • It will take a photon, get a positive charge and become protonated.

• If it's protonated, that means associated with it is an anion.

• Amine + hydrochloric acid → ammonium ion.

PKa

• In water, amines are protolytic (depending on the pKa).

• Bronsted-Lowry acids and bases: simply the transfer of a hydrogen.

• Acid + Base \rightleftharpoons Conjugate Acid + Conjugate Base

• K_A: equilibrium constant, measuring how many protons will be transferred onto a base.

• pKA = -log{10}K_A

• Basicity is measured by looking at the pKa of the conjugate acid.

• The less acidic the ammonium ion is with its hydrogen, the more basic the original amine is.

• Ethylamine: pKa = 10.8 of conjugate acid.

• NaOH pKa is 15.7 (strong base).

• Ethanol pKa = -2.4 (incredibly weak base).

• Carboxylic acids:

  • The higher the Ka the weaker the acid.

  • The lower the pKa the stronger the acid.

  • Acetic acid (vinegar) pKa = 4.8.

  • Sulfuric acid pKa = -2.8.

  • Ethanol is a feeble acid.

• The pKa tells you the pH at which the molecule is 50% deprotonated.

Stereochemistry

• All but one of the amino acids are chiral (can exist in mirror image forms).

• Mirror image forms are called enantiomers.

• Assign them as R or S.

• Assign the groups priorities looking at Newman projections.

• Four different substituents gives rise for optical activity.

• R configuration: clockwise.

• S configuration: counterclockwise.

• Example: iodobromoethane.

• Methamphetamine:

  • Sinister form is an illicit substance.

  • R form is a decongestant sold over the counter.

• Phenylalanine:

  • Chiral.

  • S configuration.

• Glycine is not chiral because it has two hydrogens.

• Nature only uses one of the two forms.

Nature of the Side Groups

• Nonpolar side groups:

  • Alkyl (methyl, propyl, butyl).

  • Hydrophobic groups (hydrophobic effect).

  • Sulfur (methionine).

  • Aromatic ring (pie pie stacking, hydrophobicity).

• Polar side groups: OH or amide.

• Charged side groups:

  • Aspartic acid, glutamic acid (negative).

  • Arginine, histidine, lysine (positive).

• Other:

  • Glycine, cysteine, proline.

  • Proline: amine is part of a closed ring.

  • Cysteine: sulfur group cross-links.

Zwitterionic Form

• Amino acids can have a positively charged amine, be negatively charged, or both (zwitterionic form).

• Cation, anion, zwitterion.

• Need to know when it exists in each form for analysis.

Assessments

• Dates are believed to be correct. If there are any issues, let the instructor know well in advance. It's crucial to verify these early to accommodate any scheduling conflicts or required adjustments.

• Standard format: online quiz, written work, online quiz, written work. This alternating pattern ensures a mix of assessment types to evaluate different aspects of understanding and application.

• There will be a workshop before the first online quiz. This workshop aims to prepare students by reviewing key concepts, providing practice questions, and offering tips for success.

Biomolecules, Enzymes, or Biochemistry

• Intermolecular interactions between biomolecules: These interactions are critical for the structure and function of biological molecules.

  • Electrostatic interactions (ion-ion, ion-dipole, dipole-dipole):

    • Ion-ion: Strong interactions between fully charged species.

    • Ion-dipole: Interactions between an ion and a polar molecule.

    • Dipole-dipole: Interactions between two polar molecules.

  • Hydrogen bonding: A special type of dipole-dipole interaction that is crucial for stabilizing protein and DNA structures.

  • Van der Waals forces: Weak, short-range interactions including London dispersion forces.

  • Hydrophobic effect: The tendency of nonpolar substances to aggregate in aqueous solutions, which plays a key role in protein folding and membrane formation.

Amino Acids

• Amino acids contain an acid group (carboxylic acid group) and an amino group. These functional groups give amino acids their amphoteric properties, allowing them to act as both acids and bases.

• The amino acids that are mostly talked about in nature are known as alpha amino acids. In alpha amino acids, the amino and carboxylic acid groups are attached to the same carbon atom.

• Generic structure:

  • NH_2 (amino group).

  • CO_2H (carboxylic acid group).

  • Alpha carbon in between with a possible substituent (R group). This R group is unique to each amino acid and determines its specific properties.

• Other types of amino acids: beta, gamma (not naturally occurring, research for drug development). These amino acids have the amino group located on the beta or gamma carbon, respectively, and are often synthesized for specific pharmaceutical applications.

• The substituent on the central carbon determines a lot of an amino acids feature in addition to the amine and the acid. The R group dictates whether an amino acid is polar, nonpolar, acidic, or basic, thereby influencing its role in protein structure and function.

  • R group can be polar, nonpolar, basic, or acidic.

• There are 21 amino acids that we are concerned with. These are the building blocks of proteins in most organisms.

  • Amino acids all have a CO2H and the NH2 separated by a carbon.

  • Glycine has no R group: Its R group is simply a hydrogen atom, making it the smallest amino acid.

  • Alanine has an R group of CH_3: It is a simple, nonpolar amino acid.

  • Other R groups: hydroxy, amide, amines, methylmalines, acid groups. These diverse R groups contribute to the wide range of properties observed in proteins.

• A table of common amino acids will be provided in the exam. Referencing this table will help in identifying and understanding the properties of different amino acids.

• Amino acids are grouped according to aliphatic, aromatic, and their different side groups. This classification aids in understanding their chemical behavior and interactions.

• Animals need amino acids, plants need amino acids, microorganisms need amino acids. Amino acids are essential for protein synthesis and various metabolic processes in all living organisms.

• Two types of amino acids:

  • Plants and microorganisms synthesize their amino acids from inorganic precursors (carbon dioxide, water, nitrogen sources). This capability allows them to produce all necessary amino acids.

  • Animals obtain essential amino acids from their diet. Animals lack the metabolic pathways to synthesize these amino acids and must obtain them through food.

• Essential amino acids: arginine, histidine, lysine, threonine, methionine, isoleucine, valine, phenylalanine, and tryptophan. These must be obtained from the diet because the body cannot synthesize them.

• If you get enough of these nine in your diet, your body will be able to synthesize all the other amino acids. The non-essential amino acids are synthesized from intermediates of metabolic pathways, using the essential amino acids as precursors.

Amines

• Primary amines: one R group attached to the nitrogen.

• Secondary amines: two R groups attached to the nitrogen.

• Tertiary amines: three R groups attached to the nitrogen.

• Examples:

  • Methylamine (CH3NH2): A primary amine.

  • Dimethylamine ((CH3)2NH): A secondary amine.

  • Methylethylamine (CH3(C2H_5)NH): A secondary amine with different alkyl groups.

• Amines are bases: They have a lone pair of electrons on the nitrogen atom that can accept a proton.

• Pyridine is a commonly used organic base: It is a heterocyclic amine with a nitrogen atom in the ring.

• The amine group is a nucleophile (likes a nucleus because the nucleus has a positive charge): The lone pair of electrons on the nitrogen atom can attack electron-deficient centers.

• Nucleophilic reaction:

  • Amine attacks a delta positive carbon on an acid chloride.

  • Formation of an amide.

  • R-NH_2 + R'-COCl \rightarrow R-NH-CO-R' + HCl

• The amines and amine groups will react with acids. This is due to the basic nature of the amine group.

  • It will take a photon, get a positive charge and become protonated.

• If it's protonated, that means associated with it is an anion: The positively charged ammonium ion will be associated with a negatively charged counterion to balance the charge.

• Amine + hydrochloric acid → ammonium ion. This is a common reaction where the amine acts as a base and accepts a proton from the acid.

PKa

• In water, amines are protolytic (depending on the pKa): They can either accept or donate protons depending on the pH of the solution and their pKa values.

• Bronsted-Lowry acids and bases: simply the transfer of a hydrogen. Acids donate protons, while bases accept protons.

• Acid + Base \rightleftharpoons Conjugate Acid + Conjugate Base

• K_A: equilibrium constant, measuring how many protons will be transferred onto a base. It indicates the strength of an acid.

• pKA = -log{10}K_A

• Basicity is measured by looking at the pKa of the conjugate acid: A higher pKa of the conjugate acid indicates a stronger base.

• The less acidic the ammonium ion is with its hydrogen, the more basic the original amine is: This inverse relationship is important for understanding amine basicity.

• Ethylamine: pKa = 10.8 of conjugate acid. This indicates that ethylamine is a relatively strong base.

• NaOH pKa is 15.7 (strong base). Sodium hydroxide is a very strong base commonly used in chemical reactions.

• Ethanol pKa = -2.4 (incredibly weak base). Ethanol is a very weak base and does not readily accept protons.

• Carboxylic acids:

  • The higher the Ka the weaker the acid.

  • The lower the pKa the stronger the acid.

  • Acetic acid (vinegar) pKa = 4.8. Acetic acid is a weak acid commonly found in vinegar.

  • Sulfuric acid pKa = -2.8. Sulfuric acid is a strong acid widely used in industrial processes.

  • Ethanol is a feeble acid.

• The pKa tells you the pH at which the molecule is 50% deprotonated. This is also known as the half-equivalence point and is useful for buffer preparation.

Stereochemistry

• All but one of the amino acids are chiral (can exist in mirror image forms). Glycine is the only achiral amino acid.

• Mirror image forms are called enantiomers: These are non-superimposable mirror images of each other.

• Assign them as R or S: The Cahn-Ingold-Prelog priority rules are used to assign R or S configurations to chiral centers.

• Assign the groups priorities looking at Newman projections: This helps visualize the spatial arrangement of substituents around a chiral center.

• Four different substituents gives rise for optical activity: A chiral center must have four different groups attached to it.

• R configuration: clockwise.

• S configuration: counterclockwise.

• Example: iodobromoethane.

• Methamphetamine:

  • Sinister form is an illicit substance.

  • R form is a decongestant sold over the counter.

• Phenylalanine:

  • Chiral.

  • S configuration.

• Glycine is not chiral because it has two hydrogens: The presence of two identical substituents on the alpha carbon makes it achiral.

• Nature only uses one of the two forms: This is known as homochirality and is a fundamental aspect of biological systems.

Nature of the Side Groups

• Nonpolar side groups:

  • Alkyl (methyl, propyl, butyl): These groups are hydrophobic and tend to cluster together in aqueous solutions.

  • Hydrophobic groups (hydrophobic effect): This effect drives protein folding and membrane formation.

  • Sulfur (methionine): Methionine contains a thioether group, which is relatively nonpolar.

  • Aromatic ring (pie pie stacking, hydrophobicity): Aromatic rings can participate in hydrophobic interactions and pi-pi stacking.

• Polar side groups: OH or amide. These groups can form hydrogen bonds with water and other polar molecules.

• Charged side groups:

  • Aspartic acid, glutamic acid (negative): These are acidic amino acids with negatively charged side chains at physiological pH.

  • Arginine, histidine, lysine (positive): These are basic amino acids with positively charged side chains at physiological pH.

• Other:

  • Glycine, cysteine, proline.

  • Proline: amine is part of a closed ring. This unique structure restricts the conformational flexibility of the peptide backbone.

  • Cysteine: sulfur group cross-links. The thiol group can form disulfide bonds, which stabilize protein structures.

Zwitterionic Form

• Amino acids can have a positively charged amine, be negatively charged, or both (zwitterionic form). The zwitterionic form is the predominant form at physiological pH.

• Cation, anion, zwitterion. The charge state depends on the pH of the solution relative to the pKa values of the amino and carboxyl groups.

• Need to know