CHEM4500: Amino Acids, Protein Structure, and Purification Flashcards

Flashcard deck containing 100 vocabulary cards covering amino acid structure, stereochemistry, peptide bonds, protein purification, sequencing, and evolution based on lecture slides.

Standard Amino Acids

The 20 amino acids that serve as the fundamental building blocks of proteins, combining in various sequences to produce structurally and functionally diverse proteins.

Condensation Reaction

A chemical reaction in which two molecules combine to form a covalent bond with the elimination of a water molecule ($\text{H}_2\text{O}$).

Peptide Bond

The covalent amide linkage formed between the $\alpha$-carboxyl group of one amino acid and the $\alpha$-amino group of another via a condensation reaction.

Dipeptide

A peptide polymer composed of exactly two amino acid units linked by a single peptide bond.

Tripeptide

A peptide polymer composed of three amino acid units joined by two peptide bonds.

Oligopeptide

A peptide chain composed of a relatively small number (a few) of joined amino acid residues.

Polypeptide

A long, continuous, and unbranched peptide chain composed of many amino acid residues linked by peptide bonds.

Amino Terminus (N-terminus)

The residue at the end of a polypeptide chain that retains a free, unbonded primary or secondary amino group.

Carboxy Terminus (C-terminus)

The residue at the end of a polypeptide chain that retains a free, unbonded carboxylate group.

Alpha-amino Acid ($\alpha$-amino acid)

An organic molecule containing a primary amino group ($-\text{NH}_2$) bonded to the $\alpha$-carbon atom directly adjacent to the carboxyl group.

Proline Structure

The sole standard amino acid containing a secondary amino group ($-\text{NH}-$) held in a rigid cyclic ring structure, which reduces polypeptide conformational flexibility.

Asparagine (Etymology)

Standard amino acid named after asparagus, from which it was first isolated.

Glutamate (Etymology)

Standard amino acid named after wheat gluten, from which it was originally isolated.

Tyrosine (Etymology)

Standard amino acid named from the Greek word tyros, meaning cheese.

Glycine (Etymology)

Standard amino acid named from the Greek word glykos, meaning sweet.

Biochemical Carbon Labeling

A convention naming amino acid carbons using Greek letters ($\beta, \gamma, \delta, \epsilon$) proceeding outward sequentially from the $\alpha$-carbon.

Organic Chemistry Carbon Numbering

A systematic numbering system assigned from one end of a molecule, assigning C-1 highest priority to the carboxyl carbon containing the highest atomic number substituent.

Optically Active Molecules

Asymmetric molecules that rotate the plane of plane-polarized light because they are non-superimposable on their mirror image.

Glycine Stereochemistry Exception

The only standard amino acid that is not optically active because its $\alpha$-carbon is bonded to two identical hydrogen atoms, making it achiral.

Chiral Center

An atom (such as the $\alpha$-carbon in 19 of the standard amino acids) bonded to four distinct chemical groups in a tetrahedral spatial arrangement.

Enantiomers

Pair of stereoisomers that are non-superimposable mirror images of one another around a chiral center.

D, L System

A stereochemical configuration system proposed by Emil Fischer in 1891 that relates the absolute configuration of chiral molecules to glyceraldehyde.

Optical Rotation of L-leucine

Rotates plane-polarized light $10.4^\text{o}$ to the left.

Optical Rotation of L-arginine

Rotates plane-polarized light $12.5^\text{o}$ to the right.

Fischer Convention for Amino Acids

Convention mapping amino acid groups around $C_\alpha$ (amino, carboxyl, R, H) directly to glyceraldehyde groups (hydroxyl, aldehyde, $\text{CH}_2\text{OH}$, H).

Racemic Mixture

An equimolar mixture of left- and right-handed enantiomers that shows no net optical rotation.

CHIMSV Rule

Mnemonic rule for the one-letter codes of Cys (C), His (H), Ile (I), Met (M), Ser (S), and Val (V), where the unique first letter of each amino acid name is used as its single-letter symbol.

AGLPT Naming Rule

Mnemonic rule assigning the non-unique starting letter to the most abundant amino acid in proteins among those sharing that initial (e.g., Leucine receives L over Lysine).

Phonetic Amino Acid Naming (RFYW)

Assigns single-letter codes based on phonetic spelling: aRginine (R), Fenylalanine (F), tYrosine (Y), and tWiptophan (W).

Name-Derived Amino Acid Symbols (DNEQ)

Assigns single-letter symbols based on letters found in or suggested by names: asparDic acid (D), asparagine (N), glutamEke (E), and Q-tamine (Q).

Lysine Single-Letter Code

Designated by the single letter K.

Nonpolar, Aliphatic R Groups

Amino acid group comprising Glycine, Alanine, Proline, Valine, Leucine, Isoleucine, and Methionine, characterized by nonpolar hydrocarbon side chains.

Hydrophobic Core Clustering

The tendency of aliphatic amino acid side chains (Ala, Val, Leu, Ile) to aggregate inside folded proteins, stabilizing structure via hydrophobic interactions.

Aromatic R Groups

Amino acid group comprising Phenylalanine, Tyrosine, and Tryptophan, containing aromatic ring systems that contribute to hydrophobic interactions.

Polarity of Aromatic Amino Acids

Tyrosine and Tryptophan are significantly more polar than Phenylalanine due to the Tyrosine hydroxyl group ($-\text{OH}$) and the nitrogen atom in the Tryptophan indole ring.

Ultraviolet Light Absorption at 280 nm

Strong light absorption exhibited by Tryptophan and Tyrosine residues near $280\,\text{nm}$, used to measure protein concentration.

Absorbance Extinction Coefficient Formula

Equation calculating molar extinction coefficient at $280\,\text{nm}$: $\epsilon_{280} = (\#\text{Trp})(5500) + (\#\text{Tyr})(1490)\,\text{M}^{-1}\,\text{cm}^{-1}$.

Polar, Uncharged R Groups

Amino acid group comprising Serine, Threonine, Cysteine, Asparagine, and Glutamine, which are hydrophilic and form hydrogen bonds with water.

Cysteine Polarity

Exhibits modest polarity due to its terminal sulfhydryl group ($-\text{SH}$).

Cystine

A dimeric, strongly hydrophobic amino acid formed when two Cysteine residues undergo oxidation to create a covalent disulfide bond.

Disulfide Bond

A covalent cross-link bond ($-\text{S}-\text{S}-$) formed by oxidation of two Cysteine sulfhydryl groups, stabilizing protein tertiary and quaternary structure.

Positively Charged (Basic) R Groups

Hydrophilic amino acids (Lysine, Arginine, Histidine) bearing net positive charges at physiological $\text{pH} = 7$.

Lysine Side Chain

Basic side chain containing an aliphatic chain terminating in a primary amino group at the $\epsilon$ position.

Arginine Side Chain

Basic side chain containing a positively charged, resonance-stabilized guanidinium group.

Histidine Side Chain

Basic side chain containing an aromatic imidazole ring with a $pKa$ near physiological pH ($pKa_R = 6.00$).

Negatively Charged (Acidic) R Groups

Amino acids (Aspartate and Glutamate) possessing a second carboxyl group that carries a net negative charge at $\text{pH} = 7$.

Aspartate Side Chain pKa

The side-chain carboxyl $pKa_R$ value is $3.65$.

Glutamate Side Chain pKa

The side-chain carboxyl $pKa_R$ value is $4.25$.

Post-synthetic Modification

Chemical modification of common amino acid residues occurring after their assembly into a polypeptide chain, producing uncommon amino acids.

Transient Amino Acid Modifications

Reversible addition of chemical groups (such as phosphoryl, methyl, acetyl, adenylyl, or ADP-ribosyl) to alter protein function or enzyme activity.

Zwitterion

A dipolar molecule containing separate positively ($-\text{NH}_3^+$) and negatively ($-\text{COO}^-$) charged functional groups with an overall net charge of zero.

Isoelectric Point (pI)

The precise pH value at which a molecule carries no net electrical charge in aqueous solution.

Isoelectric Point Formula (Non-ionizable Side Chain)

Equation used to calculate $pI$ when side chains lack ionizable groups: $\text{pI} = \frac{1}{2}(pK_1 + pK_2)$.

Isoelectric Point of Glycine

Calculated as $\text{pI} = \frac{2.34 + 9.60}{2} = 5.97$.

Acetic Acid Carboxyl pKa

Standard $pKa$ value for an uninfluenced carboxyl group, which is about $4.8$.

Methylamine Amino pKa

Standard $pKa$ value for an uninfluenced primary amino group, which is about $10.6$.

Primary Structure (1°)

The linear sequence of amino acid residues linked by covalent peptide bonds in a polypeptide chain.

Polypeptide Sequence Options Formula

Equation defining total theoretical sequence combinations for a polypeptide of $n$ residues: $20^n$.

Average Polypeptide Length

The mean length of naturally occurring polypeptides, which is $355$ amino acid residues.

Minimum Polypeptide Length

Approximately $40$ residues required for a polypeptide chain to fold into a stable, functional three-dimensional shape.

Upper Polypeptide Length Constraint

Efficiency limit near 1000 residues beyond which the frequency of transcriptional and translational errors increases significantly.

Most Abundant Amino Acids

The standard amino acids occurring most frequently in proteins: Leu, Ala, Gly, Val, Glu, and Ser.

Rarest Amino Acids

The standard amino acids occurring least frequently in proteins: Trp, Cys, Met, and His.

Conformation

The complete spatial arrangement and three-dimensional architecture of a protein molecule.

Specific Activity

The catalytic activity of an enzyme per milligram of total protein, expressed in $\text{mmol}\,\text{mg}^{-1}\,\text{min}^{-1}$ or $\text{katal}\,\text{kg}^{-1}$.

Percent Yield

The percentage of total enzyme activity remaining after a specific purification procedure relative to the initial extract.

Salting In

Increased protein solubility observed at low salt concentrations as added ions shield ionic charges and decrease inter-protein attractive forces.

Salting Out

Decreased protein solubility at very high salt concentrations caused by competition for solvation, leaving insufficient free bulk solvent to dissolve proteins.

Column Chromatography

Preparative technique where a mobile liquid phase carries a protein mixture through a column containing a stationary solid porous matrix.

Stationary Phase

The solid or gel porous matrix held within a chromatography column.

Mobile Phase

The liquid buffer solution flowing through a chromatography column.

Ion-Exchange Chromatography

Separation method that exploits differences in the net charge of proteins at a specific pH.

Cation Exchanger

Chromatographic resin containing negatively charged functional groups that binds positively charged proteins (cations).

Anion Exchanger

Chromatographic resin containing positively charged functional groups that binds negatively charged proteins (anions).

Size-Exclusion Chromatography

Technique separating proteins based on molecular size using porous polymer beads (also known as gel filtration chromatography).

Elution Order in Size-Exclusion Chromatography

Large proteins elute first because they are excluded from internal bead pores, whereas small proteins enter pores and elute later.

Affinity Chromatography

Purification method isolating proteins based on specific binding interactions with a ligand covalently attached to column matrix beads.

Ligand

A specific molecule or functional group bound covalently to matrix beads in affinity chromatography to selectively bind a target protein.

Polyacrylamide Gel Electrophoresis (PAGE)

Analytical method separating macromolecules in a polyacrylamide matrix under an electric field based on net charge, size, and shape.

Sodium Dodecyl Sulfate (SDS)

An anionic detergent that denatures proteins and binds at a constant ratio (~1 molecule per amino acid), imparting a uniform negative charge-to-mass ratio.

SDS-PAGE Separation Basis

Separates unfolded polypeptide chains exclusively on the basis of molecular weight.

Dansyl Chloride

Fluorescent labeling reagent (5-dimethylamino-1-naphthalenesulfonyl chloride) that reacts with primary amino groups to identify N-terminal residues.

Edman Degradation

Chemical procedure that sequentially labels and cleaves the N-terminal amino acid residue of a peptide without breaking other peptide bonds.

Phenylisothiocyanate (PITC)

Reagent used in the initial high-pH step of Edman degradation to react with the unprotonated $\alpha$-amino group of a peptide.

Phenylthiohydantoin (PTH) Derivative

The stable cyclic derivative released and identified after each cycle of Edman degradation.

Anilinothiazolinone Derivative

The intermediate compound formed immediately after low-pH cleavage in Edman degradation before conversion to a PTH-amino acid.

Endopeptidase

An enzyme that catalyzes the cleavage of internal peptide bonds within a polypeptide chain.

Exopeptidase

An enzyme that catalyzes the sequential cleavage of terminal amino acid residues from the N- or C-terminus.

Trypsin Cleavage Specificity

Digestive endopeptidase that specifically cleaves peptide bonds on the C-terminal side of positively charged Lys and Arg residues (unless followed by Pro).

Cyanogen Bromide Cleavage

A chemical reagent that selectively hydrolyzes peptide bonds on the C-terminal side of Methionine residues.

Peptidyl Homoserine Lactone

The C-terminal modified structure formed at former Methionine positions following cleavage by cyanogen bromide.

Mass Spectrometry (m/z)

Analytical technique that measures the mass-to-charge ratio ($m/z$) of gas-phase ions with high precision.

Electrospray Ionization Mass Spectrometry (ESI MS)

Mass spectrometry technique that converts macromolecules in solution into intact gas-phase ions with multiple positive charges.

MALDI MS

Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry, an ionization technique used to analyze intact biomolecules.

Tandem Mass Spectrometry (MS/MS)

Sequence analysis method using two mass spectrometers in series separated by a collision cell to fragment and sequence peptides.

Homologous Proteins

Evolutionarily related proteins that share sequence similarity and structural ancestry across different species.

Invariant Residues

Amino acid positions in homologous proteins that are identical across species because they perform essential functional roles.

Conservatively Substituted Residues

Amino acid positions in homologous proteins replaced across species by residues possessing similar chemical characteristics.

Hypervariable Residues

Amino acid positions in homologous proteins that tolerate many different amino acid substitutions due to nonspecific functional constraints.