Biochemistry Chapter 3 (Amino Acids, Peptides, and Proteins)

Uncommon Amino Acids (8)

1. 4-hydroxyproline 2. 5-hydroxylysine 3. 6-N-Methyllysine 4. Gamma-carboxyglutamate 5. Desmosine 6. Selenocysteine 7. Ornithine 8. Citrulline

Nonpolar, Aliphatic R Groups (7)

1. Alanine 2. Valine 3. Leucine 4. Isoleucine 5. Glycine 6. Methionine 7. Proline

Negatively Charged (Acidic) R Groups (2)

1. Aspartate 2. Glutamate

R groups

1. Formally, an abbreviation denoting any alkyl group. 2. Occasionally, used in a more general sense to denote virtually any organic substituent (R-group of an amino acid).

4 chromatographic procedures that makes use of differences in size, binding affinities, charge and other properties.

1. Ion-exchange chromatography 2. size-exclusion chromatography 3. Affinity chromatography 4. High-performance liquid chromatography (HPLC)

Three chromatographic methods used in protein purification

1. Ion-exchange chromatography exploits differences in the sign and magnitude of the net electric charges of proteins at a given pH 2. Size-exclusion chromatography, also called gel filtration, separates proteins according to size 3. Affinity chromatography separates proteins by their binding specificities.

Positively Charged (Basic) R Groups (3)

1. Lysine 2. Arginine 3. Histidine

Aromatic R Groups (9)

1. Phenylalanine 2. Tyrosine 3. Tryptophan 4. Threonine 5. Serine 6. Cysteine 7. Asparagine 8. Glutamine 9. Cystine

4 structures of proteins

1. Primary structure 2. Secondary structure 3. Tertiary structure 4. Quaternary structure

3 amino acids that can act as Acids and Bases

1. Zwitterion 2. Amphoteric 3. Ampholytes

The 20 amino acids commonly found as residues in proteins contain what 3 groups?

1. alpha-carboxyl group 2. alpha-amino group 3. distinctive R group substituted on the alpha-carbon

Polarity

1. in chemistry, the nonuniform distribution of electrons in a molecule; polar molecules are usually soluble in water. 2. In molecular biology, the distinction between the 5' and 3' ends of nucleic acids.

Consensus sequences

A DNA or amino acid sequence consisting of the residues that most commonly occur at each position in a set of similar sequences.

6-N-Methyllysine

A constituent of myosin, a contractile protein of muscle.

Desmosine

A derivative of four Lys residues, which is found in the fibrous protein elastin.

Primary structure

A description of the covalent backbone of a polymer (macromolecule), including the sequence of monomeric subunits and any interchain and intrachain covalent bonds.

Oligopeptide

A few amino acids joined by peptide bonds.

Protomers

A general term describing any repeated unit of one or more stably associated protein subunits in a larger protein structure. If a protomer has multiple subunits, the subunits may be identical or different.

Lipoproteins

A lipid protein aggregate that serves to carry water insoluble lipids in the blood. The protein component alone is an apolipoprotein.

Polypeptide

A long chain of amino acids linked by peptide bonds; the molecular weight is generally less than 10,000.

Prosthetic group

A metal ion or an organic compound (other than amino acid) that is covalently bound to a protein and is essential to its activity.

Analytes

A molecule to be analyzed by mass spectrometry.

Anion exchangers

A polymeric resin with fixed cationic groups, used in the chromatographic separation of anions.

Fractions

A portion of a biological sample that has been subjected to a procedure designed to separate macromolecules based on a property such as solubility, net charge, molecular weight, or function.

Ion-exchange chromatography

A process for separating complex mixtures of ionic compounds by many repeated partitioning's between a flowing (mobile) phase and a stationary phase consisting of a polymeric resin that contains fixed charged groups.

Glycoproteins

A protein containing a carbohydrate group.

Conjugated proteins

A protein containing one or more prosthetic groups.

Metalloproteins

A protein with a metal ion as its prosthetic group.

Ampholytes

A substance that can act as either a base or an acid.

Peptide bond

A substituted amide linkage between the alpha amino group of one amino acid and the alpha carboxyl group of another, with the elimination of the elements of water.

Affinity chromatography

Affinity chromatography is a method of separating biochemical mixtures based on a highly specific interaction such as that between antigen and antibody, enzyme and substrate, or receptor and ligand.

Alanine

Alanine is an ɑ-amino acid that is used in the biosynthesis of proteins. It contains an α-amino group, an α-carboxylic acid group, and a side chain methyl group, classifying it as a nonpolar, aliphatic amino acid

Signature sequences

An amino acid sequence, often at the amino terminus, that signals the cellular fate or destination of a newly synthesized protein.

Chiral center

An atom with substituents arranged so that the molecule is not superposable and its mirror image.

Isoelectric focusing

An electrophoretic method for separating macromolecules on the basis of isoelectric pH.

Cation exchangers

An insoluble polymer with fixed negative charges, used in the chromatographic separation of cationic substances.

Phenylalanine

An α-amino acid with the formula C₆H₅CH₂CHCOOH. This essential amino acid is classified as neutral, and nonpolar because of the inert and hydrophobic nature of the benzyl side chain.

Arginine

Arginine encoded by the codons CGU, CGC, CGA, CGG, AGA, and AGG is an ɑ-amino acid that is used in the biosynthesis of proteins.

Asparagine

Asparagine encoded by the codons AAU and AAC. is an ɑ-amino acid that is used in the biosynthesis of proteins. It contains an α-amino group, an α-carboxylic acid group, and a side chain carboxamide, classifying it as a polar, aliphatic amino acid

Aspartate

Aspartic acid is an ɑ-amino acid that is used in the biosynthesis of proteins. It contains an α-amino group, an α-carboxylic acid group, and a side chain CH₂COOH, classifying it as a charged, aliphatic amino acid.

Amphoteric

Capable of donating and accepting protons, thus able to serve as an acid or a base.

Proteases

Catalyze the hydrolytic cleavage of peptide bonds.

Column chromatography

Column chromatography in chemistry is a method used to purify individual chemical compounds from mixtures of compounds. It is often used for preparative applications on scales from micrograms up to kilograms

Cysteine

Cysteine is a semi-essential proteinogenic amino acid with the formula HO₂CCHCH₂SH>. It is encoded by the codons UGU and UGC. The thiol side chain in Cys often participates in enzymatic reactions, as a nucleophile.

Cystine

Cystine is the amino acid with the formula (SCH₂CH(NH₂)CO₂H)₂. It is a white solid that is slightly soluble in water.

4-hydroxyproline

Derivative of proline. Found in collagen.

Polymorphic

Describes a protein for which amino acid sequence variants exist in a population of organisms, but the variations do not destroy the protein's function.

To determine the amino acid sequence of each fragment by using the automated _____ degradation procedure. Then ordering the peptide fragments by finding _________ overlaps between fragments generated by different reagents.

Edman, sequence

Electrospray ionization mass spectrometry (ESI MS)

Electrospray ionization is a soft ionization technique that is typically used to determine the molecular weights of proteins, peptides, and other biological macromolecules. Soft ionization is a useful technique when considering biological molecules of large molecular mass, such as the aforementioned, because this process does not fragment the macromolecules into smaller charged particles, rather it turns the macromolecule being ionized into small droplets. These droplets will then be further desolvated into even smaller droplets, which creates molecules with attached protons. These protonated and desolvated molecular ions will then be passed through the mass analyzer to the detector, and the mass of the sample can be determined

Gamma-carboxyglutamate

Found in the blood clotting protein prothrombin and in certain other proteins that bind Ca2+ as part of their biological function.

Orthologs

Genes or proteins from different species that possess a clear sequence and functional relationship to each other.

Paralogs

Genes or proteins present in the same species that possess a clear sequence and functional relationship to each other.

Glutamate

Glutamic acid is an ɑ-amino acid that is used in the biosynthesis of proteins. It contains an α-amino group, an α-carboxylic acid group, and a side chain carboxylic acid, classifying it as a polar negatively charged, aliphatic amino acid.

Glutamine

Glutamine (abbreviated as Gln or Q; encoded by the codons CAA and CAG) is an ɑ-amino acid that is used in the biosynthesis of proteins. It contains an α-amino group (which is in the protonated -+NH3 form under biological conditions), an α-carboxylic acid group (which is in the deprotonated -COO- form under biological conditions), and a side chain amide which replaces the side chain hydroxyl of glutamic acid with an amine functional group, classifying it as a charge neutral, polar (at physiological pH) amino acid. It is non-essential and conditionally essential in humans, meaning the body can usually synthesize sufficient amounts of it, but in some instances of stress, the body's demand for glutamine increases and glutamine must be obtained from the diet. In human blood, glutamine is the most abundant free amino acid, with a concentration of about 500-900 µmol/l.

Glycine

Glycine is the smallest of the 20 amino acids commonly found in proteins, and indeed is the smallest possible. The formula is NH₂CH₂COOH. Its codons are GGU, GGC, GGA, GGG of the genetic code

High-performance liquid chromatography (HPLC)

High-performance liquid chromatography (HPLC; formerly referred to as high-pressure liquid chromatography), is a technique in analytical chemistry used to separate, identify, and quantify each component in a mixture.

Histidine

Histidine is an ɑ-amino acid that is used in the biosynthesis of proteins. It contains an α-amino group, a carboxylic acid group, and a side chain imidazole, classifying it as a positively charged, aromatic amino acid.

Horizontal gene transfer

Horizontal gene transfer (HGT) refers to the transfer of genes between organisms in a manner other than traditional reproduction. Also termed lateral gene transfer (LGT), it contrasts with vertical transfer, the transmission of genes from the parental generation to offspring via sexual or asexual reproduction.

Zwitterion

In chemistry, a zwitterion is a neutral molecule with a positive and a negative electrical charge, though multiple positive and negative charges can be present. Zwitterions are distinct from dipoles, at different locations within that molecule.

Absorbance (A)

In chemistry, absorbance or decadic absorbance is the common logarithm of the ratio of incident to transmitted radiant power through a material, and spectral absorbance or spectral decadic absorbance is the common logarithm of the ratio of incident to transmitted spectral radiant power through a material.[2] Absorbance is dimensionless, and in particular is not a length, though it is a monotonically increasing function of path length, and approaches zero as the path length approaches zero. The use of the term "optical density" for absorbance is discouraged.[2] In physics, a closely related quantity called "optical depth" is used instead of absorbance: the natural logarithm of the ratio of incident to transmitted radiant power through a material. The optical depth equals the absorbance times ln. The term absorption refers to the physical process of absorbing light, while absorbance does not always measure absorption: it measures attenuation (of transmitted radiant power). Attenuation can be caused by absorption, but also reflection, scattering, and other physical processes.

Oligomeric

In chemistry, an oligomer is a molecular complex that consists of a few monomer units, in contrast to a polymer, where the number of monomers is, in principle, not limited

Cation-exchange chromatography

Ion-exchange chromatography (or ion chromatography) is a chromatography process that separates ions and polar molecules based on their affinity to the ion exchanger. It works on almost any kind of charged molecule—including large proteins, small nucleotides, and amino acids. It is often used in protein purification, water analysis, and quality control.

Peptides can be distinguished by their _________ behavior.

Ionization

Isoleucine

Isoleucine encoded by the codons AUU, AUC, and AUA is an ɑ-amino acid that is used in the biosynthesis of proteins.

Ornithine and Citrulline

Key intermediates (metabolites) in the biosynthesis of arginine and in the urea cycle.

Leucine

Leucine is an ɑ-amino acid that is used in the biosynthesis of proteins. It contains an α-amino group, an α-carboxylic acid group, and an isobutyl side chain, classifying it as a nonpolar amino acid.

Lysine

Lysine, encoded by the codons AAA and AAG is an ɑ-amino acid that is used in the biosynthesis of proteins. It contains an α-amino group, an α-carboxylic acid group, and a side chain lysyl, classifying it as a charged, aliphatic amino acid.

Mass spectrometry

Mass spectrometry (MS) is an analytical chemistry technique that helps identify the amount and type of chemicals present in a sample by measuring the mass-to-charge ratio and abundance of gas-phase ions. A mass spectrum (plural spectra) is a plot of the ion signal as a function of the mass-to-charge ratio.

Matrix-assisted laser desorption/ionization mass spectrometry (MALDI MS)

Matrix-assisted laser desorption/ionization (MALDI) is a soft ionization technique used in mass spectrometry, allowing the analysis of biomolecules (biopolymers such as DNA, proteins, peptides and sugars) and large organic molecules (such as polymers, dendrimers and other macromolecules), which tend to be fragile and fragment when ionized by more conventional ionization methods. It is similar in character to electrospray ionization (ESI) in that both techniques are relatively soft ways of obtaining ions of large molecules in the gas phase, though MALDI produces far fewer multiply charged ions. MALDI methodology is a three-step process. First, the sample is mixed with a suitable matrix material and applied to a metal plate. Second, a pulsed laser irradiates the sample, triggering ablation and desorption of the sample and matrix material. Finally, the analyte molecules are ionized by being protonated or deprotonated in the hot plume of ablated gases, and can then be accelerated into whichever mass spectrometer is used to analyze them.

Methionine

Methionine is an ɑ-amino acid that is used in the biosynthesis of proteins. It contains an α-amino group, an α-carboxylic acid group, and an S-methyl thioether side chain, classifying it as a non-polar, aliphatic amino acid.

Electrophoresis

Movement of charged solutes in response to an electrical field; often used to separate mixtures of ions, proteins, or nucleic acids.

Proline

Proline (abbreviated as Pro or P; encoded by the codons CCU, CCC, CCA, and CCG) is an ɑ-amino acid that is used in the biosynthesis of proteins. It contains an α-amino group (which is in the protonated -+NH3 form under biological conditions), an α-carboxylic acid group (which is in the deprotonated -COO- form under biological conditions), and a side chain pyrrolidine, classifying it as a nonpolar(at physiological pH), aliphatic amino acid. It is non-essential in humans, meaning the body can synthesize it from the essential amino acid glutamine. Proline is the only amino acid with a secondary amine, classifying it as an imino acid. Furthermore, it is unique in that the alpha-amino group is attached directly to the side chain, making the alpha carbon a direct substituent of the side chain.

Protein

Proteins are large biomolecules, or macromolecules, consisting of one or more long chains of amino acid residues.

Homologous proteins (homologs)

Proteins having similar sequences and functions in different species; for example, the hemoglobin's.

Dialysis

Removal of small molecules from a solution of a macromolecule by their diffusion through a semipermeable membrane into a suitably buffered solution.

Size exclusion chromatography (gel filtration)

Separates proteins according to size.

Serine

Serine encoded by the codons UCU, UCC, UCA, UCG, AGU and AGC is an ɑ-amino acid that is used in the biosynthesis of proteins. It contains an α-amino group, a carboxyl group, and a side chain hydroxyl group, classifying it as a polar amino acid.

Sodium dodecyl sulfate (SDS)

Sodium dodecyl sulfate, sodium laurilsulfate or sodium lauryl sulfate is an organic compound with the formula CH₃(CH₂)₁₁SO₄Na. It is an anionic surfactant used in many cleaning and hygiene products

Multisubunit

Some proteins consist of a single polypeptide chain, but other, called Multisubunit proteins, have two or more polypeptides associated noncovalently.

Enantiomers

Stereoisomers that are nonsuperposable mirror images of each other.

Tandem MS (MS/MS)

Tandem mass spectrometry (MS/MS) is perhaps the most significant advance in newborn screening in the past 30 years. A tandem mass spectrometer is a specialized instrument that detects molecules by measuring their weight (mass).

Optically active

The capacity of a substance to rotate the plane of plane-polarized light.

Isoelectric point or Isoelectric pH (pI)

The characteristic pH at which the net electric charge is zero. The Isoelectric point is simple the arithmetic mean of the two pKa values: pI = 1/2 (pK1 + pK2)

Edman degradation

The chemical sequencing process itself is based on a two step process developed by Pehr Edman. Procedure labels and removes only the amino terminal residue from a peptide, leaving all other peptide bonds intact.

Bioinformatics

The computerized analysis of biological data, using methods derived from statistics, linguistics, mathematics, chemistry, biochemistry, and physics. The data are often nucleic acid or protein sequence or structural data, but can also involve experimental data from many sources, patient statistics, and materials in the scientific literature. Bioinformatics research focuses on methods for data storage, retrieval, and analysis.

Absolute configuration

The configuration of four different substituent groups around an asymmetric carbon atom, in relation to D and L-glyceraldehyde.

D, L system

The convention that is used to designate the configurations of chiral carbons of naturally occurring compounds is called the D and L convention or system

Secondary structure

The local spatial arrangement of the main chain atoms in a segment of a polypeptide chain; also applied to polynucleotide structure.

Specific activity

The number of micromoles of a substrate transformed by an enzyme preparation per minute per milligram of protein at 25 degrees Celsius, a measure of enzyme purity.

Amino-terminal (N-terminal)

The only amino acid residue in a polypeptide chain with a free alpha-amino group; defines the amino terminus of the polypeptide.

Carboxyl-terminal (C-terminal)

The only amino acid residue in a polypeptide chain with a free alpha-carboxyl group; defines the carboxyl terminal of the polypeptide.

Fractionation

The process of separating the proteins or other components of a complex molecular mixture into fractions based on differences in properties such as solubility, net charge, molecular weight, or function.

Crude extract

The source of a protein is generally tissue or microbial cells. The first step in any protein purification procedure is to break open these cells, releasing their proteins into a solution called a crude extract.

Tertiary structure

The three dimensional conformation of a polymer in its native folded state.

Quaternary structure

The three dimensional structure of a Multisubunit protein, particularly the manner in which the subunits fit together.

Activity

The true thermodynamic activity or potential of a substance, as distinct from its molar concentration.

Selenocysteine

This rare amino acid residue is introduced during protein synthesis rather than created through a post synthetic modification.

Threonine

Threonine encoded by the codons ACU, ACC, ACA, and ACG is an ɑ-amino acid that is used in the biosynthesis of proteins

RS system

To name the enantiomers of a compound unambiguously, their names must include the "handedness" of the molecule. The method for this is formally known as R/S nomenclature.

Tryptophan

Tryptophan is an ɑ-amino acid that is used in the biosynthesis of proteins. It contains an α-amino group, an α-carboxylic acid group, and a side chain indole, classifying it as a non-polar, aromatic amino acid.

Peptide

Two or more amino acids covalently joined by peptide bonds.

Two-dimensional electrophoresis

Two-dimensional gel electrophoresis, abbreviated as 2-DE or 2-D electrophoresis, is a form of gel electrophoresis commonly used to analyze proteins. Mixtures of proteins are separated by two properties in two dimensions on 2D gels.

Tyrosine

Tyrosine or 4-hydroxyphenylalanine, is one of the 22 amino acids that are used by cells to synthesize proteins. It is a non-essential amino acid with a polar side group. Its codons are UAC and UAU.

Valine

Valine encoded by the codons GUU, GUC, GUA, and GUG is an ɑ-amino acid that is used in the biosynthesis of proteins.

Amino acid residue

alpha-Amino-substituted carboxylic acids, the building blocks of proteins.

Proteins can be very long polypeptide chains of 100 to several thousand _____ ____ residues.

amino acid

The peptide is built up, one _____ ____ residue at a time, while _________ to a solid support.

amino acid, tethered

The alpha-carbon atom of all amino acids except glycine is __________, and thus amino acids can exist in at least two ______________ forms.

asymmetric, stereoisomeric

Short proteins and peptides (up to about 100 residues) can be __________ synthesized.

chemically

Differences in protein function result from differences in amino acid ___________ and ________.

composition, sequence

Other, less common amino acids also occur, either as ____________ of proteins (through modification of common amino acid residues after protein synthesis) or as free ___________.

constituents, metabolites

5-hydroxylysine

derived from lysine. Found in plant cell wall proteins, and collagen, a fibrous protein of connective tissues.

Monoamino monocarboxylic amino acids (with nonionizable R groups) are ________ acids at low pH and exist in several different _____ forms as the pH is increased.

diprotic, ionic

Some naturally occurring peptides have only a ___ amino acid residues.

few

Amino acid sequences are deduced by ____________ polypeptides into smaller peptides with reagents known to _______ specific peptide bonds.

fragmenting, cleave

Some variations in sequence may occur in a particular protein, with little or no effect on its ________.

function

Simple proteins yield only amino acids on __________.

hydrolysis

Some proteins are composed of several _____________ associated polypeptide chains, called subunits.

noncovalently

A protein sequence can also be deduced from the __________sequence of its corresponding gene in DNA, or be ____ ____________.

nucleotide, mass spectrometry

Amino acids with ionizable R groups have additional ionic species, depending on the __ of the medium and the ___ of the R group.

pH, pKa

Proteins can be selectively precipitated by changes in __ or ___________, and particularly by the addition of certain _____.

pH, temperature, salts

Amino acids can be joined covalently through _______ _____ to form peptides and proteins.

peptide bonds

Biologically active ________ and ____________ occur in a vast range of sizes and compositions.

peptides, polypeptides

Amino acids can be classified into five types on the basis of the ________ and ______ (at pH 7) of their R groups.

polarity, charge

Proteins are separated and purified on the basis of differences in their __________.

properties

Conjugated proteins contain in addition some other component, such as a metal or organic __________ group.

prosthetic

Protein sequences are a rich source of information about ________ structure and _________ as well as the _____________ of life on earth.

protein, function, evolution

Cells generally contain thousands of different ________, each with a different __________ activity.

proteins, biological

Sophisticated methods are being developed to trace evolution by analyzing the resultant _____ changes in amino acid sequences of _____________ proteins.

slow, homologous

Amino acids vary in their acid base properties and have characteristic _________ ______.

titration curves