Biochemistry: Proteins

protein

a naturally occurring, unbranched polymer consisting of amino acid monomers; forms many of the functional components of a biological organism; a peptide with at least 40 amino acid residues

amino acid

compound with an amino group on one end and a carboxyl group on the other end and a side chain which provides uniqueness that is the building block of peptides and proteins; 20 common occurring varieties separated according to acidity, basicity, and polarity

alpha amino acid

an amino acid in which the amino group is bonded to the carbon atom next to the -COOH group

standard amino acids

one of twenty amino acids coded by DNA; some amino acids (such as selenocysteine and hydroxyproline) are nonstandard amino acids, because they are not coded by DNA but instead are biosynthesized from standard amino acids

nonstandard amino acids

amino acids that are derivatives of amino acids coded by DNA; these amino acids are not themselves coded by any codon; examples include selenocysteine and hydroxyproline

nonpolar amino acids

amino acids that are composed mainly of carbon and hydrogen and do not possess any polar bonds; 8 amino acids; form hydrophobic interactions in secondary structure

polar neutral amino acids

amino acids that contain a polar bond as well as carbon and hydrogen atoms; can hydrogen bond with components of other amino acids; 6 amino acids

polar acidic amino acids

amino acids that contain a carboxylic acid on their side chain; can hydrogen bond with components of other amino acids; 2 amino acids

polar basic amino acids

amino acids that contain a basic nitrogen atom on their side chain; can hydrogen bond with components of other amino acids; 3 amino acids

essential amino acids

amino acids that are needed, but cannot be made by the body; they must be eaten in foods

complete dietary protein

protein that provides essential amino acids in the proportions needed to support protein synthesis

complementary dietary proteins

proteins in which two or more incomplete dietary proteins that, when combined, provide an adequate amount of all essential amino acids relative to the body's needs

limiting amino acid

the essential amino acid in lowest concentration in a food or diet relative to body needs

zwitterion

a molecule or ion having separate positively and negatively charged groups, like an amino acids

isoelectric point

the pH at which an amino acids exists primarily in its zwitterion form; more than 99% are in zwitterion form; calculated by taking the average of the pKa values of the amine and carboxyl group of non basic/acidic side chain amino acids; for amino acids that have a pKa for their side chain, pI is determined by taking the average pKa of either both acidic (COOH) or both basic sites (NH3+)

amphoteric

a substance that can act as both an acid and a base and can react with both acids and bases; for example, amino acids

peptide

an unbranched chain of amino acids that can be further classified by length

polypeptide

a long unbranched chain of amino acids

peptide bond

a covalent bond between the carboxyl group of one amino acid and the amino group of another amino acid; amide linkage; forms via dehydration synthesis

N terminus

the end of a polypeptide or protein that has a free amino group

C terminus

the end of a polypeptide or protein that has a free carboxyl group

amino acid residue

the portion of an amino acid structure that remains, after the release of H2O, when an amino acid participates in peptide bond formation as it becomes part of a peptide chain

polypeptide backbone

repeating sequence of atoms (-N-C-C-) that forms the core of a protein molecule and to which the amino acid side chains are attached

peptide hormones

hormones composed of amino acids; examples include oxytocin and vasopressin or enkephalins, glutathione, etc

enkephalins

pentapeptide neurotransmitters produced by the brain itself that bind at receptor sites in the brain to reduce pain

small peptide hormones

hormones that are composed of short chains of amino acid

glutathione

reducing agent that can help reverse radical formation before damage is done to the cell; antioxidant

monomeric protein

a protein in which only one peptide chain is present

multimeric protein

a protein in which more than one peptide chain is present; may be identical or different

simple protein

a protein in which only amino acid residues are present

conjugated protein

a protein that has one or more non amino acid entities present in addition to one or more peptide chains; in other words, it has a prosthetic group

prosthetic group

a non-amino acid group present in a conjugated protein; examples include a fatty acid, saccharide, metal, etc;

primary protein structure

protein structure that details the order of amino acid residues from the N-terminus to the C-terminus; amino acids can be diastereoisomers if arranged differently; stereoisomers do not exist as amino acids are always in the L configuration

secondary protein structure

protein structure that details the folding and twisting patterns of the polypeptide backbone; the two most common types of this structure are the alpha helix and the beta pleated sheet; amino acids like to be trans, with respect to their side chain

tertiary protein structure

protein structure that details the overall 3D shape of a protein that results from interactions between amino acid side chains that are widely separated from each other within a peptide chain

quaternary protein structure

protein structure that details the organization among the various peptide subunits in a multimeric protein

alpha helix structure

type of secondary structure of proteins formed by folding of the polypeptide into a helix shape with hydrogen bonds (from the amino group to the carboxyl group) stabilizing the structure; the twist is a clockwise spiral; the side chains extend outwards from the helix

beta pleated sheet structure

type of secondary structure in which two fully extended protein chain segments in the same or different molecules are held together by hydrogen bonds; in molecules were the pleated sheet involves a single peptide, several U-turns in the protein chain arrangement are needed in order to form the structure; the side chains are found above or below the plane of the sheet, alternating between top and bottom (trans)

unstructured protein segment

the portions of a protein that have neither an alpha helix or a beta pleated sheet

intramolecular disulfide bond

a bond involving two oxidized cysteine residues that form a covalent bond and contribute to tertiary structure; can be between different polypeptides or the same one

electrostatic interactions

interactions between an acidic side chain and a basic side chain that occurs at an appropriate pH and causes two portions of a peptide (or two peptides) to be drawn towards each other, contributing to tertiary structure

hydrophobic interactions

interactions between non polar side groups in which London forces cause these groups to coalesce to exclude polar molecules; contributes to tertiary structure

hydrogen bonds

very weak bonds; occurs when a hydrogen atom in one molecule is attracted to the electrostatic atom in another molecule; contributes to both secondary and tertiary structure

complete protein hydrolysis

when all of a protein's peptide bonds are cleaved and all amino acid residues are freed up

incomplete protein hydrolysis

when some, but not all, of a protein's peptides bonds are cleaved and amino acid residues are freed up

protein denaturation

when proteins are subject to heat, acid or other conditions that disturb their stability; protein uncoils, loses its secondary, tertiary, and quaternary structure, and loses its function

coagulation

the precipitation out of biochemical solution of denatured protein

fibrous protein

a protein that has only a secondary structure; generally insoluble; includes collagens, elastins, and keratins

globular protein

a protein that has peptide chains that are folded into spherical or glover shapes with most of the hydrophobic side chains pointing inwards

membrane protein

a protein that is found associated with a membrane system of a cell

alpha keratin

a fibrous protein that forms a dimer,is extremely stable and found in hair, horns and nails; acts as a protective coating in organisms; is the major constituent of hair, feathers, wool, fingernails, toenails, claws, scales, horns, shells, quills, and hooves;

collagen

the most abundant of all proteins in humans (30%); a major constituent of structural material, including tendons, ligaments, blood vessels, and skin; also the organic component of bones and teeth; is composed of a triple helix; chains of collagen are very long, thin, and rigid

triple helix

the protein structure found in collagen, consisting of three polypeptide chains woven together like a braid

hemoglobin

a globular protein that transports oxygen from the lungs to tissues; a tetramer with each subunit also containing a heme group that binds to oxygen

myoglobin

a globular protein that functions as an oxygen storage molecule in muscles; a monomer; only 1 O2 molecule can be carried; tertiary structure similar to hemoglobin;

immunoglobulin

a protein involved in the immune system's active immunity

antigen

a protein that, when introduced in the blood, triggers the production of an antibody

lipoprotein

a protein with a fatty acid prosthetic group that it transports to and from regions of the body

plasma lipoprotein

clusters of lipids associated with proteins that serve as transport vehicles for lipids in the lymph and blood

chylomicrons

the class of lipoproteins that transport lipids from the intestinal cells to the rest of the body

very low density lipoprotein

lipoproteins that function in transporting triacylglyerols synthesized in the liver to adipose tissue

low density lipoprotein

lipoproteins that function in the transport of cholesterol synthesized in the liver to cells throughout the body

high density lipoprotein

lipoproteins that function to collect excess cholesterol from the body tissues and transport it back to the liver for degradation to bile acids

info

protein are not very soluble in water, they are crystalline solids with high decomposition points

info

in acids, the carboxyl group of a protein is protonated and the amino acid/protein/peptide carries a net positive charge; in bases, the amino group is deprotonated and the amino acid/protein/peptide carries a net negative charge

info

we have L amino acids but D carbohydrates

info

cysteine dimerizes when mild oxidizing agent is present and is broken with reducing agents

info

proteins like to be trans, orienting their side groups to be on opposite sides

info

R groups need to be as small as possible to make an alpha helix as the secondary structure

info

the “U-turn” structure is a common secondary protein structure

info

amino acids can be separated by breaking the peptide bonds under acid/base + heat

info

all amino acids have an “S” configuration, except cysteine

info

To separate amino acids, a few drops of solution are added to a filter paper in a buffered solution between two electrodes. Amino acids then migrate by their net charge (negative to the cathode positive to the anode) and by their size (bigger are slower and smaller are faster to migrate). Then, the paper is treated with Ninhydrin to reveal the spots on the filter to which the amino acids migrate.

ninhydrin

a chemical reagent that reacts with amino acids to form compounds that have conjugated pi systems and have color

Hell-Volhard-Zelinsky halogenation

a chemical reaction in which bromine is installed at the alpha position of a carboxylic acid; this reaction can be used to form a racemic mixture of an amino acid after the bromine atom is reacted, via an SN2 reaction, with an amine

amidomalonate synthesis

a chemical synthesis of amino aicids that uses amidomalonate as a reactant to form amino acids on; the alpha carbon is alkylated with the side chain the specific amino acid and then with heating and acid catalysis, a racemic mixture of the amino acid can be formed after base workup

Strecker synthesis

a chemical synthesis of a racemic mixture of amino acids in which ammonia is added to an aldehyde, in which the R group is the side chain of the amino acid, and eventually forms an imine ion that is attacked by CN and then hydrolyzed to form he amino acid

enantioselective synthesis of L amino acids

a chemical synthesis of an optically active solution of L amino acids in which a chiral catalyst utilizing ruthenium (Ru) is complexed to a chiral ligand to form amino acids of only one configuration

BINAP

bis(diphenylphosphino)-1,1'binaphthyl; a chemical ligand that is complex to ruthenium that can be used to form a solution of optically active amino acids

info

amino acids are read from the N-term to the C-term

Edman degradation

a method of sequencing amino acids by removing an amino acid residue from the N-terminus by cleaving the peptide bond with phenylthiohydantoin; is only useful for small peptides

Phenylthiohydantoin

a reagent used in Edman degradation that cleaves a single amino acid from the N-terminus and forms a derivative that can be determined

enzymatic degradation

peptide sequencing of larger peptides in which small peptides are sequenced by Edman degradation and then stitched back together by determination of the primary structure; enzymes cleave only certain linkages

peptidases

enzymes that break down proteins into amino acids; can be used for peptide sequencing

trypsin

an enzyme from the pancreas that digests proteins in the small intestine; hydrolyzes the carboxyl end of the amino acids lysine and arginine

chymotrypsin

an enzyme that breaks down proteins in the small intestine; cleaves the carboxyl end of amino acids with aromatic side chains (tyrosine, phenylalanine, and tryptophan)

peptide bond formation

a type of bond that forms between a carboxyl group and an amine group; an amide linkage; a reagent that can be used to form it is DCC (dicyclohexylcarbodiimide)

dicyclohexylcarbodiimide (DCC)

a reagent used in laboratories that directs the formation of a peptide bond between a carboxyl and amine group

info

in order to make peptide bonds with DCC, you need to protect the carboxyl group of one amino acid and the amine group of another amino acid to prevent unwanted side reactions; you can protect an amino group by converting it to a carbamate with (BoC)2O and protect a carboxyl group by converting it into a benzyl or methyl ester; cleavage of the protecting group with trifluoroacetic acid and acid catalysis, respectively

Merrifield synthesis

a peptide synthesis technique in which amino acids are added to a growing chain tethered to an insoluble polymer; unwanted side products are simply washed away while the desired growing amino acid chain remains tethered until released

exopeptidases

a type of protease which hydrolyses the peptide bonds on the terminal amino acids of the peptide molecules formed by endopeptidases; they progressively release dipeptides and single amino acids

endopeptidases

a type of protease which hydrolyses the peptide bonds between amino acids in the central region of a protein molecule forming a series of peptide molecules

ion pair

amino acid residues with opposite charges that stabilize each other in the core/surface

zinc fingers

a structure forming/stabilizing chemical feature in which a zinc atom binds to negative regions of chains of amino acids

molecular chaperones

a protein that helps other proteins fold or refold from a partially denatured state

post-translational processing

alteration in the structure of a protein such as phosphorylation, glycosylation, or proteolytic cleavage, that occurs after it is translated

intrinsically unstructured proteins

proteins or protein segments that lack a fixed structure and depend on other compounds and environments to form their tertiary structure

homodimer

protein composed of two identical subunits

homotrimer

protein composed of three identical subunits

homotetramer

protein composed of four identical subunits