Biochemistry 1: Proteins

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glycine, alanine, valine, leucine, isoleucine, phenylalanine, tryptophan, methionine, proline

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nonpolar amino acids (9)

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serine, threonine, tyrosine, asparagine, glutamine, cysteine

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uncharged polar amino acids (6)

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aspartic acid, glutamic acid

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acidic amino acid (2)

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histidine, lysine, arginine

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basic amino acids (3)

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hydrophobic effect

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tendency of nonpolar R groups to cluster together

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sickle cell anemia

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disease resulting from a single substitution of polar glutamate for nonpolar valine at the 6th position in the beta subunit of Hb

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disulfide bond

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a bond between sulfurs of the sulfhydryl side chains of two cysteine amino acids

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serine, threonine, tyrosine

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amino acids that can be phosphorylated (3)

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asparagine, serine, threonine

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amino acids that can be glycosylated

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glycine

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optically inactive amino acid

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L-configuration

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steric conformation of amino acids found in proteins

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D-configuration

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steric conformation found in amino acids of antibiotics, and plant and bacterial cell walls

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pH=pKa + log ([A-]/[HA])

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Henderson-Hasselbalch equation

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buffers

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solutions containing both an acid and its conjugate base, which are efficient at keeping the pH of a solution constant, especially when pH=pKa

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Form I

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amino acid state when pH<2; net charge of +1; amino group is -NH3+ and carboxy group has -COOH

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Form II (zwitterrion)

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amino acid state when pH=6; net charge of 0; amino group is -NH3+ and carboxy group is -COO-

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Form III

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amino acid state when pH>10; net charge of -1; amino group is -NH2 and carboxy group is -COO-

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K1=([H+][II])/[I]

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dissociation constant of the carboxyl group of an amino acid

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K2

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dissociation constant of the amino group of an amino acid

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isoelectric point (pI)

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the pH at which an amino acid is electrically neutral; for a nonpolar amino acid, it is the average of pK1 and pK2; corresponds to the pH at which form II predominates

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ampholyte (amphoteric electrolyte)

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a substance, such as an amino acid, that can act as either an acid or base

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primary structure of a protein

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sequence of amino acids in a protein

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peptide bonds

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amide linkages between the alpha-carboxyl group of one amino acid and the alpha-amino group of another; planar double bond; trans configuration due to steric hindrance of R groups

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exopeptidases

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enzymes that cut the ends of proteins; divided into aminopeptidases and carboxypeptidases

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endopeptidases

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enzymes that cut within a protein

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alpha-helix

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a spiral structure consisting of a tightly packed, coiled polypeptide backbone core, with the side chains of the component amino acids extending outwardly; contain 3.6 amino acids per turn

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beta-sheet

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a form of secondary structure in which all the peptide bond components are involved in hydrogen bonding; composed to two or more segments of polypeptide chains; can be parallel or antiparallel

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beta-bends

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secondary structure that reverses the direction of a polypeptide chain; usually include charged residues; composed of four amino acids, including proline; usually have glycine

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supersecondary structures

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structures produced by packing side chains from adjacent secondary structural elements close together; e.g. helix-loop-helix, beta-alpha-beta unit, beta-meander, beta-barrel

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domains

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fundamental functional and three-dimensional structural units of polypeptides; core usually built from supersecondary structural elements

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ionic interactions

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interactions between charged groups of aspartic/glutamic acid and lysine

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chaperones

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proteins which are required for proper folding of many species of proteins; explains why denatured proteins do not refold again

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quaternary structure of protein

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the arrangement of different polypeptides into one structure; subunits are held together by noncovalent interactions

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isoforms

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proteins that perform the same function but have different primary structures

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amyloids

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insoluble, spontaneously aggregating cleaved proteins; accumulation of them can cause degenerative diseases

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amyloid beta

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the dominant component of amyloid plaque that accumulates in Alzheimer's disease; aggregates in the beta-sheet configuration and is neurotoxic

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tau protein

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a protein which, in the healthy version, helps assembly of microtubule structure; defective protein causes neurofibrillary tangles inside neurons that lead to Alzheimer's

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prion protein (PrP)

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protein that is implicated as the causative agent of transmissible spongiform encephalopathies (TSEs); alpha helices in the healthy noninfectious form are replaced by beta-sheets in the infectious form; infectious form cannot be degraded and acts as template for converting normal protein to pathogenic form

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Scrapie

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disease involving prion protein in sheep

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Creutzfeldt-Jakob disease

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disease involving defective prion protein in humans

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bovine spongiform encephalopathy

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disease involving defective prion protein in cattle; "mad cow" disease

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hemeproteins

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group of specialized proteins that contain heme as a tightly bound prosthetic group;

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cytochrome

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protein in which the heme group functions as an electron carrier

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catalase

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protein in which the heme group is part of the active site which catalyzes the breakdown of hydrogen peroxide

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heme

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a complex of protoporphyrin IX and ferrous iron

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proximal histidine

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amino acid which is coordinated with one side of the ferrous iron, leaving the other available to bind oxygen

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myoglobin

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a hemeprotein present in heart and skeletal muscle that functions as an oxygen reservoir and oxygen carrier; structurally similar to hemoglobin; single polypeptide

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80

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percentage of myoglobin polypeptide folded into 8 portions alpha-helix

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distal histidine

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amino acid in myoglobin which stabilizes the binding of oxygen to the ferrous iron

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hemoglobin

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hemeprotein found exclusively in red blood cells

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hemoglobin A

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adult hemoglobin; contains two alpha and two beta chains; can transport H+ and CO2 from tissues to lungs; can carry four molecules of O2;

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alpha-beta dimer

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dimer which comprises half of each hemoglobin molecule; joined primarily by strong hydrophobic interactions; weak ionic and hydrogen bonds bind adjacent dimers

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T form

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deoxy form of hemoglobin; the two alpha-beta dimers interact through network of ionic and hydrogen bonds; low-oxygen-affinity form

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R form

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oxygenated form of hemoglobin; the two alpha-beta dimers have fewer ionic and hydrogen bonds; high-oxygen-affinity form

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Y

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degree of saturation of oxygen binding sites on on myoglobin or hemoglobin molecules; measured as percentage

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oxygen dissociation curve

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a plot of Y measured at different partial pressures of oxygen

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P50 for hemoglobin

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26mmHg; partial pressure of oxygen required for half of the oxygen sites to be occupied

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P50 for myoglobin

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1mmHg; partial pressure of oxygen required for half the oxygen sites to be occupied

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cooperative binding of oxygen

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the phenomenon where binding of an oxygen molecule at one heme group increases the oxygen affinity of the remaining heme groups of the hemoglobin molecule

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Bohr effect

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phenomenon where release of oxygen from hemoglobin is enhanced when the pH is lowered or pCO2 is high (shift of O2 dissociation curve to the right); low pH and high pCO2 stabilize the T form

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carbonic anhydrase

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enzyme that converts carbon dioxide and water to carbonic acid, which spontaneously loses a hydrogen and becomes bicarbonate

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2,3-bisphosphoglycerate (2,3-BPG)

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molecule synthesized from an intermediate of the glycolytic pathway; similar concentration as hemoglobin; preferentially binds deoxyhemoglobin and shifts the oxygen dissociation curve to the right

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chronic hypoxia, chronic anemia

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states in which the levels of 2,3-BPG are elevated; lowers oxygen affinity of hemoglobin

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transfused blood

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blood which has abnormally low 2,3-BPG, and thus has hemoglobin with high oxygen affinity that does not deliver oxygen well to tissues

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carbamate

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form of carbon dioxide which is carried on the N-terminal amino acid groups of hemoglobin; stabilizes the T form

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carbaminohemoglobin

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hemoglobin which has carbon dioxide bound

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carbon monoxide

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molecule that binds tightly to hemoglobin, and shifts Hb to the relaxed form; causes increased affinity for oxygen in other subunits; shifts oxygen dissociation curve to the left

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phenylisothyocyanate (Edman's reagent)

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a reagent used to label the amino-terminal residue of a polypeptide; used to sequence peptide from N-terminal end

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Complex IV

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portion of electron transport chain that is inhibited by carbon monoxide

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NO

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a potent vasodilator that can also be carried by hemoglobin