Biomolecules- Chapter 4 Proteins
directly sequenced, peptides, overlapping, Trypsin, Chymotrypsin, Pepsin, Cyanogen Bromide
4. Cleavage of the polypeptide into fragments Because of technical problems, long polypeptides cannot be ________. For this reason the polypeptide is broken into smaller _______. The use of several reagents, each of which cuts the chain at different sites, creates _______ sets of fragments. After the amino acids sequence of each fragment is determined, the investigator uses this information to work out the entire sequence of the polypeptide. There are several methods for fragmenting polypeptides: a. _____________ b. _____________ c. ____________ d. __________________ (CNBr)
Trypsin, Chymotrypsin, Pepsin, Cyanogen Bromide
4. Cleavage of the polypeptide into fragments Summary: _________ AA1 = lys or arg _________ AA1 = phe, trp, tyr ________ AA2 = phe, trp, tyr, asp, glu, ile __________ AA1 = met
Pepsin, Cyanogen Bromide
4. Cleavage of the polypeptide into fragments c. ____________ It cleaves peptide bonds at the amino end of aromatic amino acids (phe, trp, tyr), acidic amino acids (asp ,glu) and ile. d. ______________ (CNBr) It specifically cleaves peptide bonds on the carboxyl side of methionine residues.
histidine, positively charged, uncharged, 7.0, donors/acceptors
4. Positively Charged (Basic) R Groups. As the only common amino acid having an ionizable side chain with pKa near neutrality, __________ may be _________ (protonated form) or _________ at pH ____. Histidine residues facilitate many enzyme-catalyzed reactions by serving as proton ___________.
hydrophilic, lysine, arginine, histidine
4. Positively Charged (Basic) R Groups. The most _________ R groups are those that are either positively or negatively charged. The amino acids in which the R groups have significant positive charge at pH 7.0 are _________, which has a second primary amino group at the Ɛ position on its aliphatic chain; __________, which has a positively charged guanidinium group; and __________, which has an aromatic imidazole group.
aspartate, glutamate, second
5. Negatively Charged (Acidic) R Groups. The two amino acids having R groups with a net negative charge at pH 7.0 are ________ and _________, each of which has a ________ carboxyl group.
overlapping segments
5. Ordering the peptide fragments The amino acid sequence information derived from two or more sets of polypeptide fragments are next examined for ___________. Such segments make it possible to piece together the overall sequence.
peptide, polypeptide, protein
_________- An amino acid polymer of short chain length. __________- An amino acid polymer of intermediate chain length containing up to 50 amino acid residues. _________- An amino acid polymer made up of more than 50 amino acids.
amino acid residue, N-terminal residue, C-terminal residue
___________- An amino acid that is a part of a peptide, polypeptide, or protein chain. ___________- An amino acid on the end of a chain that has an unreacted or free amino group. _____________- An amino acid on the end of a chain that has an unreacted or free carboxylate group.
oxidized, cystine, disulfide bond, hydrophobic, covalent links
3. Polar, Uncharged R Groups. Cysteine is readily ________ to form a covalently linked dimeric amino acid called ________, in which two cysteine molecules or residues are joined by a ___________. The disulfide-linked residues are strongly __________ (nonpolar). Disulfide bonds play a special role in the structures of many proteins by forming _________ between parts of a polypeptide molecule or between two different polypeptide chains.
serine, threonine, cysteine, asparagine, glutamine
3. Polar, Uncharged R Groups. The polarity of _______ and ________ is contributed by their hydroxyl groups; that of _______ by its sulfhydryl group, which is a weak acid and can make weak hydrogen bonds with oxygen or nitrogen; and that of _______ and ________ by their amide group.
Asparagine, glutamine, hydrolyzed
3. Polar, Uncharged R Groups. _______ and ________ are the amides of two other amino acids also found in proteins, aspartate and glutamate, respectively, to which asparagine and glutamine are easily _______ by acid or base.
nonpolar, hydrophobic, alanine, valine, leucine, isoleucine, hydrophobic
1. Nonpolar, Aliphatic R Groups The R groups in this class of amino acids are _________ and _______. The side chains of _________, _______, ________, and _______ tend to cluster together within proteins, stabilizing protein structure by means of _________ interactions.
Methionine, Proline, imino, reduces
1. Nonpolar, Aliphatic R Groups _________, one of the two sulfur-containing amino acids, has a nonpolar thioether group in its side chain. ________ has an aliphatic side chain with a distinctive cyclic structure. The secondary amino (_______) group of proline residues is held in a rigid conformation that _______ the structural flexibility of polypeptide regions containing proline.
Glycine, hydrophobic
1. Nonpolar, Aliphatic R Groups __________ has the simplest structure. Although it is most easily grouped with the nonpolar amino acids, its very small side chain makes no real contribution to _________ interactions.
Tyrosine, tryptophan, phenylalanine, hydroxyl group, nitrogen, indole
2. Aromatic R Groups. _________ and _______ are significantly more polar than _________ because of the tyrosine ________ and the ________ of the tryptophan _______ ring.
Phenylalanine, tyrosine, tryptophan, hydrophobic, tyrosine
2. Aromatic R Groups. _________, _________, and _______, with their aromatic side chains, are relatively nonpolar (_________). All can participate in hydrophobic interactions. The hydroxyl group of _______ can form hydrogen bonds, and it is an important functional group in some enzymes.
Edman degradation, PITC, phenylthiohydantoin derivative, sequenator
2. Determination of the N-terminal amino acid. b. _______________- uses phenylisothiocyanate (______), often referred to as Edman's reagent. Treatment of the product of this reaction with acid cleaves the N-terminal residue as a _________. The derivative is then identified by comparing it with known standards, using electrophoresis or various chromatographic methods. Because of the large number of steps involved in the sequencing peptide fragments, Edman degradation is usually carried out by using a computer - programmed machine called a ________.
carboxypeptidases, Carboxypeptidase A, Carboxypeptidase B, C-terminal residue
3. Determination of the C-terminal amino acid A group of enzymes called the _________ are used to identify the C - terminal residue. Carboxypeptidases A and B, both secreted by the pancreas, hydrolyze peptides one residue at a time from the C-terminal end. a. ___________ - preferentially cleaves peptide bonds when an aromatic amino acid is the C-terminal residue. b. _________ - cleaves basic amino acid residues. Because these enzymes sequentially cleave peptide bonds starting at the C-terminal residue, the first amino acid liberated is the ___________.
more hydrophilic, hydrogen bonds, serine, threonine, cysteine, asparagine, glutamine
3. Polar, Uncharged R Groups. The R groups of these amino acids are more soluble in water, or __________, than those of the nonpolar amino acids, because they contain functional groups that form _______ with water. This class of amino acids includes __________, _______, _______, __________, and ________.
sickle cell trait, malaria, sickle cell anemia, resist, maintained
An interesting relationship exists between _________ and resistance to __________. In some parts of Africa, up to 20% of the population has sickle cell trait. In those same parts of Africa, one of the leading causes of death is malaria. The presence of sickle cell trait is linked to an increased resistance to malaria because the malarial parasite cannot feed efficiently on sickled red blood cells. People who have sickle cell disease die young; those without sickle cell trait have a high probability of succumbing to malaria. Occupying the middle ground, people who have sickle cell trait do not suffer much from ________ and simultaneously _________ deadly malaria. Because those with sickle cell trait have a greater chance of survival and reproduction, the sickle cell hemoglobin gene is _________ in the population.
Peptides, homeostasis, opposing
Atrial natriuretic factor, Substance P and Bradykinin _______ are one class of messenger molecules that multicellular organism use to regulate their complex activities. Recall that multicellular organisms, consisting of several hundred cell types, must coordinate a huge number of biochemical processes. A stable internal environment, called ___________, is maintained by the dynamic interplay between __________ processes.
α-amino acids, α-carbon, side chains, R groups
All 20 of the common amino acids are ________. They have a carboxyl group and an amino group bonded to the same carbon atom (the ________) as seen in Figure 1. They differ from each other in their ______, or _______, which vary in structure, size, and electric charge and which influence the __________ of the amino acids in water.
L-isomer, D amino acids, L configuration, D-glyceraldehyde
All the amino acids in all the proteins in our body are the _______. ________ are extremely rare in nature; some are found, for example, in the cell walls of a few types of bacteria. The ________ has been determined based upon comparison of amino acids with _______.
Sanger's method, DNFB, DNP,
Amino Acid Sequencing 1. Cleavage of all disulfide bonds-oxidation with performic acid is commonly used. 2. Determination of the N-terminal amino acid. Several methods are available to determine the N-terminal amino acid a. ___________ - the polypeptide chain is reacted with 1-fluoro-2,4-dinitrobenzene (______). The dinitrophenyl (______) derivative of the N-terminal amino acid can be isolated and identified by ion - exchange chromatography after the polypeptide is hydrolyzed.
disulfide bonds-oxidation, performic acid, N-terminal, C-terminal, polypeptide, fragments, peptide fragments
Amino Acid Sequencing Determining a protein's primary structure is similar to solving a complex puzzle. Several steps are involved in solving the amino acid sequence of any protein. 1. Cleavage of all _________ with ________ is commonly used. 2. Determination of the ________ amino acid. 3. Determination of the ________ amino acid 4. Cleavage of the _________ into ________ 5. Ordering the _________
complex titration curves, Glutamic acid, +1, carboxylate group, no, proton, -1, base
Amino acids with ionizable side chains have more ___________(Figure 5b). _________, for example, has a carboxyl side chain group. At low pH, glutamic acid has net charge _______. As base is added, the α-carboxyl group loses a proton to become a ________. Glutamate now has ______ net charge. As still more base is added, the second carboxyl group loses a _______, and the molecule has a _____ charge. Adding additional ________ results in the ammonium ion losing its proton.
ammonium, uncharged, net negative, carboxylate
As the titration continues, the _________ group loses its proton, leaving an _______ amino group. The molecule then has a _________ charge because of the ________ group.
acids, bases, protons, ampholytes
At pH values below or above their isoelectric points, zwitterions act as _________ and ________ because they are able to donate or accept ________ (H+). Substances having this dual (acid-base) nature are amphoteric and are often called ___________ (from "amphoteric electrolytes").
no, electrically neutral, isoelectric point, least soluble, crystallize
At this point, alanine has _______ net charge and is __________. The pH at which this occurs is called _________ (pI). Because there is no net charge at the isoelectric point, amino acids are __________ at this pH (zwitterions _________ relatively easily).
-2, pK values
At this point, glutamate has a net charge of _____. The pI value for glutamate is the pH halfway between the ________ for the two carboxyl groups: pI=(2.19+4.25)/2=3.22 The isoelectric point for histidine is the pH value halfway between pK values for the two nitrogen - containing groups. The pKa and pI values of amino acids in peptides and proteins differ somewhat from those of free amino acids, principally because most of the α-amino and α-carboxyl groups are not ionized but are covalently joined in peptide bonds
tetrahedral, L, D, enantiomers, optical isomers
Because of the ________ arrangement of the bonding orbitals around the α-carbon atom, the four different groups can occupy two unique spatial arrangements and thus amino acids have two possible stereoisomers, the _______ and _____ (Figure 2). These nonsuperposable mirror image forms are called ________ or ________.
Glutathione, Oxytocin and Vasopressin, Met-enkephalin and leu-enkephalin, Atrial natriuretic factor, Substance P and Bradykinin
Biologically Important Peptides Although their structures are less complex than the larger protein molecules, peptides have significant biological activities. hint: g,o,v,m,l,a,s,b
proline
General structure of an α-amino acid. All amino acids isolated from proteins, with the exception of _________, have this general structure.
chemical properties, amino acids, polarity, pH 7.0, water-insoluble, water-soluble
Classification of Amino Acids Knowledge of the __________ of the common amino acids is central to an understanding of biochemistry. The topic can be simplified by grouping the ______ into five main classes based on the properties of their R groups, in particular, their _________, or tendency to interact with water at biological pH (near _______). The polarity of the R groups varies widely, from nonpolar and hydrophobic (_______) to highly polar and hydrophilic (_______).
fibrous proteins, globular proteins
Classification of proteins Proteins have been classified according to structural features and function: _________ _________
Structural, Contractile, Transport, Hormonal, Catalytic, Antibodies, Storage
Classification of proteins by function ________- collagen, keratin _______- myosin, actin _________- hemoglobin, lipoproteins ________-insulin, growth hormones, estradiol, testosterone ________- sucrase, trypsin, dehydrogenase __________- immunoglobulins _________- casein, ferritin
Dihedral Angles, α helix, β conformation, collagen, phi, sci, Ramachandran plot
Common Secondary Structures have Characteristic _________ The _______ and the _________ are the major repetitive secondary structures in a wide variety of proteins, although other repetitive structures do exist in some specialized proteins (an example is _________). Every type of secondary structure can be completely described by the dihedral angles Φ (______) and Ψ (______) associated with each residue. As shown by a __________, the α helix and β conformation fall within a relatively restricted range of sterically allowed structures.
Complete protein, animal sources
Complementary Proteins __________ foods contain all the essential amino acids in the proper amounts. Proteins from _________such as meat, poultry, eggs, dairy and fish are complete.
Incomplete protein, vegetable sources, lysine, tryptophan, methionine, animal protein, saturated fats, cholesterol,
Complementary Proteins __________ obtained from ___________ is low in one or more of the essential amino acids, usually ________, ______ or ________. In a diet that includes ________, all the essential amino acids are supplied. However, because these foods also contain ________ and ________, many people obtain their protein from a diet of grains and vegetables.
interferon, lipoproteins, hemoglobin, ribosomes, casein
Conjugated proteins glycoproteins- ___________ lipoproteins- _________ metalloproteins- __________ nucleoproteins- _________ phosphoproteins- _________
glutathione peroxidase, two tripeptides, disulfide bond, intracellular reducing agent
Glutathione (γ-glutamyl-L-cysteinylglycine) Glutathione protects against the formation of methemoglobin by reducing H2O2 in a reaction catalyzed by the enzyme ____________. In the oxidized product GSSG, __________ are linked by a _________: 2 GSH + H2O2 ----> GSSG + 2 H2O Because of the high GSH:GSSG ratio normally present in cells, glutathione is an important ____________.
reducing agent, -SH group, GSH, peroxides, hydrogen peroxide, ferric form, Methemoglobin
Glutathione (γ-glutamyl-L-cysteinylglycine) One group of glutathione's functions exploits its effectiveness as a ___________. (Because the reducing component of the molecule is the __________ of the cysteine residue, the abbreviation for glutathione is _____.) Glutathione protects cells from the destructive effects of oxidation by reacting with substances such as _________ (R -O -O -R, byproducts of O2 metabolism). For example, in red blood cells, __________ (H2O2) oxidizes the iron of hemoglobin to its _________ (Fe3+). __________, the product of this reaction, is incapable of binding O2.
parallel, Antiparallel, stable, colinear
In _______ β-pleated sheet structures, the polypeptide chains are arranged in the same direction. _________ chains run in opposite direction. Antiparallel β-pleated sheets are more ________ than parallel β-pleated sheets because fully _______ hydrogen bonds form. Occasionally, mixed parallel - antiparallel β-sheets are observed.
below, +, above, -
We can summarize the changes in ionic charge with the addition of acid or base to the solution of an amino acid at its isoelectric point. (H+) pH _______---isoelectric point ion (____) --- zwitterion (OH-) isoelectric point---pH ______ zwitterion---ion (___)
lysine
Draw the structural formula for the zwitterion of: __________
serine
Draw the structural formula for the zwitterion of: __________
acidic, uncharged, +1, proton, negatively, polyprotic acid
In a strongly ____________ solution (e.g., at pH 0), alanine is present mainly in the form in which the carboxylic group is __________. Under this circumstance, the molecule's net charge is _________, since the ammonium group is protonated. Lowering of the H+ concentration results in the carboxyl group losing its _______ to become a ___________ charged carboxylate group (in a __________, the protons are first lost from the group with the lowest pKa)
nitrogen, sulfur, fats, carbohydrates, indispensable
In addition, they provide an organism not only with carbon and hydrogen, but also with _________ and ______. These latter two elements are unavailable from ________ and ________, the other major classes of food molecules. Indeed, proteins are _______ components of all living things.
20, nonessential, essential, diet
Essential Amino Acids All _____ amino acids are needed to make proteins but our body can synthesize only 10, the ________ amino acids because we don't have to get them from food. The remaining 10 are _________ amino acids which must be obtained from proteins in the _____.
Peptide, carboxyl group, amino group, water, amino acid residues
Formation of Peptides ________ is a chain of amino acids held together by peptide bonds or amide bonds. Peptide bonds occur between the __________ of one amino acid and the _________ of the next with the loss of ________. The amino acid units that remain after a peptide bond has formed are known as ____________.
mercury, lead, negatively, salt bridges, sulfhydryl,
Heavy metals such as _______ (Hg2+) or _______ (Pb2+) may form bonds with ________ charged side chain groups. This interferes with the _______ formed between amino acid R groups of the protein chain, resulting in loss of conformation. Heavy metals may also bind to ________ groups of a protein. This may cause a profound change in the three-dimensional structure of the protein, accompanied by loss of function.
disulfide bridge, reducing agent, oxidizing agent
Humans take advantage of the _________ content of hair during the permanent waving process. After the hair strands are arranged in the desired shape, the disulfide bonds are broken with a _________. New disulfide bond, are then formed by an ________, thus creating curled hair.
water, electrolytes, red blood cells, fibrinogen, immunoglobulins, albumins
Imagine for a moment what would happen if the pH of the blood were to become too acidic or too basic. Blood is a fluid that contains _______ and dissolved _______, a variety of cells, including the ______________ responsible for oxygen transport, and many different proteins. These proteins include ________, which is involved in the clotting reaction; _______, which protect us from disease; and _______, which carry hydrophobic molecules in the blood.
-1800, +1800, steric interference, psi, phi
In principle, Φ and Ψ can have any value between _______ and ________, but many values are prohibited by _________ between atoms in the polypeptide backbone and amino acid side chains. The conformation in which both Φ and Ψ are 0 degrees is prohibited for this reason; this conformation is merely a reference point for describing the dihedral angles. Allowed values for Φ and Ψ become evident when Ψ (_____) is plotted versus Φ (_____) in a Ramachandran plot
prosthetic group, glycoproteins, heme, prosthetic, iron
In some cases the quaternary structure of a functional protein involves binding to a nonprotein group. This additional group is called a __________. For example, many of the receptor proteins on cell surfaces are __________. These are proteins with sugar groups covalently attached. Each of the subunits of hemoglobin is bound to an iron-containing heme group. The _______ group is a large, unsaturated organic cyclic amine with an iron ion coordinated within it. As in the case of hemoglobin, the _________ group often determines the function of a protein. For instance, in hemoglobin it is the ______-containing heme groups that have the ability to bind reversibly to oxygen.
dipolar ion, zwitterion, hybrid ion, nonionic form, zwitterion
Isoelectric Point When an amino acid lacking an ionizable R group is dissolved in water at neutral pH, it exists in solution as the ________, or _______ (German for "______") (Figure 5). Figure 5. Nonionic and zwitterionic forms of amino acids. The _________ does not occur in significant amounts in aqueous solutions. The ________ predominates at neutral pH.
Primary structure, Secondary structure, Tertiary structure, Quaternary structure
Levels of Protein Structure 1. __________- the sequence of amino acids linked by peptide bonds. various ways that proteins fold into the shapes essential for their function 2. ____________ 3. ____________ 4. ____________
enzymes, three-dimensional, denatured, disinfect
Many of the proteins of our cells, for instance, the _________, are in the same kind of viscous solution within the cytoplasm. To continue to function properly, they must remain in solution and maintain the correct ________ configuration. If the body temperature becomes too high, or if local regions of the body are subjected to very high temperatures, as when you touch a hot cookie sheet, cellular proteins become ______. They lose their function, and the cell or the organism dies. In the same way high temperatures are used to _______ surgical instruments, gowns, and gloves. When these materials are subjected to the high temperatures of an autoclave, the proteins of any bacteria present will be denatured, making the bacteria inactive.
opioid peptides, pain, pleasant sensations, morphine, Leu-enkephalin, met-enkephalin
Met-enkephalin and leu-enkephalin Belong to a group of peptides called the __________, found predominantly in the nervous tissue cells. Opioid peptides are molecules that relieve ______ and produce ________. They were discovered after researchers suspected that the physiological effects of opiate drugs such as ________ resulted from their binding to nerve cell receptors for endogenous molecules. __________ and _________ are pentapeptides that differ only in their C-terminal amino acid residues.
α helix, β conformation, glycine, small
Most values of Φ and Ψ taken from known protein structures fall into the expected regions, with high concentrations near the ________ and _________ values as predicted. The only amino acid residue often found in a conformation outside these regions is _______. Because its side chain is ______, a Gly residue can take part in many conformations that are sterically forbidden for other amino acids.
x-ray, myoglobin, muscle cells, heme
Myoglobin The first breakthrough in understanding the three-dimensional structure of a globular protein came from _________ diffraction studies of _______ carried out by John Kendrew and his colleagues in the 1950s. Myoglobin is a relatively small (M, 16,700), oxygen-binding protein of _________. It functions both to store oxygen and to facilitate oxygen diffusion in rapidly contracting muscle tissue. Myoglobin contains a single polypeptide chain of 153 amino acid residues of known sequence and a single iron protoporphyrin, or _________, group.
hemoglobin, erythrocytes, diving
Myoglobin The same heme group that is found in myoglobin is found in _________, the oxygen-binding protein of _________ and is responsible for the deep red-brown color of both myoglobin and hemoglobin. Myoglobin is particularly abundant in the muscles of _________ mammals such as the whale, seal, and porpoise-so abundant that the muscles of these animals are brown. Storage and distribution of oxygen by muscle myoglobin permits diving mammals to remain submerged for long periods.
heme, prosthetic group
Myoglobin. The _______ group has an iron atom to which oxygen binds. Structure of the heme _________, which binds to myoglobin and hemoglobin.
C terminal, yl, alanylglycylserine, ala-gly-ser
Naming of a peptide With the exception of the ________ amino acid, the names of all the other amino acids in a peptide end with ____. For example, a tripeptide consisting of alanine at the N terminal, glycine, and serine at the C terminal is named as one word: _________. For convenience, the order of amino acids in the peptide is often written as the sequence of three-letter abbreviations (________).
sickle-cell anemia, Polar acidic amino acid, Nonpolar amino acid
Primary structure So crucial is primary structure to function that the change of only one amino acid out of several hundreds can drastically alter a protein's biological properties. A striking demonstration to this is __________, in which the red blood cells assume the sickle shape, giving the disease its name. This is due to the substitution of an amino acid in the primary structure (gluβ6 ---> val, see discussion below). Normal beta chain: Val-His-Leu-Thr-Pro-Glu [__________]- Glu-Lys- Sickled beta chain: Val-His-Leu-Thr-Pro-Val [__________]- Glu-Lys-
standard amino acids, nonstandard amino acids
Nonstandard Amino Acids Also Have Important Functions All 20 amino acids that are found in proteins are _____________ (common amino acids), whereas _____________ (uncommon amino acids) are residues that have been chemically modified after they have been incorporated into a polypeptide and also amino acids that occur in living organisms but are not found in proteins.
chiral center, carboxyl group, amino group, R group, hydrogen atom, glycine
Optical Isomerism The α-carbon of the amino acid is a ________ in which it is bonded to four different groups: a __________, an _______, an _______, and a ________. With the exception of ________ all of the amino acids are chiral and optically active.
Polar organic solvents, hydrogen bonds, nonpolar, 70
Organic Solvents ___________, such as rubbing alcohol (2-propanol), denature proteins by disrupting _______ within the protein, in addition to forming hydrogen bonds with the solvent, water. The _________ regions of these solvents interfere with hydrophobic interactions in the interior of the protein molecule, thereby disrupting the conformation. Traditionally, a _____% solution of rubbing alcohol was often used as a disinfectant or antiseptic. However, recent evidence suggests that it is not an effective agent in this capacity.
torsion angles, phi, psi, omega, dihedral angle, bond vectors, plane, two planes, protein conformation
Peptide conformation is defined by three dihedral angles (also known as __________) called Φ (______), Ψ, (_______), and ω (_______), reflecting rotation about each of the three repeating bonds in the peptide backbone. A ___________ is the angle at the intersection of two planes. In the case of peptides, the planes are defined by _________ in the peptide backbone. Two successive bond vectors describe a ______. Three successive bond vectors describe _________ (the central bond vector is common to both; Fig. 8c), and the angle between these two planes is what we measure to describe __________.
regulation, atrial natriuretic factor, vasopressin
Peptide molecules with opposing functions are now known to affect the ________ of several processes. For example, _________, a peptide produced by specialized cells in the heart and the nervous system, stimulates the production of dilute urine (an effect opposite to that of _________).
important, shape, function, properties, sequence of the gene
Primary structure It is the most _________ of the four structural levels because it is a proteins' amino acid sequence that determines its overall _______, _______ and _________. The primary structures of proteins are translations of information contained in genes. Each protein has a different primary structure with different amino acids in different places along the chain. This sequence of amino acids is dictated by the _________.
amino terminal, Hydrolysis, chromatographic method
Sample Problems: 1. Consider the following peptide: Gly - Ile - Glu - Trp - Thr - Pro - Tyr - Gln - Phe - Arg - Lys What amino acids and peptides are produced when the above peptide is treated with each of the following reagents? d. DNFB DNFB tags the _______ amino acid. The product is DNP - Gly and Ile - Glu - Trp - Thr - Pro Tyr - Gln - Phe - Arg - Lys __________ then cleaves all the peptide bonds. DNP - Gly can then be identified by a ________________.
linear polymers, amino acids, 20, amino acids
Proteins are ________ built of monomer units called ___________. Most proteins in an organism are made from a set of _______ structurally similar ________ - these are the building blocks of proteins.
membranes, cartilage, connective tissue, oxygen, enzymes, infection, hormones, energy
Proteins provide structure in _________, build _______ and ________, transport _______ in blood and muscle, direct biological reactions as _______, defend the body against ________ and control metabolic processes as ________. They can even be a source of __________.
hemoglobin, α-subunits, β-subunits, functional, quaternary structure, hydrogen bonds, ionic bridges, van der Waals forces, disulfide bridges.
Quaternary structure of proteins For many proteins the functional form is not composed of a single peptide but is rather an aggregate of smaller globular peptides. For instance, the protein ________ is composed of four individual globular peptide subunits: two identical ________ and two identical _________. Only when the four peptides are bound to one another is the protein molecule ________. The association of several polypeptides to produce a functional protein defines the ________ of a protein. The forces that hold the quaternary structure of a protein are the same as those that hold the tertiary structure. These include ________ between polar amino acids, ________ between oppositely charged amino acids, __________ between nonpolar amino acids, and ________
phi, psi, steric interference, van der Waals radii, dihedral angles, dark blue, medium blue, lightest blue, yellow
Ramachandran plot for L-Ala Residues. Peptide conformations are defined by the values of Φ (_____) and Ψ (_____). Conformations deemed possible are those that involve little or no _________, based on calculations using known _________ and ________. The areas shaded ________ represent conformations that involve no steric overlap and thus are fully allowed; ________ indicates conformations allowed at the extreme limits for unfavorable atomic contacts; the ________ indicates conformations that are permissible if a little flexibility is allowed in the dihedral angles. The ______ regions are conformations that are not allowed.
N-Cα, Cα-C, Iimit
Rotation is permitted about the ________, and the _______ bonds. The backbone of a polypeptide chain can thus be pictured as a series of rigid planes, with consecutive planes sharing a common point of rotation at Cα. (Fig. 8b). The rigid peptide bonds ________ the range of conformations possible for a polypeptide chain.
carboxyl end
Sample Problems: 1. Consider the following peptide: Gly - Ile - Glu - Trp - Thr - Pro - Tyr - Gln - Phe - Arg - Lys What amino acids and peptides are produced when the above peptide is treated with each of the following reagents? a. Carboxypeptidase Because carboxypeptidase cleaves at the __________ of peptides, the products are Gly - Ile - Glu - Trp - Thr - Pro - Tyr - Gln - Phe - Arg and Lys
aromatic amino acids, Phe, Tyr, Trp
Sample Problems: 1. Consider the following peptide: Gly - Ile - Glu - Trp - Thr - Pro - Tyr - Gln - Phe - Arg - Lys What amino acids and peptides are produced when the above peptide is treated with each of the following reagents? b. Chymotrypsin Because chymotrypsin cleaves peptide bonds in which __________ (i.e., _______, ______and ______) contribute a carboxyl group, the products are Gly - Ile - Glu - Trp, Thr - Pro - Tyr, Gln - Phe and Arg - Lys
lysine, arginine
Sample Problems: 1. Consider the following peptide: Gly - Ile - Glu - Trp - Thr - Pro - Tyr - Gln - Phe - Arg - Lys What amino acids and peptides are produced when the above peptide is treated with each of the following reagents? c. Trypsin Trypsin cleaves at the carboxyl end of _______ and _______. The products are Gly - Ile - Glu - Tyr - Thr - Pro - Tyr - Gln - Phe - Arg and Lys
stretch, flexible, weak, covalent bonds
Silk does not _______, because the β conformation is already highly extended. However, the structure is _________ because the sheets are held together by numerous ________ interactions rather than by _______ such as the disulfide bonds in α-keratins.
primary, secondary structure, hydrogen, hydrogens, oxygens, hydrogen bonds, α-helix, β-pleated sheet
Secondary Structure The _______ sequence of a protein, the chain of covalently linked amino acids, folds into regularly repeating structures that resemble designs in a tapestry. These repeating structures define the _______ of the protein. The secondary structure is the result of _________ bonding between the amide _________ and carbonyl ________ of the peptide bonds. Many ________ are needed to maintain the secondary structure and thereby the overall structure of the protein. Different regions of a protein chain may have different types of secondary structure. The two most common types of secondary structure are the _________ and the __________ because they maximize hydrogen bonding in the backbone.
single, valine, glutamic acid, valine, sickling effect
Sickle cell hemoglobin differs from normal hemoglobin by a _______ amino acid. In the β-chain of sickle cell hemoglobin, a _______ (a hydrophobic amino acid) has replaced a ________ (a negatively charged amino acid). This substitution provides a basis for the binding of hemoglobin S molecules to one another. When oxyhemoglobin S unloads its oxygen, individual deoxyhemoglobin S molecules bind to one another as long polymeric fibers. This occurs because the ________ fits into a hydrophobic pocket on the surface of a second deoxyhemoglobin S molecule. The fibers generated in this way radically alter the shape of the red blood cell, resulting in the ________.
Albuminoids, albumins, globulins, histones
Simple proteins __________- keratin, collagen ___________- egg, serum __________- antibodies __________- chromatin
Pro, Gly, sizes, charges
Some amino acids are accommodated better than others in the different types of secondary structures. Some biases, such as the common presence of _____ and ______ residues in β turns and their relative absence in α helices, are readily explained by the known constraints on the different secondary structures. Other evident biases may be explained by taking into account the _____ or _____ of side chains.
4-hydroxyproline and 5-hydroxylysine, γ-carboxyglutamic acid, O-phosphoserine, cystine, ornithine and citrulline
Some examples of modified amino acid residues are:
chirality, L-glyceraldehyde, D-glyceraldehyde
Stereochemistry of alanine and glyceraldehyde. The amino acids found in proteins have the same ______ as __________, which is opposite to that of _________.
protofibrils, microfibril
Structure of the α - keratins. These proteins are assemblies of triple-helical __________ that are assembled in an array known as a _________. Hair is a collection of macrofibrils and hair cells.
Heat, acids and bases, organic solvents, Heavy metal ions
Summary of the factors that denature protein and their effects. ________- disrupts hydrogen bonds and hydrophobic attractions; can cause coagulation ____________- disrupt salt bridges ___________- disrupts hydrogen bonds ___________- react with disulfide bonds and acidic amino acid
Agitation, Detergents, Mechanical Stress
Summary of the factors that denature protein and their effects. ________- stretches a protein until cross-links break forming a solid _________- Disrupt hydrophobic interaction, causing the protein chain to unfold. _________- Disrupt the weak interactions that maintain protein conformation.
6.0, positive, OH-, H+, negative
Suppose that some acid is added to a glycine solution at its isoelectric pH value of _______. The zwitterion of glycine picks up H+ and becomes an ion with a _________ charge. However, when base is added to the zwitterion, the ______ is neutralized by an _____ from the glycine. In a base, glycine becomes a ________ ion.
egg white, hydrogen bonds, hydrophobic interactions, denatured
Temperature Consider the effect of increasing temperature on a solution of proteins—for instance, ________. At first, increasing the temperature simply increases the rate of molecular movement, the movement of the individual molecules within the solution. Then, as the temperature continues to increase, the bonds within the proteins begin to vibrate more violently. Eventually, the weak interactions, like ________ and __________, that maintain the protein structure are disrupted. The protein molecules are _________ as they lose their characteristic three-dimensional conformation and become completely disorganized.
Globular, tertiary structure, folds
Tertiary structure of proteins ______ proteins have three-dimensional structures called the ________ of the protein, which are distinct from their secondary structure. The polypeptide chain with its regions of secondary structure, α -helix and β -pleated sheet, further _____ on itself to achieve the tertiary structure.
phenylalanine, valine, threonine, tryptophan, isoleucine, methionine, histidine, arginine, leucine, lysine
The mnemonic given below is an aid to remember the 10 essential amino acids. PVT. TIM HALL P= __________ V= __________ T= _________ T=____________ I= __________ M = ____________ H= __________ A= ___________ L= __________ L= _____________
Covalent bonds, Linus Pauling, Robert Corey, covalent, Cα-C-N-Cα, shorter, carbonyl oxygen, amide nitrogen
The Peptide Bond is Rigid and Planar ____________, too, place important constraints on the conformation of a polypeptide. In the late 1930s, ________ and _________ embarked on a series of studies that laid the foundation for our current understanding of protein structure. They began with a careful analysis of the peptide bond. The α carbons of adjacent amino acid residues are separated by three _______ bonds, arranged as ________. X-ray diffraction studies of crystals of amino acids and of simple dipeptides and tripeptides showed that the peptide C-N bond is somewhat _______ than the C-N bond in a simple amine and that the atoms associated with the peptide bond are coplanar. This indicated a resonance or partial sharing of two pairs of electrons between the ________ and the ________ (Fig. 8a).
N-terminal end, C-terminal end, left
The _________ is the amino acid with the free amino group (-NH3); the amino acid with the free carboxyl group (-COO-) is the _________. Structures of proteins are conventionally written with the N-terminal residue on the ______.
carbonyl oxygen, amide nitrogen,
The __________ has a partial negative charge and the ________ a partial positive charge, setting up a small ____________. Virtually all peptide bonds in proteins occur in this _______ configuration.
D-glyceraldehyde, L-amino acids, alanine, glyceraldehyde, top, left
The configuration of α-amino acids isolated from proteins is opposite to that of __________, that is, the spatial relationship of the functional groups around the chiral carbon in _______, as in L-_________, resembles that of L-_________. When we put the carbonyl groups of both compounds in the same position (______), the -OH of L-glyceraldehyde and the NH3+ of L-alanine lie to the ______ of the chiral carbon.
base, isoelectric, acid, isoelectric
The effect of pH on proteins. (a) protein has an overall charge of 2+. When a ______ is added, some of the protonated amino groups lose their protons. Now the protein is _______; it has an equal number of positive and negative charges. (b) protein has an overall charge of 2-. As ______ is added, some of the carboxylate groups are protonated. The result is that the protein becomes ________.
Van der Waals forces, Hydrogen bonds, Ionic bonds, Covalent bonds, cystine, disulfide bond
The following types of interaction stabilize tertiary structure: __________ between the R groups of nonpolar amino acids that are hydrophobic ___________ between the polar R groups of the polar amino acids _________ (salt bridges) between the R groups of oppositely charged amino acids __________ between the thiol-containing amino acids. Two of the polar cysteines can be oxidized to a dimeric amino acid called _______ . The _______ of cystine can be a cross-link between different proteins, or it can tie two segments within a protein together.
hydrophobic interactions, globular, Polar, charged
The importance of these bonds becomes clear when we realize that it is the tertiary structure of the protein that defines its biological function. The most important forces stabilizing a protein's tertiary structure are the _____________of the nonpolar amino acid residues which are buried, closely packed, in the interior of a _________ protein, out of contact with water. ________ and _______ amino acids lie on the surfaces of globular proteins.
6.02
The isoelectric point for alanine may be calculated as follows: The pK1 and pK2 values for alanine are 2.34 and 9.7, respectively. The pI value for alanine is therefore is ________
mechanical strength, skin, muscle,
The major structural property of a coiled coil superstructure of α -helices is its great _________. This property is applied very efficiently in both the fibrous proteins of ________ and those of _______. As you can imagine, these proteins must be very strong to carry out their functions of mechanical support and muscle contraction.
α-helix, hydrogen bond, coil, outward
The most common type of secondary structure is a coiled, helical conformation known as the ________. It has several important features. Every amide hydrogen and carbonyl oxygen associated with the peptide backbone is involved in a _________ when the chain coils into an α-helix. These hydrogen bonds lock the α-helix into place. Because many H-bonds occur within the polypeptide, the chain is pulled into a tight _______ that looks like a spring or telephone cord. The side chains of the amino acids in the polypeptide extend ________ from the α -helix backbone.
proteios, of first importance
The name protein is derived from the Greek word _________ which means "__________."
partial negative, partial positive, electric dipole, single, trans, partial double-bond
The oxygen has a _________ charge and the nitrogen a _________ charge, setting up a small __________. The six atoms of the peptide group lie in a _______ plane, with the oxygen atom of the carbonyl group _______ to the hydrogen atom of the amide nitrogen. From these findings Pauling and Corey concluded that the peptide C-N bonds, because of their ___________ character, cannot rotate freely.
phi, psi, 180, -180, first, fourth, increase, clockwise, steric overlap
The planar peptide group. By convention, Φ (_____) and Ψ (____) are ______ degrees (or ______ degrees) when the _____ and _____ atoms are farthest apart and the peptide is fully extended. As the viewer looks out along the bond undergoing rotation (from either direction) the Φ and Ψ angles ________ as the fourth atom rotates ______ relative to the first. In a protein, some of the conformations shown here (e.g. 0 degrees) are prohibited by ________ of atoms. the balls representing atoms are smaller than the van der Waal's radii for this scale
resonance, rotate, Three, N-Cα, Cα-C, phi, psi, C-N, hindered, R groups
The planar peptide group. -Each peptide bond has some double-bond character due to _______ and cannot _____. -______ bonds separate sequential alpha carbons in a polypeptide chain. The ______ and _____ bonds can rotate, described by dihedral angles designated Φ (______) and Ψ (_____), respectively. The peptide ______ bond is not free to rotate. Other single bonds in the backbone may also be rationally ________, depending on the size and charge of the ________. - The atoms and planes defining Ψ.
parallel β-pleated sheet, antiparallel β -pleated sheet
The polypeptide chains in a β-pleated sheet can have two orientations: 1. __________-N-termini are head to head. 2. __________ - N-terminus of one chain is aligned with the C-terminus of a second chain (head to tail).
NaOH, amino groups, neutral, isoelectric point, carboxylate, zero, isoelectric point
The protein shown has a net charge of 2+ because it has two extra -N+H3 groups. If we add 2 moles of base, such as ________, the protonated _________ lose their protons and thus become electrically _______. Now the net charge of the protein is zero. The pH at which a protein has an equal number of positive and negative charges, that is, a net charge of zero, is called the _________. The protein has a net charge of 2- because of two additional carboxylate groups. When 2 moles of acid are added, the _________ groups become protonated. They are now electrically neutral, and the net charge on the protein is ________. As in the preceding example, the protein solution is at the ________.
Collagen, helical, triple helix, tropocollagen, hydrogen bonds.
Triple helix _________, which is the most abundant protein in the body, makes up from 25% to 35% of all protein in vertebrates. It is found in connective tissue, blood vessels, skin, tendons, ligaments, the cornea of the eye, and cartilage. The strong structure of collagen is a result of three __________ polypeptides woven together like a braid to form a _______, also called __________. Collagen fibers are triple helices of polypeptide chains held together by _________
backbone of the protein, amino acid side chains
The repeating chain of amide linkages is called the ____________ and the __________ are substituents on the backbone.
L stereochemistry, identical, smaller, Gly, -350, -850
The symmetry of the plot results from the __________ of the amino acid residues. The plots for the other L residues with unbranched side chains are nearly _______. Allowed ranges for branched residues such as Val, Ile, and Thr are somewhat _______ than for Ala. The _____ residue, which is less sterically hindered, has a much broader range of allowed conformations. The range for Pro residues is greatly restricted because Φ is limited by the cyclic side chain to the range _______ to ________.
mechanical agitation
The whipping of cream and the beating of egg whites into meringue are examples of _______ that denatures a protein. The violent whipping action causes the protein to stretch until the cross-linkages break apart.
isoelectric point, neutral, anode, cathode, Nonpolar, basic, acidic
The zwitterion form of an amino acid exists at a pH value called the __________________. At this pH, the molecule is electrically _______ and would not move toward a positive (_______) or negative (______) electrode. ___________ amino acids have isoelectric points at pH values close to 7. The _________ amino acids have isoelectric points at much higher pH values, whereas ________ amino acids become electrically neutral at low pH values.
parallel, away, carbonyl oxygen, amide hydrogen, parallel, right-handed, normal screw, clockwise, counterclockwise, 5.4, 3.6
The α -helix. Note that all of the hydrogen bonds between C=O and N-H groups are ________ to the long axis of the helix. The side chains of the helix point ______ from the long axis of the helix. Every ________ is hydrogen-bonded to an _________ four amino acids away in the chain. The hydrogen bonds of the α -helix are _____ to the long axis of the helix The polypeptide chain in an α -helix is _______. It is oriented like a ________. If you turn a screw ________ it goes into the wall; turned ________, it comes out of the wall. The repeat distance of the helix, or its pitch, is _____ Å, and there are ______ amino acids per turn of the helix.
lactose, lactic acid, increases, isoelectric, coagulate
This is a reaction that you have probably observed in your own kitchen. When milk sits in the refrigerator for a prolonged period, the bacteria in the milk begin to grow. They use the milk sugar, __________, as an energy source in the process of fermentation and produce ________ as a by-product. As the bacteria continue to grow, the concentration of lactic acid ______. The additional acid results in the protonation of exposed carboxylate groups on the surface of the dissolved milk proteins. They become _______ and _______ into a solid curd.
ionizable, Titration, reactivity, alanine, strong base, two, stepwise reaction
Titration of Amino Acids Because amino acids contain ________ groups, the predominant ionic form of these molecules in solution depends on the pH. __________ of an amino acid illustrates the effect of pH on amino acid structure. Titration is also a useful tool in determining the ____________ of amino acid side chains. Consider __________, a simple amino acid, which has two titratable groups. During titration with a __________ such as NaOH, alanine loses ______ protons in a ____________.
dipeptide, tripeptide, tetrapeptide, polypeptides
Two amino acids form a ________, three a _______, and four a ________. Long chains of amino acids are called _________.
enkephalins and endorphins
Two neurotransmitters that act like *opiates* to block pain.
α-helix, β-pleated sheet, triple helix
Types of secondary structure patterns: 1. ___________ 2. ___________ 3. ___________ (less common)
polycations, polyanions, unfold, functions, enzymes, hemoglobin
When the blood pH drops too low, blood proteins become _______. Similarly, when the blood pH rises too high, the proteins become ________. In either case, the proteins will _______ because of charge repulsion and loss of stabilizing ionic interactions. Under these extreme conditions, the denatured blood proteins would no longer be able to carry out their required ________. The blood cells would also die as their critical _______ were denatured. The _______ in the red blood cells would become denatured and would no longer be able to transport oxygen. Fortunately, the body has a number of mechanisms to avoid the radical changes in the blood pH that can occur as a result of metabolic or respiratory difficulties.
negative, positive, repel, isoelectric point, coagulate
When the pH of a protein solution is above the isoelectric point, all the protein molecules will have a net ________ surface charge. Below the isoelectric point, they will have a net _________ charge. In either case, these like-charged molecules ______ one another, and this repulsion helps keep these very large molecules in solution. At the _________, the protein molecules no longer have a net surface charge. As a result they no longer strongly repel one another and are at their least soluble. Under these conditions, there is a tendency for them to clump together and precipitate out of solution. In this case, proteins may _________ even though they are not denatured.
ornithine, citrulline
________ and _________ - metabolites of the urea cycle.
Collagen
________ is another well understood example of proteins with quaternary structure.
Human hair, protofibril, microfibril, molecular pigtails
________ provides a typical example of the structure of the α-keratins. The proteins of hair consist almost exclusively of polypeptide chains coiled up into α-helices. A single α -helix is coiled in a bundle with two other helices to give a three-stranded superstructure called a __________ that is part of an array known as a _________. These structures, which resemble "_________," possess great mechanical strength, and they are virtually insoluble in water.
cystine
_________ - made up of two cysteine molecules or residues joined together by a disulfide bond. The disulfide bonds play a special role in the structures of many proteins (e.g. hair) by forming covalent cross-links.
Oxytocin, Vasopressin, two, nine, hypothalamus, posterior pituitary gland, hypothalamus
_________ and ________ (cyclic peptides) The amino acid sequences of the peptide hormones oxytocin and vasopressin differ only by ______ residues. Both molecules contain _______ amino acids and are produced by the cleavage of polypeptide precursors within different specialized cells in the __________. (The hypothalamus is a small structure in the vertebrate brain that regulates functions such as water balance, hunger, thirst, and sleep.) After synthesis, oxytocin and vasopressin are transported down nerve tracts into the ____________, where they are stored. Then each peptide is secreted in response to specific signals from the _________.
Substance P, Bradykinin, opioid peptides
_________ and _________ stimulate the perception of pain, an effect opposed by the __________. (Pain is a protective mechanism in animals that warns of tissue damage.)
Detergents, hydrophobic interactions
_________ have both a hydrophobic region (the fatty acid tail) and a polar or hydrophilic region. When detergents interact with proteins, they disrupt ________, causing the protein chain to unfold.
Coagulation, egg albumins,
_________ occurs as the protein molecules then unfold and become entangled. At this point they are no longer in solution; they have aggregated to become a solid. The egg white began as a viscous solution of ________; but when it was cooked, the proteins were denatured and coagulated to become solid.
Denaturation, primary structure
_________ of a protein occurs when there is a change that disrupts the interactions between R groups that stabilize the secondary, tertiary, or quaternary structure. However, the covalent amide bonds of the ___________ are not affected.
Myosin, two
_________, one of the major proteins of muscle which has a rodlike structure has _____ α-helices coiled around one another.
Fibroin, Ala, GIy, close, van der Waals
_________, the protein of silk, is produced by insects and spiders. Its polypeptide chains are predominantly in the β conformation. Fibroin is rich in _____ and ______ residues permitting a _______ packing of β sheets and an interlocking arrangement of R groups. The overall structure is stabilized by extensive hydrogen bonding between all peptide linkages in the polypeptides of each β sheet and by the optimization of _________ interactions between sheets.
Silk fibroin
__________ - fibrous proteins composed of antiparallel β -pleated sheets
Sickle cell anemia, normal, altered β-chains, sickle cell trait, 50%
__________ occurs in individuals who have inherited the gene for sickle cell hemoglobin from both parents. Afflicted individuals produce 90-100% defective β-chains. Individuals who inherit one normal gene and one defective gene produce both _____ and _______. About 10% of African Americans carry a single copy of the defective gene, a condition known as _________. Although not severely affected, they have a ______ chance of passing the gene to each of their children.
Fibrous proteins
___________ - insoluble in water, make up the tough fibers of skin, cartilage, nails, and collagen of connective tissue; in this category, we include the α-keratins, β-pleated sheet of silk fibroin, and collagen.
Globular proteins
___________ - water soluble and so compact that they are nearly spherical in shape; they function in the cells as enzymes, hormones, and antibodies.
Sickle cell anemia, sickle cell hemoglobin, sickled, small capillaries, hindered,
____________ It is a human genetic disease that first appeared in tropical west and central Africa. It afflicts about 0.4% of African Americans. These individuals produce a mutant hemoglobin known as __________ (Hb S). Sickle cell anemia receives its name from the _______ appearance of the red blood cells that form in this condition (Figure 7). The sickled cells are unable to pass through the ________ of the circulatory system, and circulation is ___________. This results in damage to many organs, especially bone and kidney, and can lead to death at an early age.
Glutathione, γ-amide bond, protein, DNA, metabolism, amino acid
____________ (γ-glutamyl-L-cysteinylglycine) This tripeptide contains an unusual _________ (note that the γ-carboxyl group of the glutamic acid residue, not the α-carboxyl group, contributes to the peptide bond). Found in almost all organisms, glutathione is involved in many important biological processes. Among these are __________ and ________ synthesis, drug and environment toxin ________, and ______ transport.
Fibrous proteins, α-keratins
____________ - structural proteins arranged in fibers or sheets that have only one type of secondary structure. The __________ are fibrous proteins that form the covering (hair, wool, nails, hooves, and fur) of most land animals.
Oxytocin, regulatory role, testosterone
____________ stimulates contraction of uterine muscles during childbirth and the ejection of milk by mammary glands during lactation. (Recently, oxytocin production by the uterus itself during childbirth has been detected.) In males, oxytocin may have a ________ in the synthesis of the sex hormone ___________.
β-pleated sheet, β-strand, hydrogen bonds, extended
_____________- Formed when two or more polypeptide chain segments line up side by side; each individual segment is referred to as a _______; all of the carbonyl oxygens and amide hydrogens in a β -pleated sheet are involved in ________, and the polypeptide chain is nearly completely ________.
Vasopressin, antidiuretic hormone, blood pressure, blood Na+ concentration, Oxytocin, vasopressin
______________, also known as __________ (ADH), is secreted in response to low ________ or a high _________. ADH acts by stimulating the kidneys to retain water. Because oxytocin and vasopressin have similar structures, it is not surprising that the functions of the two molecules overlap. ________ has a mild antidiuretic activity, and the __________ has some oxytocinlike activity.
1. Nonpolar, Aliphatic R Groups 2. Aromatic R Groups 3. Polar, Uncharged R Groups 4. Positively Charged (Basic) R Groups 5. Negatively Charged (Acidic) R Groups
gradations of polarity, size, and shape of the R groups (five main classes of amino acids based on the properties of their R groups, in particular, their polarity) Hint: NAPPN
γ-carboxyglutamic acid, O-phosphoserine
modified amino acid residues ___________ - constituent of several proteins involved in blood clotting. ___________ - presence of P regulates the activity of proteins.
4-hydroxyproline, 5-hydroxylysine
modified amino acid residues ________ and __________- both of these amino acid residues are important structural constituents of the fibrous protein collagen, the most abundant protein in mammals.
electric charge, solution
pH Because of the R groups of the amino acids, all proteins have a characteristic _______. Because every protein has a different amino acid composition, each will have a characteristic net electric charge on its surface. The positively and negatively charged R groups on the surface of the molecule interact with ions and water molecules, and these interactions keep the protein in _________ within the cytoplasm.
globular, reverses, β turns, 180, carbonyl oxygen, amino-group hydrogen
β Turns are common in proteins In _______ proteins, which have a compact folded structure, nearly one-third of the amino acid residues are in turns or loops where the polypeptide chain ________ direction. These are the connecting elements that link successive runs of α helix or β conformation. Particularly common are _______ that connect the ends of two adjacent segments of an antiparallel β sheet. The structure is a ______ degrees turn involving four amino acid residues, with the _________ of the first residue forming a hydrogen bond with the __________ of the fourth.
central two, Glycine, proline, flexible, cis-configuration, surface, γ-turn
β Turns are common in proteins The peptide groups of the _______ residues do not participate in any interresidue hydrogen bonding. _______ and _______ residues often occur in β turns, the former (glycine) because it is small and _______, the latter because peptide bonds involving the amino nitrogen of proline readily assume the _________, a form that is particularly amenable to a tight turn. Of the several types of β turns, the two shown are the most common. Beta turns are often found near the _____ of a protein, where the peptide groups of the central two amino acid residues in the turn can hydrogen-bond with water. Considerably less common is the _______, a three residue turn with a hydrogen bond between the first and third residues.
