Chapter 6 Flashcards
The alpha carbon amino acid has four substituents, distinct from each other except in the case of the simplest amino acid, ___.
An amino group, a carboxyl group, and a proton are three of the substituents on all of the naturally occurring amino acids. The fourth, is the R group, which is the only______.
Glycine
Distinguishable feature.
Because it’s 4 substituents are distinct, except for glycine, the alpha carbon is a ___. Amino acids that occur in ordinary proteins all have ___ configuration at that center.
D amino acids are present in other kinds of molecules, such as
chiral center. L configuration
Small protein like polypeptides in microorganisms
The R group is responsible for determining the amino acid’s ____& ___.
Amino acids are put into 3 categories:
The size of the sidechain is important for ___ amino acids because these side chains ____ and therefore, the functional roles in proteins such as glycine and alanine are quite different from those of phenylalanine and tryptophan.
Polarity (which correlates with its solubility in water) and it’s size.
- Neutral (uncharged) and nonpolar
- Neutral and polar
- charged
Nonpolar, pack into the compact interior of a protein
The ___ bonds are the covalent links between amino acids in a protein. One forms by a ___ reaction, with elimination of a water molecule.
Polypeptide chain is successive links of multiple ___ into a linear chain.
The components of the chain are called amino acid ___.
Peptide
Condensation
Amino acids
Residues
The peptide bond has partial double-character (the length of the bond is intermediate relative to single and double carbon-nitrogen bond).
The amide and carboxyl components are nearly coplanar and in a ___ configuration.
The peptide bond presents a significant barrier to rotation, and thus is central to a roughly planar, rigid group of __ atoms.
The peptide bond has partial double-character (the length of the bond is intermediate relative to single and double carbon- nitrogen bond).
The amide and carboxyl components are nearly coplanar and in a TRANS configuration.
The peptide bond presents a significant barrier to rotation, and thus is central to a roughly planar, rigid group of SIX atoms.
The φ torsion angle corresponds to the rotation about the __ bond; in the conformation here φ=180°.
(c) The ψ torsionangle corresponds to the rotation about the ___ bond. In the conformation here ψ=0°.
So there are ___ bonds per amino acid residue in a peptides. The peptide bond is rigid, the other two have relative free rotation ability.
N-Cα bond, Cα-C,
Three,
If the two negatively charged oxygen atoms of a peptide bond are too close together they will repel one another. This clash is called ____ and it further limits the ____.
This clash is called STERIC HINDRANCE and it further limits the number of possible conformations of the polypeptide chain.
Because its R group is just a proton, glycine is not ___, and it has more conformational freedom than any other amino acids.
Proline: in which the side chain has a ____, has less conformational freedom than many other amino acids.
Chiral
covalent bond with N as well as Cα
Cysteine, with a sulfhydryl (-SH) group on its side chain, is one amino acid that is sensitive to ___under roughly physiological conditions. Two cysteines can form___
oxidation-reduction
A disulfide bond by oxidation of the two – SH groups to S—S.
Proteins on the cell surface or which are secreted into extracellular space are exposed to an environment with ___ that favors ___ formation; most such proteins have disulfide bonds and no ____.
Living cells maintain a more reducing internal environment, and intracellular protein very rarely have _____
.
Disulfide bonds enhance the stability of a folded protein by adding ____.
Proteins on the cell surface or which are secreted into extracellular space are exposed to an environment with REDOX POTENTIAL that favors DISULFIDE formation; most such proteins have disulfide bonds and no UNOXIDIZED cysteines. Living cells maintain a more reducing internal environment, and intracellular protein very rarely have DISULFIDE BONDS.
covalent cross-links
Hydrophobic molecules avoid the network of hydrogen bonds; hydrophilic molecules participate in it. It is therefore favorable for hydrophobic molecules to ___
remain adjacent to each other than to disperse into a aqueous medium.
Some amino acid side chains are hydrophilic (I.e___), some are hydrophobic (ie ____).
Some hydrophilic side chains can have hydrophobic parts (ie ___)
The hydrophobic character of many amino acid side chains makes it favorable to ____, and the hydrophilic character of others allows them to ___.
aspartic acid
Phenylalanine
methylene groups in lysine
The hydrophobic character of many amino acid side chains makes it favorable to cluster away from water, and the hydrophilic character of others allows them to project into water.
Primary structure: ?
Secondary structure: ?
Tertiary structure: the usually compact, three-dimensionally folded arrangement
that the peptide chain adopts under ___ conditions. Segments of the chain may have ____
Quaternary structure: for proteins composed of ___, quaternary structure refers to multi-subunit organization of an oligomeric protein or protein assembly.
Primary structure: the sequence of amino acid residues in the polypeptide chain
Secondary structure: the local conformation of it polypeptide chain—the 3D arrangement of a short stretch of amino acid residue;
Tertiary structure: the usually compact, three-dimensionally folded arrangement that the peptide chain adopts under physiological conditions. Segments of the chain may have α-helix, or β-strand, or less regular conformations (turns, loops)
Quaternary structure: for proteins composed of more than one peptide chains, quaternary structure refers to a multi-subunit organization of an oligomeric protein or protein assembly.
The α-helix: the polypeptide backbone spirals in a ___ sense around a helical axis, so that hydrogen bonds form between _____. (one turn: 5.4A, 3.6 residues)
right-handed
so that hydrogen bonds form between the main chain carbonyl group of one residue and the main-chain amide group of a reside at four positions further along in the chain. (one turn = 5.4A, 3.6 residues)
Secondary structure β- strand: is an extended conformation, in which the side chains ___, and the amide and carbonyl groups project ____.
The backbone is not quite fully stretched, so the strands has a slightly zigzag or pleated character.
β- strand: is an extended conformation, in which the side chains project alternatively to either side of the backbone, and the amide and carbonyl groups project alternatively to either side of the backbone.
The backbone is not quite fully stretched, so the strands has a slightly zigzag or pleated character.
Parallel beta sheet: the chains run ___. Anti parallel: the chains run___
in the same directions
Different directions (but it looks straighter)
Quaternary structures: (determined by ____)
In simple cases, the way in which the subunits associate doesn’t change how individual peptides fold. However, often, the ____or even the __ of the components of a protein oligomer ( a protein composed of a small number of subunits) depend on their association with each other.
Example: Transcription factor GCN4 α-helical coiled-coil: two polypeptide chains, either identical or different, adopt α-helical conformation and wrap very gently around each other. The individual chains are not, in general, stable as α-helices on their own—if oligomeric interaction is lost, the separated helices unravel into disordered polypeptide chains.
primary sequence and the interaction between the subunits
However, often, the tertiary structure or even secondary structures of the components of a protein oligomer ( a protein composed of a small number of subunits) depend on their association with each other.
Polypeptide chains typically fold into one or more ____.
Folding of polypeptide chain creates an “inside” and an “outside”, and therefore generating __&__. If the polypeptide chain is too short, there are no conformations that bury enough hydrophobic groups to stabilize the folded structure. It the chain is too long, the complexity of the folding process is likely to generate errors. As a result of these restrictions, ____. The structures of individual domains of such a protein are similar to the structure of smaller, single-domain proteins.
Polypeptide chains typically fold into one or more DOMAINS.
Folding of polypeptide chain creates an “inside” and an “outside”, and therefore generating buried and exposed amino acid side chains. If the polypeptide chain is too short, there are no conformations that BURY enough hydrophobic groups to stabilize the folded structure. It the chain is too long, the complexity of the folding process is likely to generate errors. As a result of these restrictions, MOST stably folded conformations include between 50 and 300 amino acid residues. Larger polypeptide chains generally fold into discrete modules known as domains.
The structures of individual domains of such a protein are similar to the structure of smaller, single-domain proteins.
If a functional group that donates or accepts a hydrogen bond is buried, it almost always has a ___.
• Fulfilling the main-chain hydrogen bonding is probably an important reason for the prevalence of ____, even within compactly folded protein domains.
• All known domain structures don’t form a __, so if you imagine pulling on one ends, the whole thing would open into a straight line.
hydrogen-bonding partner
Fulfilling the main-chain hydrogen bonding is probably an important reason for the prevalence of REGULAR secondary structures, even within compactly folded protein domains.
All known domain structures don’t form a KNOT—that is, if you imagine pulling on one ends, the whole thing would open into a straight line.
Domain: a part of a polypeptide chain with a ___ structure that doe not depend on any of the remaining part of the protein for its stability.
Motif: a domain substructure that occurs in many proteins, often having some characteristic ___ (e.g., the helix-turn-helix motif in many DNA-recognition domains)
Domain: a part of a polypeptide chain with a FOLDED structure that doe not depend for its stability on any of the remaining part of the protein.
Motif: a domain substructure that occurs in many proteins, often having some characteristic amino acid sequence properties (e.g., the helix-turn-helix motif in many DNA-recognition domains)
Protein domains can be classified according to their principle secondary structures:
(1) Mostly α-helix (left): myoglobin
(2) Mostly β-strand (middle): immunoglobin
(3) A mixture of the two (right): small GTPase RAS protein.
(4) Small domain with little secondary structure.
Protein domains can be classified according to their principle secondary structures: (1) Mostly α-helix (left): myoglobin
(2) Mostly β-strand (middle): immunoglobin
(3) A mixture of the two (right): small GTPase RAS protein.
(4) Smalldomainwithlittlesecondarystructure.
The most important levels in the protein classification hierarchy are \_\_&\_\_. The fold class takes into account not only the secondary structures, but also the \_\_\_\_. A group of homologous proteins are ones with \_\_ great enough to assume that they have a common evolutionary origin. All domains of a given fold class have a common origin– unanswered but reasonable assumption.
The most important levels in the classification hierarchy are FOLD (topology) and HOMOLOGY. The fold class takes into account not only the secondary structures, but also the CHAIN passes from one helix or strand to another. A group of homologous proteins are ones with SEQUENCE similarities great enough to assume that they have a common evolutionary origin.
The links between domains for folded protein can be very short, allowing a ___ interface between them, or quite long, allowing considerable ___.
• The amino acid sequences of long linkers generally lack large hydrophobic groups, since ____. Instead they have other simplified features.
Antibody molecule as a example.
The links between domains for folded protein can be very short, allowing a tight and rigid interface between them, or quite long, allowing considerable flexibility.
• The amino acid sequences of long linkers generally lack large hydrophobic groups, since the EXTENDABLE, flexible linker conformation cannot sequester from water. Instead they have other simplified features.
• Antibody molecule as a example.
Immunoglobulin G (IgG) is an antibody isotype. It is a protein complex composed of four peptide chains—two identical heavy chains and two identical light chains arranged in a Y-shape typical of antibody monomers. Each IgG has ___ antigen binding sites. Representing approximately 75% of serum immunoglobulins in humans, IgG is the most abundant antibody isotype found in the circulation.
Each IgG has two antigen binding sites.
Both light chains and heavy chains of the Ig2 have variable domains. CH2 and CH3 domains form the Fc fragment. Controlled proteolytic attack selectively cleaves the hinge, allowing _____. Note the β-strand domains in the Fab and Fc domains. The ___ between C and V domains allows restricted flexibility. The ___allows greater flexibility for antigen binding.
Both light chains and heavy chains of the Ig2 have variable domains. CH2 and CH3 domains form the Fc fragment. Controlled proteolytic attack selectively cleaves the hinge, allowing isolation of the Fab and Fc moieties. Note the β-strand domains in the Fab and Fc domains. The SHORT LINK between C and V domains allows restricted flexibility. The LONGER HINGE hinge allows greater flexibility for antigen binding.
Following emergence from the ribosome, modification of the ___ can modulate the structure and function of a protein.
• One of the most important is glycosylation, which is the ____ to an asparagine side chain, a serine or a threonine side chain. It is generally takes place in the ___ of eukaryotic cells, and therefore it is a nearly universal characteristic of the ectodomains of cell surface proteins and secreted proteins.
Following emergence from the a ribosome, modification of the peptide side chains can modulate the structure and function of a protein.
• One of the most important is glycosylation—addition of one ore more sugars (“glycans”) to an asparagine side chain or a serine or threonine side chain. It is generally takes place in the endoplasmic reticulum of eukaryotic cells, and therefore it is a nearly universal characteristic of the ectodomains of cell surface or secreted proteins.
Protein bearing glycans are called ___. Enzymes that transfer glycans to asparagine side chains recognize a short seqeunce motif, ____(where X can be any amino acid residues).
• ____] of serine, threonine, tyrosine (common in eukaryotes), or histidine (common in prokaryotes) side chains is another widespread modification, critical for intracellular regulation.
Protein bearing glycans are called glycoproteins. Enzymes that transfer glycans to asparagine side chains recognize a short seqeunce motif, Asn-X-Ser/Thr (where X can be any amino acid residues.)
• Phosphorylation of serine, threonine, tyrosine (common in eukaryotes), or histidine (common in prokaryotes) side chains is another widespread modification, critical for intracellular regulation.
The amino acid sequence of a protein determines the ____&___of that protein. The Anfisen experiment first established this point. They showed that a peptide chain can fold correctly without ____.
The amino acid sequence of a protein determines the 3D structure and function of that protein. The Anfisen experiment first established this point. They showed that peptide chain an fold correctly without additional cellular machinery.
