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84 Cards in this Set
- Front
- Back
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What is the primary structure of an amino acid?
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-Linear amino acid sequence
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Peptides Size
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2-20 amino acids long
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Polypeptides Size
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20 and up amino acids long
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Protein Size
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50 and up amino acids long
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What type of reaction joins two amino acids?
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Condensation: joins the carboxyl group of one to the amino group of the other, eliminating water, and forms a peptide bond (an unfavorable reaction energetically, costing +21 kJ/mole)
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Describe the partial double-bond character of peptide bonds.
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-Because the carbonyl double-bond character is now shared across the C-N bond, six atoms become co-planar
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In a peptide, the planar structure of each peptide bond introduces significant constraints on the possible ______ ____ that the molecule can occupy. Where is rotation only possible?
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-Conformational Space
-Around the two bonds extending from the alpha-carbon to its nitrogen (the phi bond) or its carbonyl carbon (the psi bond) |
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What is Ramanchandran plot used for?
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Phi and Psi angles are plotted on a graph of the theoretical range of each (from -180 to 180 degrees)
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_______ is not a good predictor of importance of a cell.
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Size
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What is the weighted average of an average amino acid?
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MW of 128-->110 daltons is usually used in converting between molecular weight and length in amino acids
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Why are most proteins less than 1000 amino acids long?
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Because of fidelity and processivity concerns with both RNA and protein biosynthesis
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Processivity
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-Longer length
-Both RNA polymerase and ribosome have more time to fall off |
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Fidelity
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-A single error in a long protein may completely disrupt its function
-Cell uses small proteins to make longer |
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Hydrolysis
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Used to form free amino acids from proteins for compositional analysis
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What are among the most abundant amino acids in a typical polypeptide, with frequencies from 7-9% on a molar basis.
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-Ala
-Leu -Gly -Ser -Lys |
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What is the rarest amino acid at 1%?
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-Trp
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What are the close to rarest amino acids often present at only 2-3%?
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-Met
-His -Cys |
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How can the exact identity of many proteins can be elucidated via a combination?
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Large scale 2D gels
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Large scale 2D gels
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-Separates protein based upon size and charge (or pI)
-Efficient way of resolving and identifying proteins that interact in large macromolecular complexes based upon co-purification |
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The final composition of a protein depends upon amino acid _____, usually by _______ to together functional groups or essential cofactors.
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-Modification
-Conjugation |
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What does the overall net charge of a protein depend on?
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-Total number of charged side-chain residues (plus the amino- and carboxy-termini)
-pH at which it is being measured |
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Isoelectric Point (pI)
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pH at which the net charge is zero and is generally the point of lowest solubility for a protein
-TELLS NOTHING ABOUT TOTAL CHARGES |
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When a protein is at its pI, .......
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-Its mobility in an electric field is zero
-Process can help purify using affinity chromatography or 2D gel electrophoresis |
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In addition to the diversity from the 20 standard amino acid R-groups, many peptides and proteins undergo ____ ___ ___ which further increase the _____ _____.
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-Post-translational modification
-Compositional variation |
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List possible side chains
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-Methyl
-Hydroxyl -Carboxyl -Phosphoryl -Glycosyl -Isoprenyl -Oxo |
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What does modification of proteins do to themselves?
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-Alters their properties in desirable ways for the cell or organism
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What is evident in examining proteins that carry out similar functions in different organisms?
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-Similar structural motifs are employed, usually displaying an evolutionary relationship
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What do evolutionary comparisons of related proteins generally suggest?
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-Conserved segments of sequence are functionally important, while those with high variation are not; the latter characteristic is used as a measure of evolutionary "distance"
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What do comparisons of conserved vs. non-conserved residues in such proteins often reveal?
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-(inferred) role of specific amino acid side-chains in the protein's FUNCTION and can lead to 'STRUCTURE FUNCTION" analysis via recombinant technology
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What may allow insight into the intracellular distribution (and thus presumed function) of proteins?
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-Distance Maps
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Alpha-Helix
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-Stable structure, exploiting the max H-bond within the strand, parallel to the axis of the helix, with a pitch of 5.4 Angstroms and 3.6 residues/turn
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Why are alpha-helixes so stable?
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-Van der Waal's forces in the interior of the helix, where the atoms are very closely packed
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Distortion or destabilization of the helix occurs with the inclusion of ____ (generally considered a "helix-breaker") since it cannot form hydrogen bonds and its cyclic structure forces a ______ in the helical structure where it is found.
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-Proline
-Kink |
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If similarly charged residues are nearby, they destabilize by ____ ____, and bulky side-chains can destabilize by _____ ____.
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-Charge repulsion
-Steric hindrance |
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What can result in a dipole moment in an alpha-helix?
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-Distribution of a slight electrical charge along the helix
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____ is rarely prevalent in an alpha-helix---but only because its backbone flexibility favors other structures instead.
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Glycine
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What is the structure of peptides in Beta-structures?
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-Peptide backbone is fully extended, with each residue's amino-hydrogen pointed to the same side and carbonyl-oxygen to the other side, both perpendicular to the direction of the backbone
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When 2 strands are adjacent, they form a _______ stabilized by hydrogen bonds (between N-H and C=O)
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Beta ribbon
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With multiple adjacent strands it becomes a pleated _____.
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Beta sheet
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What is the average size of a beta sheet?
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~6 strands, with about 6 amino acids in each
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Antiparallel
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-Fully extended backbone
-N- and C-termini of adjacent segments at opposite ends -Often joined by Beta-bends -H-bonds between chains |
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Antiparallel Beta-sheet (or Beta-ribbon)
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-Slight natural right-handed twist
-Adjacent strands are often connected by a Beta-bend -Inter-strand b-bond are straight, and thus a max strength, contributing to a very tough but flexible structure (this is used in silk fibroin) |
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Parallel
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-N- and C- termini of adjacent segments at the same end
-Often connected by alpha-helices -Less stable than antiparallel=usually comprised of 5 or more strands -Each backbone segment is slightly less extended than in the antiparallel case |
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Parallel Beta-strands
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-Have the same N-tp-C directionality
-Cannot be connected directly at their ends -When connections occur from one to the next, they employ a right-hand crossover (often using alpha-helical segment) |
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Beta-Turns
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-4 residue bend (reverses direction of polypeptide strand)
-Pro at amino acid #2, Gly at amino acid #3 (in Type II) -Can connect antiparallel Beta-strands |
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What are beta turns held together by?
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-H-bond between the carbonyl-oxygen of amino acid #1 and the amino-hydrogen of amino acid #4
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Other Right-handed helices
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-3(10) helix: long and thin with 3 residues/turn
-4.4(16) or Beta-helix: which is short and fat |
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What happens if glycine predominates in a helical structure? Where can this occur?
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-Left-handed helical structure can form that has 3 residues per turn, and 3 of these assemble in a triple-helical bundle (right hand twist)
-In collagen |
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What form frequently used motifs in the tertiary structure of proteins?
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-Various combinations of secondary structural elements
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Common secondary structures
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-4-helix bundle
-Beta-Beta saddle -Beta-alpha-Beta loop -Alpha/Beta barrel |
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Supersecondary Structures
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-Cannot always (or even often) be isolated as specific substructures upon chopping the protein into smaller parts
-Do not necessarily comprise a biologically functional sub0region of the protein -May be assembled from distant linear sequence elements |
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Domain
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-100-200 amino acid segment of a larger protein that is stably self-folding and FUNCTIONALLY self-contained
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Where are proteins generally present?
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In multiple proteins
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What do domains contain?
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-May contain multiple elements of secondary structure
-Often separable from their larger protein by gentle proteolytic treatment -Have biological function after being isolated from their original context as part of a larger protein |
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What are types of secondary structures?
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-Alpha-Helices
-Beta Ribbon -Beta Sheet |
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What are types of tertiary structures?
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-Fibrous proteins
-Globular proteins |
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Alpha Keratins (Fibrous Protein)
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-Right Handed Helices
-2 Chain left-handed coiled coil -Surfaces touching made up of hydrophobic residues -Protofilament, protofiber -Cross-linking within and between adjacent chains for strength |
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The ____, ranging from ____ to ____ ____, are representatives of the broad class of intermediate filament proteins, and are built up form polypeptides folded into a long right-handed alpha-helix.
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-keratins
-Hair -Rhino horn |
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What amino acid are keratins rich in? What percentage in rhino horn? What does this allow?
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-Cysteine (18%)
-Allows for innumerable disulfide linkages at all levels of assembly, which includes the formation of protofilaments from coiled coils, and protofibrils from protofilaments; about 4 of the protofibrils combine to form an intermediate filament |
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Collagen
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-Left-Handed Helices
-3 amino acids per turn of helix -Gly-X-Y with X often being Pro and Y often being 4-Hyp -RIght handed triple helix stabilzed by Lys, HyLys bonds |
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What diseases occurs from single amino acid substitutions in collagen?
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-Osteogenesis imperfecta and Ehlers-Danlos
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A connective tissue band that holds bones together is called
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ligament
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For assembly of collagen, much of the ____ is _______, allowing hydrogne bonds between adjacent helical bundles, and the incorporation of ________ allows covalent bonding to occur through a unique linkage.
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-Proline
-Hydroxylated -Hydroxylysine |
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What are collagen fibrils formed from?
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-From staggered bundles that are also crosslinked to strengthed inter-strand connections, making collagen an ideal protein for strength and inflexibility
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What causes serious genetic diseases involved with collagen?
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-Serious genetic diseases of connective tissue occur when glycine residues are mutated, because the helical bundle is greatly destabilized
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Silk Fibroin (Building from Sheets)
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-Predominantly Beta-conformation
-Rich in Ala and Gly -Chains oriented for max h-bonds and van der Waals -Highly extended conformation (no stretch)-->resists longitudianl forces but remains flexible to bending |
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The folded structure (conformation) of a protein in its native states depends upon its ____ ____.
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Primary Sequence
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What will the coformational space of a protein be delimited by?
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-Planar peptide bond
-Occurrence of proline -Interactions between secondary structural elements -Disulfide bridges between cysteine side chains |
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What do work forces do for protein conformation?
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-Govern how the protein settles in to its final 3D configuration
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With globular proteins, _____ residues predominate internally, while ____ and especially ____ residues tend to be on the surface.
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-Hydrophobic
-Polar -Charged |
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Why are salt bridges strong when formed inside a protein?
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-Low dielectric constant of the protein interior
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Denaturation
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-Structural unfolding, and generally implies a loss of function, but is gradual rather than an all-or-none phenomenon-mutated proteins may be partially functional because they are partly "denatured"
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Effects Agents that can denature a protein
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-Thermal denaturation
-Chemical denaturants (urea or guanidine) -Organic solvents or detergents (SDS-PAGE) -extremes of pH |
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Is it possible to reverse aggregation once it occurs?
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No-
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____% of proteins synthesized do not fold correctly.
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15%
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Chaperones
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A class of proteins that aid the cell in correctly folding its proteins
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2 Classes of Chaperones that Have Been Well Studied
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-Heat-shock proteins
-Chaperonins: huge multimeric protein |
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Functions of Chaperones
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-Bind misfolded proteins
-Bind partially folded proteins -Facilitate translocation of partially folded proteins -Provide a microenvironment for folding to occur |
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Quaternary Structure
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the assembly of individual polypeptide chains into larger specific aggregates, called multimers or oligomeric proteins
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Desirable Aspects to multimeric assembly of proteins
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1.Better to make many short proteins than one long one
2. There can be cooperative interactions b/w subunits that provide functional attributes not readily possible with a single chain 3.2 or more substrate binding sites can be combined to increase the specificity and binding energy of a protein 4. Oligomerization allows selective association of subunits to achieve combinatorial variety 5.Assembling capsids for large viruses such as tobacco mosaic virus and poliovirus would not be possible without capsid proteins that could form large multimers |
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How is the organization of subunits in an oligomer in space usually symmetric? (3 ways)
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-Rotational Symmetry
-Dihedral Symmetry -Helical Symmetry |
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Helical Symmetry
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-Employs end-to-end stacking of subunits in a circular form to build a rod-like structure
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Dihedral symmetry
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-Has 2-fold axis intersecting an n-fold axis at right angeles
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Rotational Symmetry
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Wheel-like or cyclic, and specified by the number of superposable forms in a full turn
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