Term
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Definition
| contains the uracil O2 and guanine N2 atoms, narrow in A tracts |
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Term
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Definition
| where DNA duplexes cross in a loop or supercoil |
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Term
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Definition
| contains almost 2 residues/turn and extends 3.2-3.4Amstrong/residue |
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Term
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Definition
| classification ofhe 3d path of polypeptide or nucleic acid |
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Term
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Definition
| most common geometry of RNA helix |
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Term
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Definition
| regular structures characterized by repeating backbone torsion angles and maximal backbone H-bonds. |
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Term
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Definition
| side-chain conformation classification based on frequent occurrence |
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Term
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Definition
| provides the widest access to the basepairs in B-DNA helices |
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Term
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Definition
| a protein complex, contains more than one subunit |
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Term
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Definition
| proteins from a different organisms with a similar functions |
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Term
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Definition
| result of London dispersion forces between planar bases |
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Term
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Definition
| a protein sequence pattern that places residues on one side of an α-helix |
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Term
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Definition
| 3-D contacts between residues that are far apart in sequence |
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Term
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Definition
| polypeptide segment of a folded protein which does not adopt compact “regular” secondary structure |
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Term
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Definition
| 4 polynucleotide strands joined by Hoogstien-paired guanine bases |
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Term
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Definition
| two consecutive base pairs |
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Term
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Definition
| disrupts backbone hydrogen bonding when in helices and sheets |
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Term
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Definition
| a fluorophore that absorbs light maximallly at 280 nm |
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Term
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Definition
| often found in turns with phi-psi angles near (90,0) |
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Term
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Definition
| side chain contains an amide group |
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Term
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Definition
| alternates with deoxycytosine to form Z-DNA |
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Term
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Definition
| side chain is contains only one CH2, pKa ~4 |
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Term
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Definition
| Isosteric to (same shape as) threonine |
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Term
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Definition
| nucleotide base that is the deamination product of 5-methyl cytosine |
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Term
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Definition
| is most stabilizing for alpha helices |
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Term
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Definition
| phenolic side chain found in topoisomerase active sites |
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Term
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Definition
| cross-links polypeptides in the presence of oxygen |
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Term
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Definition
| has a basic side chain that contains a primary amino group |
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Term
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Definition
| side chain pKa is near physiological pH |
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Term
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Definition
| contains three nitrogens, pKa ~12 |
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Term
| 3 structural properties of alpha helices and beta strands |
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Definition
compacted conformation
Hbond minimizes free energy and minimizing backbone torsional energies
minimize excluded volume and surface tension |
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Term
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Definition
| regular structures characterized by repeating backbone torsion angles and maximal backbone H-bonds |
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Term
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Definition
| protein segment that does not adopt compact "regular" 2* structure |
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Term
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Definition
| most common geometry of RNA helix |
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Term
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Definition
| two consecutive base pairs |
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Term
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Definition
| a four way junction created from two (nearly)-identical DNA duplexes |
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Term
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Definition
| 3.6 residues/turn and etends 1.5 A/residue |
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Term
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Definition
| conserved sequence patterns that indicate a specific fold or function |
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Term
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Definition
| proteins from a different organisms with a similar functions |
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Term
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Definition
| provides the widest access to the basepairs in B-DNA helices |
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Term
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Definition
| where DNA duplexes cross in a loop or supercoil |
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Term
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Definition
| connect two polypeptide sequences with mininal loss of H-bonds |
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Term
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Definition
| result of London dispersion forces between planar bases |
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Term
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Definition
| a protein sequence pattern that places residues on one side of an alpha helix |
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Term
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Definition
| 3-D contacts between residues that are far apart in sequence |
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Term
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Definition
| a protein complex, contains more than one subunit |
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Term
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Definition
| classification of the 3-D path of a polypeptide of RNA |
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Term
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Definition
| double stranded DNA or RNA |
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Term
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Definition
| binds to GNRA loops in folded RNAs |
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Term
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Definition
| contains almost 2 residues/turn and extends 3.2-3.4 A/residue |
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Term
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Definition
| contains the cytosine O2 and adenine N3 atoms, arrow in A-tracts |
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Term
| what drive duplex formation DNA |
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Definition
| Duplex formation is driven by base stacking. In the ssDNA only 70% stacked while B DNA, they are 100%. The base H bonds provide no stabilization, but do provide specificity. Cations minimize the repulsion between phosphate |
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Term
| T/F compared to a 2.5 A crystal structure, a 5 crystal structure has twice the definition |
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Definition
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Term
| T/F CryoEM images are of good quality because of their high contrast |
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Definition
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Term
| T/F Electron microscopy can, in theory, have as high a resolution as Xray crystallography |
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Definition
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Term
| T/F Electron microscopy is a good technique for studying ez catalytic mechanisms |
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Definition
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Term
| T/F Crystallography is a good way to study filamentous proteins |
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Definition
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Term
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Definition
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Term
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Definition
| S-OH and converts from non polar to polar, disrupt hydrophobic connection |
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Term
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Definition
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Term
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Definition
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Term
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Definition
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Term
| Hydrophobic (hydrocarbon side chain) |
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Definition
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Term
| Hydrophobic(contains small side chain) |
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Definition
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Term
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Definition
| same sequence will have the same structure |
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Term
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Definition
| helices, strands, turns, loops |
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Term
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Definition
| connect 2* structure elements together (turns and loops) |
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Term
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Definition
| relaxed torsion angles, compactness, cooperativity, relaxed torsion angles, main chain H bonds are satisfied |
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Term
| Cooperativity of helix assembly |
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Definition
| Limiting step = formation of the first turn. Adding the next residue is easier |
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Term
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Definition
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Term
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Definition
| the terminal 3 Os and HNs are not satisfied in H bonding. |
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Term
| consequence of extended strand |
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Definition
| Peptide bonds of adjacent residues point in opposite directions. Side chains are in opp direction. no intra strand hydrogen bonding |
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Term
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Definition
| B strands have a right hand twist -> b sheets have a left hand twist |
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Term
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Definition
| Supersecondary structure,short peptides, redirect chain with minimal loss of H bonds. Fairly rigid, WELL DEFINED GEOMETRY. |
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Term
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Definition
| can be floopy, varies in structures and length. OFTEN CONTAIN IMPORTANT INTERACTION SURFACES (ACTIVE SITES) |
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Term
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Definition
| A unit of "stand alone" protein structure. Compact, contiguously self interacting, and is able achieve its structure without additional interactions (at least in some protein, somewhere). Usually associated with a particular function. |
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Term
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Definition
| the path of the polypeptide bacbone of an entire protein or "domain". Could be a collection of domains |
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Term
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Definition
| collections of interacting secondary structures connected by super secondary structures. May contain several motifs. |
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Term
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Definition
| A well defined (and usually conserved) collection of several secondary structures. Usually smaller than a domain, but sometimes interchangeable |
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Term
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Definition
| a sequence pattern, contiguous or interrupted, that is a "signature" of a folding motif and or domain. Indicative of a particular function-functional residues are the most conserved. |
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Term
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Definition
| the best match of two or more sequences believed to be related, based on identity, homology or structure. Some gaps are allowed |
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Term
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Definition
| the % of exact residue matche within a set of sequences after alignment(random 5%) |
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Term
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Definition
| the % of close residue matches (based on chemical or genetic similarities)after alignment. More generous than identity |
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Term
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Definition
| proteins that are related in sequence and/or structure, and overall functions |
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Term
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Definition
| proteins that have the same biological function but slightly different sequences. Can be coexpressed or have organelluar or tissue-specific expression |
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Term
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Definition
| set of proteins that have similar biochemical activities but separate biological functions, contain homologous domains |
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Term
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Definition
| similar folds = similar functions. It also could indicate convergent/divergent evolution, does not mean same sequence |
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Term
| Tertiary structure classification |
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Definition
| CATH: class, architecture, topology, and homologous superfamily. |
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Term
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Definition
| dominant type of 2*structure |
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Term
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Definition
| overall shape and relative positioning of 2*structural elements. ARRANGEMENT |
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Term
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Definition
| the order and nature of the connections (loops and turns)between 2*structural elements. CONNECTION PATH OF ARRANGEMENT |
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Term
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Definition
| Members are believe to have elvolved from a common ancestor based on sequence and/or structural similarity |
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Term
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Definition
| creates a cylinder, satisfies backbone H-bonding. Barrel interior is not hollow-packed with hydrophobic sidechain |
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Term
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Definition
| At least two interaction surfaces(heterologous association). Head-to-tail interactions. Cannot close a ring. Usually super-helical. |
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Term
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Definition
| at least two interaction surfaces(except dimer). Head-to-tail interactions, head-to-head(oligomerization domains), closes a ring, can be symmetric or asymmetric dimer, trimer, tetramer, hexamer. |
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Term
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Definition
| >600A, charge distribution, types of interface:interdigitation, hydrophobic surface, polar interaction(salt bridge,H-bond,water bridge) |
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Term
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Definition
| when one protein can have more than 1 aggregation state. Usually utilizes a mixture of shared and new interfaces. Often seen in virus capsids. UNUSUAL. |
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Term
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Definition
| similar to homo except more than oen subunit type:-asymmetric multimer(G protein), pseudo-symmetric(hemoglobin),symmetric multimer of asymmetric multimers(ATCase) |
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Term
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Definition
| more than one subunit type in a mostly asymmetric or mixed symmetry/asymmetry(ribomose, RNA polymerase, ATP synthase complex) |
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Term
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Definition
1) Increased Stability/Resistance to mutations. 2)Regulation(allostery,"checkpoint")3)Higher specificity due to larger interaction surface(DNA BP)
Architectural (actin/myosin) |
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Term
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Definition
| when more than one monomer donates residues to form a single active site due to evolution |
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Term
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Definition
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Term
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Definition
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Term
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Definition
| active forms linked to 5'OH of sugar. 2' or 3'linked forms are products of degradation |
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Term
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Definition
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Term
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Definition
| causes: 3-2 migration, depurination |
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