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Biochem 2-1, protein
UMDNJSOM
| Question | Answer |
|---|---|
| Peptide Bond | covalent bonds holding amino acids together in a protein. formed by condensation reaction. partial double bond character. No rotation around peptide bond. |
| oligopeptide | less than 50 AA |
| polypeptide | 50-100AA |
| protein | greater than 100AA |
| Peptide polarity | goes from NH2 to COOH end. |
| Possible number of different proteins | 20^n n= number of AA in the chain. |
| What determines proteins function | Proteins shape. it must be correctly shaped to do its particular job correctly. |
| Primary structure | Has polarity. linear sequence. each AA called residue. |
| homologous structure | similar proteins in different organisms. similiar primary structure. Conserved regions - similarity in sequence. Variable region - differences in sequences. |
| conserved region | Regions in homologous structures that are similiar. Usually structural and functional regions, such as enzyme binding, oxygen binding, catalytic site, ATP binding, and phosphorlyation site. |
| Secondary structure | hydrogen bonding between AA within protein. Two most common - alpha helix , beta sheet Remainder is random coils or loops, have defined structures and are functionally important. Alpha Helices and Beta Sheets are the core of proteins. Can predict from |
| Alpha Helices | 2* structure. 10 residues long, 3.6 residues per turn. R groups every 100 degrees. H bond between C=O and N-H stabilize. R groups cant sterically or electrostatically interfere. arginine - bad, long. proline/tyrosine - bad, hydrophobic. |
| Beta Sheets | parallel or antiparallel. H bonded through backbone C=O and N-H to each other. |
| Beta Turn | tight 180 degree turn between two antiparallel beta strands. usualy has a Pro or a Gly because its R group is small. |
| Tertiary Structure | 3-d structure. Irregular twisting and looping of 1* and 2* due to interactions among side chains. Portions described in domains(functional regions) |
| Quaternary Structure | 2 or more polypeptides to form a functional protein. MUST have TWO polypeptides before displays this. major groups are fibrous and globular |
| Multisubunit proteins | two or more polypeptide chains act as a single functional unit. Each one is a subunit. entire grouping is a single protein. |
| Forces that hold together primary sequence | Peptide Bond |
| Forces that hold together secondary structure | Hydrogen Bond |
| Forces that hold together Tertiary structure | H bonding, disulfide bridges, Hydrophobic interaction, Van der waals ionic. |
| Forces that hold together quaternary structure | Disulfide, ionic, hydrogen bonds, hydrophobic forces. |
| Conjugated Proteins | Glycoprotein - CHO Lipoprotein - Lipid. |
| Types of proteins and locations | Globular (C,ECM),fibrous(C,M,ECF), glycoproteins/proteoglycans(BM), lipoproteins(B,Lym), nucleoproteins(C,N), metalloproteins(C,N,ECF) |
| Shape of a protein | Primarily a function of its tertiary and quarternary structure. |
| Denaturing a protein | destroys its function by hydrolyzing it but not by altering its higher levels of structure. |
| Changing 1* structure of protein effect on shape. | Will change 3* and 4*, depend on R group interactions. shape changed, function altered or lost. 1* is coded by DNA. |
| Protein folding | Driven by hydrophobic forces. Hydrophobic residues on interior, hydrophilic residues on exterior, decrease in entropy is reduced. Chaperone protein help to stabilize the folding and unfolding intermediates. Also, SS bonds. |
| Protein Disulfide Isomerase | Assists in formation, rearrangement, and breaking of S-S bonds. |
| Most proteins are | Globular. Presenting smallest surface area to aqueous environment. Also maximizes H bond between AA and water molecules. |
| Charged Resides | Rarely found inside a protein. When they are, they are covalently paired with an oppositely charged AA. |
| Protein stability | connected with protein folding. proteins have to be folded to be stable. folded state is more stable, lower deltaG than unfolded. |
| Folding and DeltaG | DeltaG<0 = spontaneously. favorable. exergonic. DeltaG>0 = nonspontanous. unfavorable. endergonic. |
| why are most proteins only marginally stable | Both folded and unfolded states form a large number of H bonds + other interactons. gain of H bonds is offset by loss of H bonds. |
| Information for protein folding | all information necessary to specify the native 3D fold is in its AA sequence. reversible for small proteins, under ideal conditions. |
| Levinthal Paradox | It would take too long for a protein to fold if it tried every single state. 10^n. Protein folding is non random and highly cooperative. |
| Two state transition model | there is a folded state and an unfolded state |
| unfolded state | Loose, expanded. most of local 2* structures in place. only a few long range interactions |
| folded state | compact, ordered. Large number of long range interactions,along with local 2* interactions. |
| Chaperones | Prevent inappropriate association or aggregation of exposed hydrophobic surfaces. interact with unfolded or partially folded protein subunits, ie nascent chains emerging from ribosome or extended chains being translocated across subcellular membranes. |
| Properties of chaperones | stabilize non native conformations. facilitate correct folding. Do not interact with native proteins. Not part of final structure. Couple ATP binding/hydrolysis. increased by cellular stress. Often stress or heat shock factors. |
| HSP70 | binds short exposed hydrophobic stretches on unfolded proteins, assist in folding by preventing aggregation. Stabilize extended chains, membrane translocation, regulate heat shock response. Collaborate with HSP40 and BAG1. |
| HSP60 | chaperonins. form folding cage with large central cavity. provide protective environment for proteins to fold. GroEL in E. Coli. Two states binding Active state and folding active state |
| Binding Active State HSP60 | ATP bound to inner ring, end of tube open. Hydrophobic residues line walls of tube, serve to capture unfolded proteins. |
| Folding active state HSP60 | Bind Substrate protein + ATP, conformational change, allows GroES(lid structure) to bind. Causes subunits to rotate, hphobic is removed from interior, eject substrate into h-philic chamber. induces burying hphobic Residues of substrate. |
| Hydrolysis of ATP + binding new substrate protein in folding active state HSP60 | sends allosteric signal, GroES and encapsulated protein to be released into cytosol. |
| HSP70 vs HSP60 | HSP70 - blocks aggregation and improper folding. HSP60 - provide isolated chamber. promote proper folding. |
| HSP90 | most common. Assist in protein folding, cell signaling, tumor repression. collaborates with p23. |
| HSP mutations | HSP important in membrane stabilization. mutations responsible for cataract neuropathies, desmin related myopathy. Often found as components of protein aggregates in protein folding diseases. |
| Neurogenerative Disease Histopathological hallmark | accumulation or inclusion of disease causing proteins in residual neurons in targeted regions of nervous system. This combines with components of molecular chaperone pathways. |
| Overexpression of HSP | reduce # and size of inclusions and accumulation of disease causing proteins. ameliorate the phenotypes in neuronal cell and mouse models. |
| HSP 90 inhibitor drugs | bind to ATP binding pocket of HSP90. disrupt it. HSP90 brought to proteosome, degraded into AA. Geldanamycin. cell cycle arrest and apoptosis. 17-AAG better tolerated. |
Created by:
nady
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