Term
| how do you separate polypeptide chains? (4 methods) |
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Definition
1. pH extremes
2. 8 M urea
3. 6 M guanidine HCl
4. high salt concentration (ammonium sulfate) |
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Term
| what does performic acid oxidation do? |
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Definition
| cleaves disulfide bridges |
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Term
| what are 2 sulfhydryl-reducing agents? what do they do?? |
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Definition
1. mercaptoethanol
2. dithiothreitol/dithioerythritol
-->treat w/ alkylating agent after (like 3-bromopropylamine)
--cleaves disulfide bridges |
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Term
| what does carboxypeptidase A do? |
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Definition
| cleave any residue except Pro, Arg, or Lys (for C-terminal ID) |
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Term
| what does carboxypeptidase B do? |
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Definition
| cleave residues only at Arg & Lys |
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Term
| What does carboxypeptidase C and Y do? |
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Definition
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Term
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Definition
| cleave on C-side of Lys and Arg |
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Term
| what does Chymotrypsin do? |
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Definition
| cleave on C-side of Phe, Tyr, Trp |
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Term
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Definition
| attacks Arg more than Lys (similar to trypsin) |
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Term
| what does staphylococcal protease do? |
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Definition
| cleaves C-side of Glu or Asp |
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Term
| What does cyanogen bromide act on? |
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Definition
| acts on methionine residues only |
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Term
| a-helix: how many residues per turn? |
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Definition
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Term
| a-helix: rise per residue? |
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Definition
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Term
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Definition
| 3.5 * 1.5 A= 5.4 A = .54 nm |
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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
| a-helix: angle circumscribed per helix unit |
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Definition
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Term
| a-helix: backbone loop that is closed by any H bond contains how many atoms? |
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Definition
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Term
| B-pleated sheet: rise per residue |
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Definition
.347 nm (antiparallel)
.325 nm (parallel) |
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Term
| B-pleated sheet: rise per turn |
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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
| B-pleated sheet: angle circumscribed per helix unit |
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Definition
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Term
| B-turn contains how many residues? |
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Definition
|
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Term
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Definition
| carbonyl C of one residue is H bonded to amide proton of residue 3 residues away |
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Term
| proline is preferred in what position for what types of B-turns? |
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Definition
| proline fits best at position 3 in type I turns, best at position 2 in type II turns |
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Term
VDW:
-strength range?
-distance range? |
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Definition
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|
Term
H-bond:
-strength range?
-distance? |
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Definition
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|
Term
Ionic interactions:
-strength
-distance |
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Definition
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Term
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Definition
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Term
| looking at the table 1.5 life times- what can you conclude as time increases? |
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Definition
| as time increases, more stable interactions (covalent bonds) and phenomena involving agents of genetic info (nucleic acids) come into play |
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Term
| what are 3 things a simplest cell must show a degree of? |
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Definition
1. degree of metabolism & energy production
2. genetic replication based on template molecule that encodes genetic info
3. formation & maintenance of cell boundary |
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Term
| why do hydrophobic substances tend to coalesce? |
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Definition
| more H-bonded interactions between H2O molecules are possible when they coalesce=entropy driven |
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Term
| what is the formula for dG standard? |
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Definition
dG standard = -RTln(Keq)
=-2.3*RT*log(Keq) |
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Term
| what does dG standard ' specify? |
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Definition
| dG' specifices that reactants & products are in the ionized form prevailing at pH 7 |
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Term
| what is a group transfer potential defined as? |
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Definition
| the free energy change that occurs upon hydrolysis (transfer of a group to water) |
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Term
| what are the 3 reasons for large negative dG' in group transfer potentials? |
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Definition
1. electrostatic repulsion
2. competing resonance
3. entropy |
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Term
| what is the dG' hydrolysis of ATP? |
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Definition
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Term
| what is the dG' of the hydrolysis of PEP (an enol phosphate) & tautomerization? |
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Definition
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Term
| what does an enol phosphate after hydrolysis tautomerize to? |
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Definition
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Term
| what is the dG' of creatine phosphate? |
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Definition
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Term
| what is the main reason why hydrolysis of creatine phosphate so favorable? |
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Definition
| has an unstable resonance form- where the 2 oxygens attached to the phosphate and interacting w/ each other and with the NH2+ group of creatine |
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Term
| what is the dG' for hydrolysis of acetyl CoA? |
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Definition
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Term
| why is the hydrolysis of acetyl CoA favorable? |
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Definition
| thio-ester resonance stabilization is less favorable than oxy-ester |
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Term
| what are the nonpolar amino acids? |
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Definition
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Term
| proline is technically not an amino acid but a |
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Definition
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Term
| tryptophan has what type of R group? |
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Definition
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Term
| polar, uncharged amino acids? |
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Definition
Asn/N, Gln/Q, Tyr/Y, Thr/T, Ser/S, Cys/C, Gly/G
(Guards, Stop The Next Queen, You C*nt) |
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Term
| which group of amino acids can form hydrogen bonds with water? |
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Definition
| polar, uncharged amino acids (except glycine) |
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Term
| which amino acids have a net negative charge at neutral pH? |
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Definition
| aspartic acid & glutamic acid (the acidic amino acids) |
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Term
| which amino acids have a positive net charge at neutral pH? |
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Definition
| histidine, arginine, and lysine |
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Term
| histidine contains what type of R group? |
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Definition
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Term
| arginine contains what type of R group? |
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Definition
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|
Term
| which amino acids are hydrophobic? |
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Definition
A, G, L, I, F, P, V
(All Good Ladies, If Fucked, Put Viagra) |
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Term
| which amino acids are hydrophilic? |
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Definition
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|
Term
| which amino acids are amphipathic? |
|
Definition
K, M, W, Y
(Kill Mary in WY (Wyoming)) |
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Term
| what 3 amino acids absorb UV light? |
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Definition
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|
Term
| which amino acid is destroyed by acid hydrolysis? |
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Definition
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Term
| which 2 amino acids convert to 2 other amino acids? what gets released in the process? |
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Definition
| Asparagine & Glutamine are converted to Aspartic acid & glutamic acid; the amide-N released as NH4+ |
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Term
| peptide bond between what type of amino acids are resistant to acid hydrolysis? |
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Definition
| peptide bonds between hydrophobic amino acids |
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Term
| what role does the amino acid sequence play in protein structure? |
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Definition
| all the information necessary for folding the chain into its native structure is contained in the primary structure of the polypeptide |
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Term
| the angle about the Ca-N bond is denoted as? |
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Definition
| phi (o w/ line through it) |
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Term
| angle about the Ca-C bond is denoted as? |
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Definition
| psi (triton looking symbol) |
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Term
| left handed helices tend to have positive/negative values of phi/psi? |
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Definition
| phi and psi values are both positive |
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Term
| right handed helices tend to have positive/negative values of phi/psi? |
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Definition
| phi and psi values are both negative |
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Term
| right handed alpha helices are made with only D/L amino acids? |
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Definition
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|
Term
| right handed alpha helices are CCW/CW? |
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Definition
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|
Term
| left handed alpha helices are CCW/CW? |
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Definition
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Term
| secondary structures form when what 2 constraints are met? |
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Definition
1. sterically permissible phi & psi values
2. stablization through H-bond formation |
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Term
| what amino acids tend to be helix formers? |
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Definition
| A, E, F, H, I, L, M, Q, R, W, Y |
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Term
| what amino acids tend to be helix breakers? |
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Definition
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Term
| proteins fold to form the most stable structures. stability arises from: (2) |
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Definition
1. formation of large # of intramolecular H bonds
2. reduction in solvent accessible surface area of the proetin when it folds |
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Term
| a-Keratin has what type of secondary structure? |
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Definition
| 311-314 residue-long alpha helical rod secments capped w/ non helical N & C termini |
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Term
| a-Keratin's primary structure of the helical rod consists of what type of repeats? |
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Definition
| 7 residue repeats, where first and 4th positions are nonpolar |
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Term
| what is the usual sequence for fibroin & B-keratin? |
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Definition
| Gly-Ala/Ser-Gly-Ala/Ser-Gly... |
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Term
| what is unique about the structure of B-keratin? |
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Definition
| residues of B-sheet extend alternatively above & blow the place-->placing all glycines on one side & all alanines and/or serines on the other side |
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Term
| what is the basic unit of collagen? |
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Definition
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Term
| what is unique about tropocollagen and why does it happen? |
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Definition
| unusual amino acid composition of collagen creates 3 intertwined helical strands, the amino acid composition that includes lots of prolines and hydroxyprolines |
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Term
| what is the rise per residue of tropocollagen? |
|
Definition
|
|
Term
| what is the # of residues per turn of tropocollagen? |
|
Definition
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|
Term
| what does the amino acid sequence of tropocollagen usually contain? |
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Definition
| long stretches of Gly-Pro-Pro/HyP |
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Term
| every 3rd residue of tropocollagen is what? why? |
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Definition
| every 3rd residue of each chain faces the crowded center of the helix- only glycine fits here |
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|
Term
| what bonds stabilize the helix? |
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Definition
| interchain H bonds involving HyP |
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Term
| why does the protein core consist primary of a-helices & b-sheets? |
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Definition
| highly polar NH & C=O moieties of peptide backbone must be neutralized in hydrophobic core==>extensive H bonded nature of the 2 structures is ideal for this purpose |
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Term
| the peptide chain of globular proteins, to adopt the most stable 3' structure must do what 2 things |
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Definition
1. satisfy constraints inherent in structure building
2. fold to bury hydrophobic side chains |
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Term
| what are the 2 forces that drive 3' folding |
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Definition
-peptide chain must fold so as to "bury" the hydrophobic side chains, minimizing their contact w/ water
-peptide chains, composed of L-aino acids, have tendency to undergo a "right handed twist" |
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Term
| what is the large contribution to the thermodynamic driving force for folding of proteins? |
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Definition
| the largest favorable contribution to folding is the entropy term for the interaction of nonpolar residues w/ the solvent |
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Term
| intrinsically unstructured proteins are usually composed of what amino acids? |
|
Definition
| abundance of polar residues & lack of hydrophobic residues |
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Term
| What are the 4 advantages of 4' association? |
|
Definition
1. stability: surface to volume ratio becomes smaller
2. genetic economy & efficiency: less DNA is needed to encode monomer that assembles into a multimer vs. DNA needed to encode one large polypeptide
3. bringing catalytic sites togehter
4. cooperativity: binding of ligand to one subunit alters the likelihood of binding ligand at other subunits |
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Term
| sugars with an amino group at C2 are what types of sugars? |
|
Definition
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|
Term
|
Definition
| plant storage polysaccharide |
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|
Term
| what are the 2 forms of starch? |
|
Definition
|
|
Term
| amylopectin branches per how many residues? |
|
Definition
| branches in amylopection occur every 12-30 residues |
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|
Term
| what type of bond does amylose have? |
|
Definition
|
|
Term
| what type of linkage do amylopectin branches have? |
|
Definition
|
|
Term
| what can glucoamylase cleave? |
|
Definition
| a(1-->4) and a(1-->6) glycosidic bonds=break oligosaccharides down to free glucose |
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Term
| what are the structural differences between amylose and cellulose? |
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Definition
| amylose are a-1,4-linked D glucose units vs. cellulose that has B-1,4-linked D glucose units |
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Term
| what makes cellulose so strong? |
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Definition
| the H bonds between the sheets strengthen the structure (interchain H bonds) |
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|
Term
| what are glycosaminoglycans? |
|
Definition
| linear chains of repeating disaccharied in which one unit is an amino sugar and one/both are negatively charged |
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|
Term
| glycoasminoglycans are components to what? |
|
Definition
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|
Term
| N-linked saccharides are attached via what? |
|
Definition
| via amide nitrogens of asparagine residues |
|
|
Term
| O linked saccharides are attached via what? |
|
Definition
| attached to hydroxyl groups of serine, threonine, or hydroxylysine |
|
|
Term
| what is the structure of peptidoglycan? |
|
Definition
tetrapeptides link adjacent backbone chains
-notice the isogluatmate linkage in the tetrapeptide chain
-here is wehre there is an unusual gamma-carboxyl linkage (rather than at the alpha carbon) |
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Term
|
Definition
| glycoproteins whos carbohydrates are mostly glycosaminoglycans |
|
|
Term
| what are fatty acids comprised of? |
|
Definition
| alkyl chains terminated by caroxylic acid groups |
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|
Term
| what is the X:Y symbol for palmitic & stearic acid? |
|
Definition
|
|
Term
| what is the X:Y symbol for oleic and linoleic acid? where are the double bonds |
|
Definition
|
|
Term
| what is the X:Y symbol for linolenic & arachidonic acid? |
|
Definition
C18:3, 9, 12, 15
C20:4, 5, 8, 11, 14 |
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Term
|
Definition
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|
Term
|
Definition
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Term
|
Definition
|
|
Term
|
Definition
|
|
Term
|
Definition
|
|
Term
| globular or fibrous proteins are soluble in aqueous solutions? |
|
Definition
| globular- fibrous proteins tend to be structural proteins that are insoluble |
|
|
Term
| how do membrane proteins fold? |
|
Definition
| fold so that hydrophobic amino acid side chains are exposed in membrane associated regions |
|
|
Term
| secondary structures are a result of what? |
|
Definition
|
|
Term
| what are the forces driving quaternary association? |
|
Definition
-dimerization=gives you energy
-loss in degrees of freedom upon that dimerization=loss of energy
[-favorable VDW interactions offset by VDW lost due to removal of solvent]
BUT-- favorable hydrophobic interactions you energy AND so does making the surface area smaller
=all together net free energy of -50 kJ |
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