Biochemistry Chapter 4: Proteins – Flashcards
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What type of conformation do protein molecules adopt?
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A three-dimensional conformation. This structure is able to fill a biological function.
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What is a native fold?
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A structure that is able to fill a biological function due to three-dimensional conformation.
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What does the native fold contain within the protein?
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A large number of favorable interactions within the protein.
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What does the hydrophobic effect do as an interaction in a protein?
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Releases molecules of water from the structured salvation layer around the molecule as protein folds increases the net entropy.
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What do hydrogen bonds do as an interaction in a protein?
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Interaction of N-H and C=O of the peptide bond leads to local regular structures such as alpha-helices and beta-sheets.
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What does london dispersion do as an interaction in a protein?
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Medium-range weak attraction between all atoms contributes significantly to the stability in the interior of the protein.
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What do electrostatic interactions do as an interaction in a protein?
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Long-range strong interactions between permanently charged groups; salt-bridges, esp. buried in the hydrophobic environment strongly stabilizes the protein.
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What are the four levels of protein structure?
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Primary, secondary, tertiary, and quaternary structure.
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What is the structure of a protein partially dictated by?
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The properties of a peptide bond.
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What is a peptide bond a resonance hybrid of?
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Two canonical structures.
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What does resonance cause peptide bonds to do?
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To be less reactive (compared to esters, for example), to be quite rigid and nearly planar, and to exhibit a large dipole moment in the favored trans configuration.
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Is rotation around the peptide bond permitted?
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No.
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Is rotation around the bonds connected to the alpha carbon permitted?
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Yes.
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What is the phi angle?
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The angle around the alpha-carbon—amide nitrogen bond.
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What is the psi angle?
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The angle around the alpha-carbon—carbonyl carbon bond.
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What are the angles for the phi and psi angles in a fully extended peptide?
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180 degrees.
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Why are some phi and psi combinations unfavorable?
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Steric crowding of backbone atoms with other atoms in the backbone or side chains.
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Why are some phi and psi combinations more favorable?
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Because of chance to form favorable H-bonding interactions along the backbone.
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What does a Ramachandran plot show?
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The distributions of phi and psi dihedral angles that are found in a protein. Also shows common secondary structure elements and reveals regions with unusual backbone structure.
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What does secondary structure refer to?
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A local spatial arrangement of the polypeptide backbone.
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What are the two common regular arrangements of secondary structure?
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Alpha-helices and beta-sheets.
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What is an alpha-helix?
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A secondary structure that is stabilized by hydrogen bonds between nearby residues.
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What is a beta-sheet?
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A secondary structure that is stabilized by hydrogen bonds between adjacent segments that may not be nearby.
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What is a random coil?
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Irregular arrangement of the polypeptide chain.
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What is the helical backbone of the alpha-helix held together by?
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Hydrogen bonds between the backbone amides of an n and n+4 amino acid.
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What are the peptide bonds in an alpha-helix like?
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They are roughly parallel with the helical axis.
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What are the side chains in an alpha-helix like?
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They point out and are roughly perpendicular with the helical axis.
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What is the inner diameter of the alpha-helix?
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About 4-5 angstroms. Too small for anything to fit "inside".
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What is the outer diameter of the alpha-helix?
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With side chains it is 10-12 angstroms. Happens to fit well into the major groove of dsDNA. Residues 1 and 8 align nicely on top of each other.
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What residues are strong helix formers?
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Small hydrophobic residues, such as alanine and leucine.
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What residue acts as a helix breaker because rotation around the N-Ca bond is impossible?
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Proline.
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Which residue acts as a helix breaker because the tiny R-group supports other conformations?
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Glysine.
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What will attractive or repulsive interactions between side chains 3-4 amino acids apart affect?
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Formation of alpha-helices.
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What type of dipole moment does an alpha helix have?
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The alpha-helix has a strong macroscopic dipole moment.
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What type of residues normally occur near the positive end of the helix dipole?
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Negatively charged residues.
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What creates a pleated sheet-like structure in beta sheets?
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The planarity of the peptide bond and tetrahedral geometry of the alpha-carbon.
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What is the sheet-like arrangement of the backbone in beta-sheets held together by?
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Hydrogen bonds between the backbone amides in different strands.
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How are side chains arranged in beta-sheets?
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Side chains protrude from the sheet alternating in up and down direction.
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What are the two orientations that are possible within a beta-sheet?
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Parallel and antiparallel.
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What are parallel beta-sheets?
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The hydrogen-bonded strands in the beta-sheet run in the same direction, resulting in bent hydrogen bonds (weaker).
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What are antiparallel beta-sheets?
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The hydrogen-bonded strands in the beta sheet run in opposite directions resulting in liner hydrogen bonds (stronger).
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What are beta-turns?
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Happen frequently whenever strands in beta-sheets change the direction. It is 180 degrees and is accomplished over four amino acids.
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What are beta-turns stabilized by?
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By a hydrogen bond from a carbonyl oxygen to amide proton three residues down the sequence.
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What residues are common in beta-turns?
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Proline in position 2, or Glycine in positon 3.
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What is the conformation of most peptide bonds not involving Proline?
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Trans configuration.
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What is the conformation of about 6% of peptide bonds involving Proline?
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Cis, most of this 6% involve beta-turns.
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What is protein isomerization catalyzed by?
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Proline isomerases.
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What does circular dichroism (CD) measure?
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The molar absorption difference of left and right-circularly polarized light.
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What do chromophores in the chiral environment of CD analysis produce?
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Characteristic signals.
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What do CD signals from peptide bonds depend on?
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The chain conformation.
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What does tertiary structure refer to?
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To the overall spatial arrangement of atoms in a protein.
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What is tertiary structure stabilized by?
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Numerous weak interactions between amino acid side chains. Largely hydrophobic and polar interactions; can be stabilized by disulfide bonds.
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What are the two major classes of tertiary structure?
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Fibrous and globular (water or lipid soluble).
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What is collagen an important constituent of?
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Connective tissue: tendons, cartilage, bones, cornea of the eye.
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What is collagen made up of?
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Each collagen chain is a long Gly- and Pro-rich left-handed helix.
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What does 4-hydroxyproline in collagen do?
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Forces the proline ring into a favorable pucker and offers more hydrogen bonds between the three strands of collagen.
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What are motifs?
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Specific arrangement of several secondary structure elements.
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How can motifs be found?
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As reoccurring structures in numerous proteins. Proteins are made of different motifs folded together. May just be a fold that isn't stable by itself.
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What is a domain?
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A functional unit of a protein; stable if it were to be "cut off". A domain can be a motif.
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What is a family?
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A group of proteins that has a common fold or motif or domain.
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What is quaternary structure formed by?
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The assembly of individual polypeptides into a larger functional cluster.
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What are the steps needed for x-ray crystallography?
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Purify the protein, crystallize the protein, collect diffraction data, calculate electron density, fit residues into density
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What are the pros of x-ray crystallography?
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No size limits, well-established.
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What are the cons of x-ray crystallography?
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Difficult for membrane proteins, cannot see hydrogens.
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What are the steps needed for biomolecular NMR?
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Purify protein, dissolve the protein, collect NMR data, assign NMR signals, calculate the structure.
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What are the pros of bimolecular NMR?
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No need to crystallize the protein, can see hydrogens.
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What are the cons of bimolecular NMR?
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Difficult for insoluble proteins, works best with small proteins.
