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78 Cards in this Set
- Front
- Back
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What does the "Native Structure" of proteins refer to?
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The unique 3-dimensional structure that has the lowest free energy of all possible FUNCTIONAL folding patterns.
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What force drives protein folding?
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Hydrophobic force -> sequesters nonpolar AA's in the protein's core.
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What is the central carbon in each amino acid?
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The alpha carbon - it's chiral except for glycine.
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What configuration are all amino acids in the body?
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L-form
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Why are amino acids classified based on hydration characteristics?
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-HydroPHOBIC prefer to be on the protein's INTERIOR.
-HydroPHILIC prefer to be on the protein's SURFACE. |
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What are the 2 subcategories of HydroPHOBIC amino acids?
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1. Aliphatic
2. Aromatic |
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List the aliphatic AA's:
(7) |
GAVLIMP
Glycine Alanine Valine Leucine Isoleucine Methionine Proline |
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List the aromatic AA's:
(3) |
PTT
Phenylalanine Tyrosine Tryptophan |
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What makes proline unique?
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It posseses an IMINO group which facilitates turns in B-sheets.
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What's the difference btwn an IMINO and AMINO side group?
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Imino = NH2+ in 5-memb ring
Amino = independent NH3+ |
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What is common to all the hydrophobic aliphatic AA's?
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-Methyl group spacer to prevent steric repulsion
-Ring structure |
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What is the ring structure in:
-Phe -Tyr -Trp |
Phe = benzene
Tyr = benzene + OH Trp = indole |
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What are the letters for the aromatics?
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F = Phe
Y = Tyr W = Trp |
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What does aromaticity of F/Y/W allow?
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The ability to measure unique UV Spectra at 280 nm
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Which aromatic AA has the highest absorbance? Lowest?
Which 2 are more similar/Why? |
Highest = Trp/W
Lowest = Phe/F Phe/Tyr are similar b/c both have the benzene ring. The indole makes Trp the oddball. |
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What about the aliphatics do we measure based on absorbance?
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Protein concentration
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What are the 2 subcategories of hydrophilic amino acids?
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Uncharged
Charged |
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What are the 5 uncharged polar amino acids?
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STAGC
Serine Threonine Asparagine Glutamine Cysteine |
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What are the 5 charged polar amino acids?
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LAAGH
Lys Argine Aspartate Glutamate Histidine |
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Which uncharged polar AA contains sulfar?
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Cysteine
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What other amino acid contains sulfar?
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Methionine
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What are the basic polar amino acids?
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Lys, Arg, His
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What are the acidic polar amino acids?
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Glu and Asp
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What 2 AA's not classified as polar have dissociable protons?
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Tyr (OH) and Cys (SH)
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Relative pKA of
-Amino group -Carboxyl group |
NH3 = 8.0
COOH = 3.1 |
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Relative pKA of:
-Asp/Glu |
4.4
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Relative pKA of:
Histidine |
6.5
(NH in the imino group) |
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Relative pKA of:
Cysteine |
8.5
(SH sulfhydryl) |
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Relative pKA of:
Tyrosine |
10.0
(phenol) |
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Relative pKA of:
Lysine |
10.0 (NH3+)
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Relative pKA of:
Arginine |
12.0
(NH2+ --- NH2+) |
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What is the isolectric point?
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The unique pH at which an amino acid has 0 net charge.
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What is the pKa?
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The pH where 50% of the ionizable R groups in solution are ionized and 50% are not.
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What is the unique characteristic of Met?
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Always the first amino acid in nascent protein
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What clinical correlation can be made with Met?
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The amino group is oxidizable b/c it's the end terminal.
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What proteolytic enzyme that has Met in its active site protects alveoli from degradn?
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alpha-Antitrypsin
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What happens when the Met in alpha-AT gets oxidized?
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It no longer works and the alveoli get chewed up.
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What oxidizes alpha-AT and what is the result?
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Cigarette smoke; Emphysema.
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What else can cause alpha-AT to be unavailable?
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Transport failure from genetic mutation
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What type of bonds constitute primary protein structure?
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Covalent peptide bonds
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What type of bonds constitute Secondary protein structure?
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Only Hydrogen Bonds btwn carbonyl Oxygens and Amino Nitrogens in peptide backbone.
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What is super secondary structure?
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Folding motifs composed of different combos of secondary structures.
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Why do super-secondary structures exist?
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To solve the packing and folding requirements of proteins by minimizing energy.
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What type of bonds constitute super-secondary structure?
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Interactions between R groups.
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What is a domain?
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The smallest thermodynamically stable unit of protein structure - result of 2ndary/Super-2ndary structure associations.
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What is tertiary structure?
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The smallest COMPLETE unit of a protein; the final 3-D structure of 1 polypep chain.
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What is quaternary structure?
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Tertiary combined into a globular protein.
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How do polypeptide bonds form?
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A carboxyl combines with amino group with loss of one water.
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What is the nature of a peptide bond?
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Resonance:
-Double bond C=O 60% of time; -Double bond C=N 40% of time. |
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What results from the delocalized resonance of peptide bonds?
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The bond is unable to rotate.
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What orientation of R groups at the peptide bond is favored by ribosomes?
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TRANS - R's pointed away from each other.
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Which bond CAN rotate in pp chains?
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The bonds between:
-Amino -> alpha-Carbon (Phi) -Alpha-carbon -> Carboxyl (Psi) |
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What are the bond angles in:
-RH alpha helices? -LH alpha helices? -Beta sheets? |
RH alpha: -60/-60
LH alpha: 60/60 Beta: 120/-120 |
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What's a characteristic of Cysteine to take note of?
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Its ability to spontaneously oxidize and form a disulfide bond within a protein.
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What proteins from disulfide bridges more often?
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Extracellular - for more stability.
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What molecule were Disulfide bonds first seen in?
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Insulin
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What are the important features of Right-hand alpha helix?
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-3.6 res/turn
-H-bonds between C=O of i and NH3+ of (i+4) |
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What does amphipathic mean?
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Hydrophilic face points out;
Hydrophobic face points in; -Refers to R groups in alpha helices. |
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So the outside of an alpha helix is:
And the inside of it is: |
Outside = hydrophilic
Inside core = hydrophobic |
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The difference between H bonds in B-sheets and a-helices is:
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-Helices have H bonds perpendicular to the aa chain.
-Sheets have H bonds parallel to the sheet. |
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What are 3 types of b-sheets?
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1. Parallel
2. Antiparallel 3. Mixed beta |
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What distinguishes an Antiparallel sheet?
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Peptides alternate in direction.
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What distinguishes Parallel sheets?
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Peptides are lined up.
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What distinguishes a mixed beta sheet?
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It contains both parallel and antiparallel sheets.
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Where are beta sheets typically found?
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In the interior of proteins.
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What are "reverse turns"?
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Aka beta turns or hairpin loops;
-A 2dry structure that connects runs of antiparallel B-sheets. |
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What is the structure of a Reverse Turn?
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-4 residues
-H bond connects AA1 to AA4 |
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What is the difference btwn Type I and Type II reverse turns?
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Orientation of peptide bond between AA2 and AA3
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What is unique about Type II reverse turns?
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The close proximity of AA3's R group to the C=O of peptide between AA2 and AA3 only accomadates Gly at AA3.
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What is the least common type of reverse turn?
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3 ten helix
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What characterizes supersecondary structure?
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Stability achieved by intramolecular interactions of R groups.
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What is the most common type of supersecondary element observed?
Why are they needed? |
Cross-over elements for parallel beta sheets.
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What 2 categories of crossover elements exist, which is preferred?
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RH or LH; RH is preferred.
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What are the 3 main types of beta-sheet crossover elements?
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-Beta-coil-beta
-Betabetabeta -Beta-alpha-beta |
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What is the most common beta crsossover element?
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Beta-alpha-beta
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What stabilizes the B-a-B motif?
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Intercalation of R groups projecting up from B-sheets, and R groups radiating out from amphipathic a-helices.
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What is a Rossmann fold?
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A series of BaB motif repeats that make a donut-shaped a-B barrel.
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Where are rossmann folds commonly found?
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In enzymes of the glycolytic metabolic pathway.
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