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107 Cards in this Set
- Front
- Back
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folding of polypeptide into a closely packed three-dimensional structure
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tertiary structure
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includes prosthetic groups and metal ions
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tertiary structure
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provides a stable three-dimensional platform to spatially organize and orient functionally
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tertiary structure
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What forms unique binding sites for interactions? |
tertiary structure
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What forms unique active sites for chemistry? |
tertiary structure
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What integrates multiple functions? |
tertiary structure
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What enables movements associated with activity? |
tertiary structure
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What stabilize tertiary structure?
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non-covalent interactions, especially the hydrophobic effect
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What are three features of tertiary structure?
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motifs domains folds |
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combinations of secondary structures
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motifs
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combinations of linked motifs |
domains
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overall protein architecture, one or more domains |
folds
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What are the two common ways to represent tertiary structure? |
ribbon model solvent-accessible surface model |
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shows only the backbone |
ribbon model
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gives an outline of the van der Waal's surface |
solvent-accessible surface model
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What are eight examples of motifs?
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helix-loop-helix coiled coil helix bundle beta-alpha-beta unit hairpin beta meander Greek key beta sandwich |
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What is a helix bundle?
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helix-turn-helix-turn-helix
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What is a beta-alpha-beta unit? |
parallel beta sheets with alpha in-between
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What is a hairpin?
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antiparallel beta sheets connected with a turn
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What is a beta meander? |
string of hairpins
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What is a Greek key? |
anti-parallel strands where 2 is joined to 3, 3 to 4, and 4 to 1
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What is a beta sandwich?
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two antiparallel beta sheets
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What happens to domains when cut out of proteins?
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remain folded
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independently folded, compact units within proteins |
domains
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What is the general size of a domain? |
25 to 300 amino acid residues
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How are different domains connected?
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by loops and bound by weak interactions between side chains
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overall architecture of a protein |
folds
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one or more domains |
folds
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regular elements (secondary structure/motifs) |
fold |
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similar overall structure, no significant sequence similarity |
super-family
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similar overall structure and sequence similarity |
family
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How are domains classified?
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according to presence of secondary features
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contain supersecondary structures such as the alpha-beta-alpha motif |
mixed alpha/beta domains
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consist of local clusters of alpha helices and beta sheet in separate, contiguous regions of the polypeptide chain |
alpha + beta domains
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What does an alpha + beta domain look like?
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Not intertwined, group of alphas meshed with group of betas.
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What have a heptad repeat? |
coiled coils
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At what positions are nonpolar residues present in coiled coils? |
a/a' d/d' |
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At what positions do electrostatic interactions occur between in coiled coils? |
e/g' g/e' |
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leucines located at 1 and 4 positions |
nonpolar leucine zipper
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True or false: electrostatic interaction between residues e/g' provide stability in coiled coils. |
false, but they don't destabilize
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Why does DNA need cations around?
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polyanion
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What motif is present for DNA binding?
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helix-loop-helix
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Where does recognition helix lie in DNA? |
across major groove
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Where are non-covalent interactions occurring in DNA? |
between helix and base sequence of the DNA
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Where are porins found?
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outer membranes of bacteria and in mitochondria
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What is the point of porins? |
big enough to pass small molecules through an aqueous channel
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What is a feature of some porin? |
gated, others just holes
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What motif is present in the beta archetype: beta-barrel domain?
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beta meander
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What is the principal component of connective tissue such as tendons and cartilage? |
collagen
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What is collagen?
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Three intertwined polypeptide chains: left-handed helical chains coiled to form a right-handed supercoil.
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What does collagen consist of?
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hydroxylated amino acids that provide additional inter-chain hydrogen bonds (and require vitamin C for their synthesis)
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What do fingernails and hair consist of?
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karyotin
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What happens to collagen as it's pulled and why? |
It becomes stronger because force is directed in.
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What amino acids are prevalent in collagen? |
G P
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What is true of every third residue in collagen? |
glycine
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True or false: intraresidue hydrogen bonding is prevalent in collagen. |
False, all is between the strands.
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Why is glycine at every third residue in collagen? |
Nothing larger can fit in the triple helix.
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Where are proline rings located in collagen? |
on the outside
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What are six generalizations about the interior of membrane proteins?
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compact with little solvent inside protein well-packed side chains relatively little conformational freedom of backbone bumpy surface hydrophobic interior no knots in the chain |
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What is the purpose of a G protein-coupled receptor (GPCR)?
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Cells communicate information from outside to inside.
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What are the targets of many drugs we use? |
G protein-coupled receptors (GPCRs)
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alternating, transmembrane helices connected by loops
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G protein-coupled receptors (GPCRs)
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What does transmembrane mean?
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embedded in membrane
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Are transmembrane proteins prominently hydrophilic or hydrophobic residues? |
hydrophobic
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Describe globular protein in two words. |
tight bundle
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How many proteins are in the human genome?
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30,000
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How many different protein folds have been discovered? |
1,000
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disrupting the native conformation of a protein
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denaturation
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How can denaturation occur? |
environmental changes (heat) chemical agents physical alteration of protein |
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What are four examples of chemical agents that cause denaturation? |
detergents pH changes thiols chaotropic agents (urea) |
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enhance solubility of non-polar substances in water |
chaotropic agents
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disrupt the formation of water |
chaotropic agents
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What are two physical alterations of protein? |
mutations proteolysis |
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restoring the native conformation of a protein when environmental agents are removed
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renaturation
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Native or denatured state: unique shape. |
native
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Native or denatured state: precisely ordered. |
native
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Native or denatured state: stable. |
native
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Native or denatured state: functional. |
native
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Native or denatured state: active site. |
native
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Native or denatured state: random shape. |
denatured
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Native or denatured state: highly mobile. |
denatured
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Native or denatured state: subject to degradation. |
denatured
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Native or denatured state: inactive. |
denatured
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Native or denatured state: no active site. |
denatured
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Why is protein folding represented as a descent into an energy well?
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Funnel represents the free energy change as folding progresses (ΔG is negative, spontaneous) but pathway must avoid local minima.
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What are the axes of folding funnels? |
x: conformation y: free energy |
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How is the bottom of a folding funnel labelled?
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N: native conformation
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What occurs as polypeptide backbone chain collides with itself? (2)
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contacts and rapid hydrophobic collapse clathrated hydrophobic residues hit and release waters |
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Why does rapid hydrophobic collapse occur? |
more energetically stable
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What happens to number of conformations down the folding funnel and why? |
rapidly shrink because chain can't slide through the core
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What is the time range of protein folding? |
1 μs - 1 ms
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What three things drive protein folding?
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entropy hydrogen bonding van der Waals and charge-charge interactions |
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What is the hydrophobic collapse model? |
Driven by entropy, protein collapses rapidly around hydrophobic side-chains with the release of bound water molecules.
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What is the nucleation model? |
Neighboring residues in sequence form some element of the native secondary structure that acts as a nucleus for cooperative folding.
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How is protein folding cooperative? |
It goes faster as more and more residues get involved.
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Does a chain prefer to be unfolded or folded and why? |
Unfolded because it can adopt more conformations.
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Does a system have higher entropy when protein is folded or unfolded? |
folded
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True or false: hydrogen bonding contributes to energy of folding. |
false
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True or false: similar topology can emerge from very different protein sequences.
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true
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When is it useful to use a ribbon model? |
when showing secondary structures or comparing structures
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What sequence exploits the structural properties of beta strands to make a stable, four-strand fold?
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Place a hydrophobic residue at every 2nd position in the sequence.
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Which residues are more likely to be found in turns, GWV or RGD?
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RGD
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Which of the following residues are most likely to be found in DNA binding helixes? NAF EFH |
KRQ
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Which of the following residues are most likely to be found on the inside surface of a porin? NLF GWV |
KSQ
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What sequence of porin beta strands allows nonpolar residues to interact with membrane lipids and polar residues to interact with the aqueous channel?
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Place a hydrophobic residue at every 2nd position in the sequence.
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Which sequence repeat destabilizes the collagen triple helix? GPR |
APP |
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What sequence exploits the structural properties of alpha helixes to make a stable, 7-helix bundle in rhodopsin? |
Place a hydrophobic residue at every position in the sequence.
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