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64 Cards in this Set
- Front
- Back
What are polymers of amino acids? |
Proteins |
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What determines the function of a protein? |
It's structure |
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What are five of the main functions of proteins? |
1. Structural components 2. Motors for movement 3. Catalyzing chemical reactions 4. Mediate communication between cell and environment 5. Expression of genetic information |
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What are the four different levels of proteins? |
1. Primary structure 2. Secondary structure 3. Tertiary structure 4. Quaternary structure |
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What is the primary structure of a protein? |
The sequence of amino acid residues |
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What is the secondary structure of a protein? |
The localized conformation of the polypeptide backbone |
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What is the tertiary structure of a protein? |
The three-dimensional structure of an entire polypeptide, including its side chain |
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What is the quaternary structure of a protein? |
The spatial arrangement of polypeptide chains in a protein with multiple subunits |
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What are the three categories of R groups for amino acids? |
1. Nonpolar R groups 2. Polar uncharged R groups 3. Polar charged R groups |
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What type of R groups do hydrophobic amino acids have? |
Nonpolar R groups |
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What type of R groups do hydrophilic amino acids have? |
Polar R groups |
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What is unique about the amino acid proline (Pro, P)? |
Proline is the only amino acid whose side chain loops back onto its own backbone |
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What is unique about the amino acid tryptophan (Trp, W)? |
Tryptophan is the only amino acid with a fused ring system |
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What is unique about the amino acid cysteine (Cys, C)? |
Cysteine residues can form disulfide bonds |
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What is unique about the amino acid methionine (Met, M)? |
Methionine is one of only two amino acids with a sulfur in its R group |
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What amino acid do most proteins contain at least one of? |
Tryptophan |
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What can tryptophan be used to determine? |
The protein concentrations |
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How can tryptophan be used to determine protein concentrations? |
Trp absorbs UV light at 280 nm Protein concentrations can be determined based on detection of Trp in proteins Beer's Law |
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What is the equation for Beer's Law? |
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What facilitates crosslinking? |
Disulfide bonds |
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What can form intra-strand crosslinks? |
Disulfide bonds |
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What can occur when a protein contains more than one polypeptide chain? |
Disulfide bonds can also form inter-chain crosslinks |
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How are amino acids linked? |
Via peptide bonds |
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What do amino acids link to form? |
A polypeptide |
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T or F: Amino acids have many amino acid residues |
True |
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What reaction links amino acids? |
Condensation reaction |
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What does pK reveal? |
The cutoff pH for protonation of species |
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What is the pH of this amino acid? |
pH < 3.5 |
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What is the pH of this amino acid? |
3.5 < pH < 9 |
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What is the pH of this amino acid? |
pH > 9 |
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T or F: Amino acid structure does not affect solubility |
False |
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What determines a molecules solubility? |
The structure of the molecule |
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What does solubility of an amino acid refer to? |
Polar, charged Polar, uncharged Nonpolar |
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What are the two characteristics of structural proteins (collagen, keratin)? |
1. Insoluble 2. Made of mostly nonpolar amino acids |
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What are the two characteristics of proteins that need to function in the cell? |
1. Soluble 2. Have hydrophilic amino acids on the surface |
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Why are secondary structures formed? |
To minimize steric strain and maximize the hydrogen bonds between the polar groups of the backbone |
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What are common secondary structures that are characterized by hydrogen bonding between backbone groups? |
Alpha helix and beta sheet |
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What does an H-bond in an alpha helix form between? |
The carbonyl oxygen and the amino hydrogen |
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How many residues are there per turn for an alpha helix? |
3.6 |
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How is the core of an alpha helix packed? |
Densley |
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What is the value of a pitch of an alpha helix? |
5.4A |
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What type of interactions are there between the backbone atoms of an alpha helix? |
van der Waals |
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What is a beta sheet? |
Aligned strands of polypeptides hydrogen bond with neighboring strands that are either parallel or antiparallel to each other |
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What are the two characteristics of alpha helixes backbone atoms? |
1. H-bones: C=O bonds with NH that is four positions away 2. Glycine and proline are rar |
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What does proline do to alpha helixes backbone atoms? |
Proline introduce destabilizing kink, lacks N-H for H-bonding |
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What does glycine do to alpha helixes backbone atoms? |
Glycine is able to rotate too freely and distorts the helix |
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What amino acid is uncommon in beta sheets? |
Proline |
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How are secondary structures linked? |
Via polypeptide loops |
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What type of structure do loops that link beta-strands and alpha-helices have? |
Irregular secondary structure: does not adopt a defined secondary structure, but is not random |
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T or F: Proteins can have limited combinations of secondary structures |
False |
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What shape does a folded polypeptide assume? |
A shape with a hydrophilic surface and a hydrophobic core |
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What is the stabilization of a protein structure? |
Delicate balance between forces |
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What interactions should be considered for the stabilization of a protein structure? |
Hydrophobic interaction H-bonds Electrostatic Charge/charge vdW interactions Disulfide bonds |
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What are hydrophobic interactions? |
The aggregation/association of nonpolar molecules due to the hydrophobic effect |
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Is a folded or unfolded protein more favorable? |
Folded |
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What bonds are able to form in the folded or unfolded state? |
Hydrogen bonds and charge/charge interactions --> equally favor the unfolded and folded state |
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What are the characteristics of disulfide bonds? |
Rare and have been demonstrated to not be essential for stabilizing protein structures in which they are present. May help prevent unfolding in harsh conditions, but do not have a strong effect on stability in normal conditions |
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Which interaction is the most important to consider? |
Hydrophobic interaction |
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What is the other interaction, along with hydrophobic interaction, that needs to be considered? |
van der Waals interactio |
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What interactions are not as important to consider? |
H-bonds Charge/charge Disulfide bonds |
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What are the four steps for the protein folding process? |
1. Folding of a protein is not random! 2. Protein folds through one or a few alternate pathways 3. Small element of the secondary structure form first 4. Hydrophobic effect causes secondary structures to coalesce with a hydrophobic core |
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What one or two pathways occur if a misfolded protein is detected? |
1. Another protein can help refold the misfolded protein 2. The misfolded protein is degraded |
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What happens if a misfolded protein is not detected or degraded? |
It can aggregate and cause diseases |
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What are two examples of diseases that can be caused when a misfolded protein is not detected or degraded? |
Alzheimer's or Parkinson's |