Term
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Definition
| linear polymers of amino acids |
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Term
| Where do amino acids connect? |
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Definition
| Carboxy end of one amino acid connects to the amino end of another |
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|
Term
| What are the characteristics of peptide bonds? |
|
Definition
extremely stable
rigid and planar
no freedom of rotation
resonance interaction |
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Term
| What are the dipoles of a peptide bond? |
|
Definition
Partial negative charge on Carboxy
Partial positive charge on Amine |
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Term
| What is the the most energetically favorable conformation for peptide bonds? |
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Definition
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Term
| What amino acid on occasion will assume the Cis transformation? |
|
Definition
Proline
10-15% percent of the time |
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|
Term
| What was the primary structure of a protein? |
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Definition
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|
Term
| What amino acid can form disulfide bridges? |
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Definition
|
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Term
| In what sort of environment do proteins have to be to form disulfide bridges? |
|
Definition
Oxidizing environments
-typically outside of cells |
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|
Term
| The two chains of insulin are combined via what mechanism? |
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Definition
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Term
| What is the secondary structure of a protein? |
|
Definition
| Regular arrangments of portions of a polypeptide chain |
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|
Term
| What are the two broadly described protein shapes? |
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Definition
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|
Term
| Fibrous proteins serve what role? |
|
Definition
| mostly structural material, although some have motion function |
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Term
| Fibrous proteins are predominantly what structure? |
|
Definition
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|
Term
| The interior of proteins tend to be? |
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Definition
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|
Term
| If peptide bonds are polar and all amino acids are formed with peptide bonds, how do proteins fold the hydrophobic side chains into the core? |
|
Definition
| main chains bond with each other |
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|
Term
| What are the two types of secondary structures? |
|
Definition
| alpha helices and beta sheets |
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|
Term
| How are secondary structures formed? |
|
Definition
| Hydrogen bonding between NH and C=O groups on the main chain |
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|
Term
| How many residues per turn on an alpha helix? |
|
Definition
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|
Term
| How does the hydrogen bonding work on alpha helices? |
|
Definition
| C=O of residue n bonds with NH residue of n+4 |
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|
Term
| What is the average length of an alpha helix? |
|
Definition
10 residues (3 turns)
wide variability |
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|
Term
| What are the preferred amino acids for alpha helices? Which amino acids are poor for alpha helices? |
|
Definition
Good: Glu, Leu, Met
Bad: Pro, Gly, Tyr, Ser |
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|
Term
| What amino acid can predict kinks in an alpha helix? |
|
Definition
|
|
Term
| What is the most common location of an alpha helix? |
|
Definition
along the outside of a protein
-half outside and half inside hydrophobic interior of protein |
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|
Term
| True or false. Beta sheets are made up of contiguous residues? |
|
Definition
| False, beta sheets grab different residues along the chain |
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|
Term
| What is the typical length of a beta sheet? |
|
Definition
|
|
Term
| What are the two way that beta strands can align? |
|
Definition
| parallel and antiparallel |
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|
Term
| How is the hydrogen bonding different in beta sheet bonding of parallel and antiparallel alignments? |
|
Definition
antiparallel has hydrogen bonding in groups
parallel has hydrogen bonding that bridges the gap in an uneven angle |
|
|
Term
| what is a mixed beta sheet? |
|
Definition
| sheet with parallel and antiparallel elements (not common) |
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|
Term
|
Definition
Structures that link secondary structures.
Some have other functions (enzyme activating sites, binding sites)
Hydrogen bond with water molecules |
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|
Term
| What is the easiest region to predict? |
|
Definition
|
|
Term
|
Definition
also called: reverse turns, turns, beta bends
loop regions that connect antiparallel B strands |
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|
Term
| What are long loop regions? |
|
Definition
| long flexible loop regions that often are involved in protein function |
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