Term
| What is tertiary protein structure? |
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Definition
| Tertiary structure is the folding of protein into it's native state |
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Term
| What are supersecondary structures or motiffs? |
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Definition
| specific geometric arrangments of secondary structures |
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Term
| What is the name of the motiff that has 2 helices joined by a loop? |
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Definition
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Term
| What is the primary function of a helix loop helix motiff? |
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Definition
| binding sites (DNA and Calcium) |
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Term
| What are the three helix-loop-helix domains of Parvalbumin? |
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Definition
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Term
| What part of the helix-loop-helix actually binds to the calcium? |
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Definition
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Term
| What is a hairpin beta motiff? |
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Definition
| 2 adjacent antiparallel strands joined by a loop |
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Term
| What is a Greek Key motiff? |
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Definition
| 4 adjacent antiparallel beta strands |
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Term
| What is a Beta-alpha-Beta motiff? |
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Definition
Beta strand-loop-alpha helix-loop-beta strand
top loop often found in the binding or active site of a protein |
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Term
| What is an alpha alpha motiff? |
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Definition
| two antiparallel alpha helices with axes inclined so side chains can indterdigitate |
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Term
| What are protein domains? |
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Definition
| polypeptide chain that can fold independently into a tertiary structure (can have many domains in one protein) |
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Term
| What are the 3 main domains? |
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Definition
alpha domains
beta domains
alpha/beta domains |
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Term
| What are alpha domains? where are they founds? |
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Definition
conglomerates of alpha helices.
seen in globular proteins and transmembrane proteins
myoglobin has alpha domains |
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Term
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Definition
contain 4 to >10 predominantly antiparallel Beta strands
>6 strands roll up into Beta barrels
8 succesive barrels make and up and down beta barrel |
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Term
| What are alpha/beta domains? |
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Definition
8 overlapping beta-alpha-beta motiffs
almost all alpha-beta barrels are enzymes |
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Term
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Definition
specific alpha/beta domain:
8 stranda alpha/beta domain
-8 parallel beta strands in center
- 7-8 alpha helices around beta strand [protect]
loops of c termini beta strands are active sites |
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Term
| most domains are composed of how many residues? |
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Definition
| 100-200. If you see a protein greater then 200 residues, start thinking domains |
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Term
| Where do non-polar sidechains tend to aggregate? |
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Definition
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Term
| Where do charged polar residues tend to aggregate? |
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Definition
| on surface of proteins in contact with the aqueous solution |
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Term
| What do uncharged polar residues ten to aggregate? |
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Definition
| eithier inside or outside of cell membrane [if inside it is neutralized by hydrogen bonding] |
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Term
| Do domains act independently or together? |
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Definition
| either, depends on the function of the protein |
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Term
| What is protein quaternary structure? |
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Definition
| arrangement of protein polypeptide chains (most have more than 1) |
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Term
| What are identical subunits of a protein called? |
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Definition
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Term
| Protein with >1 subunit are called? |
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Definition
| Oligomer. Specifically can be named relative to the number [4 subunits will be called a tetramer, etc] |
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Term
| How do oligomers bond with each other? |
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Definition
| much like any protein structures: non-polar packing, hydrogen bonding, and occasionally disulfide bridges |
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Term
| What is the role of fibrous proteins? |
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Definition
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Term
| How water soluble are fibrous proteins? |
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Definition
| have low water solubility |
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Term
| What is the major structural motiff of fibrous proteins? |
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Definition
| Composed mainly of secondary structures |
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Term
| When is hydroxyproline and hydroxylysine hydroxalated? |
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Definition
| Already in the peptide chain when they get hydroxylated |
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Term
| What is the enzyme that puts the hydroxyl group on proline? |
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Definition
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Term
| What does prolyl hydroxylase need to function correctly? |
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Definition
| Vitamin C. Deficiencies in area can lead to scurvy |
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Term
| What is the specific properties of collagen chains? Why are they formed like this? |
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Definition
Glycine is repeates as the third residue and proline [or hydroxyproline] also occurs three residues apart in the same regions.
this formation allows the super helix to form |
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Term
| what is a polyproline type II helix? |
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Definition
| 3 residues per turn combined wholly of prolines |
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Term
| Why is glycine important for the formation of the super helix? |
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Definition
| Small side chain (H) reduces steric hindrance and allows the super helix to form |
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Term
| Why are prolines important for the super helix? |
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Definition
| Proline's distinctive side chain (ring) grants rigidity to the helix |
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Term
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Definition
| collagen "super structures" that are crosslinked. Arrangment depends on specific function of the fibril |
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Term
| What are the collagens that form fibrils? |
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Definition
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Term
| How are collagens crosslinked? |
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Definition
| interactions of the Lys and His side chains |
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Term
| What is the enzyme involved in collagen cross linking? |
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Definition
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Term
| What is the mechanism of collagen crosslinking? |
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Definition
lysyl oxidase connect two lysines
histindine connects and reacts with C=
then 5-hydroxy lysine connects |
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Term
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Definition
| primitive collagen that has extra residues on its termini (allowing for water solubility) |
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Term
| What are diseases caused by abnormal collagen synthesis? |
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Definition
| Ehler-Danlos, osteogenesis imperfecta, and scurvy |
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Term
| What are examples of collagen vascular disease? |
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Definition
| Systemic lupus erythematosus, rheumatoid arthritis, scleroderma, polymyositis, dermatomyositis |
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