Term
| #32. what is the relationship between folding and energy? |
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Definition
| Proteins always try to fold into the lowest energy state for the environment they are in. As the environment changes the shape changes, this can be done with heat, ph or chemically. |
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Term
| #33. what's denaturation? Why is it important? Name two ways to denature a protein. |
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Definition
| Denaturation is when proteins are unfolded. It's important because the shape of the protein determines it's function. Two ways to denature a protein is by applying heat or changing the pH. |
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Term
| #34. what are molecular chaperones proteins? What are their uses? |
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Definition
| chaperones are proteins that assist the non-covalent folding or unfolding and the assembly or disassembly of other macromolecular structures, but do not occur in these structures when the structures are performing their normal biological functions having completed the processes of folding and/or assembly. |
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Term
| #35. Describe secondary structure . Name two types. What are the roles for hydrogen bonds and R groups in these structures. |
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Definition
Location of repetitive coiling or folding of a protein.
Common forms, alpha helix, beta plate sheets.
The roles of h-bonds and r groups.
Non polar R groups make it wrap around each other to produce coil strands, h-bond is made every 4th peptide bond linking the c=o of one amino acid with the n-h of another, which allows for periodicity of the turn of the helix which regulates internal structure for helix.
For beta h-bonds between backbone c=o groups to form a rigid planer surface, R groups alternatively project above and below the plane of the sheet which allows it to make good interfaces between aqueous and non aqueous environments |
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Term
| #48. how can you classify proteins into gene families? |
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Definition
After it has gone through a functional state
- it has to go trough gene duplication
- their three dimensional structure is similar
- function similar |
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Term
| #49. describe the serine protease gene family in terms of structure and domain. |
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Definition
Serine protease, begin as zymogens and are activated by proteolysis, this changes their architecture of the active site.
Their domain is a conserved domain. Enzyme activation, and degradative functions in different cellular or extra cellular compartments |
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Term
| #48. how can you classify proteins into gene families? |
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Definition
Recurring units in molecular evolution, which can be determined by sequence and structure analysis.
-they contain conceived sequence patterns or motifs which allow detection in polypeptide sequences.
Look for domains because Database searching, sequence alignment, phylogeny and protein modeling are all better performed on a single domain, rather than a multi-domain polypeptide. |
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Term
| #52. what are the properties of domains |
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Definition
Part of a polypeptide, but when folded it creates it's own hydrophobic core.
Some regions are conserved through recombination events because of their own functionality for example shuffling
Inter domain regions will be more divergent
Region between domains are fairly simple in sequence level because they are rich in one or two specific amino acids
Can be reverse Ingeneered because they have independent folding units |
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Term
| #53 how does domain shuffle work to give you different proteins? |
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Definition
1 it's a process put together to give you a three dimensional part to form a complete structure.
It allows to use the same piece in many different proteins this allow to see
Allows to regulate amino acids tightly. |
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Term
| #36 Describe the formation of an alpha helix in diagram bond formation |
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Definition
| Generated when a single polypeptide chain twist around itself to form a rigid cylinder |
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Term
| #37. describe how helix's can interact? Why are alpha helixes so useful? |
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Definition
They can wrap around each other to produce coil strands,
They are important because they can be hydrophilic and hydrophobic regions. |
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Term
| #38. how do alpha helix's interact to form strong structures such as hair and collagen. |
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Definition
They wrap around each other
this happens by the non polar R which leads to interacting with each other and letting polar R groups face the aqueous environment |
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Term
#39
diagram and describe the formation of a plated sheet |
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Definition
Two or more extended strands of polypeptide chain lay side by side held by a h bond.
Pg 17 lecture notes 1 |
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Term
| #40 describe how turns are formed in secondary protein structure |
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Definition
| Type three single turn of 3.10 helix contain h-bond between the carbon and oxygen and the amide nitrogen of i+3 |
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Term
#41
why do proteins try to fold into the lowest energy shape? |
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Definition
| It is so that the folded state is very stable, it happens faster, allowing folding through many pathways, |
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Term
#45
what is the quartenary structure and what types of bonds are important in forming one? |
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Definition
| Quartenary structure is Many proteins consist of two or more chains folded into their specific tertiary structure, bonds between sulfur residues |
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Term
| #47 Why is folding so important? Give an ex. Of how proteins with different primary structures can fold to make similar structures. |
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Definition
| A protein needs to be in the proper shape to do it's job. When denature, proteins cannot return to their original shape and loose or change function. |
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Term
| #46Why aren't all folding patterns useful? Give an ex of pathology |
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Definition
| Ways of polypeptide chain can fold are limited bc structure are determined by cellular location of protein. Example: Alzheimer's due to improper folding |
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Term
| #43 describe the basic physical nature of turns -what are 2 common amino acids found in turns? |
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Definition
| Turns have several unsatisfactory backbone hydrogen bond donors and acceptors they are polar and are found near the surface of the protein. Two common amino acids are proline and glycene |
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Term
| #44 how do domains go together to form a protein? Why is the especially important in the? immune system |
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Definition
| It goes trough the sh3 domain continuing to the small kinase domain, large kinase domain, finally sh2 domain. |
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Term
| #42. how can alpha helix's and beta sheets be polar on one side and non polar on the other |
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Definition
In beta sheets hydrogen bonds occur between strands and the R groups alternately project above and below the plain of the sheet.
In alpha helix the polar R groups face the aqueous environment |
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Term
| #56 why are some proteins also are founded to be covalently conjugated with carbohydrates? |
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Definition
| These occur due to translation of proteins. It I parts specialized functions upon the resultant proteins. Those covalently associated termed glycoproteins. |
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Term
| #54 Why are we more complicated than simple organisms? Think proteins. |
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Definition
| Yes bc we have twice as many types of combinations as found in simpler organisms. |
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Term
| 55. Describe how conserved domains are used in tertiary structure. |
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Definition
| Is due to amino acid substitutions |
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