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1 What enables proteins to participate in a wide range of functions?
- a. They are linear polymers made up of a group of 20 amino acids that dictate the structure and interactions they undergo
- b. They contain functional groups that allow it to function
- c. They can come together to form complexes to accomplish tasks that the individual proteins could not initially complete
- d. Some are rigid and can be structural and others are flexible and can act as levers, hinges, etc.
1) What is a special characteristic of polar amino acids?
- a. They are important in proteins involved in signaling, which is done in a series of steps
- b. Hydrogen of the hydroxyl group can be replaced by a phosphate, changing size and charge dramaticallyà regulatory switches
- Good for pathways
1) How did this particular set of amino acids become the building blocks of prtoeins?
- a. Diverse
- b. Previously available from prebiotic reactions; evolution chose them
- c. Other proteins may have been too reactive
1) How many different combinations can there be? Is it limited? Why or why not?
Several different compounds. It is not infinite, but in fact limited by factors such as the backbone being rigid and planar, the psi and phi angles, trans and cis, steric hindrance, and the protein not being coded by the genetic code. The psi and phi angles were discovered to be limited by Ramachandran, who saw steric exclusion as a strong organizing principle
1) Why is knowing the amino acid sequence important?
- a. The amino acid sequence is important because
- i. the amino acid sequence can elucidate the mechanism of action
- ii. They can reveal the structure and thus the function
- iii. It is a component of molecular pathology and can lead to the discovery of alterations in sequence, which lead to disease
- iv. Much can be revealed about the evolutionary history of that protein
1) In Beta strands, how far is the separation of the side chains?
1) What are some preferences regarding secondary structure?
- a. Alpha helix is the default confirmation, but many things don’t fit in alpha helix:
- i. Branching at the beta carbon causes destabilization of the alpha helix
- ii. Polar amino acids have –OH groups, which compete for the NH and CO on main chains
- iii. Glycine is the smallest and can exist in any motif, but it does not prefer alpha helices
- iv. Proline disrupts the structure of both alpha helices and beta pleated sheets. It fits better in turns.
1) Name modifications proteins go through.
- a. Acetyl groups: make proteins more resistant to degradation
- b. Hydroxyl groups: stabilizes fibers of newly made collagen
- c. Carbohydrate units: many proteins, especially surface proteins or secretion proteins, acquire carbohydrate units on specific asparagine residues; also gives membrane directionality
- i. If you want export from a cell, glycosylate (adding carbohydrate units to proteins)
- d. Sugars: make protein more hydrophilic and able to interact with other proteins
- e. Phosphate additions: makes the protein useful as regulatory switches, for cellular processes
- i. Hormones stimulate the phosphorylation of hydroxyl amino acids of serine and threonine
- ii. Growth factors stimulate phosphorylation of hydroxyl group of tyrosine
- f. Fatty acids: added to alpha amino group or cysteine SH group to produce a more hydrophobic protein
- g. Can be trimmed and cleaved