Biologically Important Molecules Flashcards
Amino acid structure:
Tetrahedral a-carbon with side chain (variable R-group); a-carboxylic acid (COOH), and a-amino group (NH2)
___ different kinds of AA exist.
20
4 different broad categories of AA by property are ___.
- Non-polar, hydrophobic AA; R=hydrocarbon
Non-polar hydrophobic AA have R-groups that are___. The hydrophobic character is due to ___; this characteristic is amplified when ___. These AA are found ___.
hydrocarbon chains; affinity of hydrocarbon residues for each other; hydrocarbon chain is larger; dry interior of folded globular proteins.
Polar and neutral AA have R-groups that are ___ compared to non-polar hydrophobic AA and ___ compared to polar acidic or polar basic AA. In general, these R-groups tend to contain ___ atoms like ___.
more polar; less polar. Electrophillic; O, N, S.
___ groups of serine, threonine, and tyrosine are modified by addition of ___ by ___. The effect of the modification is ___. This modification is significant because ___.
hydroxyl (-OH); phosphate group (-PO4) by kinase; AA becoming highly hydrophillic; this will cause a change in protein conformation.
Polar and acidic AA have R-groups that are ___. There are ___ acidic proteins in these AA, which are ___. At physiological pH, these AA are ___.
carboxylic acid (-COOH); 2; glutamic acid, and aspartic acid; anions (deprotonated with - charge).
Polar and basic AA have R-groups that ___. At physiological pH, these AA are ___.
contain :N(s); cations (protonated with + charge), except Histidine.
AA with N: are neither acidic nor basic when ___.
it is connected to an electrophillic O that “weaken” the effect of the :
AA that is amphopheric at physiological pH is ___; this is because ___. As a result of its flexible nature, it is often found in ___.
histidine; its R-group pKa is ~7; protein active sites. “His goes both ways.”
AA that has sulfur: Two sulfur-containing organic groups are ___. Cysteine has ___ and is (a/b/n). Methionine has ___ and is (a/b/n).
thiol and thioether; thiol (-SH); acidic; thioether (R-S-R); neutral.
AA with a secondary a-amino group is ___. Its structure is important for ___.
Proline; protein folding.
Describe the formation of polypeptide bond; what is the leftover product?
:NH2 alpha to central C of one AA attacks nucleophilic center of COOH of another AA; H20 leaves
The backbone of PP is ___; which functional groups do each atoms come from?
N-C-C-N-C-C (Amine, central Carbon, Carboxylic acid)
A PP made of just glycine has ___ acidic or basic sites
2; N- and C-terminus are basic and acidic
Given it is of 2 AA vs. dipeptide, how is the bond formed and maintained? Use the terms kinetically and thermodynamically favored
Formed by using stored energy to overcome the activation energy;
maintained because the high activation energy makes the hydrolysis reaction thermodynamically favored but kinetically unfavored.
Proteolysis/Proteolytic cleavage is an enzyme reaction by proteolytic enzyme/protease; therefore, the reaction is (non/specific) to ___
specific to the relative position of the AA the protease recognize
Disulfide bond is formed by AA ___, specifically due to the interaction of functional groups ___, which is (oxidized/reduced). The result of disulfide bonding is ____.
Cysteine;
Thiol (-SH); reduced to S-S
Cystine
Define denaturation and 4 examples of denaturing forces. Mention which structures are being disrupted.
Disruption of protien’s shape (and therefore its function) without breaking peptide bonds;
- Urea (disrupt H-bonding in 2’ structure)
- pH
- T
- [Salt]
1’ Structure: What is it, and what bond determines 1’ structure?
AA sequence; peptide bond
2’ Structure: What is it, and what bonds determine it?
Initial folding of chain stabilized by bonds between bacbone NH and CO groups;
H-bonding in alpha-helix or beta-sheets
2’ Structure: What AA is never found in one of the 2’ structures (and what is that structure)? Why?
Proline residue never appears in alpha-helix because its ring structure (with NH embedded in it) kinks the chain
2’ Structure: Why would alpha-helix be a good structure found in ion channels and hormone receptors? 2 structural reasons.
Integrated within the hydrophobic membrane;
all polar groups (NH and CO of the backbone) interact with each other via H-bonding in the center of the helix & side chains are hydrophobic and interact with the hydrophobic membrane
2’ Structure: The differences between alpha helix and beta sheets, and similarities?
Similarities: both H-bonding between NH and CO of backbone
Difference: that same H-bonding occurs in distant residues in beta sheets; otherwise in alpha helix
