Term
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Definition
| valine, Val, V; nonpolar side chain, hydrophobic, aliphatic |
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Term
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Definition
| proline, Pro, P; nonpolar side chain, hydrophobic, aliphatic |
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Term
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Definition
| methionine, Met, M; nonpolar side chain, hydrophobic, methionine is the start codon |
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Term
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Definition
| leucine, Leu, L; nonpolar side chain, hydrophobic, aliphatic |
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Term
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Definition
| isoleucine, Ile, I; nonpolar side chain, hydrophobic, aliphatic |
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Term
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Definition
| glycine, Gly, G; nonpolar side chain, hydrophobic, smallest amino acid, only optically inactive amino acid due to H R-group, aliphatic |
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Term
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Definition
| alanine, Ala, A; nonpolar side chain, hydrophobic, aliphatic |
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Term
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Definition
| histidine, His, H; polar, hydrophilic, positively charged (basic) side chain, aromatic |
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Term
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Definition
| arginine, Arg, R; polar, hydrophilic, positively charged (basic) side chain, positive charge is delocalized over all three N atoms of its structure |
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Term
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Definition
| lysine, Lys, K; polar, hydrophilic, positively charge (basic) side chain |
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Term
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Definition
| glutamic acid (glutamate), Glu, E; polar, hydrophilic, negatively charge (acidic) side chain; similar to Gln but contains carboxylate group instead of amide. glutamate is simply the deprotonated form of glutamic acid |
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Term
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Definition
| aspartic acid (aspartate), Asp, D; polar hyrophilic, negatively charged (acidic) side chain; similar to Asn but contains carboxylate group instead of amide. Aspartate is deprotonated form of aspartic acid |
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Term
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Definition
| cysteine, Cys, C; polar, hydrophilic, thiol (-SH) containing side chain |
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Term
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Definition
| glutamine, Gln, Q; polar hydrophilic, amide containing side chain |
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Term
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Definition
| asparagine, Asn, N; polar, hydrophilic, amide containing side chain |
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Term
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Definition
| Threonine, Thr, T; polar, hydrophilic side chain |
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Term
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Definition
| Serine, Ser, S; polar, hydrophilic side chain |
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Term
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Definition
| tyrosine, Tyr, Y; relatively polar, relatively hydrophilic, aromatic side chain; absorbs in the UV spectrum due to aromaticity |
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Term
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Definition
| phenylalanine, Phe, F; nonpolar, hydrophobic, aromatic side chain; absorbs in the UV spectrum due to aromaticity |
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Term
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Definition
| tryptophan, Trp, W; nonpolar, hydrophobic, aromatic side chain; absorbs in the UV spectrum due to aromaticity |
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Term
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Definition
[image]
Val, V; nonpolar side chain, hydrophobic, aliphatic |
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Term
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Definition
[image]
Pro, P; nonpolar side chain, hydrophobic, aliphatic |
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Term
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Definition
[image]
Met, M; nonpolar side chain, hydrophobic, methionine is the start codon |
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Term
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Definition
[image]
Leu, L; nonpolar side chain, hydrophobic, aliphatic |
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Term
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Definition
[image]
Ile, I; nonpolar side chain, hydrophobic, aliphatic |
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Term
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Definition
[image]
Gly, G; nonpolar side chain, hydrophobic, smallest amino acid, only optically inactive amino acid due to H R-group, aliphatic |
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Term
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Definition
[image]
Ala, A; nonpolar side chain, hydrophobic, aliphatic |
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Term
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Definition
[image]
His, H; polar, hydrophilic, positively charged (basic) side chain, aromatic |
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Term
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Definition
[image]
Arg, R; polar, hydrophilic, positively charged (basic) side chain, positive charge is delocalized over all three N atoms of its structure |
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Term
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Definition
[image]
Lys, K; polar, hydrophilic, positively charge (basic) side chain |
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Term
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Definition
[image]
Glu, E; polar, hydrophilic, negatively charge (acidic) side chain; similar to Gln but contains carboxylate group instead of amide. glutamate is simply the deprotonated form of glutamic acid |
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Term
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Definition
[image]
Asp, D; polar hyrophilic, negatively charged (acidic) side chain; similar to Asn but contains carboxylate group instead of amide. Aspartate is deprotonated form of aspartic acid |
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Term
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Definition
[image]
Cys, C; polar, hydrophilic, thiol (-SH) containing side chain |
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Term
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Definition
[image]
Gln, Q; polar hydrophilic, amide containing side chain |
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Term
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Definition
[image]
Asn, N; polar, hydrophilic, amide containing side chain |
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Term
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Definition
[image]
Thr, T; polar, hydrophilic side chain |
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Term
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Definition
[image]
Ser, S; polar, hydrophilic side chain |
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Term
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Definition
[image]
Tyr, Y; relatively polar, relatively hydrophilic, aromatic side chain; absorbs in the UV spectrum due to aromaticity |
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Term
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Definition
[image]
Phe, F; nonpolar, hydrophobic, aromatic side chain; absorbs in the UV spectrum due to aromaticity |
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Term
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Definition
[image]
Trp, W; nonpolar, hydrophobic, aromatic side chain; absorbs in the UV spectrum due to aromaticity |
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Term
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Definition
| one that can either donate or accept an electron |
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Term
| general pKa values for amino acids |
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Definition
pKa is the pH value at which, on average, half of the molecules of that species are deprotonated.
The carboxyl group of amino acids has a pKa of around 2. The amino group has a pKa usually between 9 and 10. |
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Term
[image]
Determine the pKa and pI using the titration curve above. |
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Definition
| The half equivalent point where half of glycine is protonated and half is deprotonated at 2.3 pH is pKa1. When the carboxyl group becomes fully deprotonated the amino acid stops acting like a buffer and pH increases rapidly. The midpoint of this rapid increase is the pI of the amino acid. 9.6 marks pKa2 where the amino group becomes half protonated and half deprotonated |
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Term
| Describe peptide bond formation |
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Definition
| A bond forms between the carboxylate group of one amino acid and the amide cation group of another amino acid. The hydroxyl oxygen is removed as water along with the two hydrogens from the nitrogen. This is a condensation or dehydration reaction because the water is removed. The new bond will be between the carbonyl carbon and the nitrogen |
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Term
| primary protein structure |
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Definition
| the sequence of amino acids |
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Term
| secondary protein structure |
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Definition
local structure of neighboring amino acids; alpha helices and beta pleated sheets are the two most common secondary structures and are held together by intramolecular hydrogen bonds.
note: proline is rarely found in these structures due to its rigid cyclic structure. It introduces a kink and is often found in turns between chain of secondary structures |
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Term
| tertiary protein structure |
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Definition
| the three dimensional shape of a protein that results from how it folds. Folding occurs due to an overall increase in entropy that results from putting the hydrophilic residues on the outside of the protein and the hydrophobic residues on the inside. |
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Term
| quaternary protein structure |
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Definition
the interactions between multiple protein subunits.
-increase stability of protein complex
-reduce amount of DNA needed to encode the protein complex;
-can bring catalytic sites closer together
-cooperativity (allosteric effects) |
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Term
| What amino acids have one letter abbreviations that don't match their first letter? |
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Definition
Tryptophan - W
Tyrosine - Y
Lysine - K
Asparagine - N
Glutamine - Q
Aspartic Acid - D
Glutamic Acid - E
Phenylalanine - F
Arginine - R |
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