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What are the two forms in which you can draw the structure of a peptide containing the sequence:
H3N+1-DYNVPL-COO-1
- Form 1: Where we show ALL atoms (except for RING-containing amino acid R-groups)
- Form 2: Draw the correct peptide structure using correct skeletal representations
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In the figure below, what does the encircled region depict?
The circled region shows SIX atoms that comprise the repeating unit of a peptide (protein) backbone
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Draw both form 1 and form 2. Please note that each a-carbon has an _____ _____ (____ ____) emanating/protruding from it. However, please note that we are just showing the backbone atoms in two representations
- R group (side chains)
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A peptide has 29 amino acids, how many peptide bonds does it have?
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A protein when translated released 489 water molecules. How long is it?
490 (one water molecule released for every peptide bond formed)
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Amino acids end in ____, ____ or ____.
-ine, -ate, or -an
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State the amino acid name ending when within a peptide or protein for the following:
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Amino acids that have name endings that end in have name ending that end in -ine, -ate and -an are replaced with ___. What are the three exceptions and how are they replaced?
- -yl
- 3 amino acids: asparagine, glutamine, and cysteine have the e removed and replaced with a -yl
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Consider the peptide:
H3N+1-EGAK-COO-1
1) Write the 3-letter abbreviated name for this peptide
2) Write the systematic name for this peptide
3) How many ionizable groups are in this peptide?
4) How many peptide bonds are in this peptide
5) How many water molecules were released during the process of making these peptide bonds
- 1) H3N+1-Glu-Gly-Ala-Lys-COO-1
- 2) H3N+1-glutamyl-glycyl-alanyl-lysine-COO-1
- 3) 4, ALWAYS count the ends of a peptide
- 4) 3
- 5) 3
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Consider the hypothetical H3N+1-DSRHNAYQ-COO-1
A) Calculate the overall charge on this peptide at a pH of ~7.40. Before going over this, make certain to go over oxygen, sulfur and nitrogen-containing functional groups
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- if unclear see pg 33/ans = 0 (at a pH of ~7.40)
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Consider the hypothetical H3N+1-DSRHNAYQ-COO-1
B) Calculate the isoelectric point of this peptide with the sequence
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- Ans: pl = 7.00 (pg 34-35)
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Consider the hypothetical H3N+1-DSRHNAYQ-COO-1
Ca) How many ionizable groups (if any) are there within this peptide?
Cb) Which amino acids (if any) exhibit resonance in this peptide?
- Ca) 7 ionizable groups: H3N+1, D, S, R, H, Y, and COOH
- Cb) 4 display resonance: D, R, H, Y
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Sketch a titration curve for the free amino acid lysine and determine its isoelectric point. Assume that the lysine solution is present at a very acidic pH of around 1.00
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Sketch a titration curve for the free amino acid, Histidine. Assume (like we did for lysine) that it is initially present in an acidic solution at a pH of 1.00
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Sketch a titration curve of the peptide, EGAK, (assume that the peptide is solubilized in an acidic pH of around 1.00)
Important pKa values:
Amino group: 8.0
Carboxyl Group: 3.0
What functional groups are represented by each number in your graph?
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- 1= carboxylate group of peptide
- 2= R group (side chain) of aspartate
- 3= amino group of peptide
- 4= R group of lysine
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Explain the Edman sequencing technique (Name the amino acid residues that become present and what is causing them to shift from one configuration to the next)
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What is the main idea here:
The idea is that cyanogen bromide treatment of a methionine residue leads to the formation of a homeoserine
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Name two proteases and what is their function?
- Trypsin: cleaves peptide bonds C-terminal to Lysine and/or Arginine (*still used today)
- Chymotrypsin: cleaves peptide bonds C -terminal to Phenylalanine, Tyrosine and/or Tryptophan
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What are the exceptions to Trypsin's cleaving capabilities?
- If proline (P) follows the lysine (K) or arginine (R), trypsin will be unable to cleave it
- If lysine (K) or arginine (R) is the LAST residue in a peptide or protein, trypsin will be unable to cleave it
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What are the exceptions to Chymotrypsin's cleaving capabilities?
- If proline (P) follows phenylalanine (F), tyrosine (Y) and/or tryptophan (W), chymotrypsin will be unable to cleave it
- If phenylalanine (F), tyrosine (Y) and/or tryptophan (W) is the LAST residue in a peptide or protein, chymotrypsin will be unable to cleave it
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Why can't trypsin or chymotrypsin cleave a target amino acid when it is the last residue in the peptide or protein?
It is not a peptide bond, a peptide is a bond between two amino acids
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An octapeptide is composed of Pro, Met, Trp, Tyr, Arg, Lys, Ser, and Gln
One cycle of Edman degradation yields PTH-Gln
Treatment with trypsin yields two tetrapeptides. One tetrapeptide was composed of Arg, Trp, Pro and Gln and the other tetrapepitde was comprised of the remaining residues
Treatment with chymortypsin yields a hexapeptide composed of Trp, Pro, Arg, Gln, Met and Tyr as well as a dipeptide composed of Ser and Lys residues
Using cyanogen bromide yields a pentapeptide composed of Hsr, Gln, Pro Trp and Arg as well as a tripeptide composed of Tyr, Lys and Ser
Based on these collective pieces of information, please determine the sequence of this octapeptide. Please make sure to indicate the proper ends of the peptide.
Please write the sequence in two ways: using the three-letter and the one-letter codes
Also, after you determine the sequence, please determine the number of cuts AND the number of fragments generated as a results of the cuts made by TRYPSIN and CHYMOTRYPSIN
How many total ionizable groups are in this peptide?
- H3N+1-Gln-Trp-Pro-Arg-Met-Tyr-Ser-Lys-COO-1
- H3N+1-Q-W-P-R-M-Y-S-K-COO-1
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An octapeptide consists of 2 Arg, Pro, Tyr, Phe, Met, His and Ser
One cycle of Edman degradation yields a PTH-Arg derivative
Treatment with tyrpsin yields a free Arg, a tripeptide consisting of Arg, Pro, and Tyr; and a tetrapeptide consisting of Phe, Ser, Met and His
Using cyanogen bromide on his peptide yields a pentapeptide containing Hsr, 2 Arg, Pro and Tyr as well as a tripeptide consisting of His, Ser and Phe
Treatment with chymotrypsin yields a free His and a heptapeptide consisting of the remaining residues
Based on these pieces of information, please determine the correct sequence of the octapeptide. Please make sure to indicate the proper ends of the peptide
Please write both the three-letter and the one-letter code
Also, after you determine the sequence, please determine the number of cuts AND the number of fragments generated as a results of the cuts made by TRYPSIN and CHYMOTRYPSIN
How many total ionizable groups are in this peptide?
- H3N+1-Arg-Tyr-Pro-Arg-Met-Ser-Phe-His-COO-1
- H3N+1-R-Y-P-R-M-S-F-H-COO-1
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