ChemActivity
46
Part A: Amino Acids and Peptides
(Is the peptide IAG the same as the peptide GAI?)
Model 1: The 20 Amino Acids at Biological pH
See diagram of AA structures at the end of this ChemActivity.Side chains are classified into three general types: those with… i) nonpolar sidechains
ii) polar sidechains
iii) charged sidechains (at biological pH)
A working definition of nonpolar = the sidechain has more than 2 C's per neutral heteroatom. ("hetero" = "other" and refers to atoms "other" than C or H.)
Critical Thinking Questions
1. Each amino acid has a distinct side chain attached to a carbon referred to as the "alpha carbon."
a) Why is this carbon called the "alpha carbon."
It is the first carbon next to the carbonyl. This is the same nomenclature used previously.
b) Identify a example of an amino acid with a nonpolar sidechain… a polar sidechain… a charged sidechain.
See examples on chart at the end of this activity.
2. All but one amino acid is chiral. a) Which amino acid is not chiral.
proline
b) What is the absolute configuration (R or S) of alanine?
c) Chiral, naturally occurring amino acids are called "L-amino acids." Confirm that, at the alpha carbon, all L-amino acids have the same spatial arrangement of the ammonium, carboxylate, H and sidechain groups at the alpha C.
Note that because of the rules for assigning R and S, cysteine has an R assignment even though it is an L amino acid.
d) Use wedge and dash bonds to draw a "D-amino acid" (one not found in nature).
O O H3N
Model 2: Peptide Bonds/Dipeptides/Polypeptide Chains
• Specially designed enzyme catalysts can hold two amino acids in the right conformation and covalently link them together, forming a dipeptide.
• Enzyme catalysts can add more amino acids to the carboxy terminal end, one at a time, building a long unbranched chain of amino acids called a polypeptide.
N H O H3N CH2SH O O CH2OH "Amino
Terminus" "Carboxy Terminus" (chain extended by adding amino acids to carboxy end)
Critical Thinking Questions
3. A peptide bond is the bond formed with the help of an enzyme that connects two amino acids.
a) Put a slash through the peptide bond in Model 2, as if you were retrosynthesizing this molecule from its constituent amino acids.
b) When a peptide bond is made, a carboxylic acid functional group and an amine functional group are combined to form a functional group called an “amide.” Put a box around the atoms comprising the amide functional group in the dipeptide above.
c) On the structure in Model 2, circle together all the atoms that came from an individual amino acid, and identify each of these amino acids by name.
Cysteine and serine.
4. The dipeptide shown in Model 2 is named "Cys-Ser" or "CS". a) Explain each of these names.
These are the three-letter code and one-letter code names, respectively.
b) Draw the tri-peptide IAG.
H3N O HN O CH H3C CH2CH3 O HN O IAG H3C
5. A polypeptide chain is a long chain of amino acids.
a) Write the name (using the three-letter codes) of a 5 amino-acid polypeptide chain that you expect to be very insoluble in water. Such polypeptides are called hydrophobic because they appear to "run away from water."
Any polypeptide containing mostly nonpolar (and very few polar) amino acid residues.
b) Write the name (using the three-letter codes) of a 5 amino-acid polypeptide chain that you expect to be very soluble in water. Such polypeptides are called hydrophilic because they appear to "love water."
Any polypeptide containing mostly polar (and very few nonpolar) amino acid residues.
Part B: Proteins
(What is the difference between the 1o, 2o, 3o and 40 structures of a protein?)
Model 3:
α-Helix and β-Pleated Sheet
• part of a polypeptide chain can coil up into a hollow rod-like structure called an α-helix. This coil can be 10 amino acids long or hundreds of amino acids long.
• A part of a polypeptide chain can line up with other parts of the chain to form a fabric-like array called a β-pleated sheet.
• Both α-helices and β-pleated sheets are held together by hydrogen bonding between different amino acids in the polypeptide backbone (backbone shown in bold, below).
amino terminus carboxy terminus N H O N H O N H O N H O N H N H O N H O N H O O
Schematic of polypeptide backbone (only atoms involved in hydrogen bonding are shown)
N N N N O O O O O H H H H R R R R N H R N N N N O O O O O H H H H R R R R N H N H R O N H R O N N N N O O O O O H H H H R R R R N H R N H O S S disulfide bond
Critical Thinking Questions
6. Label the two structures in Model 3 as being either an α-helix or a β-pleated sheet, based on the descriptions at the top of the page.
The alpha helix is at the top of the page.
7. What do the dotted lines on these structures represent?
8. A thiol is like an alcohol, but with S replacing O. Two thiols can be oxidized (loss of H2) to form a disulfide bond (shown below).
R S H H S R oxidize R S S R
thiol thiol disulfide
H2
a) What amino acid has a thiol sidechain? cysteine
b) Modify the drawing of the β-pleated sheet in Model 3 to show how the sidechains shown at the bottom right of the drawing can be oxidized to covalently link two strands of the β-pleated sheet.
Model 4: Protein Folding
• Parts of a large polypeptide chain will spontaneously organize into α-helices, β -pleated sheets and sometimes other less common sub-structures.
• These "sub-structures" will organize themselves into a specific 3D super-structure, which is mostly held together by non-covalent interactions like hydrogen bonds.
• A given sequence of amino acids will fold the same way to form the same 3D structure every time. This structure is called a protein.
• Many proteins are comprised of a single polypeptide chain between 50 and 500 amino acids long.
ALIVFYWMGPSTNGCFPCHEGQVIMNDRTWLAYSKRDEHCGNTSPQMWYFVILA...etc. spontaneously forms helices and sheets
helix A helix B helix C helix D sheet A sheet B amino terminus carboxy terminus Linear polypeptide chain:
sub-structures spontaneously and repeatably organize into a very specific 3D structure
= indicates a binding
site for another molecule
schematic of protein protein
Critical Thinking Questions
9. Model 4 describes three levels of protein structure, usually called primary (1o), secondary (2o), and tertiary (3o) structure.
a) If you know the primary structure of a protein, what do you know?
You know the linear sequence of amino acids in the protein.
b) If you know the secondary structure of a protein, what do you know?
You know what sections of the protein fold into alpha helices, beta pleated sheets (and other substructures).
c) If you know the tertiary structure of a protein, what do you know?
You know the three dimensional shape of the folded protein.
Model 5: Protein Function
Proteins (on average) make up 50% of the dry weight of a cell. They serve a myriad of chemical and structural functions including…
• structure (hair, skin, connective tissue, muscle etc.)
• enzymes (very specific and efficient catalysts such as those in Model 2)
• antibodies
• hormones
• transport for smaller molecules (e.g. O2/CO2 to and from the lungs and
mitochondria = the tiny combustion engine that provides power to each of our cells).
Critical Thinking Questions
10. The chicken and the egg paradox speaks to the problem of how the first chicken got here. Explain how this parable relates to proteins. (Hint: see Model 2).
Since proteins are needed to make other proteins, this creates a paradox… how was the first protein synthesized?
Exercises for Part A
2. Simply mixing the three amino acids shown below results in an extremely low yield of the tripeptide IAG.
O H3N O CH3 O H3N O CH H3C CH2CH3 O H3N O
This is partly because a carboxylate ion is a terrible electrophile and an ammonium ion is a terrible nucleophile. The enzymes involved in peptide synthesis overcomes these problems by activating the amino and carboxy ends of each amino acid.
O H3N O R EnzymeA withdraws e-O N H O R' EnzymeB withdraws donates donates
e-a) EnzymeA and EnzymeB, above, either donate or withdraw electron density. For each enzyme, circle the correct function and cross out the wrong one. b) What other function must the enzyme perform to ensure a 100% yield of the
tripeptide IAG?
c) Name one possible peptide sideproduct that would form if the protein simply activated both ends of the three amino acids shown above.
Exercises for Part B
3. In the 1960's Linus Pauling and E.J. Corey discovered that certain sequences of amino acids tend to organize themselves into rod-like structures (α-helix) while other sequences organize into sheet-like structures (β-pleated sheet). Still other sequences form neither. For example, a sequence that has many proline amino acids will double back on itself too often to be able to form either an α-helix or a β -pleated sheet. Among all amino acids, what is unique about proline?
4. Some very large proteins are actually made up of smaller protein sub-units. For example, the transport protein, hemoglobin is comprised of four nearly identical polypeptide chains. Each chain undergoes folding to produce a specific secondary (2o) then tertiary (3o) structure. Finally, the four 3o structures come together to form the quaternary (4o) structure of the protein hemoglobin. What is the difference between tertiary structure and quaternary structure of a protein?
5. Explain the following statement: "At this point in time, we are very bad at
predicting the tertiary structure of a protein based on its linear amino acid sequence. Nevertheless, the amino acid sequence of a protein determines the tertiary structure of the protein."
6. The following pathway is an example of the trouble a chemist has to go through to create a single peptide bond in the laboratory. Describe at least two things this cumbersome synthesis accomplishes that simply adding two amino acids together cannot accomplish. H N O O H2N R' Cl O O O R' O H N OH O R' O SOCl2 H N Cl O R' O electrophile O O H2N R" nucleophile STEP 1 STEP 2 STEP 3 H N N H O R' O R" O O H3O H2N N H O R' R" O OH STEP 4 STEP 5 neutralize
This is an amino acid with the carboxy end protected to make it a poor nucleophile. O O H2N R" dipeptide
O H3N O O H3N O O H3N O O H3N O O H3N O Alanine (Ala) A Leucine (Leu) L Isoleucine (Ile) I Valine (Val) V Phenylalanine (Phe) F O H3N O O H3N O O H3N O O H3N O O N H2 O Tyrosine (Tyr) Y Tryptophan (Trp) W Methionine (Met) M Glycine (Gly) G Proline (Pro) P N H OH S O H3N O O H3N O O H3N O HO O H3N O O H3N O Serine (Ser) S Threonine (Thr) T Asparagine (Asn) N Glutamine (Gln) Q Cysteine (Cys) C HO O NH2 NH2 O SH O H3N O O H3N O O H3N O O H3N O Lysine (Lys) K Arginine (Arg) R
Aspartic Acid (Asp) D
Glutamic Acid (Glu) E Histidine (His) H O O O H3N O O O NH3 H N NH2 NH2 NH HN
The 20 Amino Acids at Biological pH (with three-letter and one-letter abbreviations)
non-polar sidechains
polar sidechains
