Amino Acids, Peptides, and Proteins Flashcards
(24 cards)
Alpha-amino acid
Amino group and carboxyl group attached to the same carbon. Does not always have to be the case: -Gamma: 3 carbons apart
Stereochemistry of amino acids
All amino acids are chiral (stereogenic) and optically active EXCEPT glycine. All eukaryotic amino acids are L-amino acids (amino group drawn to the left in a Fischer projection) and S-configuration. EXCEPTION: Cysteine is still an L-amino acids, but it is in the R configuration.
Nonpolar, non-aromatic side chains
Glycine, alanine, valine, leucine, isoleucine, methionine, proline
Proline can have contrainsts on flexibility, which limits where it can appear in a protein and can have significant effects on proline’s role in secondary structure.
Aromatic (Uncharged) Side Chains
Tryptophan: Non-polar
Phenylalanine: Non-polar
Tyrosine: Relatively polar
Polar, non-aromatic side chains
Serine, threonine, asparagine, glutamine, cysteine
- Serine and threonine have -OH groups making them highly polar and able to participate in hydrogen bonding
- Asparagine and glutamine have amide side chains (DO NOT gain or lose proteons with changes in pH)
- Cysteine has a thiol group (-SH). Prone to oxidation.
Negatively Charged (Acidic) Side Chains
Aspartic acid (aspartate) and glutamic acid (glutamate)
- Negatively charged at physiological pH (~7.4)
- Carboxylate groups
- “Ate” version is the deprotonated version of the acid
Positively Charged (Basic) Side Chains
Lysine, Arginine, Histidine
- All have positively charged nitrogen atoms
- Histidine has an aromatic ring called an imidazole
- Hydrophilic
Amino Acid Abbreviations
pKa
pKa of a group is the pH at which, on average, half of the molecules of that species are deprotonated
[HA] = [A-]
If the pH is less than the pLa, a majority of the species will be protonated. If the pH is higher than the pKa, a major of the species will be deprotonated.
Titration of Amion Acids
pI
pH at which the molecule is electricall neutral.
Neutral amino acids:
- pI = (pKa(NH3+) + pKa(COOH))/2
Acidic amino acid:
- pI = (pKa(R group) + pKa(COOH))/2
Basic amino acid:
- pI = ((pKa(NH3+) + pka(Rgroup))/2
Overall: Amino acids with acidic side chains have relatively low isolectric points, while those with basic side chains have relatively high ones.
Peptide Bond Formation
- Condensation or dehydration reaction (removal of a water molecule)
- Peptide bond has partial double bond characer due to resonance
- This causes restriction of rotation of the protein backbone around its C-N amide bond
- The other bonds of the backbone are not restricted
Peptide Bond Hydrolysis
- Hydrolysis is catalyzed by hydrolytic enzymes such as trypsin and chymotrypsin
-
Each cleaves at specific points:
- Trypsin cleaves the carboxyl end of arginine and lysine
- Chymotrypsin cleaves the carboxyl end of phenylalanine, tryptophan, and tyrosine
- They break apart the amide bond by adding a hydrogen atom to the amide nitrogen and an OH group to the carboyl carbon
-
Each cleaves at specific points:
Oligopeptide
Peptide with up to 20 amino acids. A single amino acid is not considered an oligopeptide.
Alpha-helices
- Coils clockwise around a central axis
- Stabilized by intramolecular hydrogen bonds between a carbonyl oxygen and an amide hydrogen four residues down a chain (n+4).
- Side chains of the amino acids point away from the helix core
- Important in keratin
Beta-Pleated Sheet
- Can be parallel or antiparallel
- Peptide chains lie alongside one another, forming rows held together by intramolecular hydrogen bonds between carbonyl oxygen atoms on one chain and amide hydrogen atoms in an adjacent chain
- Assume a pleated shape to accomodate as many hydrogen bonds as possible
- R groups of amino residues point above and below the plane of the sheet (alternate)
Secondary Structure: Proline (in alpha helices)
Disulfide Bonds
- Part of teritiary structure
- When two cysteine moelcules become oxidized to from cystine
- Create loops in protein chain (why they determine how curly hair is)
Tertiary Structure Formation
- Secondary structures probably form first.
- Then, hydrophobic interactions and hydrogen bonds cause the protein to “collapse” into its proper three-dimensional structure.
- Adopts intermediate states called molten globules along the way
Solvation Layer and Entropy
- When a hydrophobic side chain is placed in aqueous solution, the water molecules in the solvation layer cannot form hydrogen bonds with the side chain. This forces the nearby water molecules to rearrange themselves into specific arrangements to maximize hydrogen bonding. Negative change in entropy. Nonspontaneous. Unfavorable.
- Putting hydrophilic residues on the exterior of the protein allows nearby water molecules more latitude in their positioning. Increase in entropy. Spontaneous.
Quarternary Structure
- Cooperativity (allosteric effects): One subunit can undergo conformational or structural changes, which either enhance of reduce the activity of the oterh subunits.
Conjugated Proteins
- Proteins covalently attached to prosthetic groups (organic molecules or metal ions)
- Lipoproteins, glycoproteins, nucleoproteins
- Determine function of respective protein
- Example: Hemoglobin has a prosthetic group called heme. It is inactive without the heme group.
- Prosthetic groups can also direct the protein to be delived to a certain location.
Denaturation
- Heat: Average kinetic energy increases; extra energy can be enough to overcome the hydrophobic interaction that hold a protein together
- Urea: Denatures proteins by directly interfering with tertiary and quarternary structures by breaking disulfide bridges. Can also overcome the hydrogen bonds of seconary structure.
- s
Finding how many distinct peptides can be formed from x amount of amino acids:
Tripeptides with 3 amino acids: 3 x 2 x 1
