Lecture 3 - Amino Acids Flashcards
What is the orientation of biological amino acids?
L-amino acids only. D-groups exist, but not biologically
Name the 9 hydrophobic amino acids (mostly found on interior of cell or protein)
Study Hint: Broken off into 4 similar rows
GAP FILM WV
- (Glycine - Gly - G), 2. (Alanine - Ala - A)
- (Proline - Pro - P)
- (Valine - Val - V), 5. (Leucine - Leu - L), 6. (Isoleucine - Ile - I)
7. (Methionine - Met - M) - (Phenylalanine - Phe - F), 9. (Tryptophan - Trp - W)
Name the 11 Polar Amino Acids:
Study Tip: Try to memorize by row
- (Serine - Ser - S), 2. (Threonine - Thr - T),
- (Tyrosine - Tyr -Y), 4. (Asparagine - Asn - N),
- (Glutamine, Gln, Q), 6. (Cysteine, Cys, C)
- (Aspartate - Asp - D), 8. (Glutamate - Glu - E)
- (Lysine - Lys - K), 10. (Arginine - Arg - R),
- (Histidine - His - H)
Go through that other biochem’s 3-letter code Amino Quiz, and 1-Letter Code Amino Quiz.
Do it.
Name the 10 Essential Amino Acids
PVT TIM HALL (Doesn’t follow 1-letter codes)
Phenyalanine, Valine, Tryptophan
Threonine, Isoleucine, Methionine
Histidine, Arginine, Leucine, Lysine
- What is the relationship comparison between pKa and the charge of the amino acid?
- Name what’s considered the most neutrally charged AA
- Name the two amino acids that commonly have negative charges (low pKa).
- Name the two amino acids that commonly have positive (high pKa) charges).
- The lower the pKa, the lower the affinity the AA has for protons (as in more basic. So pKa “Might” be the opposite of pH in this case…don’t quote me on that)
- Histidine - pKa = 6, often called “half-protonated”
- Aspartate, Glutamate (at pKa: 4)
- Lysine and Arginine (pKa: 10, and 12 respectively)
Give some characteristics about the amino acid: Glycine
Smallest Amino Acid, Nonessential, cheap to make, However, collagen proteins are made up of 33% glycine
Give some characteristics about the amino acid, Proline
Technically, since this AA forms a ring onto itself, proline is regarded as an Imino Acid. Proline is found solely on the end of the alpha helices structure, but is also found in collagen as a GP? Pattern. So glycine-proline-something. Glycine-Proline-Something.
Name the 3 BCAAs and describe their significance
There’s three BCAAs: Valine, Leucine, and Isoleucine. These are vital because of their length/size. These will maintain the structural interior of proteins. The first step of folding proteins is the hydrophobic collapse, which is kind of important. Misfolding can cause conformational diseases such as Parkinson’s, Alzheimer’s and others.
Describe the significance of methionine
Methionine is regarded as Very essential. The intermediate group is SAM (not sure what that stands for). Neurotransmitters rely on this.
Describe some characteristics about the Amino Acid, Valine
Valine is an essential amino acid, one of the BCAAs. Muscle tissues are comprised of this, as well as mitochondrial function.
Why are the aromatic amino acid structures significant
Aromatic structures such as phenylalanine allow protein detection/absorption to occur with protein detection.
Tryptophan - The inclusion of tryptophan in a protein usually indicates a deep, core functionality. These can’t really be removed or mutated out of the protein without severe consequences. Like Phenylalanine, this is good for absorbance, but unlike phe, this also fluoresces.
What do the amino acids Serine, Threonine, And Tyrosine have in common, and where are they often found?
These top 3 aminos are generally grouped together. Not just because of their polarity, but more because of the attached hydroxyl group attached to the end of the chains.
These amino acids are found in the peripheral ends of proteins due to their polar, hydrophilic properties. The ends are sites for reversible phosphorylation, which hydroxys are quite good for. This is a nice fast way to change the function (usually these take the form of kinases).
Describe some characteristics of the amino acid, Glutamine
Glutamine is thought to be involved in cell repair, as well as breaking down amines into urea, which can be released through urination.
What do the amino acids Cysteine and Methionine have in common and where are they generally found.
Both have that Sulfur chemical in their structures.
Cysteine isn’t really essential because it can be constructed from methionine.
Disulfide bonds are only found in extracellular proteins (Such as cysteine), never intracellular, unless you’re sick. This is seen in insulin as an example.
Note: Tyrosine isn’t considered essential for similar reasons
