Amino Acids Structure, Name Function

Which amino acids are aromatic?

"Smelly lunch=Cheese and turkey sandwich with a Diet Coke" aromatic="smelly" Tyrosine (Y) "cheese" Tryptophan (W) "turkey" Phenylaline (F) "why phenylketonurics can't drink diet coke"

Serine

-OH in side chain allows it to make temporary bonds -OH also means it has the ability to phosphorylate

A region rich in which of the following amino acid residues is most likely to be found buried in the interior of a globular protein? A. Aspartic acid B. Lysine C. Threonine D. Isoleucine

A. Aspartic acid (polar) B. Lysine (polar) C. Threonine (polar) D. Isoleucine (nonpolar) Answer is D.

A

Alanine

Asparagine-Asn-N

Amide amino acid = polar Able to act as

Glutamine-Glu-Q

Amide amino acid. "Glutton" has one more CH2 than asparagine.

Phenylalanine

Aromatic R groups

Tryptophan

Aromatic R groups

Tyrosine

Aromatic R groups

Tyrosine

Aromatic. Has -OH so can participate in reversible binding and phosphorylation. Polar -OH competing with aromatic ring, still nonpolar as a whole.

Which amino acids are amidic?

Asparagine (ASN) N Glutamine (GLN) Q Their 3-letter abbreviations are the only ones ending with -n. Their one-letter abbreviations are not obvious. Q for Glutamine looks like G.

Cysteine

Barely polar - some would say nonpolar. Difference in electronegativity is 0.58. Not strong enough to want to interact with water so it is hydrophobic. One of two amino acids that has S in an R group. Has ability to oxidize the S on two different cysteines and form a covalent bond between them (disulphide bridge). This is the only covalent bond seen in the tertiary and quaternary structure of polypeptide chains. This helps stabilize the overall structure of proteins and enzymes.

Forms disulphide bridges

Cysteine

Which amino acid is involved in S-S bonds?

Cysteine (but not methionine, the other S-containing amino acid)

Aromatic Amino Acids

Diet Coke (Phenylalanine) with a Cheese (Tyrosine) and Turkey (Tryptophan) sandwich...smells (aromatic) good!

Which amino acids have aliphatic side chains?

GAVLI Glycine Alanine Valine Leucine Isoleucine

Which AA have aliphatic side chains?

GAVLI Glycine (Gly, G) R= H Alanine (Ala, A) R= CH₃ Valine (Val, V) R= CHCH₃CH₃ Leucine (Leu, L) R=CH₂CHCH₃CH₃ Isoleucine (Ile, I) R=CHCH₃CH₂CH₃

Which amino acids are negatively charged?

Glutamate ()

What amino acids can undergo deamidation? What are the products?

Glutamine (Q), Asparagine (N), kcat Deamidation is a chemical reaction in which an amide functional group in the side chain of the amino acids asparagine or glutamine is removed or converted to another functional group. Typically, asparagine is converted to aspartic acid or isoaspartic acid. Glutamine is converted to glutamic acid or pyroglutamic acid (5-oxoproline). In a protein or peptide, these reactions are important because they may alter its structure, stability or function and may lead to protein degradation. In the deamidation of an asparagine residue under physiological conditions, the side chain is attacked by the nitrogen atom of the following peptide group (in black at top right of Figure), forming an asymmetric succinimide intermediate (in red). The asymmetry of the intermediate results in two products of its hydrolysis, either aspartic acid (in black at left) or isoaspartic acid, which is a beta amino acid (in green at bottom right). The deamidation of a glutamine residue may proceed via the same mechanism but at a much slower rate since formation of the six-member-ring glutarimide intermediate is less favoured than the succinimide intermediate for asparagine.

Which of the following amino acids is aliphatic?

Glycine Alanine Valine Leucine Isoleucine

Which of these is achiral? A. Proline B. Valine C. Isoleucine D. Glycine

Glycine has a side chain with only one hydrogen. It's the only achiral amino acid. So glycine is special in that regard.

Threonine

Has 3 groups on its side chain. Looks like a valine but one methyl is replaced with an alcohol. -OH makes it ideal for temporary reversible binding -OH also means it has the ability to phosphorylate Second chiral carbon in its side chain

Which Basic Amino Acid is Cyclic?

Histidine (because history is cyclic)

Aspartate

Negatively charged R groups

Glutamate

Negatively charged R groups

Alanine

Nonpolar, aliphatic R Groups

Glycine

Nonpolar, aliphatic R Groups

Isoleucine

Nonpolar, aliphatic R Groups

Leucine

Nonpolar, aliphatic R Groups

Methionine

Nonpolar, aliphatic R Groups

Proline

Nonpolar, aliphatic R Groups

Valine

Nonpolar, aliphatic R Groups

Asparagine

Polar, uncharged R groups

Cysteine

Polar, uncharged R groups

Glutamine

Polar, uncharged R groups

Serine

Polar, uncharged R groups

Threonine

Polar, uncharged R groups

Arginine

Positively charged R groups

Histidine

Positively charged R groups

Lysine

Positively charged R groups

A particular oncogene product has an unusually high number of proline residues. These residues: (A) Aid in the formation of alpha helices (B) Are more likely to be found throughout beta-pleated sheets (C) Aid only in the formation of antiparallel beta-pleated sheets (D) Are more likely to be found in turn regions of the protein

Proline is special because its side chain connects to its own amino in the amino acid part. It has this weird little looped structure. So one is so tiny and proline has this weird, rigid self attachment structure. As a result, neither glycine or proline tends to play nice when it comes to secondary structure (alpha and beta) particularly proline. Proline is the combo breaker on your alpha and beta structures. A turn region in the protein is a loose, unstructured region where the amino acids are not locked into an alpha or beta structure. If proline is going to show up, it's going to be like it's breaking the alpha and beta sequence into a more unstructured, turn region. So the right answer here is (D).

Which AA have an -OH and can thus be phosphorylated?

STY Serine Threonine (T) Tyrosine (Y)

Which amino acids can form a bond to phosphate?

Serine, Threonine, Tyrosine

Which amino acids have an OH group?

Serine, Threonine, Tyrosine

Basic Amino Acids

The His(tory of) Arg(entine) is a Lie(Lysine)

Which amino acids are capable of forming covalent bonds?

These 7 amino acids are able to donate or accept protons to facilitate reactions as well as to form ionic bonds. Table 3.1 gives equilibria and typical pKa values for ionization of the side chains of tyrosine, cysteine, arginine, lysine, histidine, and aspartic and glutamic acids in proteins.

Which amino acids have ionizable side chains?

These 7 amino acids are able to donate or accept protons to facilitate reactions as well as to form ionic bonds. Table 3.1 gives equilibria and typical pKa values for ionization of the side chains of tyrosine, cysteine, arginine, lysine, histidine, and aspartic and glutamic acids in proteins.

What are the pka values of N and C ends of amino acids and what are pka values of ionizable side chains?

These 7 amino acids are able to donate or accept protons to facilitate reactions as well as to form ionic bonds. Table 3.1 gives equilibria and typical pKa values for ionization of the side chains of tyrosine, cysteine, arginine, lysine, histidine, and aspartic and glutamic acids in proteins. N=10 C=2 Neutral when ionized: D=4 Y=11 C=8 E=4 Positive when ionized: H=6 R=13 K=11

Which amino acid has symbol T?

Threonine (T) Not Tryptophan (W) or Tyrosine (Y)