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)
