7 and 8A Amino acids and Protein Secondary Structure Flashcards
How many amino acids do peptides have?
50 or less
How many amino acids do polypeptides and proteins have?
Greater than 50
What are zwitterions?
Molecules that have a positive and negative charge, and no net charge at pH 7
What type of side chains do acidic Amino Acids have?
Have a side chain with a carboxylate group that ionizes at physiological pH
How are amino acids characterized?
Characterized by their ability to interact with water
The only non-chiral standard amino acid is?
glycine
What is the Isoelectric Point (pI)
When amino acids have no net charge ue to ionization of both groups
Peptide bonds are formed by what type of reaction?
Amide linkages formed by nucleophilic acyl substitution (dehydration reaction)
How are Shiff bases formed?
By imine products of primary amine groups interacting with carbonyl groups, eg. in amino acid biosynthesis reactions.
What is a Schiff base?
Referred to as aldimines, are intermediates formed by the reaction of an amino group with an aldehyde group
How many standard amino acids are there?
20
How are amino acids amphoteric?
They have a carboxyl group which can act as an acid and an amino group that can act as a base
What are nonpolar amino acids (structurally)?
Contain hydrocarbon groups with no charge
What are polar amino acids?
They have functional groups that can easily interact with water through hydrogen bonding.
The functional group is either a hydroxyl group (serine, threonine and tyrosine etc.), thiol group (cysteine) or an amide group (asparigine, glutamine etc.)
What is the three and one letter abbreviation of asparigine?
ASN
N
What is the three and one letter abbreviation of aspartic acid?
Asp
D
What is the one letter abbreviation for arginine?
R
What is the three letter abbreviation for glutamine?
Gln
Q
What is the three letter abbreviation for isoleucine?
Ile
What is the three letter abbreviation for tryptophan?
Trp
W
What are the amino acids involved as metabolic intermediates in the urea cycle?
Arginine
Ornithine
Citrulline
Which amino acids can be phosphorylated?
Serine
Threonine
Tyrosine
True or false, amino acids can exist as stereoisomers. Why?
True, because the alpha-carbon is attached to four different groups, they can exist as stereoisomers.
(except glycine, which is the only nonchiral standard amino acid)
What are D and L used to signify with amino acids?
Used to indicate the similarity of the arrangement of atoms around the molecules assymmetric carbon to the asymmetric carbon of the glyceraldehyde isomers (reference compound for optical isomers)
Only L amino acids are used in translation, D can be used after post-translational modifications
What causes a more complex titration curve with amino acids?
More ionizable side chains cause a more complex titration curve, as it proceeds stepwise as each group is deprotonated by NaOH
What are peptide bonds? How are they formed (what type of reaction?)
Amide linkages formed by nucleophilic acyl substitution (a dehydration reaction).
Where is the free amino group on the peptide chain? Where is the carboxyl group found? What terminal end for each?
The N-terminal contains the free amino group, the C-terminal has a free carboxyl group.
Is the peptide bond rigid and flat? Or soft and curvy? Why?
Rigid and flat (found by Linus Pauling)
The C-N bonds between two amino acids are shorter than other C-N bonds. This gives them partial double bond characteristics (they are resonance hybrids)
How many peptide bonds in a polypeptide cannot rotate freely due to their short double-bond-like nature?
One third of the bonds in a polypeptide backbone cannot rotate freely.
This limits the number of conformational possibilities
What happens when cysteine is oxidized?
A reversible disulphide bridge between another oxidized cysteine
What does a cysteine-cysteine disulfide double bridge do for the polypeptide?
Helps stabilize it
When do Shiff base formations occur most? (most importantly)
Amino acid biosynthesis reactions
