Practice Questions - Week 3 - Amino acids & Peptides Flashcards
Consider the two peptides
1) Ser - Glu - Gly - His - Ala
2) Gly - His - Ala - Glu - Ser
Do they differ in composition? (yes/no)
No
(These peptides differ in sequence, but not in composition)
Identify the polar amino acids in the following amino acid sequence
Val - Met - Ser - Ile - Phe - Arg - Cys - Tyr - Leu
Val
Met
Ser
Ile
Phe
Arg
Cys
Tyr
Leu
Ser, Arg, Cys, Tyr, Leu
The side chains of Ser, Arg, Cys and Tyr have polar groups that can establish H-bonds. Tyr has a polar group (-OH), an aromatic ring and hydrophobic properties, so it can also be referred to as aromatic, hydrophobic or as amphipathic.
D- amino acids differ from L-amino acids due to differences around which atom?
Alpha carbon
(L and D- amino acids differ in stereochemistry around the alpha carbon)
Peptides that contain D-amino acids are found in bacterial cell walls and in some antibiotics. (True/False)
True
Choose the correct answers for the following statement: Amino acids share communal features, such as?
a) an amino group, which is normally protonated and is responsible for the basic properties of amino acids
b) an amino group, which is normally protonated and is responsible for the acidic properties of amino acids
c) a carboxylic group, which is a proton donor and is responsible for the basic properties of amino acids
d) being zwitterions, as they may contain positive and negative charges.
a, d
Are amino acids other than the usual 20 amino acids found in proteins? (yes/no)
Yes
(In addition to the 20 amino acids in the universal genetic code, there are amino acids that are obtained from post translational modifications (e.g. phospho-Tyrosine), and others that are encoded in a special way (e.g. Seleno-cysteine))
Match the following amino acid with the feature of the side chain
Hydroxyl group
Sulphur atom
Amino group
Amide group
Lysine
Serine
Cysteine
Glutamine
Glutamine - Amide group
Lysine - amino group
Cysteine - Sulfur atom
Serine - Hydroxyl group
Which of the following amino acid is more negative at pH = 7.0?
a) Histidine
b) Glutamate/glutamic acid
c) Isoleucine
d) Serine
b)
Which amino acid has a positive charge when the R group gains a proton?
a) Glutamate/glutamic acid
b) Histidine
c) Tyrosine
d) Glycine
b)
(The side chain of histidine becomes protonated (positively charged) at around pH = 6.
Glycine and Tyrosine side chains are not ionisable. The side chain of glutamate has a carboxylic group (COOH), which loses a proton and becomes negatively-charged)
Which is a correct pair of abbreviations for an amino acid?
a) Gln / N
b) Tyr / T
c) Asn / N
d) Phe / P
c)
Which of the following is a cyclic amino acid?
a) Alanine
b) Valine
c) Proline
d) Tyrosine
e) Cysteine
c)
Which of the following properties are determined by the R group of an amino acid?
a) hydrophilic or hydrophobic
b) polar or nonpolar
c) charged or uncharged
d) an acid or a base
a, b, c, d
(All of the properties in the above options are determined by the R group (side chain) of an amino acid)
Choose the correct option(s) about the peptide bond
a) is planar
b) can be written as a resonance hybrid
c) is the basis of protein structure
d) links amino acids to form a polypeptide chain
e) is an amide bond
a, b, c, d, e (all answers are correct)
Choose the correct statements about the peptide Ser-Gly-Tyr-Ala-Leu
a) It has 4 peptide bonds
b) It has 5 peptide bonds
c) It is positively-charged at pH 7
d) Its sequence can be written as SGYAL
a) d)
(This peptide has 5 amino acid residues, which are linked by 4 peptide bonds. None of the side chains of these amino acids is charged, this peptide has one positive charge from the N-terminus (NH3+) and one negative charge from the C-terminus (COO-); therefore this peptide is neutral at pH 7.
Using one-letter code, this peptide can be written as SGYAL)
Which of the following options is correct with respect to the amino acid composition of proteins?
a) Proteins contain at least one each of the 20 different standard amino acids
b) The amino acid sequence determines the three-dimensional structure of the protein
c) Proteins with the same molecular weight have the same amino acid composition.
d) The amino acid sequence has no impact in the function and structure of proteins
b)
(Proteins have some, but not necessarily all the 20 standard amino acids.
Proteins with the same molecular weight can be composed of distinct combination of amino acids.
The amino acid sequence determines intramolecular bonds, which are important for the 3D structure and function)
List all the amino acids with nonpolar aliphatic R groups
List all the amino acids with aromatic R groups
List all the amino acids with polar, uncharged R groups
List all the amino acids with positively charged R groups
List all the amino acids with negatively charged R groups
In this image opposite, this shows the Structure of the 20 common __________. The structural formulas show the state of ionisation that is predominant at pH _______? The shaded regions are the __________(___________)?
Amino acids
7.0
R groups (i.e. side chains)
Refer to the image opposite for the properties and conventions associated with the common amino acids found in proteins.
In this file you find the structure of the 20 common amino acids, and a table with pKa values and other properties of these amino acids. We will practise how to calculate the charge of amino acids and of peptides/proteins during the tutorial. The information in this file is helpful for these calculations. Do you know how to do these calculation?
Yes
