02.03 - Review of Proteins Flashcards
Enumerate the five components of the structure of an amino acid.
Central carbon (alpha-carbon)
Amino group
Carboxyl group
Side chain
Which of the following is not true about proteins?
a. It is a linear polymer of amino acids linked by glycosidic bonds.
b. It is a building block of collagen, a connective tissue framework of our body.
c. It can help regulate cellular metabolism.
d. It is the subject of proteomics.
a. It is a linear polymer of amino acids linked by glycosidic bonds.
Enumerate the five amino acids with an aliphatic side chain.
Glycine (G) Alanine (A) Valine (V) Leucine (L) Isoleucine (I)
Name the three amino acids with a hydroxyl group.
Serine (S)
Threonine (T)
Tyrosine (Y)
Name the two amino acids with a sulfur-containing group.
Methionine (M)
Cysteine (C)
What are the proteins that have an aromatic side chain?
Histidine (H) Phenylalanine (F) Tyrosine (Y) Trytophan (W) Proline (P)
What are the three amino acids that contain a basic group in their side chains?
Arginine (R)
Lysine (K)
Histidine (H)
What are the two amino acids with acidic groups and what are their respective amides?
Aspartic acid (D) - asparagine (N) Glumatic acid (E) - glumatine (Q)
According to Lippincott, what are the amino acids with non-polar side chains?
Glycine (G) Alanine (A) Valine (V) Leucine (L) Isoleucine (I) Phenylalanine (F) Tryptophan (W) Methionine (M) Proline (P)
What are the amino acids with uncharged polar side chains?
Serine (S) Threonine (S) Tyrosine (Y) Asparagine (N) Glutamine (Q) Cysteine (C)
In the classification made by Lippincott, what are the amino acids with acidic side chains?
Aspartate (D)
Glutamate (E)
What are the basic amino acids according to Lippincott?
Arginine (R)
Lysine (K)
Histidine (H)
Which of the following does not describe glycine?
a. It has the smallest side chain.
b. It is used in the first step of heme synthesis, where it combines with succinyl CoA to form aminolevulinic acid (ALA).
c. It often occurs where peptides bend sharply.
d. It carries nitrogen from peripheral tissues to the liver.
d. It carries nitrogen from peripheral tissues to the liver.
Degraded nitrogen in the form of ammonia is converted to urea in the liver. What amino acid is responsible for the transport of degraded nitrogen to the liver?
Alanine (A)
What are the three aliphatic amino acids that accumulate in the maple syrup urine disease?
Valine (V)
Leucine (L)
Isoleucine (I)
Which of the following statements regarding phenylketonuria is false?
a. It is caused by an overproduction of phenylalanine hydroxylase.
b. It accumulates phenyllactate, phenylacetate, and phenylpyruvate in the body.
c. It is characterised by the inability of the body to convert phenylalanine to tyrosine.
d. Phenylketonurics lack the necessary amount of norepinephrine and epinephrine.
a. It is caused by an overproduction of phenylalanine hydroxyls. (PKU is a deficiency of phenylalanine hydroxylase)
Which of the following is incorrectly paired?
a. Brain damage and mental retardation in PKU is caused by the absence of dopamine, norepinephrine and epinephrine.
b. Blue eyes, blond hair, and fair skin in PKU is caused by the overproduction of melanin.
c. The musty door of urine and sweat in PKU is due to the accumulation of phenyl acetic acid.
d. Thyroid hormone in PKU is insufficient due to the absence of its thyroxine precursor.
b. Blue eyes, blond hair, and fair skin in PKU is caused by the overproduction of melanin. (These phenotypic characteristics are caused by the lack of melanin).
What amino acid is the precursor of tyrosine?
Phenylalanine (F)
Enumerate the phenyalanine derivatives (in order).
Phenylalanine (P) Tyrosine (Y) L-Dopa Dopamine Norepinephrine Epinephrine
Thyroxine (from Tyrosine)
Melanin
What amino acid has the largest side chain?
Tryptophan (W)
What are the important tryptophan derivatives?
Melatonin
Serotonin
Niacin
It is a tryptophan derivative that is associated with the biological clock
a. Serotonin
b. Niacin
c. Melanin
d. Melatonin
d. Melatonin
A certain individual lacks tryptophan in his diet. Which of the following is most likely to occur?
a. Depression
b. Pellagra
c. Diarrhea
d. All of the above
d. All of the above (Note that diarrhera is a symptom of pellagra, which is a Vitamin B3 deficiency).
What amino acid is a precursor for homocysteine, which is present in rare myocardial infarction cases?
Methionine
Which of the following statements does not pertain to proline?
a. It is an imino acid.
b. It is the smallest amino acid.
c. It contributes to the fibrous structure of collagen.
d. It interrupts alpha-helices in globular proteins.
b. It is the smallest amino acid.
Which statement does not describe serine, threonine and tyrosine?
a. Nonpolar hydroxyl groups exist in their side chains.
b. The hydroxyl group present in these amino acids can serve as an attachment site for phosphate groups.
c. They have uncharged but polar side chains.
d. None of the above.
a. Nonpolar hydroxyl groups exist in their side chains. (Terminal -OH groups in the three amino acids are polar).
What amino acid is a immediate precursor for thyroxine and melanin?
Tyrosine
This amino acid is often linked to carbohydrate groups in glycoproteins and is also usually a part of the phosphorylation site of enzyme modification.
Serine
These two amino acids are sites of O-linked glycosylation in the Golgi apparatus.
a. Tyrosine and serine
b. Serine and threonine
c. Threonine and tyrosine
d. Asparagine and glutamine
b. Serine and threonine
What amino acid contains a sulfhydryl group and is often connect by covalent disulfide bonds?
Cysteine
Two cysteines linked with a disulfide bond is called a:
Cystine
This amino acid is the site for N-linked glycosylation in the endoplasmic reticulum.
Asparagine (N)
When deaminated, this amino acid results in the formation of ammonia.
Glutamine (Q)
True or False: Glutamine is also a major carrier of nitrogen to the liver from peripheral tissues.
True
What amino acid is the precursor of gamma-aminobutyric acid? (GABA) and glutathione?
Glumatate (E)
Which statement about histidine is false?
a. It is a weak base and is positively charged at physiological pH.
b. It is a precursor of histamine, which is involved in the inflammatory response.
c. It is used in the diagnosis of folic acid deficiency.
d. After ingestion of large doses of histidine, individuals deficient in folic acid excrete increased amounts of FlGlu in urine.
a. It is a weak base and is positively charged at physiological pH. (It has no charge at physiological pH!)
What amino acid is the precursor of creatinine, urea and nitric oxide?
Arginine (R)
Which of the following statements is incorrect?
a. Selenocysteine is found in peroxidases and reductases.
b. It is analogous to cysteine, only with a selenium atom instead of sulfur.
c. Selenocysteine-producing cells have a specific codon for selenocysteine.
d. None of the above.
c. Selenocysteine-producing cells have a specific codon for selenocysteine.
All amino acids are chiral except for:
Glycine
What conformation is common in amino acids? In carbohydrates?
L-conformations in amino acids
D-conformation in carbohydrates
Enumerate all the essential amino acids.
Phenyalanine (F) Valine (V) Tryptophan (W) Threonine (T) Isoleucine (I) Methionine (M) Histidine (H) Arginine (R) Leucine (L) Lysine (K)
Which of the following statements about peptide bond formation is incorrect?
a. It attaches the alpha-amino group of one amino acid to the alpha-carboxyl group of another.
b. It is very stable but can be disrupted by hydrolysis through prolonged exposure to a strong acid or base.
c. It results in the primary structure of a protein.
d. It results from the addition of water to the two participating amino acids.
d. It results from the addition of water to the two participating amino acids.
Which of the following statement about the characteristics of peptide bonds is incorrect?
a. It has a partial double-bond character due to the even distribution of electrons.
b. It is planar and rotation can easily occur.
c. Usually, the side chains are arranged in opposite directions (trans configuration)
d. It is uncharged but polar.
b. It is planar and rotation can easily occur.
(It is rigid and planar).
Which of the following statements about alpha helices is incorrect?
a. It is usually right-handed.
b. Side chains extend outward.
c. Hydrogen bonds are perpendicular to the spiral.
d. It may be disrupted by proline and large side chains.
c. Hydrogen bonds are perpendicular to the spiral. (H-bonds are parallel to the spiral.)
Which of the following statements about beta sheets is incorrect?
a. Surfaces appear flat and pleated.
b. One or more polypeptide chains are parallel to each other.
c. Intrachain H-bonds may occur.
d. None of the above
d. None of the above
What are the two main mechanisms of proteolysis?
Enzymatic or proteolytic degradation
Exposure to strong acid or base at 110 C for 24 h
What secondary structure reverses the direction of the polypeptide chain to form anti-parallel beta sheets?
Beta bends/reverse turns/beta turns
Which of the following statements about secondary structures is true?
a. Greek key is a non-repetitive loop and coil structure.
b. Beta bends are usually composed of proline and glycine.
c. Non-repetitive loop and coil structures are absent in globular proteins.
d. All of the above.
b. Beta bends are usually composed of proline and glycine.
Which of the following statements about tertiary structure is correct?
a. Globular proteins have an axial ratio of 10.
b. Hydrophobic chains are buried in the exterior, away from water.
c. Tertiary structures can only be stabilised by hydrophobic interactions.
d. None of the above.
d. None of the above.
It is the fundamental functional and three-dimensional structural unit of a polypeptide.
Domain
Quarternary structures are held together mainly by _______ bonds like hydrogen bonds, ionic bonds and hydrophobic interactions.
Non-covalent
What structures are affected by protein denaturation?
Secondary, tertiary and quarternary
Which of the following statements about protein folding is incorrect?
a. It occurs in a modular, step-wise fashion.
b. Hydrophobic regions settle in the exterior, away from the aqueous environment.
c. Chaperones may facilitate protein folding.
d. None of the above.
b. Hydrophobic regions settle in the exterior, away from the aqueous environment.
It is a protein folding chaperone that binds to hydrophobic amino acids and shields them from the solvent.
Hsp70
It is a chaperone that provides sheltered environment where polypeptide can fold until all hydrophobic groups are in the interior, preventing aggregation.
Hsp60 (chaperonins)
It facilitates the formation of disulfide bonds that stabilises the protein’s native conformation.
Protein disulfide isomerase
It catalyses the trans to cis formation in proline.
Proline cis-trans isomerase
What is true about in vitro and in vivo protein folding?
a. In vivo studies are more common that in vitro studies.
b. In vivo studies, a refolding buffer is used.
c. Co-translational folding occurs in vivo, while in vitro, the protein has to be fully synthesised before refolding.
d. In vitro folding occurs in the crowded macromolecular environment.
c. Co-translational folding occurs in vivo, while in vitro, the protein has to be fully synthesised before refolding.
Alzheimer’s disease is characterised by the aggregation of the protein __________.
Beta-amyloid
In prion diseases, normal PrPc are rich in _______ and pathogenic PrPsc are rich in _______.
Alpha-helices
Beta-sheets
