BIO285 Final Content Exam Study Set
You are studying a protein with a known structure. You decide to mutate the protein and
then study how the structure changes due to the mutation made. You want to determine
if overall surface topology (the shape of the surface of your protein) was affected by the
mutation - which type of protein modeling would be most effective to make this
determination? - ANSWER spacefill model
NH3+ - ANSWER ammonia would be found outside the folded protein
N-terminus - ANSWER the first part of the protein that exits the ribosome during protein
biosynthesis.
During protein synthesis, the covalent bond between amino acids is formed by the
process of - ANSWER condensation, also known as dehydration
You are studying a protein with a known structure. You decide to mutate the protein and
then study how the structure changes due to the mutation made. If you want to
determine how secondary structure specifically changes from the wildtype (unmated)
protein as compared to the mutated protein, which type of modeling would you use? -
ANSWER ribbon model
What is the difference between a domain and a subunit? - ANSWER Domain =
independently folded section of a single polypeptide
Subunit = a single polypeptide in a protein composed of multiple polypeptides, Ex:
Antibody
In a protein, a mutation occurs and results in phenylalanine being replaced by an
alanine. This would... - ANSWER Always change the primary structure of a protein,
sometimes affect tertiary structure and function.
In a structure where a carbon is bound to an uncharged amino group, due to differences
in electronegativity between atoms, the nitrogen is... - ANSWER partially negatively
charged
C-terminus - ANSWER the end of a polypeptide or protein that has a free carboxyl group
peptide bond - ANSWER The chemical bond that forms between the carboxyl group of
one amino acid and the amino group of another amino acid
an R group that could make covalent bonds with other R groups in tertiary and/or
quaternary folding - ANSWER SH-CH2-C-H
In a structure where a carbon is bound to an uncharged amino group, due to differences
in electronegativity between atoms, the nitrogen can form... - ANSWER Van der Waals
,interactions
an R group that will make ionic bonds with other R groups in tertiary and/or quaternary
folding: - ANSWER NH3-CH2-CH2-CH2-CH2-C
"Proteins can never be chemically modified in more than one way at the same time." -
ANSWER false
"Allostery is defined as the inhibition of enzymes by binding of molecules in the
enzyme's active site." - ANSWER False
Allosteric - ANSWER is the regulation of an enzyme by binding an effector molecule at a
site other than the enzyme's active site.
If you agree that the following statement is a way that enzymes increase rates of
chemical reactions:
Changing the free energy of the reactants in the reaction - ANSWER no
If you agree that the following statement is a way that enzymes increase rates of
chemical reactions:
Raising the activation energy - ANSWER no
If you agree that the following statement is a way that enzymes increase rates of
chemical reactions:
Temporarily increasing the temperature surrounding the reaction - ANSWER no
If you agree that the following statement is a way that enzymes increase rates of
chemical reactions:
Forming a tight binding interaction with the product - ANSWER no
If you agree that the following statement is a way that enzymes increase rates of
chemical reactions:
Stabilizing the transition state - ANSWER yes
If you agree that the following statement is a way that enzymes increase rates of
chemical reactions:
initially forming specific non-covalent bonds with the substrate - ANSWER yes
If you agree that the following statement is a way that enzymes increase rates of
chemical reactions:
Changing the Gibbs free energy of the reaction - ANSWER no
If a protein completely unfolds, would you expect its solubility in water to change? -
ANSWER yes
, Is the Kd higher for enzyme-substrate or enzyme-product? - ANSWER enzyme-product
In the protein and ligand shown below, the threonine is replaced by an arginine due to
mutation. Based on the chemistry of arginine, would you expect that it could still make
interactions with the cAMP nitrogenous base if situated correctly in the binding pocket
of the protein? - ANSWER yes
The reported Kd of a protein-ligand interaction at binding equilibrium is equal to the
concentration of the - ANSWER Ligand when Ligand (L)Unbound protein (P) and
Complex (C) (protein bound to ligand)Protein (P)Protein (P) and Ligand (L)Complex (C)
(Protein bound to Ligand) are at equal concentrations at equilibrium.
Backbone Model - ANSWER Shows only path of polypeptide backbone, doesn't show R
groups
Ribbon Model - ANSWER Only shows path of polypeptide backbone, doesn't show R
groups
Wireframe vs Ball and Stick Model - ANSWER This shows every atom/covalent bond in
the protein including backbone and R groups ▪
- Wireframe just shows sticks for covalent bonds without balls for atoms
- Ball and stick shows balls for atoms and sticks for covalent bonds between atoms
Space-fill model - ANSWER This shows all atoms as balls with van der waal radii (the
space that the entire atom takes up including electron cloud)
-This type of model is great for seeing what the protein actually looks like to other
molecules in the cell
Primary Structure - ANSWER is defined as the sequence of amino acids in the protein
Secondary Structure - ANSWER consists of particular polypeptide folds that are
common to many proteins
Tertiary Structure - ANSWER defined as the overall fold of a single polypeptide
Quaternary Structure - ANSWER is defined as the overall structure of proteins that are
made up of multiple polypeptides
You are studying a protein with a known structure. You decide to mutate the protein and
then study how the structure changes due to the mutation made. You want to determine
if overall surface topology (the shape of the surface of your protein) was affected by the
mutation - which type of protein modeling would be most effective to make this
determination? - ANSWER spacefill model
NH3+ - ANSWER ammonia would be found outside the folded protein
N-terminus - ANSWER the first part of the protein that exits the ribosome during protein
biosynthesis.
During protein synthesis, the covalent bond between amino acids is formed by the
process of - ANSWER condensation, also known as dehydration
You are studying a protein with a known structure. You decide to mutate the protein and
then study how the structure changes due to the mutation made. If you want to
determine how secondary structure specifically changes from the wildtype (unmated)
protein as compared to the mutated protein, which type of modeling would you use? -
ANSWER ribbon model
What is the difference between a domain and a subunit? - ANSWER Domain =
independently folded section of a single polypeptide
Subunit = a single polypeptide in a protein composed of multiple polypeptides, Ex:
Antibody
In a protein, a mutation occurs and results in phenylalanine being replaced by an
alanine. This would... - ANSWER Always change the primary structure of a protein,
sometimes affect tertiary structure and function.
In a structure where a carbon is bound to an uncharged amino group, due to differences
in electronegativity between atoms, the nitrogen is... - ANSWER partially negatively
charged
C-terminus - ANSWER the end of a polypeptide or protein that has a free carboxyl group
peptide bond - ANSWER The chemical bond that forms between the carboxyl group of
one amino acid and the amino group of another amino acid
an R group that could make covalent bonds with other R groups in tertiary and/or
quaternary folding - ANSWER SH-CH2-C-H
In a structure where a carbon is bound to an uncharged amino group, due to differences
in electronegativity between atoms, the nitrogen can form... - ANSWER Van der Waals
,interactions
an R group that will make ionic bonds with other R groups in tertiary and/or quaternary
folding: - ANSWER NH3-CH2-CH2-CH2-CH2-C
"Proteins can never be chemically modified in more than one way at the same time." -
ANSWER false
"Allostery is defined as the inhibition of enzymes by binding of molecules in the
enzyme's active site." - ANSWER False
Allosteric - ANSWER is the regulation of an enzyme by binding an effector molecule at a
site other than the enzyme's active site.
If you agree that the following statement is a way that enzymes increase rates of
chemical reactions:
Changing the free energy of the reactants in the reaction - ANSWER no
If you agree that the following statement is a way that enzymes increase rates of
chemical reactions:
Raising the activation energy - ANSWER no
If you agree that the following statement is a way that enzymes increase rates of
chemical reactions:
Temporarily increasing the temperature surrounding the reaction - ANSWER no
If you agree that the following statement is a way that enzymes increase rates of
chemical reactions:
Forming a tight binding interaction with the product - ANSWER no
If you agree that the following statement is a way that enzymes increase rates of
chemical reactions:
Stabilizing the transition state - ANSWER yes
If you agree that the following statement is a way that enzymes increase rates of
chemical reactions:
initially forming specific non-covalent bonds with the substrate - ANSWER yes
If you agree that the following statement is a way that enzymes increase rates of
chemical reactions:
Changing the Gibbs free energy of the reaction - ANSWER no
If a protein completely unfolds, would you expect its solubility in water to change? -
ANSWER yes
, Is the Kd higher for enzyme-substrate or enzyme-product? - ANSWER enzyme-product
In the protein and ligand shown below, the threonine is replaced by an arginine due to
mutation. Based on the chemistry of arginine, would you expect that it could still make
interactions with the cAMP nitrogenous base if situated correctly in the binding pocket
of the protein? - ANSWER yes
The reported Kd of a protein-ligand interaction at binding equilibrium is equal to the
concentration of the - ANSWER Ligand when Ligand (L)Unbound protein (P) and
Complex (C) (protein bound to ligand)Protein (P)Protein (P) and Ligand (L)Complex (C)
(Protein bound to Ligand) are at equal concentrations at equilibrium.
Backbone Model - ANSWER Shows only path of polypeptide backbone, doesn't show R
groups
Ribbon Model - ANSWER Only shows path of polypeptide backbone, doesn't show R
groups
Wireframe vs Ball and Stick Model - ANSWER This shows every atom/covalent bond in
the protein including backbone and R groups ▪
- Wireframe just shows sticks for covalent bonds without balls for atoms
- Ball and stick shows balls for atoms and sticks for covalent bonds between atoms
Space-fill model - ANSWER This shows all atoms as balls with van der waal radii (the
space that the entire atom takes up including electron cloud)
-This type of model is great for seeing what the protein actually looks like to other
molecules in the cell
Primary Structure - ANSWER is defined as the sequence of amino acids in the protein
Secondary Structure - ANSWER consists of particular polypeptide folds that are
common to many proteins
Tertiary Structure - ANSWER defined as the overall fold of a single polypeptide
Quaternary Structure - ANSWER is defined as the overall structure of proteins that are
made up of multiple polypeptides
