Proteins Flashcards
Chemical reactions in living systems occur in an ____________ environment, within a narrow range of temperatures.
aqueous
A covalent bond between two atoms is formed as a result of the ______________.
sharing of electrons
An ionic bond between two atoms is formed as a result of the ______________.
transfer of electrons from one atom to the other.
Equal sharing of electrons yields a(n) __________________ covalent bond.
nonpolar
If one atom participating in the bond has a stronger affinity for the electron, this produces a partial negative charge on one atom and a partial positive charge on the other. These __________________ covalent bonds should not be confused with the weaker ________________ bonds that are critical for the three-dimensional structure of biological molecules and for interactions between these molecules.
polar; noncovalent
Although covalent bonds are 10–100 times stronger than noncovalent interactions, many biological processes depend upon the number and type of noncovalent interactions between molecules. Which of the noncovalent interactions below will contribute most to the strong and specific binding of two molecules, such as a pair of proteins?
electrostatic attractions
The amino acids glutamine and glutamic acid are shown below. They differ only in the structure of their side chains (circled). At pH 7, glutamic acid can participate in molecular interactions that are not possible for glutamine. What types of interactions are these?
ionic bonds
Proteins are ______________ built from amino acids, which each have an amino group and a _____________ group attached to the central _______________.
polypeptides; carboxyl; alpha-carbon
There are twenty possible _______________ that differ in structure and are generally referred to as “R.”
side chains
In solutions of neutral pH, amino acids are _______________, carrying both a positive and negative charge. When a protein is made, amino acids are linked together through _______________, which are formed by condensation reactions between the carboxyl end of the last amino acid and the ___________________ end of the next amino acid to be added to the growing chain.
ionized; peptide bonds; amino
As a protein is made, the polypeptide is in an extended conformation, with every amino acid exposed to the aqueous environment. Although both polar and charged side chains can mix readily with water, this is not the case for nonpolar side chains. Explain how hydrophobic interactions may play a role in the early stages of protein folding, and have an influence on the final protein conformation.
A hydrophobic surface would organize water into a highly structured network of hydrogen bonds, which is energetically unfavorable. So you would expect the nonpolar amino acids would group together early, forming hydrophobic pockets, while the polar and charged side chains remain in the interface of the surrounding solution. In the final folded protein, most of the nonpolar atoms are prevented from contact with water and remain in contact with each other.
choose the class(es) of amino acids that are most important for the interactions:
forming ionic bonds with negatively charged DNA
basic
choose the class(es) of amino acids that are most important for the interactions:
forming hydrogen bonds to aid solubility in water
uncharged polar
choose the class(es) of amino acids that are most important for the interactions:
localizing an “integral membrane” protein that spans a lipid bilayer
nonpolar
choose the class(es) of amino acids that are most important for the interactions:
tightly packing the hydrophobic interior core of a globular protein
nonpolar
A large number of noncovalent interactions is required to hold two regions of a polypeptide chain together in a stable conformation.
True or False?
True
A single polypeptide tends to adopt 3–4 different conformations, which all have equivalent free-energy values (G).
True or False?
False.
Different conformation (3D) shape means a different function. There is a single, final fold for every polypeptide. The fold adopted is the “best” conformation, for which the free energy (G) of the molecule is at the minimum.
A newly synthesized protein generally folds up into a __________________ conformation.
stable
All the information required to determine a protein’s conformation is contained in its amino acid __________________.
sequence
On being heated, a protein molecule will become __________________ as a result of breakage of __________________ bonds.
denatured; noncovalent
Explain the protein structural level and the most important force involved in maintaining each structure.
Primary:
Covalent bond - peptide bonds.
The unique sequence of amino acids.
Explain the protein structural level and the most important force involved in maintaining each structure.
Secondary:
H bonds.
- Consists of coils and folds in the polypeptide chain
- Alpha-helix coil and beta-pleated sheets
Explain the protein structural level and the most important force involved in maintaining each structure.
Tertiary.
H bonds, ionic bonds, hydrophobic interactions, van der Waals interaction
Strong covalent bonds called disulfide bridges.
Explain the protein structural level and the most important force involved in maintaining each structure.
Quarternary
H bonds, ionic bonds, hydrophobic interactions, van der Waals interactions
2+ polypeptide chain forms form one macromolecule
What type of domain and chain do we have at 1?
antigen-binding site
What type of domain and chain do we have at 2?
variable domain of the heavy chain
What type of domain and chain do we have at 3?
constant domain of the heavy chain
What type of domain and chain do we have at 4?
constant domain of the light chain
What type of domain and chain do we have at 5?
variable domain of the light chain
