Biochemistry Quiz 4
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The Gibbs free energy of activation is the energy difference between the product and the transition state [T/F]
F; should be reactants
The native folded structure of a protein is dictated by several factors. Which is the most important?
The sequence of a protein
What are the three reasons proteins form stable quaternary structures?
- There are enhanced polar interactions between the subunits relative to polar interactions with the solvent.
- There are increased can der Waals interactions at the subunit interfaces favoring quaternary structure formation.
- There is a considerable increase in entropy as a result of water molecules being excluded from the subunit interface.
Which non-covalent interactions drive protein folding?
hydrophobic interactions and van der Waals forces
What are the major factors that favor the formation of quaternary structure?
DeltaS solvent and deltaH subunits
Which of the following non-covalent forces or interactions plays the dominant role in protein folding?
Which non-covalent forces are predominantly on the inside of a protein?
hydrophobic and van der Waals
The primary sequence of a protein governs:
- The final folded structure of the protein
- The location of the protein
- The position of disulphide bonds in the protein
- The position of post translational modifications of the protein
What are the advantages of forming a quaternary structure?
- genomic economy
- catalytic site
- substrate channeling
Which of them are found predominantly on the surface of a protein?
H-bonds and electrostatic bonds
Glycine often plays a unique role in specialized proteins because...
- because of its symmetry it can form symmetrical hydrogen bonds
- it allows close packing of triple helical structures
- Because of its symmetry, it is equally comfortable in beta structures or alpha helical structures
- Its small size allows close packing in antiparallel beta sheets
The atoms of the peptide bond lie in a ____.
The resonance stabilization energy of the planar structure is ____.
_____ degrees of freedom per residue for the peptide chain.
What are the five types of secondary structures?
- alpha helices
- other helices
- beta sheet
- tight turns
- beta bulge
What are beta sheets composed of?
What are other names for tight turns?
beta turns or beta bends
What stabilizes the a-Helix?
The backbone loop of an a-Helix contains ___ atoms.
Strands in a B-sheet may be ___ or ___.
parallel or antiparallel
What allows the peptide chain to reverse direction?
What two amino acids are prevalent in B-turns?
proline and glycine
What are the two kinds of B-turns?
Left (Type I), Right (Type II)
What are the three main types of fibrous protein?
How many alpha helical rod segment residues are in an a-Keratin sequence?
Primary structure of helical rods in a-Keratin consists of ____ -residue repeats.
In a-Keratin, there are (a-d-c-d-e-f-g)_n
residue in the sequence. Which are nonpolar?
a and d
What does the a-Keratin promote?
association of helices to form coiled coils
Which secondary shape does B-keratin contain?
B-Keratin has a ____ sequence.
What is the basic unit of collagen?
What is tropocollagen, in regards to chains?
Three intertwined polypeptide chains (1000 residues each)
What is the length and diameter of collagen?
300nm long, 1.4nm diameter
Collagen has what shape?
A triple helix
What sort of unique amino acid composition is in collagen?
hydroxylysine and hydroxyproline
Hydroxylation of proline residues is catalyzed by ______.
Nearly one residue out of three is ____ in collagen?
What makes 30% of the residues in collagen?
Pro and HyPro
What residue faces the inside of a collagen helix?
Which is more common--- fibrous proteins or globular?
What shapes make up the core of most globular proteins?
Helices and sheets
Why is a random coil called random?
because it does not conform to any frequently recurring pattern
What is a module?
compact, folded protein structures that are usually stable by themselves in aqueous solution
What do domains consist of?
a single continuous portion of the protein sequence
What are the four classification schemes for proteins?
How is class (as a classification scheme) determined?
from overall composition of secondary structure elements in a domain
What do folds (as a classification scheme) describe?
the number, arrangement, and connections of secondary structure elements
What is K-cat?
substrate molecules converted to product per second
What does a superfamily (as a classification scheme) include?
domains of similar folds and usually similar functions
What does a fmaily (as a classification scheme include?
domains with closely related amino acid sequences
What can cause denaturation?
External stresses--heat, chemical treatment, etc.
In protein folding, what types of structures form first?
What is the term for when nonpolar residues aggregate or coalesce?
What is a molten globule?
A transition state while the protein is folding
Which way to peptide chains typically twist?
What is the largest favorable contribution to folding?
the entropy term for the interaction of nonpolar residues with the solvent.
Why are nonpolar residues folded/buried inside the protein?
Unfolded, they force order on the solvent which decreases entropy
How stable is a typical folded protein?
Why are proteins often only marginally stable?
to maintain flexibility and motion
What kind of tertiary structure do globular proteins adopt?
The most stable
What type of structure predominates in alpha proteins?
What type of structure predominates in beta proteins?
What type of structure predominates in a/B proteins?
helices and sheets intermingle
What type of structure predominates in a+B proteins?
they contain separate a-helical and B-sheet domains
What proteins do not possess uniform structural properties but are still essential for cellular function?
intrinsically unstructured proteins (IUPs)
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