Chapter 4

A ___ is a part of a polypeptide chain that is independently stable or could undergo movement as a single entity with respect to the entire protein.

domain

The Φ and Ψ dihedral angles of a fibrous protein were measured to be -160 ° and +150 °, respectively, and its CD spectrum showed a strong positive Δε at 205 nm. The protein is most likely _____.

fibroin

Collagen

has fibrils consisting of cross-linked triple helices of polypeptide chains

A good way to predict whether an amino acid side chain is on the outside or inside of a protein is to consider its ______.

hydropathy (polarity)

Features associated with globular proteins

intrinsically disordered regions of structure domains motifs

The Beta-sheet

is primarily stabilized by hydrogen bonds

Proteins that are folded in their thermodynamically stable and functional form(s) are considered to be ___ proteins.

native

Which of the following terms best describes the higher order structure of α keratin, shown below?

photofibril

Which of the following types of proteins are exceptions to the two simple rules of protein folding: (1) Hydrophobic residues are found buried in the interior of a protein; and (2) the number of hydrogen bonds and ionic interactions within the protein are maximized?

proteins with intrinsically disordered segments transmembrane proteins

Quaternary structure

referes to an arrangement of tertiary protein subunits in a 3-D complex

Proteostatis

refolding, synthesis, degradation

Book 122: The negatively charged carboxyl groups of adjacent Glu residues

repel each other so strongly that they prevent formation of the α helix

The C−N bond in the peptide backbone of a protein would have a bond that is ______ the C−N bond in CH3−NH3+.

shorter than

The Ramachandran plot

shows combinations of permissible dihedral angles in a polypeptide chain.

Book 122: if there are many adjacent Lys and/or Arg residues, with positively charged R groups at pH 7.0

they also repel each other and prevent formation of the α helix.

True statements regarding tertiary structure of proteins:

- Quaternary structure is the description of how the tertiary structures in a multi-subunit protein are arranged with respect to each other. - Many proteins can be classified as either globular or fibrous (but not both) - Amino acid residues far apart in primary structure may interact with each other in the tertiary structure.

Statement about protein folding is true

- it is driven by changes in free energy - it is sometimes assisted by proteins known as chaperones - it is a stepwise process

Diseases associated with protein misfolding

amyloidosis, cystic fibrosis, Parkinson disease

Denaturing followed by renaturing of a protein

demonstrates that primary structure dictates tertiary structure.

Book 122 : if a polypeptide chain has a long block of Glu residues

this segment of the chain will not form an α helix at pH 7.0

T/F regarding the tertiary structure of proteins: the tertiary structure of a protein is destabilized by the hydrophobic effect

False

Which amino acid repeat is present in collagen? (X is often Pro; Y is often 4-Hyp)

Glu-X-Y

Which statement applies to the following sequence's α helix formation at pH 7? AIVDAEDVEID

Helices are not favored due to repulsion of negative charges.

Which of the following amino acids would be located on the exterior of a protein and not part of the hydrophobic protein core?

Ser

Why are salt bridges much stronger when they occur at the interior of a protein as compared to its surface?

The interior of the protein has a much lower dielectric constant than the solvent so there is no shielding of the charges.

Free-energy funnels are used to explain the thermodynamics of protein folding. What can be said of a protein that has the following free-energy funnel? 1 big bump around

The protein has folding intermediates with substantial stability on nearly every pathway leading to the native state.

Which statement is true about the side chains (R groups) of amino acids in an α helix?

They extend radially out from the helix.

T/F Regarding protein structure: hydrophobic side chains are usually in the interior of the native structure

True

The _____ is not an example of a type of protein secondary structures

alpha-turn

Describe peptide bond

amide bond, linkage between amino acids in a protein, rigid and planar.

All of the common secondary structural elements fall within allowed combinations of φ and ψ dihedral angles except _____.

α-helix, β-helix, triple helix, antiparallel β-sheets

The alphas helix is

affected by the identities of the residues near each end

Book 122: The bulk and shape of Asn, Ser, Thr, and Cys residues

can also destabilize an α helix if they are close together in the chain.

Hsp70 is an example of a/an ________.

chaperone that binds hydrophobic regions of unfolded proteins

Solving the X-ray crystal structure for the protein myoglobin demonstrated _____.

the existence of α-helices in proteins the close packing of hydrophobic side chains at the core of a globular protein the peptide bonds in proteins are planar and trans proline residues will occur at bends in the peptide backbone

Which item is the predominant factor in protein stability?

the hydrophobic effect

The major finding of the experiment by Christian Anfinsen in the 1950s with ribonuclease A was that _____.

the information required to fold ribonuclease A into its native structure is present in its amino acid sequence

Which of the following best defines the term secondary structure with respect to proteins?

the local spatial arrangement of the main-chain atoms in a segment of a polypeptide chain