Exam 20: Designer Proteins and Protein Folding

_____ of protein structures is a useful tool in building 3D structures for proteins that do not have a solved x-ray structure. It uses the x-ray structure of a related protein as a template and the amino acid sequence of the protein of interest.

Subtilisin is a bacterial serine protease that is commonly used as an additive in laundry detergent. In its native state, it has a methionine that becomes oxidized, surprisingly leading to enzyme inactivation. To prevent inactivation, subtilisin could be engineered by mutating methionine residues to ___________. I. isoleucine II. alanine III. cysteine IV. phenylalanine

Proteins can be engineered to express a tag that is beneficial in __________ of the protein by _______ chromatography.

In the cell, most proteins fold without assistance and within milliseconds. The information needed to fold a protein properly is found in the ______ sequence of the protein.

It is common, when making mutations in a cDNA sequence ___________________.

Using a resin in solid-phase protein synthesis allows for _______. I. efficient washing steps to remove the side products II. keeping the growing peptide in solid phase III. obtaining higher product yields IV. using lower reaction temperatures

Several neurodegenerative diseases (Alzheimer's, Parkinson's, etc.) present __________ structures at the molecular level.

Mammalian protein expression systems __________. I. sometimes use the strong viral promoter CMV II. are used when the expressed proteins require post-translational modifications III. require expensive cell culture reagents IV. are easy to handle V. are used for producing insulin analogs

Which amino acid side chains would need to be protected in SPPS? I. hydroxyl groups of tyrosine and serine II. carboxyl groups of glutamic acid and aspartic acid III. amine group of lysine IV. methyl group of alanine V. phenyl group of phenylalanine

PCR-based mutagenesis is a widely used technique due to the mutation being introduced in _________.

Expression vectors are engineered fragments of DNA that contain the necessary information, such as ______, for the cell to be able to express the protein at a high level. I. cloning sites tailored to various restriction enzymes II. promoters designed to work in the individual cell lines III. an origin of replication IV. visualization sites V. antibiotics resistance marker gene

The thermodynamic stabilization of the protein in folded state is partly due to the hydrophobic effect that accompanies protein folding. The hydrophobic effect in proteins is manifested in ________ and _________.

Protein folding can be described in terms of energy, and visualized by an energy funnel diagram .The width of the funnel is given by the________.

The purity of a peptide synthesized by SPPS is analyzed by ____________.

Choose fusion proteins from the list that could be used in biochemical or cellular assays: I. GFP-protein constructs II. extra cellular matrix proteins III. anti-His6 tag-antibody conjugated to horseradish peroxidase IV. maltose binding proteins V. subtilisin

Proteins expressed in bacterial cells ________. I. fold properly if they contain several domains II. have to be released from the cells during a cell lysis step III. do not go through post-translational modifications IV. are secreted into the growth media

When using cassette mutagenesis, in order to insert an engineered cDNA sequence into a plasmid, a __________ is used to cut out the sequence that is no longer needed, and a __________ is used to insert the new mutant cassette into the plasmid.

Mutation of a serine residue to a(n) _____ residue is a good modeling tool for a phosphorylated serine.

Protein folding is the process by which proteins ____________. I. are stored II. gain their secondary structure III. gain their tertiary structure IV. lose activity V. burry hydrophobic side chains and expose hydrophilic ones

During folding the entropy of the protein _______.