Final Flashcards
Titin is present in telomeres
False
VAST stands for Vector Alignment Search Tool
True
You need a PDB ID or MMBD ID to search VAST+
True
“VAST neighbors” are non-similar structures
False
VAST+ uses protein sequence similarities to compare the 3D structures
False
VAST+ stands for Vector Alignment Sequence Tool
False
Botulinum Toxin comes from a gram-positive bacteria
True
VAST relates proteins based on geometric and sequence criteria
False
You can filter VAST+ results based on taxonomy
True
RMSD stands for Root Mean Square Deviation
True
Malate Dehydrogenase is an enzyme that catalyzes an irreversible reaction
False
Malate Dehydrogenase is a part of the Krebs Cycle
True
The Rossman fold is not a common super secondary structure
False
Prokaryotic and Eukaryotic cells alike have malate dehydrogenase
True
CD in “CD Search” on the NCBI website stands for Conserved Daltons
False
SASA stands for solvent accessible surface area
True
The primary function of katanin is to cut intermediate filaments
False
iCn3D cannot export models for 3-D printing
False
When identifying amino acids by charge using iCn3D, red is a negative amino acids and blue is a positive amino acid
True
An example of a developmental disorder caused by katanin dysfunction is microcephaly
True
Cytoglobin was discovered in 2001 within hemoglobin cells
False (within hepatic stellate cells)
A protein does not have to fall into one of the specific symmetry operations (cyclic, dihedral, helical, or cubic)
True (a protein can be listed as asymmetric)
There are more local symmetries than global symmetries in the Protein Data Bank
False (there are more global symmetries)
A protein of cyclic symmetry has one axis of rotation
True
A homomer consists of two different subunit
False
Sonic Hedgehog was named after the video game character Sonic The Hedgehog
True
IBIS shows only observed interaction
False
Sonic Hedgehog plays a role in embryogenesis of mammals
True
The Hedgehog protein was first discovered in Mice
False
IBIS does not require a number from the PDB to do a search
False
The HMMR database focuses on the structure of the protein
False
BLAST is a better tool to identify homologs than HMMER
False
Glycine oxidase is a dioxidase
True
Hydrogen peroxidase interacts with amplex red to form a pink colored complex.
True
Glycine oxidase has two differential subunits
False
IBIS stands for Inferred Biomolecular Interactions Server
True
IBIS categorizes protein binding sites into five categories
True
One of erythropoietin’s functions is to make red blood cells
True
According to IBIS, erythropoietin only binds with proteins and peptides
True
“Singleton” means a cluster which has only one non-redundant member
True
The terms polypeptide and protein are synonymous in all situations
False
Van der Wals forces help stabilize alpha helices
True
Parallel beta-sheets are stronger than anti-parallel beta-sheets because their atoms, which form hydrogen bonds, are directly opposite each other rather than at an angle
False
Phosphatases add phosphate groups on the hydroxyl group of the R chains of serine, tyrosine, or threonine residues during the post translation process of phosphorylation
False, kinases add phosphates and phosphatases remove them
Intrinsically disordered proteins have no function and are distant evolutionary remnants
False
The mammal and bird sequences above are 90% homologous
False, there cannot be a percent homology
High throughput methods are amenable to proteomic investigations
True
A domain is a separately folded part of a polypeptide chain that often has unique functions such as binding DNA
True
Protein folding is driven by hydrogen bond formation
False, hydrophobic interactions
It makes no difference when purifying a protein whether it is being purified for industrial or analytical purposes
False
Fusion tags can be put onto recombinant proteins to help prevent inclusion body formation
True
Freezing and thawing are good for both cell disruption and to maintain proper protein folding
False, disrupts protein folding
Filter is commonly used in industrial protein processing to rid cell lysates of cell debris and non lysed cells because it is very cheap and efficient
True
In industrial settings for many therapeutic molecules reading absorbance at 280nm is a good way to check for protein contamination
True
Chromatography separates complex combinations proteins based upon their chromatographic fingerprints
True
An element of chromatographic fingerprints is hydrophobicity of the protein
True
Proteins are relatively unstable compared to DNA and RNA
False, they are more stable
Protein functionality activity can be lost at any state of protein purification
True
Proteins can be destabilized so they are non functional by sheer force
True
Proteins prefer to be in a buffer and not with other proteins
False
Reducing agents are added to break disulfide bonds between two serines
False, cysteines
Dried proteins go bad very quickly except when they are frozen
False, lyophilization is fine
To isolate a recombinant protein more steps are typically needed then for a natively produced protein
False, native proteins require more
Size exclusion chromatography is a good last step in a protein purification chromatographic scheme
False, it dilutes the protein
Most biomarkers are able to be directly assayed by one biochemical reaction
False, most will require an assay (multiple reactions)
Analytical proteins are rarely used for medical diagnostics techniques, only in the lab
False
Industry uses analytical proteins for quality control
True
Beers law is applicable to optical spectrophotometry
True
Light scattering spectrophotometry is also known as turbidimetric photometry
True
Raman photometry measures visible light absorbance
False, measures fluorescent light scattering
Analytical reactions measuring biomarkers by enzyme kinetics rename substrates as analytes
True
Potentiometric analysis is also known as electrochemical analysis
True
End point assays are quicker than kinetic assays
False, you have to wait for the reaction to reach its end point while the kinetic can be meausred quickly
Kinetic analytical techniques need a standard curve
True
Oxidation reactions in analytical assays make peroxidases that convert non-colored reactant to a colored precipitant
True
There are three parts to biosensors: biological, transducer, and detector
True
Advantages of biosensors are that there are no extra equipment and reagent needed as compared to other analytical techniques
True
Enzymes are often used in biosensors as the biological component
True
Live organisms are never used in biosensors for a fear of skewing the results
False, bacteria
A pregnancy test is not antibody-based, but enzyme based
False
Immunoassays use antibodies as a biological detector
True
Radioactive assays are the most common choice today for doing immunoassays because radioactive isotopes are so easy to work with
False
Chemiluminescence detected immunoassays utilize chemical reactions that emit light to visualize where proteins are in tissue slices or on a membrane
True
Homologously produced proteins are the same as recombinant proteins
False, heterologous is the same as recombinant and homologous is the same as native
Some recombinant proteins can be toxic to cells
True
For a protein to be homologously produced from industrial production a cell must have naturally high levels of the protein
True
Companies can patent naturally produced proteins in unaltered cells
False
Transformed cells are called transformed because their genome has been transformed or changed into something other than what it was
True, t as in transformed
Transduction of cells uses a viral vector to insert non-native DNA into the cells
True
One method to introduce DNA into mammalian cells to produce proteins is to use an inactive HIV virus called a lenta virus
True
Prokaryotic proteins can have multiple proteins produced from the same transcript; thus bacterial genes are polycistronic
True
E. coli is the most common organism which produces recombinant proteins
True
Proper post translational modifications of therapeutic proteins for mammals will not be a problem when producing them in bacteria
False
Chaperone proteins are the proteins that help other proteins fold correctly
True
Optimizing growing temperatures, media nutritional components, and bacterial host strain rarely helps the cell line produce more protein so it is discouraged
False
Inclusion bodies are partially misfolded proteins that precipitate out of solution
True
Inclusion bodies in a protein isolation experiment are always a bad thing as the protein that produced the inclusion body is non-recoverable
False
It is permissible to leave cell debris in protein isolation procedures because it is totally inert and inactive, and so it is unable to damage the protein
False
It is advantageous to have the protein secreted into the cell media rather than produced intracellularly
True
GRAS refers microorganisms used to produce proteins stands for general research aided strains
False, generally recognized as safe
The problem with engineering cells to secrete recombinant proteins is that the cell can produce so much of the protein that the cell secretory system is overwhelmed and all cells die
True
Bacteria produce most of industrially produced proteins
True
Saccromyces cerevisiae is a common bacterial strain used to produce recombinant proteins
False, it is a yeast
Most food associated yeast and bacteria are not GRAS
False
PTMs in yeast are the same as in humans because fungi and mammals are made up of eukaryotic cells
False
Yeast produces most recombinant proteins in low numbers compared to bacteria
True
Only the yeast Schizosaccharomyces pombe is used for heterologous protein production in industrial settings
False
Fungi are saprophytic organisms that live off dead tissues and cells thus their cell membranes contain proteases which is a problem for recombinant protein production
True
A baculovirus is an insect cell virus
True
Live insects are never used to produce heterologous proteins
False
Insect cells do the exact same PTMs as mouse cells
False
A problem with insect cell produced proteins is that insect cells do not create extracellular proteins well
True
Proteins produced for therapeutic reasons from animal tissues can have problems due to cross-reactive pathogens
True
PTMs from other mammalian animal tissues are totally equal to PTMs in human tissue
False, almost the same but not quite
Transgenic proteins attained through animal secretions are preferable to transgenic proteins obtained through animal tissues
True
Using animal secretions like milk for protein production causes no ethical concerns because the animal is not harmed
False
Optimized cell cultures that produce proteins can produce concentrations of proteins up to 5g/L
True
Large scale production of proteins through mammalian cell culture is relatively simple and cheap
False
Mammalian cell culture has a doubling time that is comparable to bacterial and yeast cells
False
Because plants are easy to grow and harvest, they are always the first choice for protein production
False
Plant vacuoles can be problematic to producing proteins because they degrade proteins
True
Papain produce by papaya is also an industrial produce protease and used in several processes including as a digestive aid
True
A debriding agent cleans wounds and papain can be a debriding agent
True
Agrobacterium is a plant virus that can be utilized to induce heterologous protein production in plants
True
Plant cells cannot add PTMs to proteins and so are unfit for protein production
False
Upstream plant processing requires lots of rare and expensive equipment
False
Targeting proteins to be produced in seeds is desirable because the protein is less likely to be toxic to the plant
True
Proteins can be produced using plant cell culture
True
Plant cell culture became more utilized due to concerns over releasing transgenic plants into the environment
True
The primary structure of a protein is unimportant in determining the secondary and tertiary structure of a protein
False
Structures are related to the functions of a protein
False
A dipeptide has two amino acids joined together by a glycosidic bond
False, they are joined by a peptide bond
Economics is important in upstream protein processing but not downstream
False
Scaling up production from an analytical lab setting to industrial production is simple and often presents no problems
False
In industrial level protein production and processing regulatory compliances are of no concern
False
Purification of every protein has to be 100% pure protein for every use
False
Upstream processing goes from growing the cells and producing the protein to harvesting the cells
True
Downstream processing describes the chromatographic processing only
False
Downstream processing does not include packaging and labeling of the product
False
Optimizing protein production must balance cell growth rate with optimal cell densities to maximize protein production
True
Genetic stability of cell lines does not need to be considered when choosing cells to produce a protein
False
Some cell lines may have intellectual property rights and using these may result in paying royalties and be economically unfavorable
True
The screening process of cells to use for industrial production is only needed when using heterologous cells
False
In the screening process cells that make an intermediate amount of protein of interest are usually chosen because they present fewer production cost and still make a large amounts of protein, the intermediate amount of protein production is usually accepted
False
In selecting cells for industrially producing a protein, mutations are induced in hopes that protein production will increase
True
Recombinant proteins are made by inserting the protein sequence directly into the cell
False, the plasmid is inserted
DMSO is toxic to mammalian cells at room temperature but helps maintain these cells in liquid nitrogen
True
Antibiotics are added to cell lines to prevent bacterial growth and to screen for recombinant cells
True
Cells, particularly mammalian cells, like to be cooled slowly and thawed quickly
True
Complex media has multiple components that may be unidentified and in unknown concentrations
True
Feed batch and batch systems are the method of choice for growing bacterial and mammalian cells in both academic and industrial levels
False
Some sort of agitation is used in most industrial size fermentators for the purpose of aeration and to prevent buildup of carbon dioxide in localized regions
True
Solid state media looks similar to a big agar plate in some situations
True
Prions are non-genetically inheritable particles that are always harmful
False
Prions may prove that Lamarckian evolution is at least partially right
True
Mammalian cell culture uses animal serum to give cells essential nutrient and growth factors
True
Non-continuous cell lines are primary healthy cells from a body that have a short life span
True
Single use mammalian cell culture containers are often just big plastic bags
True
Mammalian cells are often derived from cancer because they are naturally immortalized
True
Rractional purification design for the industrial production of proteins is concerned only with the choice of cells lines and not downstream events
False
Industry needs to meet marketing demands while being the most economically optimized to lower cost to consumers and increase profits
True
Per unit overhead decreases as quantity produced increases
True
New techniques for industrial processes are constantly being implemented because it is easy to get regulatory approval
False
All bulk proteins produced industrially by law have to be 100% pure
False, only therapeutic has to be 100% pure
All industrial instruments have to be disassembled every time they are cleaned and sterilized
False
Cleaning removes all dirt, debris, and microorganisms
False, only removes dirt
Endotoxins are lipopolysaccharides (LPS) from gram negative bacteria induce fevers
True
Cleaning and sterilization of plates can be done with water, sodium hydroxide and nitric acid
True
Horseshoe crab blood can detect pyrogens and proteins but not viruses
True
Protein contaminants in therapeutic protein productions are simple to detect and remove
False
Protein slurries can be used to store proteins by concentrating the protein and adding large amounts of neutral salts
True
Nuclear receptors are inside the nucleus when they are first bound by their ligand
False, they are on the nuclear envelope/membrane
Surface receptors can be g-protein coupled receptors, tyrosine-kinase receptors, and ion channels
True
Proximal signaling events include ligand binding surface receptors, and translocation of transcription factors to the nucleus
False
A distal signaling event is typically a release of calcium from the sarcoplasmic reticulum
False, it is a proximal signaling event
The intermediate steps of cell signaling are a series of protein-protein interactions called a signaling cascade
True
Ras proteins are associated with the FGF signaling pathway
True
The WNT and FGF pathway is only associated with adult cells and cancer
False, they are important in development
In the jak-stat pathway the JAK protein is part of the signal cascade but is not associated with the receptor
False, it is associated with the receptor
Autophosphorylation is: two receptors are bound by the ligand, they activate each other by a process where by one part of the receptor adds a phosphate group to another part or subunit of the receptor
True
A common proximal signaling event is activation of adenylyl cyclase to make ATP
False, makes cAMP
In the sonic hedgehog pathway, sonic hedgehog refers to the receptor
False, it refers to the ligand
Packaging labels for therapeutic proteins are not strictly regulated by the FDA
False
Synthesis of proteins is done by the ribosome from a template RNA
True
SPR stands for surface plasmon resonance and is utilized to study enzymes
False, it is utilized to study receptors
Circular dichroism can determine tertiary structure of proteins
False, determines secondary structures (alpha-helices)
Edmund sequencing is slow and tedious so it is not often used in industry for sequencing proteins
False, you only have to sequence the first few amino acids to ensure it is the protein of interest and it is cheaper than a mass spec
NMR can determine 20 amino acid long polypeptide
True
The peptide bond is formed between the side chains of two adjacent amino acids in a polypeptide chain
False
A container of mammalian cell lines can be stored in liquid nitrogen and is called a dewar
True
