Final

Question 1

Titin is present in telomeres

Answer 1

False

Question 2

VAST stands for Vector Alignment Search Tool

Answer 2

True

Question 3

You need a PDB ID or MMBD ID to search VAST+

Answer 3

True

Question 4

“VAST neighbors” are non-similar structures

Answer 4

False

Question 5

VAST+ uses protein sequence similarities to compare the 3D structures

Answer 5

False

Question 6

VAST+ stands for Vector Alignment Sequence Tool

Answer 6

False

Question 7

Botulinum Toxin comes from a gram-positive bacteria

Answer 7

True

Question 8

VAST relates proteins based on geometric and sequence criteria

Answer 8

False

Question 9

You can filter VAST+ results based on taxonomy

Answer 9

True

Question 10

RMSD stands for Root Mean Square Deviation

Answer 10

True

Question 11

Malate Dehydrogenase is an enzyme that catalyzes an irreversible reaction

Answer 11

False

Question 12

Malate Dehydrogenase is a part of the Krebs Cycle

Answer 12

True

Question 13

The Rossman fold is not a common super secondary structure

Answer 13

False

Question 14

Prokaryotic and Eukaryotic cells alike have malate dehydrogenase

Answer 14

True

Question 15

CD in “CD Search” on the NCBI website stands for Conserved Daltons

Answer 15

False

Question 16

SASA stands for solvent accessible surface area

Answer 16

True

Question 17

The primary function of katanin is to cut intermediate filaments

Answer 17

False

Question 18

iCn3D cannot export models for 3-D printing

Answer 18

False

Question 19

When identifying amino acids by charge using iCn3D, red is a negative amino acids and blue is a positive amino acid

Answer 19

True

Question 20

An example of a developmental disorder caused by katanin dysfunction is microcephaly

Answer 20

True

Question 21

Cytoglobin was discovered in 2001 within hemoglobin cells

Answer 21

False (within hepatic stellate cells)

Question 22

A protein does not have to fall into one of the specific symmetry operations (cyclic, dihedral, helical, or cubic)

Answer 22

True (a protein can be listed as asymmetric)

Question 23

There are more local symmetries than global symmetries in the Protein Data Bank

Answer 23

False (there are more global symmetries)

Question 24

A protein of cyclic symmetry has one axis of rotation

Answer 24

True

Question 25

A homomer consists of two different subunit

Answer 25

False

Question 26

Sonic Hedgehog was named after the video game character Sonic The Hedgehog

Answer 26

True

Question 27

IBIS shows only observed interaction

Answer 27

False

Question 28

Sonic Hedgehog plays a role in embryogenesis of mammals

Answer 28

True

Question 29

The Hedgehog protein was first discovered in Mice

Answer 29

False

Question 30

IBIS does not require a number from the PDB to do a search

Answer 30

False

Question 31

The HMMR database focuses on the structure of the protein

Answer 31

False

Question 32

BLAST is a better tool to identify homologs than HMMER

Answer 32

False

Question 33

Glycine oxidase is a dioxidase

Answer 33

True

Question 34

Hydrogen peroxidase interacts with amplex red to form a pink colored complex.

Answer 34

True

Question 35

Glycine oxidase has two differential subunits

Answer 35

False

Question 36

IBIS stands for Inferred Biomolecular Interactions Server

Answer 36

True

Question 37

IBIS categorizes protein binding sites into five categories

Answer 37

True

Question 38

One of erythropoietin’s functions is to make red blood cells

Answer 38

True

Question 39

According to IBIS, erythropoietin only binds with proteins and peptides

Answer 39

True

Question 40

“Singleton” means a cluster which has only one non-redundant member

Answer 40

True

Question 41

The terms polypeptide and protein are synonymous in all situations

Answer 41

False

Question 42

Van der Wals forces help stabilize alpha helices

Answer 42

True

Question 43

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

Answer 43

False

Question 44

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

Answer 44

False, kinases add phosphates and phosphatases remove them

Question 45

Intrinsically disordered proteins have no function and are distant evolutionary remnants

Answer 45

False

Question 46

The mammal and bird sequences above are 90% homologous

Answer 46

False, there cannot be a percent homology

Question 47

High throughput methods are amenable to proteomic investigations

Answer 47

True

Question 48

A domain is a separately folded part of a polypeptide chain that often has unique functions such as binding DNA

Answer 48

True

Question 49

Protein folding is driven by hydrogen bond formation

Answer 49

False, hydrophobic interactions

Question 50

It makes no difference when purifying a protein whether it is being purified for industrial or analytical purposes

Answer 50

False

Question 51

Fusion tags can be put onto recombinant proteins to help prevent inclusion body formation

Answer 51

True

Question 52

Freezing and thawing are good for both cell disruption and to maintain proper protein folding

Answer 52

False, disrupts protein folding

Question 53

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

Answer 53

True

Question 54

In industrial settings for many therapeutic molecules reading absorbance at 280nm is a good way to check for protein contamination

Answer 54

True

Question 55

Chromatography separates complex combinations proteins based upon their chromatographic fingerprints

Answer 55

True

Question 56

An element of chromatographic fingerprints is hydrophobicity of the protein

Answer 56

True

Question 57

Proteins are relatively unstable compared to DNA and RNA

Answer 57

False, they are more stable

Question 58

Protein functionality activity can be lost at any state of protein purification

Answer 58

True

Question 59

Proteins can be destabilized so they are non functional by sheer force

Answer 59

True

Question 60

Proteins prefer to be in a buffer and not with other proteins

Answer 60

False

Question 61

Reducing agents are added to break disulfide bonds between two serines

Answer 61

False, cysteines

Question 62

Dried proteins go bad very quickly except when they are frozen

Answer 62

False, lyophilization is fine

Question 63

To isolate a recombinant protein more steps are typically needed then for a natively produced protein

Answer 63

False, native proteins require more

Question 64

Size exclusion chromatography is a good last step in a protein purification chromatographic scheme

Answer 64

False, it dilutes the protein

Question 65

Most biomarkers are able to be directly assayed by one biochemical reaction

Answer 65

False, most will require an assay (multiple reactions)

Question 66

Analytical proteins are rarely used for medical diagnostics techniques, only in the lab

Answer 66

False

Question 67

Industry uses analytical proteins for quality control

Answer 67

True

Question 68

Beers law is applicable to optical spectrophotometry

Answer 68

True

Question 69

Light scattering spectrophotometry is also known as turbidimetric photometry

Answer 69

True

Question 70

Raman photometry measures visible light absorbance

Answer 70

False, measures fluorescent light scattering

Question 71

Analytical reactions measuring biomarkers by enzyme kinetics rename substrates as analytes

Answer 71

True

Question 72

Potentiometric analysis is also known as electrochemical analysis

Answer 72

True

Question 73

End point assays are quicker than kinetic assays

Answer 73

False, you have to wait for the reaction to reach its end point while the kinetic can be meausred quickly

Question 74

Kinetic analytical techniques need a standard curve

Answer 74

True

Question 75

Oxidation reactions in analytical assays make peroxidases that convert non-colored reactant to a colored precipitant

Answer 75

True

Question 76

There are three parts to biosensors: biological, transducer, and detector

Answer 76

True

Question 77

Advantages of biosensors are that there are no extra equipment and reagent needed as compared to other analytical techniques

Answer 77

True

Question 78

Enzymes are often used in biosensors as the biological component

Answer 78

True

Question 79

Live organisms are never used in biosensors for a fear of skewing the results

Answer 79

False, bacteria

Question 80

A pregnancy test is not antibody-based, but enzyme based

Answer 80

False

Question 81

Immunoassays use antibodies as a biological detector

Answer 81

True

Question 82

Radioactive assays are the most common choice today for doing immunoassays because radioactive isotopes are so easy to work with

Answer 82

False

Question 83

Chemiluminescence detected immunoassays utilize chemical reactions that emit light to visualize where proteins are in tissue slices or on a membrane

Answer 83

True

Question 84

Homologously produced proteins are the same as recombinant proteins

Answer 84

False, heterologous is the same as recombinant and homologous is the same as native

Question 85

Some recombinant proteins can be toxic to cells

Answer 85

True

Question 86

For a protein to be homologously produced from industrial production a cell must have naturally high levels of the protein

Answer 86

True

Question 87

Companies can patent naturally produced proteins in unaltered cells

Answer 87

False

Question 88

Transformed cells are called transformed because their genome has been transformed or changed into something other than what it was

Answer 88

True, t as in transformed

Question 89

Transduction of cells uses a viral vector to insert non-native DNA into the cells

Answer 89

True

Question 90

One method to introduce DNA into mammalian cells to produce proteins is to use an inactive HIV virus called a lenta virus

Answer 90

True

Question 91

Prokaryotic proteins can have multiple proteins produced from the same transcript; thus bacterial genes are polycistronic

Answer 91

True

Question 92

E. coli is the most common organism which produces recombinant proteins

Answer 92

True

Question 93

Proper post translational modifications of therapeutic proteins for mammals will not be a problem when producing them in bacteria

Answer 93

False

Question 94

Chaperone proteins are the proteins that help other proteins fold correctly

Answer 94

True

Question 95

Optimizing growing temperatures, media nutritional components, and bacterial host strain rarely helps the cell line produce more protein so it is discouraged

Answer 95

False

Question 96

Inclusion bodies are partially misfolded proteins that precipitate out of solution

Answer 96

True

Question 97

Inclusion bodies in a protein isolation experiment are always a bad thing as the protein that produced the inclusion body is non-recoverable

Answer 97

False

Question 98

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

Answer 98

False

Question 99

It is advantageous to have the protein secreted into the cell media rather than produced intracellularly

Answer 99

True

Question 100

GRAS refers microorganisms used to produce proteins stands for general research aided strains

Answer 100

False, generally recognized as safe

Question 101

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

Answer 101

True

Question 102

Bacteria produce most of industrially produced proteins

Answer 102

True

Question 103

Saccromyces cerevisiae is a common bacterial strain used to produce recombinant proteins

Answer 103

False, it is a yeast

Question 104

Most food associated yeast and bacteria are not GRAS

Answer 104

False

Question 105

PTMs in yeast are the same as in humans because fungi and mammals are made up of eukaryotic cells

Answer 105

False

Question 106

Yeast produces most recombinant proteins in low numbers compared to bacteria

Answer 106

True

Question 107

Only the yeast Schizosaccharomyces pombe is used for heterologous protein production in industrial settings

Answer 107

False

Question 108

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

Answer 108

True

Question 109

A baculovirus is an insect cell virus

Answer 109

True

Question 110

Live insects are never used to produce heterologous proteins

Answer 110

False

Question 111

Insect cells do the exact same PTMs as mouse cells

Answer 111

False

Question 112

A problem with insect cell produced proteins is that insect cells do not create extracellular proteins well

Answer 112

True

Question 113

Proteins produced for therapeutic reasons from animal tissues can have problems due to cross-reactive pathogens

Answer 113

True

Question 114

PTMs from other mammalian animal tissues are totally equal to PTMs in human tissue

Answer 114

False, almost the same but not quite

Question 115

Transgenic proteins attained through animal secretions are preferable to transgenic proteins obtained through animal tissues

Answer 115

True

Question 116

Using animal secretions like milk for protein production causes no ethical concerns because the animal is not harmed

Answer 116

False

Question 117

Optimized cell cultures that produce proteins can produce concentrations of proteins up to 5g/L

Answer 117

True

Question 118

Large scale production of proteins through mammalian cell culture is relatively simple and cheap

Answer 118

False

Question 119

Mammalian cell culture has a doubling time that is comparable to bacterial and yeast cells

Answer 119

False

Question 120

Because plants are easy to grow and harvest, they are always the first choice for protein production

Answer 120

False

Question 121

Plant vacuoles can be problematic to producing proteins because they degrade proteins

Answer 121

True

Question 122

Papain produce by papaya is also an industrial produce protease and used in several processes including as a digestive aid

Answer 122

True

Question 123

A debriding agent cleans wounds and papain can be a debriding agent

Answer 123

True

Question 124

Agrobacterium is a plant virus that can be utilized to induce heterologous protein production in plants

Answer 124

True

Question 125

Plant cells cannot add PTMs to proteins and so are unfit for protein production

Answer 125

False

Question 126

Upstream plant processing requires lots of rare and expensive equipment

Answer 126

False

Question 127

Targeting proteins to be produced in seeds is desirable because the protein is less likely to be toxic to the plant

Answer 127

True

Question 128

Proteins can be produced using plant cell culture

Answer 128

True

Question 129

Plant cell culture became more utilized due to concerns over releasing transgenic plants into the environment

Answer 129

True

Question 130

The primary structure of a protein is unimportant in determining the secondary and tertiary structure of a protein

Answer 130

False

Question 131

Structures are related to the functions of a protein

Answer 131

False

Question 132

A dipeptide has two amino acids joined together by a glycosidic bond

Answer 132

False, they are joined by a peptide bond

Question 133

Economics is important in upstream protein processing but not downstream

Answer 133

False

Question 134

Scaling up production from an analytical lab setting to industrial production is simple and often presents no problems

Answer 134

False

Question 135

In industrial level protein production and processing regulatory compliances are of no concern

Answer 135

False

Question 136

Purification of every protein has to be 100% pure protein for every use

Answer 136

False

Question 137

Upstream processing goes from growing the cells and producing the protein to harvesting the cells

Answer 137

True

Question 138

Downstream processing describes the chromatographic processing only

Answer 138

False

Question 139

Downstream processing does not include packaging and labeling of the product

Answer 139

False

Question 140

Optimizing protein production must balance cell growth rate with optimal cell densities to maximize protein production

Answer 140

True

Question 141

Genetic stability of cell lines does not need to be considered when choosing cells to produce a protein

Answer 141

False

Question 142

Some cell lines may have intellectual property rights and using these may result in paying royalties and be economically unfavorable

Answer 142

True

Question 143

The screening process of cells to use for industrial production is only needed when using heterologous cells

Answer 143

False

Question 144

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

Answer 144

False

Question 145

In selecting cells for industrially producing a protein, mutations are induced in hopes that protein production will increase

Answer 145

True

Question 146

Recombinant proteins are made by inserting the protein sequence directly into the cell

Answer 146

False, the plasmid is inserted

Question 147

DMSO is toxic to mammalian cells at room temperature but helps maintain these cells in liquid nitrogen

Answer 147

True

Question 148

Antibiotics are added to cell lines to prevent bacterial growth and to screen for recombinant cells

Answer 148

True

Question 149

Cells, particularly mammalian cells, like to be cooled slowly and thawed quickly

Answer 149

True

Question 150

Complex media has multiple components that may be unidentified and in unknown concentrations

Answer 150

True

Question 151

Feed batch and batch systems are the method of choice for growing bacterial and mammalian cells in both academic and industrial levels

Answer 151

False

Question 152

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

Answer 152

True

Question 153

Solid state media looks similar to a big agar plate in some situations

Answer 153

True

Question 154

Prions are non-genetically inheritable particles that are always harmful

Answer 154

False

Question 155

Prions may prove that Lamarckian evolution is at least partially right

Answer 155

True

Question 156

Mammalian cell culture uses animal serum to give cells essential nutrient and growth factors

Answer 156

True

Question 157

Non-continuous cell lines are primary healthy cells from a body that have a short life span

Answer 157

True

Question 158

Single use mammalian cell culture containers are often just big plastic bags

Answer 158

True

Question 159

Mammalian cells are often derived from cancer because they are naturally immortalized

Answer 159

True

Question 160

Rractional purification design for the industrial production of proteins is concerned only with the choice of cells lines and not downstream events

Answer 160

False

Question 161

Industry needs to meet marketing demands while being the most economically optimized to lower cost to consumers and increase profits

Answer 161

True

Question 162

Per unit overhead decreases as quantity produced increases

Answer 162

True

Question 163

New techniques for industrial processes are constantly being implemented because it is easy to get regulatory approval

Answer 163

False

Question 164

All bulk proteins produced industrially by law have to be 100% pure

Answer 164

False, only therapeutic has to be 100% pure

Question 165

All industrial instruments have to be disassembled every time they are cleaned and sterilized

Answer 165

False

Question 166

Cleaning removes all dirt, debris, and microorganisms

Answer 166

False, only removes dirt

Question 167

Endotoxins are lipopolysaccharides (LPS) from gram negative bacteria induce fevers

Answer 167

True

Question 168

Cleaning and sterilization of plates can be done with water, sodium hydroxide and nitric acid

Answer 168

True

Question 169

Horseshoe crab blood can detect pyrogens and proteins but not viruses

Answer 169

True

Question 170

Protein contaminants in therapeutic protein productions are simple to detect and remove

Answer 170

False

Question 171

Protein slurries can be used to store proteins by concentrating the protein and adding large amounts of neutral salts

Answer 171

True

Question 172

Nuclear receptors are inside the nucleus when they are first bound by their ligand

Answer 172

False, they are on the nuclear envelope/membrane

Question 173

Surface receptors can be g-protein coupled receptors, tyrosine-kinase receptors, and ion channels

Answer 173

True

Question 174

Proximal signaling events include ligand binding surface receptors, and translocation of transcription factors to the nucleus

Answer 174

False

Question 175

A distal signaling event is typically a release of calcium from the sarcoplasmic reticulum

Answer 175

False, it is a proximal signaling event

Question 176

The intermediate steps of cell signaling are a series of protein-protein interactions called a signaling cascade

Answer 176

True

Question 177

Ras proteins are associated with the FGF signaling pathway

Answer 177

True

Question 178

The WNT and FGF pathway is only associated with adult cells and cancer

Answer 178

False, they are important in development

Question 179

In the jak-stat pathway the JAK protein is part of the signal cascade but is not associated with the receptor

Answer 179

False, it is associated with the receptor

Question 180

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

Answer 180

True

Question 181

A common proximal signaling event is activation of adenylyl cyclase to make ATP

Answer 181

False, makes cAMP

Question 182

In the sonic hedgehog pathway, sonic hedgehog refers to the receptor

Answer 182

False, it refers to the ligand

Question 183

Packaging labels for therapeutic proteins are not strictly regulated by the FDA

Answer 183

False

Question 184

Synthesis of proteins is done by the ribosome from a template RNA

Answer 184

True

Question 185

SPR stands for surface plasmon resonance and is utilized to study enzymes

Answer 185

False, it is utilized to study receptors

Question 186

Circular dichroism can determine tertiary structure of proteins

Answer 186

False, determines secondary structures (alpha-helices)

Question 187

Edmund sequencing is slow and tedious so it is not often used in industry for sequencing proteins

Answer 187

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

Question 188

NMR can determine 20 amino acid long polypeptide

Answer 188

True

Question 189

The peptide bond is formed between the side chains of two adjacent amino acids in a polypeptide chain

Answer 189

False

Question 190

A container of mammalian cell lines can be stored in liquid nitrogen and is called a dewar

Answer 190

True