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Definition
| Maltose, high glucose content, high fructose content |
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Definition
high total carbohydrate content
source of vitamins
high mineral (ash) content
High sucrose content |
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Definition
High total protein content
high total carbohydrate content
high mineral ash content |
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Definition
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Definition
high total carbohydrate content
high sucrose content |
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Definition
high amino nitrogen content
source of vitamins |
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Definition
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Definition
high amino nitrogen content
high total protein content |
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Definition
| high amino nitrogen content, high total protein content |
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| soy protein grits or flour (3) |
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Definition
high amino nitrogen content
high total protein content
source of vitamins |
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Term
| List 4 types of biocatalysts used in commercial biomanufacturing |
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Definition
whole cells
immobilized cells
synthetic cells
enzymes |
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Term
| Explain the impact of the ability to patent isolated DNA sequences on each type of biocatalyst |
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Definition
these are considered green biocatalysts because they prevent/reduce wastes, replace toxic/hazardous chemicals, are more energy efficient, grow in renewable substrates, reduce the number of synthesis steps and in general make up safer processes
the ability to patent isolated DNA sequences gives companies a competititve edge over competitors
sequences can code for hetologous genes that code for valuable metbaolites or special phenotypes that make whole cells (growing, resting, or immobilized) more stable under production conditions. Sequnces coding for enzymes that are more stable under non-physiological conditions are also valuable as most commercial enzymes need active in a broad range of temperatures, pH and salt concentrations |
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Term
Define the following terms and their impact on biomanufacturing
Non-GMO versus GMO and how might this effect the perception by consumers of a potential health risk or the safety of products produced by biocatlaysts depending on the type of product? |
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Definition
GMO: genetically modified organism. It refers to any organism (bacteria, yeast, plants, insects, fish, mammals) whose genetic material has been modified using genetic engineering techniques. a non gmo organism has not been modified and preserves its genetic identity found in nature
the safety perception of the general public towards GMO-derived products is generally cautious. By definitions, GMO's are considered " less natural" and potentially dangerous, even if it has been demonstrated scientifically that their nutritional value is comparable or even superior compared to non-GMO products. In other cases the genetic modifications are not intended to modify the nature of the product itself but to reduce susceptibility to pests and climate changes |
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Term
| What does the concept of " over production" of a microbial metabolite refer to? why is this important in biomanufacturing? |
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Definition
| It refers to organisms that have been engineered to produce high quantities of a specific metabolite by engineering their genetic and metabolic regulation pathways. Under normal conditions, wild type strains either do not produce certain metabolites or produce only small quantities as a result of feedback regulation or lack of the necessary genetic information. There in order to achieve suitable industrial yields, production strains need to be engineered to over produce such metabolites |
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| briefly explain how patents and Freedom to Operate (FTO) can affect choices of both the upstream microbial biology and downstream recovery and purification in desinging a biomanufacturing process |
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Definition
| early during the biomanufacturing process design stage, it is necessary to build a patent map in order to identify IP that could be potentially infringed with the new technology in development. Infringement risk is managed by licensing tehcnology, using appropriate legal documentation or adjusting the product/process configuration. This freedom to operate process is repeated during the several phases in product/process development and becomes more critical as the cost of infringement increases as the product gets closer to marketing |
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| Scale and markets are two important concepts for directing research in product development and biomanufacturing. briefly describe why these concepts are important and list 2 additional concepts introduced in this class that are important for industrial biomanufacturing that are not common to bench-scale biotechnology research |
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Definition
market refers to the specific need that will be satisfied with the product in development. It includes all potential competitors and customers along with their interactions.
The scale of the market determines the size of the opportunity, the potential size of the operations and the range of customers that could benefit from the new product. other important concepts include
1. strain development and screening
2. over production
3. scale up
4. growth media design and optimization |
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Term
| both patents and trade secrets are important forms of IP that often dictate the strategy for microbial manufacturing strain construction, overall process and final product design. how do these two forms of IP differ? |
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Definition
trace secrets are based on information about processes, recipes, or designs that is highly valuable to the inventor because nobody else has the ability to duplicate it and will remain secret as long as nobody discloses it to the public
a patent is a right granted by the govt to exploit and receive profit from an invention during a fixed period of time (20 years) in exchange for disclosing its composition, applications and use to the public. After the patent expires anybody can use the disclosed information to create products for profit in an identical way |
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Term
| Outline the entire pathway of drug development and include all pre-clinical studies and phases of human clinical trials |
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Definition
discovery (variable)
pre-clinical (3.5-6.5)
IND
Phase 1 (1-1.5)
Phase 2 (2)
Phase 3 (3-3.5)
NDA
FDA Review (2-2.5)
Phase 4- product life |
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Term
| two critical FDA regulatory documents that must be submitted specify what information is needed in each document |
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Definition
1. IND (animal pharmacology and toxicology studies)
2. chemistry and manufacturing information
3. protocols for clinical trials and qualitifcations of investigators
NDA includes
* clinical trials
* drug product formulation
* pharmacokinetics
* pharmacodynamics
* manufacturing process
* packaging
* facility design |
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Term
| What determines the overall yield of recombinant protein produced by an expression system or "expression platform"? Which of these factors contributes the most to the cost of protein manufacture |
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Definition
downstream processing cost can represent as much as 70% of the total cost of protein manufacture being the most expensive factor in most biomanufacturing processes
* recombinant protein yield=cell yield* (protein yield/cell)*%recovery |
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Term
The addition of IPTG, a chemical inducer is often used in small scale bioracts to induce heterologous protein expression using the T7 expression system. Explain how the t7 induction results in high levels of protein expression. Identify the promoter and how this promoter is regulated by IPTG addition (draw picture)
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Definition
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Term
| The addition of IPTG, a chemical inducer is often used in small scale bioracts to induce heterologous protein expression using the T7 expression system. Explain how the t7 induction results in high levels of protein expression. Identify the promoter and how this promoter is regulated by IPTG addition (draw picture) |
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Definition
| the product of the lacl gene (lac repressor) is constitutively produced and, in the absence of lactose or IPTG binds to the lac operator repressing the synthesis of the T7 RNA polymerase and transcription of the target gene. If lactose or IPTG is present in the media, it binds to the lac repressor and prevents it from repressing transcription of the T7 RNA polymerase. Once transcribed the T7 RNA polymerase binds to the T7 gene 10 promoter and transcribes the target gene |
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Term
| Explain one additional method for gene induction that may be more cost effective in biomanufacturing (large scale)that does require addition of a chemical inducer for gene induction and protein accumulation. Identify the expression system you describe |
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Definition
| Temperature- inducible phage lambda promoter expression system: the temperature sensitive cl repressor that is constitutively synthesized under the control of its own promoter can bind to the operator region of the lambda promoter at 30 degrees C repressing the target gene from being transcribed. At 42 degrees C the cl repressor is inactive and can't bind to the operator region therefore allowing for transcription of the target gene |
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Term
| Starting with a gene encoding a valuable human growth factor inhibitor protein, explain in a diagram all of the steps from transcription to rhTGFI protein folding and how each step can be optimized for maximum protein production by either (1) optimization of the expression vector or (2) optimization of the host cell containing the expression vector |
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Definition
Given that the product will be used in humans and it is a relatively small peptide, suitable hosts may include yeast (P. pastoris) and mammalian cells
Steps
1. intrinsic elements- vector (plasmid/gene copy number, genes for : selection, retention, and partition, instability inducing DNA sequences- Host (selection-sensitive genotype, cell-suicide elements)
2. transcription vector (promoter and regulatory sequences appropriate for each host, transcriptional terminators and attenuators, antiterminators )host - RNAase deficient strains may increase expression
3. translation -vector (protein fusions: signal peptides for secretion, affinity sequences, secretion affinity and double affinity sequences for purification (host -protease deficient host strains)
5. folding (vector co express chaperones or PDI for correct disulfide bond formation) |
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Term
| Explain the significance of Crabtree-negative yeasts as hosts for recombinant protein production |
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Definition
| Crabtree positive yeasts will produce ethanol aerobically at high glucose concentrations when glucose is fed too fast. Crabtree negative yeasts have very low levels of ethanol production under aerobic conditions which translates into higher cell densities and recombinant protein productivities |
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Term
| Non-obviousness of an invention disclosure or patent filing |
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Definition
| non obviousness or invetiveness is one of the most important patentability requirements. Basically even if a patent applicant demonstrates novel subject matter and utility, the patent might still not be granted if the invention can be predicted from prior art |
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Term
| complex media growth nutrients |
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Definition
| complex media are agricultural commodities (seed meals, oils, starches) or extracts from plants animals or yeast that are rich in carbohydrates, amino acids, vitamins, minerals, proteins and fatty acids. Such media is complex because the precise individual components of these media vary seasonally and depend on where the plants are grown and how the materials were processed. These media can contain a wide range of nutrients that are well above the minimal nutritional requirements of the organism being cultured. They are inexpensive, available in large quantities, and are useful to support the growth of a wide range of microorganisms |
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Term
| Synthetic biology in relation to biomanufacturing |
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Definition
| it refers to the re-design of natural biological processes and metabolic pathways for the over production of useful metabolites. It uses tools as DNA sequencing and recombinant DNA technologies, DNA synthesis and synstems biology to design and incorporate new capabilities into suitable hosts |
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| An affinity "tag" gene fusion technology such as a His tag is one approach to simplify recombinant protein recovery. List the advantages of this approach. |
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Definition
Advantages
1. protect against proteolytic cleavage
2. simplified recovery and purification using affinity resins
3. can include signal sequences for secretion
4. can detoxify proteins by generating pro-proteins or dimers |
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Term
| How can more recent gene fusion technologies such as self-cleaving inteins simplify this approach |
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Definition
| self cleaving inteins are used for protein purification without chromatography and do not need enzymes to cleave fusion tag which eliminates the need to remove cleaving agents during downstream processing |
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| An affinity "tag" gene fusion technology such as a His tag is one approach to simplify recombinant protein recovery. List the disadvantages of this approach. |
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Definition
disadvantages
* fusion tag needs to be cleaved chemically or proteolytically to recover the desired protein product
- fusion tags can alter biological activity of proteins |
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