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Week 2 Principles of Biotechnology (1) Merged
Week 2 Principles of Biotechnology (1) Merged
SCIENCE OF INTEGRATION
History of Biotechnology
History of Biotechnology
History of Biotechnology
History of Biotechnology
History of Biotechnology
• 2013: Two research teams announced a fast and precise new method for editing snippets
of the genetic code. The so-called CRISPR system takes advantage of a defense strategy
used by bacteria.
• 2015: Scientists discovered a new antibiotic, the first in nearly 30 years, that may pave the
way for a new generation of antibiotics and fight growing drug-resistance. The antibiotic,
teixobactin, can treat many common bacterial infections, such as tuberculosis,
septicaemia, and C. diff.
• 2016: For the first time, bioengineers created a completely 3D-printed ‘heart on a chip.’
• 2017: Blood stem cells grown in lab for the first time.
History of Biotechnology
• 16 April 2019 – Scientists report, for the first time, the use of the CRISPR technology to
edit human genes to treat cancer patients.
• 27 April 2020– Scientists report to have genetically engineered plants to glow much
brighter than previously possible by inserting genes of the bioluminescent
mushroom Neonothopanus nambi.
• 11 December 2020 – Scientists report that they have rebuilt a human thymus using stem
cells and a bioengineered scaffold.- Tissue Engineering
2021
• Bioprinting method to produce steak-like cultured meat.
• A plant proteins-based biodegradable packaging alternative to plastic based on research
about molecularly similar spider silk known for its high strength.
• Embedded biosensors for pathogenic signatures – such as of SARS-CoV-2 – that
are wearable such as face masks.
Traditional (Ancient) Biotechnology
• Traditional biotechnology refers to the conventional techniques that have been
used for many centuries to produce beer, wine, cheese etc. These techniques
are still being used and if they do not include the use of any genetically
modified organisms, they are considered to be under traditional biotechnology.
Chinese, Sumerians and
Babylonians are considered
to understand anaerobic
principles which helped
yeast to make alcohol.
Egyptians on the other
hand showed adeptness at
using aerobic principles to
leaven bread.
Traditional (Ancient) Biotechnology
• The use of microorganisms for fermentation,
• Domesticating animals for livestock,
• Alcohol in the form of wine and beer,
• Herbal remedies,
• Plant balms for the treatment of wounds and ailments.
Modern Biotechnology
• Two important technique which enable development of modern
biotechnology:
1. Genetic engineering: Techniques to alter the chemistry of genetic
material (DNA and RNA), to introduce these into host organisms and
thus change the phenotype of the host organism.
• Hybridization procedures often lead to inclusion and multiplication of
undesirable genes along with the desired genes.
• The techniques of genetic engineering which include creation of
recombinant DNA, use of gene cloning and gene transfer allows us to
isolate and introduce only one or a set of desirable genes without
introducing undesirable genes into the target organism.
Modern Biotechnology
• Three basic steps in genetically modifying an organism:
• Identification of DNA with desirable genes
• Introduction of the identified DNA into the host
• Maintenance of introduced DNA in the host and transfer of the DNA
to its progeny.
Modern Biotechnology
2. Maintenance of sterile conditions: Microbial contamination-free
environment in processes to enable growth of only the desired
microorganism/eukaryotic cell in large quantities for the manufacture of
biotechnological products like antibiotics, vaccines, enzymes, etc.
Products of Modern Biotechnology
• Many products reflect the current needs of humans—for example,
pharmaceutical production, creating drugs for the treatment of human
health conditions.
Biopolymers
Enzymes
Biofuels
.
.
.
Types of Biotechnology
• Microbial Biotechnology
• Agricultural Biotechnology (Plant Biotechnology)
• Animal Biotechnology
• Forensic Biotechnology
• Environmental Biotechnology
• Nanobiotechnology
• Aquatic Biotechnology
• Medical Biotechnology
• Industrial Biotechnology
Biotechnology Regulations
• An essential aspect of the biotechnology business involves the regulatory
processes that govern the industry.
• Although the FDA sets the standards for biotechnology products, many times
the U.S. Department of Agriculture and the Environmental Protection Agency
are involved.
• Two important aspects of the regulatory process include quality assurance
(QA) and quality control (QC). QA measures include all activities involved in
regulating the final quality of a product, whereas QC procedures are the part
of the QA process, involving lab testing and monitoring of processes and
applications to ensure consistent product standards.
Ethics and Biotechnology
Potential promise of biotechnology
applications raises many ethical concerns.
Human cloning
Animal tests ?
An Introduction to Gene and
Genomes
**Organelles allow cells to carry out thousands of different complex reactions simultaneously. Each organelle is
responsible for specific biochemical reactions.
DNA: Inherited Genetic Material
• Genes influence how cells, tissues, and organs appear. These inherited
appearances are called traits. Through the DNA contained in your cells, you
have inherited traits from your parents, such as eye color and skin color.
• Some traits are controlled by a single gene, but many others are determined
by multiple genes, which produce many proteins that interact in complex
ways.
Chromosome Structure
• The size and number of chromosomes vary from species to species. Most
bacteria have a single circular chromosome, while eukaryotes typically contain
one or more sets of chromosomes.
Karyotype analysis for studying chromosomes
• Human Genome Project: Provided exciting insight into human genes, their
locations, and their functions.
Replication, Transcription, and Translation
Flow of genetic information in a typical cell (Central Dogma)
DNA Replication
DNA Replication
Transcription • RNA splicing is the removal of portions of
the primary transcript that are not protein
coding.
• Bacterial chromosomes are continuous – all DNA
sequence from the chromosome is found in the
mRNA.
• Eukaryotic chromosomes are discontinuous
• There are extra DNA sequences within the
genes that do not encode any amino acid
sequence called introns.
• Presence of introns makes direct translation
to synthesize proteins impossible.
• Transcription is catalyzed by RNA polymerase. • The introns are cut out and the exons (coding
• Process of transcription has 3 stages: sequences) are spliced together.
• Initiation binds RNA polymerase to the promoter
region at the beginning of the gene.
• Chain elongation then occurs forming a 3'-5'
phosphodiester bond, generating a
complementary copy.
• Termination is the final step of transcription when
the RNA polymerase releases the newly formed
RNA molecule.
The Genetic Code
• Each group of three nucleotides in the sequence of
the mRNA is called a codon, and each codes for a
single amino acid.
• All 64 codons have meaning.
• 61 code for amino acids.
• Three code for the “stop” signal.
• Multiple codes for an amino acid tend to have two
bases in common.
• CUU, CUC, CUA, CUG code for leucine.
• Makes the code mutation resistant.
• Codons are written in a 5' 3' sequence.
Translation
1. Initiation
2. Elongation
3. Termination
RNA and Protein Synthesis
Basics of gene expression control
• Gene expression refers to the production of
mRNA (and sometimes protein) by a cell.
• At any given time in a cell, only certain genes
are “turned on” to produce proteins, while
many other genes are silenced or repressed.
These genes may be expressed by cells in
response to specific cues from inside or
outside of the cell, to make proteins as
needed.
• How can genes be turned on and off in
response to different signals? Biologists call
this process gene regulation.
MicroRNAs: Gene expression regulation
MicroRNAs: Gene expression regulation
Gene silencing
Mutations: Causes and Consequences
• Mutations are a major cause of genetic diversity.
Types of Mutations
Sometimes mutations occur through spontaneous events such as errors during DNA
replication. Mutations can also be induced by environmental causes (e.g. Mutagens)
Types of Mutations
Real-time PCR
• Real-time or quantitative PCR (qPCR), enables researchers to quantify
amplification reactions as they occur in “real time”.
Gene Microarrays (DNA microarray)
Gene Microarrays (DNA microarray)
Gene mutagenesis studies
• Site-directed mutagenesis. In this technique, mutations can be created in
specific nucleotides of a cloned gene contained in a vector. The gene can
then be expressed in cells, which results in the translation of a mutated
protein.
• This allows researchers to study the effects of particular mutations on
protein structure and serves as a way of determining which nucleotides are
important for specific functions of the protein.
Bioinformatics
• An interdisciplinary field that applies computer science and information
technology to promote an understanding of biological processes.
• Databases - search the new sequence against all other sequences in the
database and create an alignment of similar nucleotide sequences if a match is
found.
• Widely used DNA sequence databases worldwide is called GenBank.
• For example, an NCBI program called Basic Local Alignment Search Tool (BLAST)
can be used to search GenBank for sequence matches between cloned genes
and to create DNA sequence alignments.
Bioinformatics and Genomics
Whole-Genome “Shotgun” Sequencing
• The entire genome, introns and exons, is sequenced. The complete genome
sequence is assembled with the help of software programs, and then individual
genes are identified through bioinformatics.
‘Omics’ Technologies
• Proteomics—studying all of the proteins in a cell.
• Metabolomics—studying the chemical processes involving metabolites, the
small molecule substrates, intermediates, and products of metabolism.
• Glycomics—studying the carbohydrates of a cell.
• Transcriptomics—studying all genes expressed (transcription) in a cell.
• Metagenomics—the analysis of genomes of organisms collected from the
environment.
• Pharmacogenomics—customized medicine based on a person’s genetic profile
for a particular condition.
• Nutrigenomics – Understanding interactions between diet and genes.
Proteins as Products
Asst. Prof. Fatma Gizem AVCI
fatmagizem.avci@uskudar.edu.tr
MA210
Protein Structures
• Proteins are large molecules required for the structure, function, and
regulation of living cells.
• Ribosomes are factories that produce proteins.
• Proteins have specific molecular weights. They also have an electrical charge
that cause them to interact with other molecules.
• The way the chemical structure and electrical charge of an amino acid can
influence its interactions with water: The molecules will be either hydrophilic
(water loving) or hydrophobic (water hating).
Protein Structures
• Primary structure: Sequence of the amino
acids. The 20 commonly occurring amino
acids are the building blocks that make up
proteins.
• Secondary structure: Hydrogen bond
formation, alpha helix, beta sheet, beta turn.
• Tertiary structure: Covalent bond formation,
determines protein’s function.
• Quaternary structure: Unique, globular, 3D
complexes built of several polypeptides
(chain).
Protein Structures
Posttranslational modifications: Phosphorylation, glycosylation, acetylation,
acylation, prenylation, methylation, ubiquitylation, and proteolytic cleavage.
Glycosylation
• In glycosylation, carbohydrate units (sugar
molecules) are added to specific locations on
proteins.
• Glycosylation can increase solubility and orient
proteins into membranes.
Protein Structures
Protein Folding
• Everything that is important about a
protein—its structure, its function—
depends on folding.
• Misfolding: Sickle cell anemia,
Alzheimer’s disease, mad cow
disease etc.
Protein Structures
Protein Engineering by Directed Molecular Evolution
• Introduction of specific, predefined alterations in the amino acid sequence can
be done with directed molecular evolution technology.
• Allows researchers to create proteins with specific enhancements.
• Production of enzymes - with high activity by random mutations
- that tolerate high concentrations of toxic compound.
• A mutation resulting in this type of organism is not possible in a natural
selection.
• Scientists have used directed evolution and rational design with varying
degrees of success to improve activity, stability, and selectivity of native
enzymes.
Protein Production
• Two major phases in producing proteins: Upstream processing and
downstream processing.
• Upstream processing: Actual expression of the protein in the cell.
• Downstream processing: Separation of the protein from other parts of the
cells and isolation from other proteins, verification of purity and
functional abilities, preserving the protein.
• The choices made during upstream processing can simplify downstream
processing.
Protein Expression: Upstream Processing
Bacteria: - The fermentation processes of bacteria are well understood.
- They can be cultured in large quantities in a short time.
- Bacteria are also relatively easy to alter genetically.
Protein Expression: Upstream Processing
Fungi: - Fungi are eukaryotic and capable of doing some posttranslational
modification.
- Many species of fungi are good hosts for engineered proteins.
Protein Expression: Upstream Processing
Separating proteins from all other cellular contents is not easy, and isolating the
target protein from the other proteins in the sample can be even more difficult.
Step one: Preparing an extract for purification
• If the protein is intracellular, the first task is cell lysis, disrupting the cell wall
to release the protein.
• Freezing and thawing
• Detergents (used to dissolve cell walls)
• Mechanical methods
• After the cells have been ruptured, organic alcohols and salts may be added
to the mixture to coalesce protein (initial concentration).
Step two: Stabilizing proteins in solution
• Maintaining a low temperature is crucial to protecting proteins, so most
purifications must occur at low temperatures.
• Maintaining the proper pH for the activity of a protein is also important.
• Natural proteases that can digest the target proteins in a preparation are
another threat. Protease inhibitors can be added.
Step three: Separating the components in the extract
Protein precipitation:
• Salts, most commonly ammonium sulfate, can be added to the protein
mixture to precipitate the proteins by removing water from between the
protein molecules (ethanol, isopropanol, acetone, and diethyl ether).
Filtration (size-based) separation methods:
• Centrifugation separates samples by spinning them at high speed.
• In membrane filtration, thin membranes of nylon or other engineered
substances with varying pore sizes are used to filter out all of the cellular
debris from a solution. First, microfiltration removes the precipitates and
bacteria. Ultrafiltration then uses filters that can catch molecules such as
proteins and nucleic acids.
Filtration (size-based) separation methods:
Step three: Separating the components in the extract
Filtration (size-based) separation methods:
• Diafiltration and dialysis are filtration methods that rely on the chemical
concept of equilibrium, the migration of dissolved substances from areas of
higher concentration to areas of lower concentration. Dialysis is often
required to remove the smaller salts, solvents, and other additives used
earlier in the purification. Diafiltration adds a filtering component to dialysis.
Step three: Separating the components in the extract
Chromatography:
Allows us to sort proteins by size or by how they cling to or separate from
other substances.
• Size-exclusion chromatography (SEC) uses gel beads as a filtering system.
• Ion-exchange chromatography, relies on an electrostatic charge to bind
proteins to resin beads in a column.
• Affinity chromatography relies on the ability of most proteins to bind
specifically and reversibly to uniquely shaped compounds called ligands.
Size-exclusion chromatography (SEC)
Ion-exchange chromatography
Affinity chromatography
Analytical methods
Preserving Proteins
• One means of preserving the protein is lyophilization, or freeze-drying.
• Many freeze-dried proteins may be stored at room temperature for
prolonged periods of time.
Proteins as Biotechnology Products
• Biotechnological drugs and other medical applications (hormones, antibodies)
• Food processing (baby food, cheeses, baked goods, beer, dietetic foods)
• Textiles and clothing (spider silk fibers)
• Detergents (proteases, lipases, amylases)
• Bioremediation-treating pollution with proteins
Proteins as Biotechnology Products
Proteins as Biotechnology Products