# data[].attributes.body
Must be completed BEFORE moving on to LT #2

Check in with Mrs. Duffy.

Complete mastery check.

Get feedback.

Move on to LT #2

# data[].attributes.headline
LT #1: Identify & Describe the levels of genetics.

# data[].attributes.subject
LT #1: Identify & Describe the levels of genetics.

# data[].attributes.body
Vocabulary + Levels of genetics … nucleic acids to populations.

# data[].attributes.attachment_link.readable_text
In the nucleus of each cell there are 23 pairs of chromosomes, i.e., a total of 46 chromosomes. Each chromosome is comprised of tightly-coiled DNA.

DNA, or deoxyribonucleic acid, is the hereditary material of all living organisms. The information in DNA is stored as a code consisting of four chemical bases that are pair-wise linked: adenine (A), guanine (G), cytosine (C) and thymine (T). The order, or sequence, of these base pairs determines the information available for building and maintaining an organism. Human DNA consists of about 3 billion base pairs, and more than 99 percent of those are identical in all people.

A gene is the basic physical and functional unit of heredity. Genes are a region of DNA that act as instructions to create molecules called proteins. In humans, genes vary in size from a few hundred to more than 2 million DNA base pairs. The Human Genome Project has estimated that humans have between 20,000 and 25,000 genes. A genome is the complete set of DNA of an organism.

The figure depicts the relationship between genes, DNA and chromosomes (2)
An important property of DNA is that it can replicate, or produce copies of itself. Each strand of DNA in the double helix can serve as a template to duplicate the sequence of the bases. This is critical when cells divide because each new cell must have an identical copy of the DNA present in the old cell.

Proteins are very important molecules and have many critical functions in the cells of the body. Proteins are comprised of smaller molecules called amino acids. In humans, there are 21 proteinogenic (protein creating) amino acids involved in the biosynthesis of proteins. A protein is formed from a sequence of hundreds up to thousands of amino acids. Shorter sequences of amino acids are termed polypeptides; however, in this context these are also regarded as peptides. The sequence of amino acids determines the unique three-dimensional structure and specific function of each protein. Proteins perform most of the activities in the cells and the body and are involved in different functions. Examples of protein function are as follows:
Different functions of proteins (3)

Antibodies (antibodies play an important role in immune defence and aid in protecting the body from infection)

Enzymes (catalyse chemical reactions and aid in reading the genetic information stored in the DNA)

Messengers (messenger proteins coordinate biological processes, e.g., hormones and transmit signals)

Structural components (provide structure and support to cells)

Transporters/storage (bind and transport molecules within and between cells)

Information concerning protein synthesis is stored in the DNA inside the nucleus. The information from the DNA is copied to mRNA (transcription). The mRNA leaves the nucleus and transports the information to the ribosomes in the cytoplasm. The proteins are generated at the ribosomes (translation).

A simplified picture of the production of proteins in a cell (4)

___

(1) http://phenomena.nationalgeographic.com/2013/10/23/how-many-cells-are-in-your-body/

(2) http://www.civilsdaily.com/blog/biotechnology-basics-of-cell-nucleus-chromosomes-dna-genes-etc

(3) http://www.masteringbiologyquiz.com

(4) https://oerpub.github.io/epubjs-demo-book/content/m46032.xhtml
READ MORE

https://ghr.nlm.nih.gov/primer/howgeneswork/protein
https://ghr.nlm.nih.gov/primer/basics/dna
https://ghr.nlm.nih.gov/primer/basics/gene
https://ghr.nlm.nih.gov/primer/hgp/description
http://dnsanalys.se/dna/
https://genteknik.nu/fran-gen-till-protein/

# data[].attributes.attachment_link.description
In the nucleus of each cell there are 23 pairs of chromosomes, i.e., a total of 46 chromosomes. Each chromosome is comprised of tightly-coiled DNA. DNA, or deoxyribonucleic acid, is the hereditary material of all living organisms. The information in DNA is stored as a code consisting of four chemical bases that are pair-wise linked: adenine (A), guanine (G), cytosine (C) and thymine (T).

# data[].attributes.attachment_caption
Genetics - Chapter 1 - Vocabulary Terms (22)

# data[].attributes.body
Option #1- Vocabulary (21 terms): Science Notebook, Notecards, Study Mrs. Duffy’s Quizlet (requires Proof!)

# data[].attributes.body
Option #2 Notes: Science Notebook, OneNote, Cornell Notes (AVID template - PDF - linked; Paper Copy - pick up in class)

1.1 Introducing Genes & Genomes & 1.2 Levels of Genetics and Genomics

Must include Essential Question, highlighting, summary or Q & A for 1.1 and 1.2

Essential Question: What are the levels of genetics 🧬 from nucleic acids (smallest) to gene pool of a population (largest).

# data[].attributes.body
Option #3 -LT #1 - Worksheet (Basic - Vocabulary, Labeling and Ordering)

# data[].attributes.body
Provide examples of how genetics is used in identification of people and in health care.

# data[].attributes.attachment_link.readable_text
"A molecular genetic technique used for the direct manipulation, alteration or modification of genes or genome of organisms in order to manipulate the phenotypes is called genetic engineering."
Or in other words, we can say,

"Genetic engineering is a technique using which the genetic composition of an organism can be altered."

The technique is often known as genetic manipulation, genetic modification or genetic alterations, broadly it is categorized as genetic engineering.

In this technique, a recombinant DNA is constructed and inserted into the host genome using a vector. Or we can delete some mutant sequences from a genome. The first recombinant DNA was constructed by Paul Berg in 1972.

Using the genetic engineering technique genetically modified organisms can be constructed which are economically very important for us.

It is employed for the production of improved plant species, therapeutic drugs or proteins, prevention of inherited genetic disorders and construction of a genetically modified organism.

In the present article, we will our major talk is genetic engineering and its applications. The content of the article is,

Humans are manipulating the genetic material of many organisms for long. Using selective breeding and cross-hybridization, economically important plant species were created by us.

The purpose of developing the genetic engineering or genetic manipulating technique is to produce organisms or phenotypes which are useful to us. Genetic engineering techniques are used for,

Construction of genetically modified plant species.

Abiotic and biotic stress resistant plant species.

Economically important plant species

Commercially valuable organism

For the production of therapeutic drugs

Prevention of genetic abnormalities.

"In genetic engineering, two different cell's DNA are combined and inserted into the host genome via vector." Important components of the gene manipulation experiments are explained here.

using the plasmid DNA like vectors the gene of interest is inserted into the host genome. Vectors are kind of vehicles which transfer the genetic material.

Definitions:

"A technique used to insert or delete a mutant gene or to manipulate a genome of an organism is known as genetic engineering."

History of genetic engineering:

The term genetic engineering was first used by the science-fiction novelist, not by any scientist. In the year, 1951, Jack Williamson used the term "genetic engineering" for the first time in his novel "Dragon's island".

Soon after that, the molecular structure of the DNA was discovered by Watson and Crick, although the genetic experiments were popular since the time of Mendel.

The first recombinant DNA was constructed by Paul Berg in 1972. In the same year, Herbert Boyer and Stanley Cohen performed gene transfer experiments. In 1974, Rudolf Jaenisch had created genetically modified mice, the first time in the history of genetics.

After the success of Rudolf, the genetically modified or genetically engineered tobacco plant species was developed in 1976.

During this period (between 1960 to 1990) restriction digestion, ligation and PCR like techniques were discovered which gave wings to genetic engineering technology.

Related article: What is a genome?

Type of genetic engineering techniques:

Recombinant DNA- A recombinant DNA technology is a type of genetic engineering technology in which an artificial DNA molecule is constructed by ligating two different DNAs using physical methods. For that, the gene of interest is inserted into the plasmid vector and used for gene transfer experiments.

Gene delivering- Gene delivering technique is employed for the insertion of a gene of interest into the host genome.

Electrophoration, solicitation and viral vector-mediated gene transfer, liposome-mediated gene transfer, transposon-mediated gene transfer are some of the methods used for that.

Gene editing- A gene-editing technique is used to edit the genome in which an undesired DNA sequence is removed or a new gene can be inserted into the host genome. CRISPR-CAS9, TALEN and ZFN are some known gene-editing tools used in gene therapy experiments.

Read more: What is gene editing and CRISPR-CAS9?

Process of genetic engineering:

The genetic engineering technique is used for many different purposes thus we must have to decide first the purpose of the experiment. The entire process of genetic engineering can be divided into 5 broader steps:

Selecting and isolating the candidate gene

Selection and construction of plasmid

Gene transformation

Insertion of DNA into the host genome

Confirmation of insert

Selecting and isolating the candidate gene:

The gene must contain a sequence of DNA that we want to study and for that, a gene has some special characteristics. A candidate gene should have high GC content and a lower repetitive DNA sequence.

In addition to this, the gene of interest must not be too long- only a few kb genes can be successfully inserted. Longer the gene higher the chance of failure. The candidate gene must have a start and stop codon in it. Related article: What is The Genetic Code?

Now, the gene of interest can be isolated from the rest of the DNA using either restriction digestion or polymerase chain reaction.

The restriction endonucleases are the bacterial enzyme having the power to digest DNA sequence at a specific location. Using a specific type of restriction endonuclease we can cut and isolated our gene of interest.

The restriction digestion method is explained in our previous article: What is restriction digestion?

In the polymerase chain reaction, using the information of the gene sequence, the gene of interest or the candidate gene is amplified in the thermocycler.

The machine, using the polymerase chain reaction makes millions of copies of a gene of our interest. Through the process of agarose gel electrophoresis, the amplified gene is isolated.

If the gene of interest is well studied, previously, then the information of a gene is accessible in the genetic library and we can use it for the artificial synthesis of a gene of our interest. (using the genetic library information, the gene can also be artificially synthesized)

In the next step, perform DNA purification, if required. Now our DNA is ready to insert in a plasmid.

Selection and construction of plasmid:

Selecting plasmid for the genetic engineering experiment is one of the crucial steps in the entire experiment. Before selecting the plasmid, we must understand why the plasmid is used in the gene transfer experiments.

The plasmid DNA is a circular, double-stranded cytoplasmic DNA of the bacteria that replicate independently.

Scientists are using it as a vehicle for transferring the gene of interest to the target location in the genome. It can efficiently transfer the gene at the target location. The structure of plasmid is explained in the figure below,

Related article: What is a plasmid?
Preparation of plasmid:
Select the plasmid which suits your experiment.

The plasmid must have the origin of replication, promoter region, antibiotic resistance gene and other important sequences. Using the restriction digestion method, an insertion site is introduced in the plasmid at which our gene of interest is ligated.

Utilizing the T4 DNA ligase like power sealer, the DNA of our interest in inserted and ligated in the plasmid. Along with the plasmid, a selectable marker is also introduced in the plasmid DNA to identify the recombinant DNA.

In addition to this, a promoter region and terminator sequences are also included in the plasmid for the effective expression of a gene of our interest. A plasmid with our gene of interest and some other important sequences is now referred to as a recombinant DNA molecule.

Now our recombinant DNA is ready for for the expression.

If we are performing gene cloning than the plasmid is inserted in the bacterial host, for that generally are commonly used. Once the bacteria starts dividing, our recombinant plasmid DNA is also replicated along with it.

Now we have the multiple copies of our plasmid DNA which are extracted using the plasmid DNA extraction kit and used for the transformation experiments.

Transformation into the host genome:

Transporting the recombinant DNA into the recipient cell or the host genome is yet another tedious and difficult task. Various methods for recombinant DNA insertion is used for various cell types because a single method can't used for all cell types.

Various method for transformation:

We have covered a whole article on it. Read it here: Electroporation- A Modern Gene Transfer Technique.

Liposome mediated gene transfer- Using an artificial cell-like outer coat known as a liposome- recombinant DNA can be inserted in the host genome.

This method is one of the popular methods and routinely used in plant genetic engineering experiments. Here, the plant species is infected with the transformed bacteria for inserting a gene of interest.

Agrobacterium tumifecian is utilized to insert recombinant DNA into the plant cell. A gene of interest is inserted into the Ti- plasmid of the Agrobacterium. The plant cells are infected by this bacteria cell culture and the transformed cells are regenerated using the plant tissue culture methods.

Chemical in gene transfer- Some metal ions, chemicals, and solutions of different chemicals are also employed in the gene transfer experiments, however, the success rate is too low as compared with the other methods.

Confirmation of insert:

Our work is still not completed.

Now we have to conform, whether the recombinant DNA is inserted in our target cell or not. Various molecular genetic technologies are used for that. In the traditional culturing method, the presence or absence of a selectable marker is used to differentiate transformed cells from the untransformed cells.

Although, it is not necessary for the PCR based detection method. The polymerase chain reaction-based detection method is widely accepted more trusted than other methods.

DNA is extracted from the transformed cell and amplified using the primers complementary to our gene of interest or our recombinant DNA.

If the recombinant DNA is present it surely amplified otherwise no amplification obtained. For the two factor conformation, one primer set complementary to recombinant DNA specific and one set of primer complementary to the selectable marker sequence are taken and multiplex PCR is performed.

For validating results, amplification must be obtained in both the reaction.

But wait a minute!

What happened if any mutation occurred during the experiment in our gene of interest? Because the PCR can only amplify the DNA. We must need sequence information to detect the mutation.

For that, the DNA sequencing method is used.

DNA is extracted from the transformed cells and the gene of interest is amplified using the PCR. Now the PCR amplicons are used for DNA sequencing in which using the fluorescent chemistry the sequence of our gene of interest is orderly determined.

Once all the parameters for determining the gene of interest fulfilled, our cells are now ready to inject in the host organism or for tissue culture experiments.

Applications of Genetic engineering:

Now coming to the important point of this topic, "What is genetic engineering used for?"

Genetic engineering has great industrial and agricultural value. It is practiced in medicine, genetic research, agriculture, crop improvement, and for production of therapeutic drugs.

It is also used in the development of genetically modified organisms. Here we are discussing some of the important applications of genetic engineering.

The recombinant DNA technology is used in the crop improvement and development of new economically important traits. Some of them are:

Herbicide resistance

Virus resistance

Delayed fruit ripening

Altered oil content

Pollen control

Development of cold and drought-tolerant plant species.

A classical example of it is the BT cotton- one of the types of genetically modified species provides resistance to the plant against bacillus thuringiensis.
Process of developing genetically modified plant species:
A gene of interest is isolated from the organism using restriction digestion or amplified by the polymerase chain reaction. Recombinant DNA is constructed by inserting a gene of interest into the plasmid, here the T- plasmid is used.

In the next step, the T- plasmid is inserted into the agrobacterium. In the last step, the plant species is infected with the transformed bacterial cells and cultured. The entire process of it is shown in the figure below,

GMF- genetically modified food is another best application of genetic engineering in which economically important food products are constructed using recombinant DNA technology.

The classical example of it is Flavr Savr tomato, a genetically modified tomato species made up of the antisense RNA technology. It has great economic values as the GM- tomato can easily be transported from one place to another place.

Another important application of genetic engineering is genetically modified or genetically engineered food.

The quality of some of the food products such as cotton, corn, and soybeans are improved using the present recombinant DNA technology. The aim of developing genetically modified crops or plant species is to make them economical important, nutritious, protein-rich, disease, and stress resistance.

Even, using genetic engineering and tissue culture techniques insecticides resistance plant species in tobacco, potato, corn, and cotton are developed.

In addition to this, some modified plants capable of generating their own fertilizers can also be created using the present genetic modification technique.

Transgenic model organisms are developed to test different parameters- the function of certain genes can be determined by designing the transgenic microorganism and animal models.

Harmful pathogens and insecticidal pasts can be destroyed using genetically modified microorganisms which are capable of degrading toxics.
Medicinal applications:
Low-cost drugs, hormones, enzymes, and vaccines are created using genetic engineering tools.

The anti-blood-clotting factor is the best example of it in which the plasminogen activating enzyme which is capable of dissolving the blood clot is artificially designed and used in the patients with coronary artery disease or heart attack.

Other examples are two other therapeutic proteins somatostatin and lymphokines which are worked against several disease conditions and can be synthesized artificially. Insulin is yet a classic example of a therapeutic protein designed using genetic engineering technology.

A gene for insulin is isolated by restriction digestion or through PCR and inserted int the plasmid. The recombinant plasmid DNA is immediately inserted into the bacterial or yeast cell in which the plasmid is multiplying. As the microorganism starts dividing it starts making artificial insulin.

A large amount of insulin produced using the same technique at an industrial scale. The detailed outline of insulin production is shown in the figure below,

The commercial production of insulin started after the FDA approval in 1982.
Recombinant vaccines:
Vaccines against smallpox, herpes simplex virus and hepatitis are produced using the genetic engineering technique. The vaccines are the inactivated viral particles used to induce an immune response against that pathogen, however, the chance of contamination is high in it.

Using the recombinant DNA technology scientists has created a unique type of vaccines that only contains the DNA for viral coat protein thus the pathogen can never be activated again. The main advantage of it is that it is safer, contamination-free and more reactive.
Genetic engineering in gene therapy:
Using the gene therapy or gene transfer technique, inherited genetic disorders can be cured. Cystic fibrosis, Duchenne muscular dystrophy and sickle cell anemia like gene therapies are now under the final clinical trial phase and ready to use on patients.

In the gene therapy, a faulty, non-function or mutated gene is replaced with the wild type one using the same technique as explained above.

We have covered amazing articles on gene therapy, read it here:

1. Gene Therapy: Types, Vectors [Viral and Non-Viral], Process, Applications and Limitations.

2. What is Gene Therapy? and How Does it Work?

3. Naked DNA Mediated Gene Therapy

4. Sleeping Beauty Transposon System: The Future of Gene Therapy

In addition to this, the genetic engineering technology is likewise used in the production of biofuel, disease, bio alcohol and other essential products.

Limitations of genetic engineering:

There are ethical issues associated with the use of gene therapy and genetically engineered products.

Also, to provide an economic value to the food product or any GM product, the nutritional values are compromised.

Because of the adverse effect of it, new resistant pathogenic strains are evolved faster.

Also, the side effects of gene therapy and the use of viruses in it are harmful to the target organism.

The technology is costlier as gene therapy cost up to 50,000 USD.

Playing with the embryo or fetus is against the natural law, people strongly believe in it, thus genetically modified food and plant products are always becoming a center of controversy.

However, using genetic engineering tools such as gene therapy and gene transfer technique, inherited disorders and cancer like lethal diseases can be prevented. Positive use of genetic engineering techniques can change the fate of mankind.
Sources:

Wallace RB. Principles of gene manipulation. An introduction to genetic engineering. Studies in microbiology. Am J Hum Genet. 1981;33(4):652-653.

# data[].attributes.attachment_link.title
What Is Genetic Engineering?- Definition, Types, Process And Application

# data[].attributes.attachment_link.description
"A molecular genetic technique used for the direct manipulation, alteration or modification of genes or genome of organisms in order to manipulate the phenotypes is called genetic engineering." Or in other words, we can say, "Genetic engineering is a technique using which the genetic composition of an organism can be altered."

# data[].attributes.body
Option #1 - Textbook page 10

Exome sequencing saves a boys life

Read article & complete worksheet

# data[].attributes.attachment_link.title
Duffy_Textbook_Pg10_Exome Sequencing Saves a Boy's Life

# data[].attributes.body
AVID 1-pager
Essential Question: What are the levels of genetics 🧬 from nucleic acids (smallest) to gene pool of a population (largest).

Colored

Fills entire page + Topic related border

More pictures/ illustrations than words

2 Quotes - textbook or credible source

Summary paragraph OR Bullet Points that answer the essential question.

# data[].attributes.body
Worksheet (concept focused)

# data[].attributes.body
Schoology Concept Check (LT #1)

Must score at least a 16/20

# data[].attributes.body
Connecting Ideas

Create a concept map using ALL 21 terms.

Need help getting started? Watch this video…

# data[].attributes.body
Scientist Social Media Page

Create a (fake) scientist social media presence.

Scientists/Individuals must have had an impact on genetics, genomes, exome or DNA sequencing.

Check with your teacher before beginning this assessment!

# data[].attributes.body
Option #2: Science Notebook or OneNote (Upload to Schoology)

Application of Genetics and Genomics (1.3) — Give an example of each …

Establishing Identity

Health care

Single-gene diseases

Gene expression

# data[].attributes.attachment_link.title
LT2 Required_Option2_Application of Genetics and Genomics

# data[].attributes.body
Science notebook or One Note

Read: Bioethic choices for the future pages 11-12

Answer questions 1-5 on page 12.

# data[].attributes.body
Bioethics - 2 Assignment Options

Research a story, article, historical event, or current issue regarding the topic of bioethics.

Read text, watch video or both!

The data bases online through the media center is a great resource and place to start!

Historical Examples to get you started ...

1945 - Nuremberg Trials

1948 - Declaration of Geneva

1951 - The Immortal Life of Henrietta Lacks

1972 - Tuskegee Syphilis Study

Feel free to find your own example!

ASSIGNMENT OPTIONS

Option 1: Write a 5 paragraph paper about your findings.

Upload paper to Schoology.

Option 2: One-on-one conversation - Share your research, findings, and thoughts directly with Mrs. Duffy.

Come prepared with notes, topics, & sources.

Article(s) you read or video(s) you watched.

# data[].attributes.body
Textbook Questions - Science notebook or OneNote

Page 9 - Key Concept Questions 1.3

Page 11 - Key Concept Questions 1.4

# data[].attributes.body
Date: Friday, September 1
Schoology Quiz - Vocabulary

# data[].attributes.body
Refresh your Biology knowledge with this Koala Karyotype!

- Individual, Pairs, or Pod Activity (Submit 1 per group to Schoology -- just make sure you include everyone's name!)

Paper Assignment -- Cut & Paste + Worksheet ?s
Take a picture and submit to Schoology when done!

# data[].attributes.body
POD, Pairs, or Individual Mastery Check
Focus: Genome-wide Associated Studies
What are they?
Learn More ... Study identifies African-specific genomic variant associated with obesity.

# data[].attributes.body
Karyotype Stations - 100 points -- Summative Assessment

Unit Ends -- Tuesday, September 12th -- Complete the following ...
* All assignments for LT #1 and LT #2
* LT #1 - Quiz (Vocabulary - Schoology)
* LT #1 - Mastery Check (1/2 Sheet Paper)
* LT #2 - Mastery Check - Individual, Pairs, or Pod must be completed. (Paper or Digital Worksheet)
* Koala Karyotype (Paper -- Cut & Paste + Worksheet ?s)
* Karyotype Stations (Paper or Digital Worksheet)

# data[].attributes.body
Grading (Weighted)

Daily Work (30% of quarter grade) - Student Choice - Required, Recommended, Rigor

Work at your own pace, BUT everything MUST be turned in by the END OF THE UNIT.

100 pts per unit - every unit!

Successfully complete: One (1) “required assignments” PER learning target 🎯 (LT)

Earn 60-69 points. D- to D+

Successfully complete: Two (2) “required assignments” PER learning target 🎯 (LT)

Earn 70-79 points. C- to C+

Successfully complete: One (1) “required assignment” PER learning target 🎯 (LT) + One (1) “recommended assignment” PER learning target 🎯 (LT)

Earn 80-89 points. B- to B+

Successfully complete: One (1) “required assignment” PER learning target 🎯 (LT) + One (1) “recommended assignment” from ANY learning target 🎯 + One (1) “rigor assignment” from ANY learning target 🎯 (LT)

Earn 90-100 points. A- to A+