Human Biology: Quiz #5

Apoptosis

- "Cell suicide" or programmed cell death

Cancer stages

- 0: in situ tumor, cells in the tumor are abnormal but still all clumped together. - I-III: Defined according to the cancer's size, degree of spread to surrounding tissues, and whether lymph nodes are now involved - IV: cancer has definitely metastasized, spreading to distant sites and organs. Targeted therapies such as radiation will not work because there are just too many targets. Treatment broad and potentially dangerous to normal cells

Advantages and drawbacks viral vectors

- Advantages: good at targeting and entering cells & some target specific cell types, can be modified so that they can't replicate and destroy cells - Drawbacks: can carry a limited amount of genetic material, so some genes might be too big to fit, can cause immune responses (sickness or could be blocked by the immune system, not successfully delivering gene)

Causative SNPs

- Affect the way protein functions, correlating w disease or influencing a person's response to medication - In gene - 2 forms: Coding and Non-coding

Benign vs. malignant tumor

- Benign: remains at the site of origin - Malignant: invades other tissues

Malignant tumor

- Cancer cells invade surrounding tissue and enter blood and lymph - Metastases may form at distant sites

Dysplasia

- Cell changes form

Ways to prevent DNA damage (DNA Damage Response)

- Cell cycle checkpoints, DNA repair mechanisms, apoptosis (cell death, cell suicide)

Hyperplasia

- Cell divides more rapidly than normal

In situ cancer

- Cell stays in one place

Significance of insulin

- First success of recombinant DNA technology in healthcare & disease treatment

What is genetic cloning?

- Gene cloning occurs when a bacterium (carrying a recombinant plasmid) reproduces, allowing for the production of multiple copies of the recombinant plasmid

What determines whether in vivo or ex vivo delivery mechanism should be used?

- Cells/tissues that need treating, where they are, how easily accessible they are, if the cells can be removed from the body, treated, and returned

Coding SNP

- Change amino acid sequences of gene's protein product

Non-coding SNP

- Change timing, location, or level of gene expression, which changes the amount that a protein is produced

As the cell cycle progresses, there are control mechanisms located at several __________, where the cell cycle may stop.

- Checkpoints

Linked SNPs

- Correspond to particular drug response or to risk of getting certain disease - Outside of gene, no effect on protein production or function

Gene guns are used as a technique for what?

- Creating transgenic plants (A mechanism by which foreign DNA can be transferred into a host cell)

What do restriction enzymes do for recombinant DNA technology (genetic engineering)?

- Cut DNA at specific nucleotide sequences (Most useful ones make their cut in palindromic DNA sequences. The resulting fragments with overhanging "sticky ends" = restriction fragments)

Process of cloning a gene

- Cut out gene of interest (insulin) from its source using restriction enzyme. - Insert into a plasmid—also cut with same restriction enzyme. Cutting with the restriction enzyme produces complementary sticky ends between gene of interest and plasmid. - Ligase pastes together the DNA fragments - Plasmid with gene of interest inserted is called a recombinant plasmid - Bacteria mutiple, and large amounts of the protein are produced

Critical factors in cancer

- DNA damage and genomic instability - If DNA damage is not repaired (repair mechanisms are deregulated) --> permanent mutations in genes related to cancer - Unregulated cell division

Why are sticky ends helpful in genetic engineering?

- DNA from different organisms that are cut w the same enzyme will have complementary sticky ends, allowing for recombination

Biotechnology uses scientific knowledge of DNA, genes, and gene expression to...

- Develop desired products (for practical applications) This includes... 1) Recombinant DNA technology (cloning + genetic engineering) 2) DNA fingerprinting (associated w/ blood) 3) Genome sequencing 4) Gene therapy

How to checkpoints work for repair?

- Facilitate repair by arresting cell cycle progression - (a) Inspecting the genome for damage & using repairing pathways - (b) Removing cell w apoptosis if cannot be repaired - (c) failing to remove cells with damage, causing permanent changes (point mutations/letter changes, chromosomal changes, deletions, translocations, and fusions)

Angiogenesis

- Formation of new blood vessels - When tumors recruit blood vessels from surrounding tissues and spread cancerous cells to other parts of the body

Differences between GMOs and transgenic organisms

- GMOs have acquired genes by artificial means - Transgenic from different species

Which of the following is used to separate fragments of DNA by size (& charge)?

- Gel electrophoresis

What is in vivo gene therapy?

- Gene is sprayed directly into the nose or introduced to the respiratory system by a virus - Used for cystic fibrosis patients - Transgene packaged into delivery vehicle and injected into patient

Gene Therapy vs. Gene Editing

- Gene therapy = adding new genes to human cells. Producing functional copy of gene to cells that have mutated version, but does not correct mutated version of gene. Functional gene is not "integrated" into genome, and corrective gene can be lost during division . - Gene editing = the precise manipulation of the sequence of the human genome for disease management. "Correcting" the mutated gene, ie CRISPR

What would be the advantage of introducing genes into germ cells rather than somatic cells?

- Genes introduced into germ cells would be passed on to gametes & future generations

How can cloning be used for disease treatment?

- Genetically engineered bacteria can make large quantities of valuable proteins to treat diseases, such as insulin

Regulation ensures _______

- Genomic stability! - Accuracy in duplication - Accuracy in division process - A cell healthy enough and not too old

Side effects of chemotherapy

- Hair loss - Anemia - Nausea - Depletion of white blood cells

History of DNA sequencing

- Have been improved since 1970's - First human genome sequence completed in 2001 - Numerous organisms' genomes have been sequenced now, providing comparative data that provides for many applications

Metastasis means that the tumor cells...

- Have broken off and traveled to new locations (remote regions) of the body

Steps leading to malignant cancer:

- Hyperplasia, dysplasia, in-situ cancer, metastasis and/or invasion

Rationale for immunotherapy, gene therapy, anti-angiogenic drugs

- Immunotherapy: promote responsiveness of immune system to fight cancer better - Gene therapy: genes introduced to replace defective genes or to direct synthesis of proteins to fight cancer - Anti-angiogenic drugs: may starve tumors by limiting blood supply,

What do bacterial plasmids do for recombinant DNA technology (genetic engineering)?

- Introduce a piece of foreign DNA into an organism & replicate that foreign DNA. (By growing the bacteria in a lab, scientists manufacture unlimited copies of a recombinant DNA plasmid)

Bioinformatics

- Learning from the human genome - Acquisition, storage, display, and analysis of info found in nucleic acid and protein sequence data - Individual and population differences are informative and are used to advance our understanding and applications in medicine, genetic engineering, evolution, biotech

Types of SNPs

- Linked - Causative

Humans have one of the _____ ratios of genes: nucleotides

- Lowest

Overview of genetic engineering

- Making recombinant DNA through "cut and paste" method, creating transgenic (GMO) organisms - Uses restriction enzymes and often a plasmid DNA from bacteria

Genetic engineering application example

- Mass producing useful proteins to treat diseases

What are the purposes of genetic engineering?

- Mass production of useful proteins to treat diseases - Pest resistance - Cleaning up toxic waste - Production of insulin - Dissolving clots

What are viral vectors and how are they valuable in gene therapy?

- Modified viruses that deliver genes into human cells - Viral vectors are unable to reproduce & cannot cause disease

Why are eyes commonly used to gene therapy treatments?

- Necessary to deal with cells, tissues, organs that are more easily accessible to deliver the gene therapy to the tissues, and eye retinas are very accessible

The process of accurately amplifying a sample of DNA is called a __________________________.

- Polymerase chain reaction (PCR)

Function of tumor suppressor genes

- Prevent the growth of mutated cells

2 key uses of recombinant DNA technology

- Produce and harvest large volumes of a protein - Be inserted into another organism, conferring the ability for that organism to express the new gene itself

Mechanisms of regulation/control

- Protein signals (like growth factors and other proteins) determine if/when the cell cycle proceeds from one stage to the next. *Growth factors activate other proteins to pass the "divide" signal along, responding to "contact" *Cyclins (and kinases)- "regulators" of checkpoints *Repair and inhibition signals, like apoptosis

Controls associated with tumor suppressor genes

- Proteins that arrest cell cycle, facilitate repair, induce apoptosis

2 main genes that regulate cell cycle

- Proto-oncogenes and tumor-suppressor genes

Proto-oncogenes vs. oncogenes

- Proto-oncogenes: control cell division, normal cells - Oncogenes: contribute to cancer cell development

RNAi

- RNA interference - Tool for studying genome, genes, and treatment against disease

Early detection methods

- Radiation techniques: X-rays, CAT scans, PET - Non-radiation techniques: ultrasound, MRI - Genetic testing: identify mutations in cancer-associated regulatory genes - Tumor markers: chemicals produced by cancer cell

Genetic engineering typically equates to making _______ DNA. It utilizes ________ enzymes that have ______ ends and a ___________ sequence.

- Recombinant - Restriction - Sticky - Palindromic

What controls cell divisions in healthy cells?

- Regulatory genes

Genome wide association studies

- Rely on linked SNPs to hone in on disease causing genetic variants - Helpful with "complex" diseases

1.5% of the genome are genes for functional proteins. What is the 98.5%?

- Repetitive sequences (repeats, duplications, viral "contamination"). These are largely ineffective or disruptive, but may allow for innovation of function - Templates for rRNA, rRNA, small RNAs - Regulatory sequences that turn genes on or off

DNA used in recombinant DNA techniques is first cut into fragments by __________.

- Restriction enzymes

After introducing recombinant plasmids into bacteria, the next step toward producing clones of a desired human gene would be...

- Selecting bacteria containing the human gene of interest and allowing it to reproduce

SNP

- Single Nucleotide Polymorphism - Single letter changes in DNA sequence, single-nucleotides substitutions of one base - 2+ versions of sequences must be present in at least 1% of population

How does X-inactivation occur?

- Small, interfering RNA & epigenetic mechanisms - Xist gene produces non-coding RNA, which binds to the X chromosome - Then works with methylation and deacetylation to inactivate the chromosome

Conventional cancer treatments pros and cons

- Surgery: has improved w better imaging techniques. May miss small groups of metastasized cancer cells - Radiation: targets tumor, but sometimes damages healthy cells. May miss small groups of metastasized cancer cells - Chemo: use of cytotoxic drugs to destroy cancer cells, targets rapidly diving cells. Causes negative side effects (nausea, hair loss, anemia), kills normal cells

Targeted therapy

- Targets specific characteristics of different types of cancer cells - Does not harm normal cells - Stops cancer cells from dividing, but cannot eliminate cancer cells that have already developed

An enzyme that occurs rarely in normal cells but frequently in cancer cells is...

- Telomerase

Angiogenesis is...

- The growth of new blood vessels that allow cancer cells to grow

For a tumor to form, which gene or genes must mutate?

- The proto-oncogene AND the tumor suppressor gene

Genetically engineered human insulin, human growth hormone, and human clotting factor VIII are made by:

- Transgenic bacteria

What do DNA ligases do for recombinant DNA technology (genetic engineering)?

- Used to rejoin DNA strands after restriction enzymes have cut/altered them

What is gene pharming?

- Using transgenic farm animals to produce human proteins for medical uses

Gene therapy requires that genes be transported to cells and incorporated into the cells' DNA; ________ transfer genes into human cells.

- Vectors

Potential carcinogens

- Viruses- vira lDNA may disrupt critical regions of DNA sequences - Tobacco-most lethal (about 30% of cancer deaths) - Radiation: UVB rays and skin cancer - Diet and metabolism (insulin-like growth factors may stimulate cell, free radicals and antioxidants plays a role)

What is ex vivo gene therapy?

- When cells containing a dysfunctional gene are removed from the patient, treated, and then returned to the patient - Cell-based delivery, with a transgene packaged into a delivery vehicle/cell, multiplied in lab, and then readministered into patient

Inheriting a mutated proto-oncogene from one or both of your parents means that __________.

- You're at an increased risk for cancer

2 controls associated with proto-oncogene s

- growth factors and cyclins, promoting cell growth

Role of free radicals and antioxidants

- radicals: highly reactive fragments of molecules that are produced by the body's biochemical processes - if detoxification processes become less efficient, free radicals may accumulate and damage other molecules, including DNA --> cancer - Antioxidants neutralize free radicals & their damage

1) What are transgenic organisms? 2) What are their uses? 3) What's most difficult to produce?

1) A living organism that has had foreign genes inserted into it. Used for many means of production... 2) Transgenic bacteria + yeast produce... - Human insulin grown in vats - Human growth hormone (GH) - Erythropoietin - Plasminogen activator (treats hemophilia) - Hepatitis B vaccine (from transgenic yeast) - Amylase (enzyme) - Citric acid & ethanol Transgenic plants produce... - GMOs (food crops that are resistant to insects) → tomato plants that resist freezing, tomatoes that last longer, apples & potatoes that resist browning, etc. 3) Transgenic animals = more difficult because animals don't take up plasmids as bacteria & plant cells do.

CRISPR-Cas9 technology (gene editing system): 1) Origin 2) Applications 3) Obstacles

1) Anti-viral defense system found in bacteria 2) Used to explore the function of a gene and edit an organism's DNA (adding, deleting, or replacing DNA at specific regions in the genome) → corrects/replaces a disease-causing mutation / cures a genetic disease. 3) Difficulties getting the CRISPR-Cas9 system into cells, whether there will be long-term effects, etc.

1) What is recombinant DNA technology? 2) What is it used for? 3) What specialized tools does it require?

1) Cutting, splicing, and cloning DNA (& the genes it contains) to transfer pieces of DNA from one organism to another. 2) Used to insert specific genes into bacteria/yeast so that the bacteria/yeast can be induced to produce useful protein products. 3) Requires restriction enzymes, DNA ligases, plasmids, and bacteria.

Protein products of recombinant DNA technology include...

1) Insulin; treatment for diabetes 2) EPO (Erythropoietin); treatment for anemia 3) GH; treatment for growth defects

How is cancer a "multi-hit" process

1) Oncogene 2) One mutated tumor suppressor 3) Second mutated tumor suppressor

1) What is DNA sequencing? 2) What are its applications?

1) Process that helps determine the nucleotide sequence of DNA. 2) Helps scientists trace the spread of diseases, aids in drug/vaccine development, and helps provide strategies for diagnosis, treatment, & prevention.

1) What is gene therapy? 2) What is a major obstacle in gene therapy?

1) The insertion of human genes into human cells to treat/eliminate a disease (Application of the Human Genome Project) 2) Difficulty delivering the normal allele into the cells of the recipient