Download Gene Expression and Regulation

AP BIOLOGY
GENETICS RESEARCH PAPER
Introduction: During the annual Nobel Week, held each December in Stockholm, the current year’s Nobel
Laureates participate in a whirlwind of events and activities leading up to the 10th of December, when they receive
their Nobel Prize and attend the Nobel Banquet.
“The event aims to stimulate discussion at the highest level on a topical science-related theme by bringing together
Nobel Laureates, the world’s leading scientists and experts, key opinion leaders, policy makers and the general
public, online as well as on site. By bridging science and society, it’s an opportunity to stimulate thinking, excite
imagination and inspire greatness!”
The theme for the 2015 Nobel Week Dialogue is The Genetic Revolution and its Impact on Society, a choice partly
inspired by the fact that 2012 marks the 50th anniversary of the award of the 1962 Nobel Prize in Physiology or
Medicine to Francis Crick, James Watson and Maurice Wilkins for their discovery of the molecular structure of
DNA. The day’s events will be dedicated to reviewing the past 50 years of progress in genetics and genomics,
assessing the implications for today’s society and looking towards future trends.
Research Goals: Your assigned task is to choose one Topic below (approval from teacher for topics other than
those listed below) and do as the Nobel Laureates do during Nobel week- (1) review the progress in genetics and
genomics for your topic, (2) assess the implications/impact for today’s society and (3) look toward future
trends. You will be summarizing your research AND discussing your personal insight based on the data you find
in a 5-7 page formal research paper (double spaced, 12 font, 1 inch margins, APA formatting, minimum 5
resources). This writing assignment will include several self/peer/teacher reviews and revisions along the way
making the process just as important as the product.
Format: There are three sections/goals to this paper (see above). In addition to an introductory paragraph the first
section must address and summarize your chosen theme including scientists and/or technology involved. The
second section must summarize one relevant piece of current research within the last five years. Your stated
research must clearly show how it is related to the topic you have chosen. What designs, methods and results were
used in the study? The third section should present potential legislation or way of life that affects society in the
future. Your presentation should be backed by the research from the first two sections. The themes are very broad,
so don’t be afraid to narrow your research.
Themes: http://www.nobelweekdialogue.org/the-genetic-revolution-and-its-impact-on-society/
 Personalized Medicine and Disease Genetics
 The Genetic Revolution in Agriculture
 Regulation of Gene Expression/Epigenetics
 Genetics and the Environment
 Human Evolution/Synthetic Biology
How to Do Library Research: http://mcldaz.org/search/misc/esources.aspx?ctx=1.1033.0.0.1&Category=477
APA Style- http://www.differencebetween.net/language/difference-between-mla-and-apa/
Your online sources are limited to reliable sources. Web sites consulted must be connected to a reliable print source (such
as Time or Newsweek), organization (like the Alzheimers Association or PETA), government agency (such as the
USDA or National Park Service), or institution (a school or medical research facility, for example).
You should document your sources for the following reasons:—information such as quotations, paraphrased or
summarized ideas, debatable or little known facts, statistics and other quantifiable data, unique phrasing or terminology,
and others opinions or assertions. You will document using APA style: http://www.apastyle.org/learn/tutorials/basicstutorial.aspx
Timeline (100 points for prep work, 100 points Final Draft, 200 points total):
11/19- Receive Genetics Research Assignment. Read through and choose a topic.
12/1- Topic due, minimum of 5 sources listed APA format, goals 1, 2, and 3 discussed in outline format
(key information in your own words). 40 pts
12/8- Supportive facts, current research and legislation due described in paragraph format. 30 pts
12/10- Rough draft due (2 copies) and peer review (in class) 30 pts
12/16- Final draft due (TurnItIn.com)
_____/ 40
_____/ 30
_____/ 30
____/ 100
TURNITIN.COM
Class ID 11126140
Enrollment Password APBio1516
Peer Review
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Provide writers with real readers who must make sense of the writing.
Help writers improve their reading/critical analysis skills.
Help writers improve their writing skills and final products.
Writers Name_______________________
Readers Name_______________________
Writer: If you have any specific questions you want your reader to answer, or places in your essay you want your
reader to respond to, list them below:
Reader: Read through the essay once without marking on it or making any notes. Read through it a second time and
respond to the following question on their paper:
1. After reading the entire essay, summarize in your own words the writers reaction at the end of their paper,
including the main idea they are reacting to. Is the reaction narrow enough for you to easily follow? Do you
have any suggestions for how the writer might narrow the focus of the reaction further?
2. Mark a (?) in any places in the text that seem tangential or unrelated to the overall focus of the reaction and
explain in the text why you think this section may stray from that focus.
3. Mark at least one effective piece of evidence (example, personal experience, personal observation, etc.) with a
(*), and then explain nearby why you found that evidence effective.
4. Write (MORE) in at least one place where the essay could use more evidence, and then explain below what
those places could use to allow the reader to more easily relate to and understand the authors reaction.
5. List below at least 2 strengths of the essay, and explain why these aspects of the paper are working well.
6. List your three main suggestions for revision.
Topic #1 Personalized Medicine
Of all the scientific and social promises that stem from advances in our understanding of the human genome,
genomic medicine may be the most eagerly awaited. The prospect of examining a person's entire genome, or
at least a large portion of it, in order to make individualized risk predictions and treatment decisions is
tantalizingly within reach. This discussion will explain the genomic basis of personalized medicine and explore
its potential for good as well as its possible risks.
What is the human genome?
The human genome is the blueprint for each person's body, influencing how we look, our genetic
predispositions for certain medical conditions, how well our bodies fight disease or metabolize food, and
which therapies our bodies do and do not respond to. The genome consists of an organism's total DNA,
including its genes. DNA—the famous "double helix"—is composed of four chemicals, which are repeated
many times in different sequences. (The names of the chemicals are abbreviated as A, T, C, and G. That's
why DNA is sometimes referred to as a code with a four-letter alphabet.) The sequence of the chemicals
dictates the type of organism that develops, as well as other critical life functions. The human genome
contains approximately 3 billion pairs of these chemicals. Genes are believed to make up only about 2
percent of the human genome, with the rest consisting of "noncoding" regions, thought to regulate the
function of genes and contribute to the structural integrity of chromosomes.
2. What is personalized medicine?
Personalized medicine is a young but rapidly advancing field of healthcare that is informed by each person's
unique clinical, genetic, genomic, and environmental information. Because these factors are different for
every person, the nature of diseases—including their onset, their course, and how they might respond to
drugs or other interventions—is as individual as the people who have them.
Personalized medicine is about making the treatment as individualized as the disease. It involves identifying
genetic, genomic, and clinical information that allows accurate predictions to be made about a person's
susceptibility of developing disease, the course of disease, and its response to treatment.
In order for personalized medicine to be used effectively by healthcare providers and their patients, these
findings must be translated into precise diagnostic tests and targeted therapies. This has begun to happen in
certain areas, such as testing patients genetically to determine their likelihood of having a serious adverse
reaction to various cancer drugs.
Because the 2003 sequencing of the human genome provided crucial insight into the biological workings
behind countless medical conditions, scientists and physicians are advancing the field of personalized
medicine at a fast pace. It is not yet an established part of clinical practice, but a number of top-tier medical
institutions now have personalized medicine programs, and many are actively conducting both basic research
and clinical studies in genomic medicine.
Specific advantages that personalized medicine may offer patients and clinicians include:
 Ability to make more informed medical decisions
 Higher probability of desired outcomes thanks to better-targeted therapies
 Reduced probability of negative side effects
 Focus on prevention and prediction of disease rather than reaction to it
 Earlier disease intervention than has been possible in the past
 Reduced healthcare costs
Personalized medicine is not to be confused with "genetic medicine." Genetics, a field more than 50 years
old, is the study of heredity. It examines individual genes and their effects as they relate to biology and
medicine. "Single cell" genetic diseases include muscular dystrophy, cystic fibrosis, and sickle cell anemia.
(However, even these seemingly "simple" hereditary disorders can be influenced by other genes, as well as
by environmental factors such as diet and exposure to toxins.)
Genomic and personalized medicine aims to tackle more complex diseases, such as cancer, heart disease,
and diabetes, for years believed to be influenced primarily by environmental factors and their interaction with
the human genome. It is now understood that because these diseases have strong multigene components—
and in some cases might be caused by errors in the DNA between genes instead of within genes—they can
be better understood using a whole-genome approach.
http://health.usnews.com/health-conditions/cancer/personalized-medicine#2
Topic # 2 The Genetic Revolution in Agriculture
Process of Genetic Modification
Deoxyribonucleic acid, commonly known as DNA, is the hereditary material in a cell's nucleus that guides an organism to
develop in a certain way from an embryo into an adult. DNA affects almost every one of the organism's characteristics by
carrying the information, in the form of genes, required for each cell to make functional proteins. In addition to their
fundamental role in an organism's growth and development, these proteins impart individual traits. In plants, these traits
include the flavor and color of fruit, the ability to resist cold and heat shock, and the presence of specific enzymes that can
detoxify some chemicals.
Genetic engineers seek to impart desired traits from one type of organism to another by transferring the genetic material (or
genes) needed to create certain proteins. For example, much of the corn and cotton grown in Georgia has been engineered to
make a protein that is toxic to harmful insects. This protein is taken from the bacterium Bacillus thuringiensis (Bt) and
inserted into a crop plant's genome (or genetic makeup). Because Bt plants resist pests better than wild-type (normal) plants,
they require smaller amounts of pesticides than do unmodified plants.
To transform an organism's genome, researchers must identify DNA that codes for a specific trait, such as insect or drought
resistance, then isolate it from the organism's other genetic material. Using restriction enzymes, which are molecules that
serve as "DNA scissors," researchers isolate the
desired gene so that it can be cloned, which is the process of making multiple copies of the gene.
The gene copies are then transferred into the genetic material of the target organism.
To transfer a gene into a cell, where the gene can make its way to the nucleus, researchers must
first overcome the protective exterior layer of the cell, known as the plasma membrane. There
are three common ways to accomplish this task. One method involves shocking a cell briefly
with heat or an electric current, causing small pores to form in the cell through which the cloned
genes are able to gain entry. Another method is to shoot small gold particles coated with the
cloned genes into the cell with a gene gun.
Gene Gun
A third method involves cloning a gene into a bacterium or virus that will infect the target cell. Restriction enzymes are used
to insert the cloned gene into a plasmid vector, or small circular DNA, which is in turn introduced into the bacterium or virus.
Once the gene is inside the bacterium or virus, it can be transferred into the genome of the target organism. For example, the
bacterium Agrobacterium tumefaciens has been successfully used to transfer genes for increased drought resistance into
loblolly pine trees, which are commercially important to Georgia's paper and pulp industries.
Regardless of the technique used, once the transgenic material is inside the plasma membrane, some of the target cells will
incorporate that material into their own genome.
Example in Agriculture: Peggy Ozais-Akins, a professor of horticulture at UGA's Coastal Plain Experiment Station,
published a study in 2003 detailing her work to engineer pearl millet (Pennisetum glaucum), a drought-resistant cereal used
for grazing in the Southeast, including Georgia. Pearl millet cultivars (or varieties) have been improved over the years by
traditional breeding, but because of the lengthy time involved with breeding, some feared that improvements would not keep
pace with the demand for high-yielding, pest-resistant cultivars. Ozais-Akins successfully developed a system to make a
transgenic pearl millet cell that can be quickly improved using genetic-engineering techniques and then coaxed to grow into a
full, fertile plant.
http://www.georgiaencyclopedia.org/nge/Article.jsp?id=h-3716
Topic #3 Regulation of Gene Expression/Epigenetics
Gene Expression and Regulation
How does a gene, which consists of a string of DNA hidden in a cell's nucleus, know when it should express itself? How
does this gene cause the production of a string of amino acids called a protein? How do different types of cells know which
types of proteins they must manufacture? The answers to such questions lie in the study of gene expression. Thus, this topic
room begins by showing how a quiet, well-guarded string of DNA is expressed to make RNA, and how the messenger RNA
is translated from nucleic acid coding to protein coding to form a protein. Along the way, the room also examines the nature
of the genetic code, how the elements of code were predicted, and how the actual codons were determined.
Next, this topic room turns to the regulation of genes. Genes can't control an organism on their own; rather, they must interact
with and respond to the organism's environment. Some genes are constitutive, or always "on," regardless of environmental
conditions. Such genes are among the most important elements of a cell's genome, and they control the ability of DNA to
replicate, express itself, and repair itself. These genes also control protein synthesis and much of an organism's central
metabolism. In contrast, regulated genes are needed only occasionally — but how do these genes get turned "on" and "off"?
What specific molecules control when they are expressed?
It turns out that the regulation of such genes differs between prokaryotes and eukaryotes. For prokaryotes, most regulatory
proteins are negative and therefore turn genes off. Here, the cells rely on protein–small molecule binding, in which a ligand
or small molecule signals the state of the cell and whether gene expression is needed. The repressor or activator protein binds
near its regulatory target: the gene. Some regulatory proteins must have a ligand attached to them to be able to bind, whereas
others are unable to bind when attached to a ligand. In prokaryotes, most regulatory proteins are specific to one gene,
although there are a few proteins that act more widely. For instance, some repressors bind near the start of mRNA production
for an entire operon, or cluster of coregulated genes. Furthermore, some repressors have a fine-tuning system known as
attenuation, which uses mRNA structure to stop both transcription and translation depending on the concentration of an
operon's end-product enzymes. (In eukaryotes, there is no exact equivalent of attenuation, because transcription occurs in the
nucleus and translation occurs in the cytoplasm, making this sort of coordinated effect impossible.) Yet another layer of
prokaryotic regulation affects the structure of RNA polymerase, which turns on large groups of genes. Here, the sigma factor
of RNA polymerase changes several times to produce heat- and desiccation-resistant spores. Within this topic room, the
articles on prokaryotic regulation delve into each of these topics, leading to primary literature in many cases.
http://www.nature.com/scitable/topic/gene-expression-and-regulation-15
Epigenetic regulation of gene expression: how the genome integrates intrinsic and environmental signals.
Abstract
Cells of a multicellular organism are genetically homogeneous but structurally and functionally heterogeneous owing to the
differential expression of genes. Many of these differences in gene expression arise during development and are subsequently
retained through mitosis. Stable alterations of this kind are said to be 'epigenetic', because they are heritable in the short term
but do not involve mutations of the DNA itself. Research over the past few years has focused on two molecular mechanisms
that mediate epigenetic phenomena: DNA methylation and histone modifications. Here, we review advances in the
understanding of the mechanism and role of DNA methylation in biological processes. Epigenetic effects by means of DNA
methylation have an important role in development but can also arise stochastically as animals age. Identification of proteins
that mediate these effects has provided insight into this complex process and diseases that occur when it is perturbed.
External influences on epigenetic processes are seen in the effects of diet on long-term diseases such as cancer. Thus,
epigenetic mechanisms seem to allow an organism to respond to the environment through changes in gene expression. The
extent to which environmental effects can provoke epigenetic responses represents an exciting area of future research.
http://www.ncbi.nlm.nih.gov/pubmed/12610534
Topic #4 Genetics and the Environment
The expression of genes in an organism can be influenced by the environment, including the external world in which the
organism is located or develops, as well as the organism's internal world, which includes such factors as its hormones and
metabolism. One major internal environmental influence that affects gene expression is gender, as is the case with sexinfluenced and sex-limited traits. Similarly, drugs, chemicals, temperature, and light are among the external environmental
factors that can determine which genes are turned on and off, thereby influencing the way an organism develops and
functions.
Sex-Influenced and Sex-Limited Traits
Sex-influenced traits are those that are expressed differently in the two sexes. Such traits are autosomal, which means that the
genes responsible for their expression are not carried on the sex chromosomes. An example of a sex-influenced trait is malepattern baldness. The baldness allele, which causes hair loss, is influenced by the hormones testosterone and
dihydrotestosterone, but only when levels of the two hormones are high. In general, males have much higher levels of these
hormones than females, so the baldness allele has a stronger effect in males than in females. However, high levels of stress
can lead to expression of the gene in women. In stressful situations, women's adrenal glands can produce testosterone and
convert it into dihydrotestosterone, which can result in hair loss.
…
Drugs and Chemicals
The presence of drugs or chemicals in an organism's environment can also influence gene expression in the organism.
Cyclops fish are a dramatic example of the way in which an environmental chemical can affect development. In 1907,
researcher C. R. Stockard created cyclopean fish embryos by placing fertilized Fundulus heteroclitus eggs in 100 mL of
seawater mixed with approximately 6 g of magnesium chloride. Normally, F. heteroclitus embryos feature two eyes;
however, in this experiment, half of the eggs placed in the magnesium chloride mixture gave rise to one-eyed embryos
(Stockard, 1907).
…
Temperature and Light
In addition to drugs and chemicals, temperature and light are external environmental factors that may influence gene
expression in certain organisms. For example, Himalayan rabbits carry the C gene, which is required for the development of
pigments in the fur, skin, and eyes, and whose expression is regulated by temperature (Sturtevant, 1913). Specifically, the C
gene is inactive above 35°C, and it is maximally active from 15°C to 25°C. This temperature regulation of gene expression
produces rabbits with a distinctive coat coloring. In the warm, central parts of the rabbit's body, the gene is inactive, and no
pigments are produced, causing the fur color to be white (Figure 1). Meanwhile, in the rabbit's extremities (i.e., the ears, tip
of the nose, and feet), where the temperature is much lower than 35°C, the C gene actively produces pigment, making these
parts of the animal black.
As these examples illustrate, there are many specific instances of environmental influences on gene expression. However, it
is important to keep in mind that there is a very complex interaction between our genes and our environment that defines our
phenotype and who we are.
http://www.nature.com/scitable/topicpage/environmental-influences-on-gene-expression-536
Topic #5 Human Evolution/Synthetic Biology
…
But he happened to be in the process of creating a new discipline, synthetic biology, which—by combining elements of
engineering, chemistry, computer science, and molecular biology—seeks to assemble the biological tools necessary to
redesign the living world.
Scientists have been manipulating genes for decades; inserting, deleting, and changing them in various microbes has become
a routine function in thousands of labs. Keasling and a rapidly growing number of colleagues around the world have
something more radical in mind. By using gene-sequence information and synthetic DNA, they are attempting to reconfigure
the metabolic pathways of cells to perform entirely new functions, such as manufacturing chemicals and drugs. Eventually,
they intend to construct genes—and new forms of life—from scratch. Keasling and others are putting together a kind of
foundry of biological components—BioBricks, as Tom Knight, a senior research scientist at the Massachusetts Institute of
Technology, who helped invent the field, has named them. Each BioBrick part, made of standardized pieces of DNA, can be
used interchangeably to create and modify living cells.
“When your hard drive dies, you can go to the nearest computer store, buy a new one, and swap it out,” Keasling said.
“That’s because it’s a standard part in a machine. The entire electronics industry is based on a plug-and-play mentality. Get a
transistor, plug it in, and off you go. What works in one cell phone or laptop should work in another. That is true for almost
everything we build: when you go to Home Depot, you don’t think about the thread size on the bolts you buy, because
they’re all made to the same standard. Why shouldn’t we use biological parts in the same way?” Keasling and others in the
field, who have formed bicoastal clusters in the Bay Area and in Cambridge, Massachusetts, see cells as hardware, and
genetic code as the software required to make them run. Synthetic biologists are convinced that, with enough knowledge,
they will be able to write programs to control those genetic components, programs that would let them not only alter nature
but guide human evolution as well.
No scientific achievement has promised so much, and none has come with greater risks or clearer possibilities for deliberate
abuse. The benefits of new technologies—from genetically engineered food to the wonders of pharmaceuticals—often have
been oversold. If the tools of synthetic biology succeed, though, they could turn specialized molecules into tiny, selfcontained factories, creating cheap drugs, clean fuels, and new organisms to siphon carbon dioxide from the atmosphere.
…
Read more: http://www.newyorker.com/reporting/2009/09/28/090928fa_fact_specter#ixzz2C3YPzOL8