Session 2-1: Cell cycle, mitosis, and cancer
Exam review
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Mitosisisatopicwherestudentshavesignificantfamiliaritywiththebasicfacts. The
purpose of mitosis is to insure that each daughter cell during cell division receives a
complete set of genetic information with a reasonable distribution of the cytoplasmic
contents. Thus a diploid cell remains diploid and the process is constitutive occurring in
somaticcells. Studentsneedtobeawareoftherelevantvocabularyformitosis,the
phasing of the process (what occurs when and how), and where mitosis fits in the
cell cycle. This material is very well covered in the assigned readings from the text book
and in the in-class presentation.
Summary of additional concepts and ideas
The in-class presentation and the pre-class video link the cell cycle and cancer into the
discussion of mitosis. If you have not watched the pre-class video it really is an excellent
review. The following points are relevant in the discussion of the cell cycle and cancer.
1. Thecellcyclehas4phases(M,G1,S,andG2)withafifthphasewherecells
that no longer divide are held (G0). This orderly sequence of events occurs in
all cells that are dividing. Not all different types of cells divide at the same rate
but a specific cell type will follow the same timing (for example epithelial cells
divide at a higher rate than many other types of cells). Mitosis in somatic cells
occurs during the M phase.
2. Thereareseveralregulatorypointsinthecellcyclethatareexplainedinclass.
All of these regulatory points are controlled by cell signaling cascades. Both
the G1 and M checkpoint regulation were described in general terms but not in
specific detail of exactly how the regulation occurs. The G1 checkpoint is
routinely impacted by growth factors. Based upon the integration of cancer
into this session, how might regulation of the cell cycle be affected in a cancer
cell?
3. Duringmitosischromosomesarebeingproperlydistributedintodaughtercells.
What do chromosomes look like or how many chromatids are there per
chromosomes at each stage of the cell cycle? What is the relationship between
an interphase chromosome and a mitotic chromosome? How does the linkage
to the mitotic spindle occur and how do the spindle microtubules impact
separation of chromosomes/chromatids? Cohesin proteins are required to
keep chromatids attached and their destruction triggers anaphase events.
4. The vast majority of cancers are diseases of somatic cells. What does this
statement mean? Can you explain the differences seen in the karyotype of the
pancreatic cancer cells when compared to normal cells?
5. Cancercellsshowmutationalchanges,chromosomeabnormalitiesandcell
cycle regulation loss. The processes that are aberrant in cancer cells are
mistakes made in normal biological regulation of the cell cycle and mitosis.
The Discovery Channel video illustrates a cancer treatment therapy using
immunological methods while a standard chemotherapy using Taxol and
Vinblastine illustrates how we currently operate to treat cancer.
For further study and background see:
the Chapter ending material for Chapter 8 (pgs 149-151);
the BioFlix pages for mitosis have more than just the animation shown inclass as there are
questions for review.
Session 2: Human Genetics and Disease I
Exam Review
Meiosis I and Meiosis II. In meiosis I the chromosome number is reduced from diploid to
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The process of meiosis is necessary for formation of gametes and involves two processes-
haploid and in meiosis II (processes very similar to mitosis) each gamete receives a
completecopyofthehaploidgenome. Meiosisonlyoccursinthegermlineandisimportant
in providing variability in the genetic composition of the gametes.
vocabulary for meiosis, the phasing of the processes (what occurs when and how),
This variation insures
geneticvariationinthepopulation. Studentsneedtobeawareoftherelevant
and the differences between mitosis and meiosis. This material is very well covered in
the assigned readings from the text book and in the in-class presentation.
You need to understand Mendelian genetics with the concepts and ideas behind the Laws of
Segregation and Independent Assortment. Traits (genes) are discrete entities and
inheritance is not blended. We expect you to know the terminology and basic analysis
involved in monohybrid and dihybrid crosses and to be able to map these crosses onto
meiosis. After all it is the process of meiosis that creates gametes and indicates how
segregation of alleles and independent assortment of chromosomes occurs. If you can
understand and map meiosis to the basics of Mendelian genetics you will have a
fundamental understanding of genetics.
You must be able to solve basic problems as covered at the end of chapter 9 in the review
pages. In fact this review in Chapter 9 makes our instructions to you simpler. Be able to
do all of the problems on pages 178-179. If you need more practice, please check out the
following site:
(http://www.biology.arizona.edu/mendelian_genetics/mendelian_genetics.html.).
Summary of additional concepts and ideas
Meiosis is a process necessary for sexually reproducing organisms. The processes of
spermatogenesis and oogenesis in humans were described. What are the essential features
of meiosis? First the diploid number of chromosomes must be reduced to the haploid
number in a systematic way such that one copy of each chromosome is represented in the
gametes. Second, there is variability of genetic information caused by the processes of
meiosis. This genetic variability (described below) maintains genetic diversity in the
population on which natural selection can act and provides tools for survival of the species.
• Variability comes from having different alleles for a particular trait on different
copies of homologous chromosomes. These will sort during meiosis.
• Variability comes from the independent assortment of the homologous
chromosomes such that with the haploid number (n) of chromosomes there are 22 3
possible combinations of chromosomes in human gametes.
• Variability is increased by genetic recombination causing new gene combinations
not present in either parental chromosome.
• Fertilization brings two different genotypes together to make a diploid organism.
• The evolutionary advantage of sex is significant.
• The main principles of genetics that were covered were the principles of
Mendelian genetics is fairly well covered and most of you have seen this in high school and
you have covered it extensively in the lab for BIOL-1010. You may or may not be good at
solving genetic problems. We suggest the end of Chapter 9 and the Arizona web site which
is a problem tutorial interactive site to fine tune your skills or to develop them if needed.
segregation and independent assortment. Can you use the basics of meiosis to
illustrate these principles?
• Understand the details of monohybrid and dihybrid crosses, phenotype and
genotype, and positioning of genes on chromosomes. How can homologous
chromosomes not have identical information (as in heterozygotes)?
• Recombination causes differences in the way alleles involved with the same trait
and on the same chromosome segregate.
• Understand how to read a family pedigree.
• Some human diseases are due to a single gene mutation. We used Tay Sachs
and Huntington’s Diseases as examples of recessive and dominant single gene
mutations.
For further study and background see:
the Chapter ending material for Chapter 8 (pgs 149-151); Chapter 9 problems on pages
178-179, the BioFlix pages for meiosis for the fundamentals. There are animations and
questions for review.
The answer to the attendance exercise:
You are crossing a homozygous dominant pea plant versus a homozygous recessive pea
plant. The traits are ROUND/wrinkled seeds (R/r) and YELLOW/green seed color (Y/y). the
capital letters indicate dominant traits.
The initial cross is easy because one parent produces only RY gametes and the other only ry
gametes. In a genetic cross, all F1 offspring are RrYy and heterozygous for ROUND and
YELLOW.
The second cross is of one of the F1 offspring, RrYy, where there are four possible gametes-
RY, Ry, rY, ry in equal proportion. When this strain is crossed versus the original parent
that is homozygous recessive for wrinkled green seeds, again there is only one type of
gamete- ry. This sets up the following:
F1
Recessive_
Pare
nt
gam
etes
Geno
Phenotype
t y p e
RY
x
ry
→
RrYy
Round Yellow
Ry
x
ry
Rryy
Round
gree
n
rY
x
ry
rrYy
Wrinkled
ow
ry
x
ry
→
rryy
Wrinkled
Yell
→
gree
n
Both the genotypic ratio and phenotypic ratios are identical and present in equal amounts or
1:1:1:1. Genotypes and phenotypes as written above.
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Session 3: Human Genetics and Disease II
Exam Review
Almost all of Chapter 9 in your text was covered in class in the two sessions on Human
Genetics. The Concept Review on pg 178 is still excellent. You need to understand
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Mendelian genetics in order to understand the topics in this session which are genetic
concepts and ideas that are not in line with the basics as understood by Mendel. While
chromosomes do not behave any differently, genetics gets much more complicated. We
have lumped all of these complications under one heading called “Non-Mendeelian Genetics.
You must be able to solve basic problems as covered at the end of chapter 9 in the review
pages. Some of these problems are examples of Mendelian genetics and some are
non-Mendelian problems. Be able to do all of the problems on pages 178-179. If you need
more practice, please check out the following site:
(http://www.biology.arizona.edu/mendelian_genetics/mendelian_genetics.html.).
This problem set from the University of Arizona contains problems of sex-linkage which we
use to introduce more complicated areas of genetic analysis that all fit under the umbrella of
Summary of Additional ideas and concepts
non-Mendelian genetics. The review concepts in Chapter 9 are again excellent along with
the problems.
The non-Mendelian genetics are often beyond what you have been taught previously.
Toward that end, be familiar with the following:
1. Sex-linkedgenesshowadifferentdistributionofphenotypesthatareshown
often by differences between the phenotypes of males and females.
Hemizygous refers to the male genotype because there is only one copy of the
X chromosome in males. How is the gender determined in humans?
2. Whatisthedifferencebetweenincompletedominanceandcodominance?
3. Onegeneticlocuscanhavemultipleallelesandonegenemayimpactmany
traits (pleiotropy).
4. Interactionsbetweengenesthataffectasinglephenotypearedefinedas
epistatic interactions.
5. Whatispolygenicinheritance?
6. Does the environment ever impact the expression of the genotype? Is this
always straightforward? Think about schizophrenia.
7. Whattypesofchromosomalrearrangementsoccurandhowdotheserelateto
genetic diseases or disorders?
8. Whatisaneuploidyandwhatareexamplesofhumandiseases/conditionsthat
are caused by changes in chromosome number? What if the change in ploidy
affects the sex chromosomes? What is nondisjunction and how might it apply
to having extra or fewer chromosomes than normal?
9. Canyoubuildapedigreefromageneticanalysisorgofromapedigreeto
determine genotypes?
10. Since we have used many human examples of traits and disease, please know
which diseases and traits go with each example of genetic phenomena. In
some cases we used plants or Labrador retrievers as examples and you should
understand these also.
Answer to attendance exercise
The genotype for a female with white eyes is Xr Xr (homozygous recessive). The only
gametes generated from this genotype are Xr .
The genotype of a male with red eyes is XR Y (hemizygous dominant). The gametes can be
either XR or Y.
The offspring must receive one of the Xr chromosomes from the mother (no other choice)
and either XR from the father (producing a daughter that is XR Xr and heterozygous for red
eyes) of Y from the father (producing a son that is Xr Y and hemizygous for white eyes).
While the distribution of phenotypes and genotypes are 50:50 red to white, only the females
have red eyes and only the males have white eyes. Such a striking difference between the
phenotypes and the sex is indicative of genes that are sex linked. Also, the male fly carried
a dominant eye color gene and none of the male offspring were “heterozygous” which would
make them red eyed. This indicates that the genes for eye color are on the sex
chromosomes.
_________________________
For those looking for additional information, please see the following:
Progeria New Hope for Patients video (mp4, 22mb) (Quicktime format)
Newblood test – Downs (pdf)
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Could gene therapy cure sickle cell anemia?
Session 2.4: Molecular Biology I
Exam Review
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The inheritable information in cells is always DNA. In a few viruses the
genetic material is RNA but these are the exception. In this session we
begin with instruction about the structure of a DNA molecule and we go into
some detail. As the heritable message that is passed from one cell to the
next, the structure gives us a point of reference to understand why DNA is
the informational molecule (instead of RNA) of cells. The structure, as
described by Watson and Crick, has certain properties that provide it with a
regularity of physical form and stability necessary for maintaining
information. The structure suggests at an elementary level how you take
one copy of a genome and convert it into two copies. The conformational
isomers of DNA molecules show us how DNA is folded to allow for
distribution between daughter cells (and to fit in the nucleus) and either
provide or deny access to the DNA molecule.
Transcription
RNA is similarly composed to DNA with a few subtle differences in composition, structure and function. What are these differences? If one knows the DNA sequence, the location where RNA polymerase binds to the DNA and the direction that the polymerase moves one can determine the sequence of the mRNA that encodes the information in the gene. Please be able to explain how the process works on an actual DNA molecule (directionality is important). There are many other roles and 3D forms for RNA molecules, often referred to as secondary structure. For example a major component of the ribosome (and the Domain system of phylogenetics), the 16s rRNA, has a significant secondary structure as do other examples provided in lecture. However, the secondary structure, dependent upon h-bonds between nucleotides is still a single strand if h-bonds are disrupted. mRNA is much more linear as it is read at the ribosome to determine the amino acid sequence of the protein encoded by the gene. Please note that all forms of RNA are represented by genes in the DNA.
Genes are described in many different ways; single-copy, families, and
multiple copies. You also learn that the information in a gene is typically
interrupted with non-coding information (exon and introns) and preceded by
regulatory information as not all genes are expressed under all conditions.
From genomic studies and using the human genome as a model of study, we
learn that not the entire DNA in the genome has an apparent function.
There are spacer regions that can be very large and contain both short and
long repeated DNA sequences, transposons, and non-functional genes.
There is some clustering of genes with similar functions as illustrated by the
close look at chromosome #11). We illustrate the techniques used to
sequence the genome. The last two slides provide some examples of
genomes that have been seque.nced and show the continuing rate of new
species genome acquisition
Summary of Additional ideas and concepts
·
· ·
·
For DNA structure, you should know:
polymer
The components of the mononucleotide building blocks of the
The base pairing rules
The components of the backbone and the opposite polarity of the
two strands
How the base pairs stack up
You should be able to extrapolate a mechanism for copying the DNA into two
sister DNA molecules simply based upon the structure.
DNA replication and transcription are described briefly and you need to
understand the process but not the names of all of the enzymes involved.
We do expect you to understand polymerase and helicase as they are
prominently featured in the lesson. Why does the DNA get unwound during
replication? We expect you to note differences in the enzymes and proteins
that do and/or control transcription.
In previous lessons you were shown that DNA molecules go from a state
where they are not visible using standard microscopes to a more highly
condensed form of the DNA where the chromatids can be distinguished
during mitosis and meiosis. Information on how DNA is packaged into
chromosomes is explained in this lesson and that should give an added
perspective on how to fit 2 meters of DNA into a tiny nucleus.
Examples or arrangements of genes are given during this lesson- single
copy, solitary, gene families or superfamilies, multiple copies, and
interrupted genes. In higher organisms, most genes are interrupted and the
interruptions are called introns and the information that encodes proteins is
called exons. You need to have some knowledge of the arrangement and
problems caused by these interruptions of genes. The “flyover” of the short
end of chromosome #11 provides fundamental information about the many
components of the chromosome that are not traditional genes as well as
providing insight into some of the types of gene arrangements.
Finally, we get to sequencing of DNA. The basic principles of automated
DNA sequencing are presented in videos and in animations. You need to
understand this sequencing process. It is astounding how little DNA in the
human genome is exons.
For additional study:
If you are interested in the players involved in determining the structure of
DNA and the role of Rosalind Franklin in this discovery, you will find the
following site full of information- http://www.pbs.org/wgbh/nova/photo51/.
To understand scientific rivalry, please see the following two videos:
https://www.youtube.com/watch?v=ojNUmQqq8Ig and https://www.youtube.com/watch?v=6W31QjzR37w. Craig Venter versus the government and Francis Collins.
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Session 2.5: Molecular Biology II Exam review
In the previous session we discussed the molecular details of DNA replication, mRNA synthesis and the genome- thus the focus was on reproduction of the genetic information that is passed on ,how that information is organized in chromosomes and how genes are transcribed. There were some surprises! In this session we discuss the molecular details of converting the genotype into the phenotype. The information in the genome is transcribed into messenger RNA (mRNA) which is a process called transcription. The transcript is then translated into polypeptides by reading the transcript and converting a language of nucleotides into a language of amino acids. The resulting polypeptides and their activity is responsible for the phenotype. Let’s look at one process at a time.
Translation
The ribosome speaks a language of amino acids but the information brought to the ribosome is in nucleotides.
The interpreter for the two languages is transfer RNA (tRNA) and the dictionary is the genetic code.
Be certain that you understand the genetic code without resorting to memorizing it. What should you know? An mRNA is not read from the first nucleotide to the last. There are special features for starting to read the
6.
nucleotides and for stopping the reading of the nucleotides. These are the start and stop codons. A codon is a 3 nucleotide letter sequence that codes for an amino acid. What other properties are inherent with regard to the genetic code?
tRNA is a perfect interpreter because it binds the amino acid at one end and has a three letter nucleotide region that base pairs with the codon in the mRNA- the anti-codon. The shape of the tRNA facilitates its interaction with the ribosome and the mRNA.
There are three major tasks for the ribosome, each with its own unique set of steps. You need to know these steps. First is initiation where the small ribosomal subunit, the mRNA, the start tRNA and finally the large subunit of the tRNA get together. Now we have the reading frame for beginning the synthesis of the polypeptide (what is reading frame?). The elongation steps involve reading the mRNA and adding the amino acids in a linear sequence that corresponds with the codons in the mRNA. tRNAs with their amino acids attached bind in special location in the ribosome. You need to be able to draw the peptide bond and know where the bond is synthesized on the ribosome and that ribosomal RNA (rRNA) is involved in the catalytic function. The final step is termination when the stop codons are in the codon/anti-codon binding sites. The ribosome and all of the other components, mRNA, tRNAs, finished polypeptide are released. You should be able to draw diagrams of the process and label all important physical locations on the ribosome.
The linear sequence of amino acids is not the active form of the polypeptide. All polypeptides fold into characteristic shapes that are unique to their activity be it enzymatic or structural. How important is this? Very important, as can be seen with diseases that are caused by misfolded proteins. We use prions and Mad Cow Disease as an example to make the point of proper folding and the function of the protein. After all, it is the action of the protein that provides your phenotype.
Gene expression is outlined in prokaryotic and eukaryotic systems. The major control in prokaryotes is at the transcriptional level and in the organization of genes involved in biochemical pathways. Eukaryotic cells in multicellular organisms have a much more broad approach and these approaches are enumerated in the summary. In multicellular organisms there are many different cell types yet they all have the same genotype. Muscle cells, pancreas cells and blood cells are compared to illustrate the concept of how gene expression is regulated to allow the same information to be available yet have different cell types (same genotype but different phenotypes). Also, the process of transcription is described as it has a central role in both prokaryotic and eukaryotic cells. At the end of chapter 11 on page 228 most of the concepts for gene expression are covered.
Summary of Additional ideas and concepts
The essential features of prokaryotic regulatory systems are efficiency, ability to
respond quickly to changes in their environment, and organization of genes in
1.
operons where the genes in an operon are those needed for a specific metabolic pathway. Approximately 70% of the genes in prokaryotes are organized in operons. An operon contains the structural genes linked together and a regulatory region preceding the genes and composed of a promoter (where RNA polymerase binds) and an operator where the regulatory protein interacts.
The transcription animation shown during class provides a quick look at transcription. In this example several regulatory proteins are involved in triggering RNA synthesis on one strand of the DNA molecule by RNA polymerase. RNA polymerase will polymerize nucleotides in the 5’ to 3’ direction using the 3’ to 5’ strand of the DNA molecule as a template. Only one strand of the DNA is copied and the direction of transcription is determined by the position of the promoter. If the other strand of the DNA were copied, the RNA polymerase would start at the other end of the gene because of the polarity of nucleic acids and make a different message. Thus copying both DNA strands will give you two different mRNAs of which only one will be correct.
Regulatory proteins or transcription factors act as environmental signals and can act in inducible, repressible, and activator roles. The conformation of the transcription factor is determined based upon binding the environmental sensor molecule and the type of regulation.
The lac operon is a classic example where the genes for lactose utilization are not routinely needed and therefore transcription of the genes is inhibited by the binding of the repressor protein to the operator (blocks binding of RNA polymerase). If lactose is present, it binds to the repressor protein (inducible system), changing its confirmation such that the repressor will not bind to the operator and RNA polymerase is free to bind at the promoter and transcribe all three genes in the operon.
The trp operon functions in a reverse manner in that the genes are routinely transcribed. If there is sufficient tryptophan, transcription is turned off by the binding of tryptophan to the inactive repressor protein such that the repressor is activated and it binds to the operator to block transcription. This is a repressible system.
Other prokaryotic regulation includes activator transcription factors which assist in RNA polymerase binding and post-translational activation/deactivation of enzymes.
2.
3.
4.
5.
Eukaryotic systems are not organized in operons and often genes for the same pathway or function are not clustered together or even on the same chromosome. We have seen some cases where genes of like function are clustered (globin genes as an example) but each will have its own individual regulatory region or promoter. RNA polymerase is responsible for transcription but in eukaryotic systems routine transcription requires protein transcriptional activators at a minimum. Other transcriptional activities include the following:
1.
There are transcription factors that serve as sensors but not toward basic biochemicals but toward signaling molecules or hormones. A transcription factor
2.
may bind to multiple promoters and not to just one promoter as in prokaryotes. Transcription factors typically activate by binding to the promoter and to other regions of the DNA near but not right next to the promoter. These regions are called enhancers. There are also negative regulatory proteins to block transcription. Protein binding to enhancers causes the DNA to bend bringing the enhancer factors and the promoter factors together to trigger transcription.
The overall state of condensation or packaging of the chromosome determines whether or not the chromosome can be transcribed. Mitotic chromosomes are inactive as are the Barr bodies or one of the two sex chromosomes in human females. X-inactivation was illustrated for the tortoiseshell cat coat color. Transcriptionally active regions have a less condensed chromosomal structure.
Eukaryotic cells have a host of post-transcriptional and post-translational regulatory mechanisms. These include:
1.
2.
3.
4. 5.
Alternative splicing of exons during the removal of introns from the pre-mRNA. Splicing out of introns is a precision process involving spliceosomes. However, as much as 50% of eukaryotic genes may have alternative splicing arrangements.
These mechanism yield similar proteins but not identical ones from the same genetic information.
Small silencer RNAs or microRNAs, that are encoded in the non-gene regions of the chromosome, bind to mRNAs and cause them to be degraded or block translation of the mRNA. This seems to be wasteful as the mRNA is made unnecessarily. Eukaryotes are not bound by efficiency as are prokaryotes.
mRNA in prokaryotes has a short half-life because of the need to respond quickly to environmental changes. Eukaryotic mRNA lasts on average several hours but the time is variable and can be prolonged under certain condition up to months (in response to hormones or other factors).
Under certain conditions, translation of mRNA can be blocked (class example was hemoglobin).
Post-translational mechanisms include activation or deactivation of proteins after they have been translated. Insulin was used as an example where the protein is modified by covalent bonds and cleavage of a portion of the molecule.
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Session 2.6: DNA Technologies and Genomics Exam review
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There is a variety of different DNA or molecular biological techniques that have been used to impact our lives and will continue to do so in the future. In fact, these techniques may lead to even more intrusive or beneficial impacts on society- depending upon your point of view. Most of these life changing impacts come in the field of medicine but we have provided examples that involve fashion (stone-washed jeans), food (golden rice), and forensics (DNA profiling). All of these examples come from a few basic facts and technologies. We have previously described the techniques used in DNA sequencing and described some of the uses of DNA sequence information.
In this session we focus on two major techniques, gene cloning and the polymerase chain reaction (PCR). It is important to understand the scientific principles of these two simple techniques and how they are used to impact medicine and other areas of modern society.
Summary of Additional ideas and concepts
In the process of gene cloning there are several tools that are utilized to accomplish the task of finding the gene of interest, moving it into a suitable vector/host system, and getting the gene to be expressed. The final steps in the process involve purification of the protein and control of manufacturing.
● We did not discuss precise techniques for finding the gene of interest other than looking for it in the correct tissue or organism. For example where would you look to isolate genes encoding proteins that regulate blood glucose levels? Also, if you really understand PCR and DNA sequencing, you could probably predict a method for finding a gene.
● DNA restriction endonucleases have important properties that allow any two DNA molecules treated with the same enzyme to be joined together. What is the reason for this statement and how do these enzymes work? What is a palindrome?
● The vector for carrying a specific gene is typically a plasmid or a virus and these are used to help in storing the genetic information or transmitting the information into another host.
● In all cases, we want a product (antithrobin III, cellulase, or factor XIII as examples). Sometimes products can be made in bacteria and sometimes they must be made in eukaryotic cells or even in whole organisms as in the genetic engineering of plants. Genes can be problematic because they have introns. If you clone eukaryotic genes into eukaryotic organisms this is less of a problem than if you clone eukaryotic genes into prokaryotic organisms. Prokaryotes can not remove introns from mRNA and therefore proteins will not be produced. However, isolation of eukaryotic mRNA from the correct tissue or organism provides a work around to this issue. Isolated mRNA with introns spliced out is treated with reverse transcriptase to make a double stranded DNA copy of the mRNA that can then be put into any organism that you wish. You should understand this process.
DNA profiling has a more limited list of techniques in that PCR is the most relevant followed by gel electrophoresis and identification of the bands on the gel. These are all techniques that you have used in the laboratory and you should understand them well. The important features of PCR are
● that you can amplify any segment of DNA for which you can design primers. You need to know what primers are and why they are needed.
● having a thermostabile DNA polymerase (commonly an enzyme isolated from a thermophilic microbe) so that the cycles can run without additional input once the reaction is started.
● 30 cycles of PCR can amplify a DNA molecule a billion fold.
Using PCR for DNA profiling or DNA fingerprinting means that you need to be able to distinguish between individuals much as you can with the old fashioned fingerprint. However, the DNA profile is much more precise that the older fingerprint using your fingers.
● The most useful DNA for profiling analysis is the short tandem repeats (STR) that are found in the non-gene DNA of the chromosomes. The number of repeats is what varies and this can be accurately determined using PCR technology. Primers are designed to look at these hypervariable regions by designing primers that bind to DNA sequences that are just outside of the STR regions. PCR will amplify small amounts of DNA as found at crime scenes into detectable amounts for gel electrophoretic analysis.
● The FBI has identified 13 of these regions on several different chromosomes and a STR markers for determining male or female. Using PCR technology, it becomes easy to rule a suspect in or out as the perpetrator of a crime based upon evidence collected at the scene of the crime compared to the DNA profile of the suspect.
● Profiling can be used for paternity testing, ancestor or genealogical studies, or identifying victims of major natural and human disasters from tissue sample.
For those students interested in further study of these topics please look at the following web site: http://www.dnai.org/d/index.html. The four applications are all highly interesting and build on the uses of DNA technologies for studies from forensics, medicine and human origins.
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Session 2.4: Emerging Diseases Exam review
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There is a variety of different DNA or molecular biological techniques that have been used to impact our lives and will continue to do so in the future. In fact, these techniques may lead to even more intrusive or beneficial impacts on society- depending upon your point of view. Most of these life changing impacts come in the field of medicine but we have provided examples that involve fashion (stone-washed jeans), food (golden rice), and forensics (DNA profiling). All of these examples come from a few basic facts and technologies. We have previously described the techniques used in DNA sequencing and described some of the uses of DNA sequence information.
In this session we focus on two major techniques, gene cloning and the polymerase chain reaction (PCR). It is important to understand the scientific principles of these two simple techniques and how they are used to impact medicine and other areas of modern society.
Summary of Additional ideas and concepts
In the process of gene cloning there are several tools that are utilized to accomplish the task of finding the gene of interest, moving it into a suitable vector/host system, and getting the gene to be expressed. The final steps in the process involve purification of the protein and control of manufacturing.
● We did not discuss precise techniques for finding the gene of interest other than looking for it in the correct tissue or organism. For example where would you look to isolate genes encoding proteins that regulate blood glucose levels? Also, if you really understand PCR and DNA sequencing, you could probably predict a method for finding a gene.
● DNA restriction endonucleases have important properties that allow any two DNA molecules treated with the same enzyme to be joined together. What is the reason for this statement and how do these enzymes work? What is a palindrome?
● The vector for carrying a specific gene is typically a plasmid or a virus and these are used to help in storing the genetic information or transmitting the information into another host.
● In all cases, we want a product (antithrobin III, cellulase, or factor XIII as examples). Sometimes products can be made in bacteria and sometimes they must be made in eukaryotic cells or even in whole organisms as in the genetic engineering of plants. Genes can be problematic because they have introns. If you clone eukaryotic genes into eukaryotic organisms this is less of a problem than if you clone eukaryotic genes into prokaryotic organisms. Prokaryotes can not
remove introns from mRNA and therefore proteins will not be produced. However, isolation of eukaryotic mRNA from the correct tissue or organism provides a work around to this issue. Isolated mRNA with introns spliced out is treated with reverse transcriptase to make a double stranded DNA copy of the mRNA that can then be put into any organism that you wish. You should understand this process.
DNA profiling has a more limited list of techniques in that PCR is the most relevant followed by gel electrophoresis and identification of the bands on the gel. These are all techniques that you have used in the laboratory and you should understand them well. The important features of PCR are
● that you can amplify any segment of DNA for which you can design primers. You need to know what primers are and why they are needed.
● having a thermostabile DNA polymerase (commonly an enzyme isolated from a thermophilic microbe) so that the cycles can run without additional input once the reaction is started.
● 30 cycles of PCR can amplify a DNA molecule a billion fold.
Using PCR for DNA profiling or DNA fingerprinting means that you need to be able to distinguish between individuals much as you can with the old fashioned fingerprint. However, the DNA profile is much more precise that the older fingerprint using your fingers.
● The most useful DNA for profiling analysis is the short tandem repeats (STR) that are found in the non-gene DNA of the chromosomes. The number of repeats is what varies and this can be accurately determined using PCR technology. Primers are designed to look at these hypervariable regions by designing primers that bind to DNA sequences that are just outside of the STR regions. PCR will amplify small amounts of DNA as found at crime scenes into detectable amounts for gel electrophoretic analysis.
● The FBI has identified 13 of these regions on several different chromosomes and a STR markers for determining male or female. Using PCR technology, it becomes easy to rule a suspect in or out as the perpetrator of a crime based upon evidence collected at the scene of the crime compared to the DNA profile of the suspect.
● Profiling can be used for paternity testing, ancestor or genealogical studies, or identifying victims of major natural and human disasters from tissue sample.
For those students interested in further study of these topics please look at the following web site: http://www.dnai.org/d/index.html. The four applications are all highly interesting and build on the uses of DNA technologies for studies from forensics, medicine and human origins.
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Session 2.8. New frontiers: Personalized Medicine. Hope or Hype? Exam review
In this session we explore the impacts of traditional and new genetic and molecular
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techniques to blend into the area of medicine and disease in humans. We explore the
details of personalized medicine based upon molecular gene mapping, individual genome
sequencing, and stem cell therapy/
Summary of Additional ideas and concepts
Personalized medicine provides the potential for medicine to switch from a reactive mode to
a preventative mode. In this session we rely upon video and animations to highlight recent
advances in personalized medicine. We describe the molecular techniques involved if they
have not been described previously. Are the new techniques hyped and spreading false
hope? What are the ethical issues concerning the techniques (stem cells) or utility of the
information (personal genomics)? The following information was covered:
1. Theutilityofpedigreeanalysisandgenemappingareexploredinrelationship
to inherited forms of breast cancer. Scientific information includes
understanding how to read a pedigree and the role of DNA markers or specific
DNA sequences within unique genes. These unique gene markers are located
at intervals along all chromosomes and their linkage to diseases or medical
conditions serve as indicators for mapping analysis, diagnostic analysis of
family members where the disease is present, and possibly for genetic
counseling in relation to life style and child bearing matters.
2. IndividualgenomesequencingdoesnotinvolvenewtechniquesforDNA
sequencing but asked whether the process can be accomplished faster and
economically. Why do we need to know our individual genome? The number
of human genomes completed is small (2-3) and extrapolating “normal” from
something less than normal is not possible with this sample size. The
arrangement of genes on a particular chromosome can have impacts on the
expression of the gene (cis effect). The significance of personal genome
information on how we live our lives is debated. Whether or not we want to
know the information is an individual decision. Since most human diseases
involve multiple genes, other than estimating the probability of getting a
disease, have we learned much? Since we do not have a mechanism to
replace genes safely, where is the sequence information leading.
3. Stemcellscomeintwoforms,embryonicstemcells(hES)andinduced
pluripotent stem (iPS) cells. There are differences between these two types of
stem cells. hES are totipotent, are isolated from embryos, and can
differentiate, under the right conditions, into all cell types whereas the
potential of iPS varies with the original tissue of origin of the cells and the
factors causing differentiation. In either case there are cell surface markers or
antigens that are used to indicate how closely the cells resemble early
embryonic cells. New techniques for converting differentiated cells into iPS are
described.