Biology Exam 3

Explain how DNA technology can be used to improve the nutritional value of crops and to develop plants that can produce pharmaceutical products

) Reducing herbivore damage. Making crops more resistant to herbicides. Improving the quality of food products. rice does contain b-carotene, which is a precursor of vitamin A. Scientists set out to develop rice enriched in b-carotene. The synthetic pathway for b-carotene has three enzymes.To produce transgenic rice strains capable of producing b-carotene, the three genes that code for these enzymes had to be inserted into rice plants. Agrobacterium tumefaciens is a bacterium that infects plants, producing a tumorlike growth called a gall.A. tumefaciens is often used for genetic transformation of plants through transfer of its Ti (tumor-inducing) plasmid.A section of the Ti plasmid, called T-DNA, is incorporated into the genome of the host plant cell.Recombinant genes added to the T-DNA will be expressed in the new host plant. To develop golden rice, researchers modified Ti plasmids so that they contained the genes for the three enzymes needed to synthesize β-carotene. They then exposed plant embryos to Agrobacterium cells containing these genetically modified Ti plasmids. A transgenic plant was produced that is now called golden rice, because its high concentration of b-carotene gives it a yellow color

Describe the natural function of restriction enzymes and explain how they are used in recombinant DNA technology. Note the growth hormone example from the book

1) The recombinant DNA strategy for producing human growth hormone involved cloning the human gene, introducing the gene into bacteria, and having the recombinant cells produce the hormone. Restriction endonucleases are bacterial enzymes that cut DNA at specific base sequences called recognition sites.

Explain how the creation of sticky ends by restriction enzymes is useful in producing a recombinant DNA molecule

2) Restriction endonucleases often make staggered cuts in the DNA, resulting in sticky ends, complementary single-stranded ends. The sticky ends of the plasmids and cDNAs will bind by complementary base pairing. DNA ligase then seals the recombinant pieces of DNA together. If restriction sites in different DNA sequences are cut with the same restriction endonuclease, the presence of the same sticky ends in both samples of DNA allows the resulting fragments to be spliced together by complementary base pairing. This is the essence of recombinant DNA technology—the ability to create novel combinations of DNA sequences by cutting specific sequences and pasting them into new locations.

Explain how linkage mapping, physical mapping, and DNA sequencing each conributed to the genome-mapping project

2) To locate the gene or genes associated with a particular phenotype, such as a disease, researchers traditionally started with a genetic map (or linkage map or meiotic map).More recently, biologists have begun using a physical map of the genome. A physical map records the absolute position of a gene—in numbers of base pairs—along a chromosome.

Outline the procedures for cloning a eukaryotic gene in a bacterial plasmid

3) Researchers used reverse transcriptase to make complementary DNA (cDNA) from mRNA isolated from pituitary cells. (cDNA is any DNA made from an RNA template.) They then used DNA cloning—the process of producing many identical copies of a gene—to copy the cDNAs for analysis to determine which encoded the growth hormone protein. Plasmids are small, circular DNA molecules often found in bacteria. They replicate independently of the chromosome .Plasmids can serve as a vector—a vehicle for transferring recombinant genes to a new host. If a recombinant plasmid can be inserted into a bacterial or yeast cell, the foreign DNA will be copied and transmitted to new cells as the host cell grows and divides. In this way plasmids can be used to produce millions of identical copies of specific genes. Plasmid vectors can be introduced into bacteria by transformation, the process of taking up DNA from the environment and incorporating it into the genome. A DNA library is a collection of transformed bacterial cells, each containing a vector with an inserted gene. A cDNA library is a collection of bacterial cells, each containing a vector with one cDNA. A genomic library is made up of cloned DNA fragments representing an entire genome. DNA libraries are important because they give researchers a way to store information from a particular cell type or genome in an accessible form. Once the researchers found the human growth hormone cDNA, they cloned it in a plasmid under the control of a bacterial promoter. The transformed E. coli cells produced human growth hormone that could be isolated and purified in large quantities.

Eukaryotes present unique problems when trying to determine DNA sequences for actual genes. Why? What is probably the most current and efficient strategy used today to try and identify a gene sequence in Eukaryotes

4) Much more difficult in eukaryotes, who have many noncoding sequences in their genomes. In eukaryotic organisms, genes contain introns, and most of the genome does not code for a product—thus, it is not possible to scan for ORFs. The most effective strategy for identifying genes is to use reverse transcriptase to produce a cDNA version of each mRNA, and sequence a portion of the resulting molecule to produce an expressed sequence tag, or EST. ESTs represent protein-coding genes. Sequencing eukaryotic genomes presents unique challenges. Eukaryotic genomes are much larger than the genomes of bacteria and archaea. The presence of noncoding repetitive sequences.

Explain lateral gene transfer

5) The movement of DNA from one species to another species is called lateral gene transfer. Lateral gene transfer often results because genes are carried on plasmids. Another way lateral gene transfer occurs is through transformation, taking up DNA fragments from the environment. Thus, mutation and genetic recombination within species are not the only sources of genetic variation in bacteria and archaea.

Understand that chromosome modifications can be inherited. Define epigenetic inheritance

5) The pattern of chemical modifications on histones varies from one cell type to another. The histone code hypothesis contends that precise patterns of chemical modifications of histones contain information that influences whether or not a particular gene is expressed. Daughter cells inherit patterns of histone modification, and thus patterns of gene expression, from the parent cells. This is an example of epigenetic inheritance, patterns of inheritance that are not due to differences in gene sequences.

Be able to explain how the following: promoter, TATA Box and TATA-binding protein regulate transcription

6) Promoter-region of DNA that initiates transcription of a particular gene. Promoters are located near the genes they transcribe, on the same strand and upstream on the DNA. Promoters contain specific DNA sequences and response elements that provide a secure initial binding site for RNA polymerase and for proteins called transcription factors that recruit RNA polymerase. These transcription factors have specific activator or repressor sequences of corresponding nucleotides that attach to specific promoters and regulate gene expressions. There are three conserved sequences and each eukaryotic promoter has two of the three. The most common sequence is the TATA box. TATA box-is a DNA sequence found in the promoter region of genes, Considered to be the core promoter sequence, it is the binding site of either general transcription factors or histones (the binding of a transcription factor blocks the binding of a histone and vice versa) and is involved in the process of transcription by RNA polymerase. All eukaryotic promoters are bound by the TATA-binding protein (TBP). TBP- is a general transcription factor that binds specifically to a DNA sequence called the TATA box. TBP, along with a variety of TBP-associated factors, make up the TFIID, a general transcription factor that in turn makes up part of the RNA polymerase II preinitiation complex. As one of the few proteins in the preinitiation complex that binds DNA in a sequence-specific manner, it helps position RNA polymerase II over the transcription start site of the gene. Another feature of TBP is modulation of DNA-binding which affects the rate of transcription complex formation and initiation of transcription.TFIID is the first protein to bind to DNA during the formation of the pre-initiation transcription complex of RNA polymerase II. Binding of TFIID to the TATA box in the promoter region of the gene initiates the recruitment of other factors required for RNA Pol II to begin transcription. When TBP binds to a TATA box within the DNA, it distorts the DNA by inserting amino acid side-chains between base pairs, partially unwinding the helix, and doubly kinking it. TBP binds with the negatively charged phosphates in the DNA backbone through positively charged lysine and arginine amino acid residues. As the DNA bends, its contact with TBP increases, thus enhancing the DNA-protein interaction. The strain imposed on the DNA through this interaction initiates melting, or separation, of the strands. Separation of the two strands exposes the bases and allows RNA polymerase II to begin transcription of the gene.

What is a transposable element? An (STR)?

6) Protein-coding sequences constitute a very small percentage of the human genome, and repetitive sequences make up more than 50 percent. In contrast, over 90 percent of the prokaryotic genome consists of genes. Repeated sequences in the human genome are often the result of transposable elements—segments of DNA that can move from one location in a genome to another. Transposable elements are examples of selfish genes—parasitic DNA sequences that survive and reproduce but that do not increase the fitness of the host genome. Transposable elements are classified as parasitic because they decrease their host's fitness: It takes time and resources to copy them along with the rest of the genome. They can disrupt gene function when they insert in a new location. Eukaryotic genomes have several thousand loci called short tandem repeats (STRs). These are small sequences repeated down the length of a chromosome. There are two types of STRs. Microsatellites, or simple sequence repeats, are repeating units of 1 to 5 bases. Minisatellites, or variable number terminal repeats (VNTRs), are repeating units of 6 to 500 bases. Repeated sequences are hypervariable and vary among individuals much more than any other type of sequence

What is a DNA fingerprint?

7) DNA fingerprinting refers to any technique for identifying individuals on the basis of unique features of their genomes. Because microsatellite and minisatellite loci vary so much among individuals, they are now the markers of choice for DNA fingerprinting.

Describe the trends that have been identified across major taxa with respect to genome size and gene density

8) At the level of base sequence, the human and chimpanzee genomes are 98.8 percent identical. This raises the question of how humans and chimps can be so similar genetically but so different in morphology and behavior. One hypothesis proposes that even though many structural genes (those that code for products) in humans and chimps are identical, regulatory genes (those that code for regulatory transcription factors) of the two species might have important differences.

What is an oncogene? Relate our understanding of oncogenes to the genetic basis of uncontrolled cell growth

Abnormal regulation of gene expression can lead to developmental abnormalities and cancer. Cancers result from defects in the proteins that control the cell cycle. All cancers are characterized by uncontrolled cell growth. Cancers become dangerous when they metastasize and stimulate the production of their own vascular supply. Many cancers are associated with mutations in regulatory transcription factors. These mutations lead to cancer when they affect one of two classes of genes: (1) genes that stop or slow the cell cycle, and (2) genes that trigger cell growth and division by initiating specific phases in the cell cycle. Tumor suppressor genes slow or stop the cell cycle. If a mutation disrupts the normal function of a tumor suppressor gene, cells are released from this negative control of the cell cycle. Genes that trigger specific phases in the cell cycle are called proto-oncogenes. Defects in the regulation of proto-oncogenes cause these genes to stimulate growth at all times. These types of mutations convert proto-oncogenes into oncogenes that promote cancer development.

what are the general mechanisms of action of gene expression? For example, what is translational control?

Among these mechanisms of gene regulation there is a clear trade off between the speed of response and the conservation of ATP, amino acids, and other responses. Variation in gene expression allows cells to respond to changes in their environment. Gene expression is not an all or none proposition. Genes are not just "on" or "off" instead, the level of expression can vary between these extremes.

Recognize and be able to answer questions involving the following terms regarding the lac Operon: operator-operon-repressor-regulatory gene-inducing agent-promoter

An Operonis a set of coordinately regulated bacterial genes that are transcribed together into one mRNA. Lac Operon is the group of genes involved in lactose metabolism. The lacAgene was found to be adjacent to lacY and lacZ and transcribed as part of the same operon. This gene codes for the enzyme transacetylase, which catalyzes the reaction that allow certain sugars to be exported from the cell when they are too abundant and could harm the cell. There are 3 hypothesis for lac-operon regulation. The first is that the lacZ, lacY and lacA genes are adjacent andtranscribed into 1 mRNA initiated from a single promoter of the lac operon, which is known as contrascriptionand results in the coordinated expression for the three genes.Second, the repressor is a protein encoded by the lacI that binds to DNA and prevents transcription of the lac operon genes (lacY, lacZ, lacA), also known as the operator. Third, the inducer (lactose) binds to the repressor and when it does the repressor changes shape, which causes the repressor to come off of the DNA, which is called Allosteric Regulation (a small molecule binds to a protein and causes it to change shape and activity, when the inducer binds to the repressor, the repressor cant bind to DNA and transcription can proceed) Transcription of lac operon is reduce when glucose present in environment because its E coli's preferred carbon source. However, when both glucose and lactose are present, the transport of lactose into the cell is inhibited because lactose does not accumulate in the cytoplasm and repressor remains bound to operator so negative control is in place. Inducer exclusion is the mechanism of glucose preventing the transport of lactose into the cell. This allows E coli to use glucose as its preferred carbon source even when other sugars are present outside.Inducer a small molecule that triggers transcription of a specific gene

Explain the difference between a chromosome and chromatin

Chromatin is the DNA before it coils. Chromosomes are coiled DNA

How does our present understanding of meiosis help to support Mendel's principle of segregation and his law of independent assortment?

Chromosomes are composed of Mendel's hereditary determinants (what we now call genes) and the physical separation of alleles during anaphase of Meiosis I is responsible for Mendel's principle of segregation. Also states that if the alleles for different genes are located on different chromosomes, they assort independently of one another at meiosis I

What is differential gene expression? How do regulatory elements affect this process? Give two examples of regulatory elements that recent research suggests have a role.

Different cell types express different genes because they have different histone modifications and contain different regulatory proteins. Differential gene expression is a result of the production or activation of specific regulatory proteins. Eukaryotic genes are turned on when specific regulatory proteins bind to enhancers and promoter-proximal elements; the genes are turned off when regulatory proteins bind to silencers or when chromatin remains condensed. This leads to certain proteins being produced only in certain types of cells. 2 types-Regulatory transcription factors bind to enhancers, silencers, and promoter-proximal elements, and are responsible for the expression of particular genes in particular cell types and at particular stages of development. Basal transcription factors interact with the promoter and are not restricted to particular cell types. Although they are required for transcription, they do not regulate gene expression.

Explain the difference between dominance-codominance-incomplete dominance.

Dominance: this genotype shows phenotypically, co-dominance: both genotypes show mutually, incomplete dominance: white + red = pink

Recombinants typically have different combinations of a set of alleles than at least one of their parents. Explain how this can happen.

Gametes with new combinations of alleles were generated when crossing over occurred during prophase of Meiosis I.

What is meant by the following expression: "The expression of a protein-coding gene is ultimately measured in terms of the amount of functional protein a cell makes..."?

Gene expression = protein produced and activated

Describe how gene therapy was used to treat severe combined immunodeficiency (SCID), with mixed success

Gene therapy has been used to treat severe combined immunodeficiency (SCID), fatal genetic disease whose sufferers have a profoundly weakened immune system. The type of SCID treated is called SCID-X1, because it is caused by mutations in a gene on the X chromosome. The gene responsible for SCID-X1 encodes a receptor protein needed for development of immune system cells called T cells. A retrovirus engineered with a normal receptor gene was used to infect cells from bone marrow that produce T cells. Cells that produced normal receptor protein were then isolated and transferred back into 10 young patients. Within four months after treatment, nine of the ten patients had normal levels of functioning T cells. Subsequently, however, four of the boys had developed a type of cancer characterized by unchecked growth of T cells. Three are responding well to treatment; the fourth has died of cancer.

Explain how global gene regulation works.

Genes are grouped into a regulon. When an environmental change triggers a regulatory protein, such as a repressor to fall off, all the genes are simultaneously activated.

Describe how DNA technology has medical applications in the diagnosis of genetic disease, the development of gene therapy, vaccine production, and the development of pharmaceutical products

Genetic markers (genes or other loci that have known locations).Each genetic marker provides a landmark at a position along a chromosome that is known relative to other markers. Genetic markers must be polymorphic in order to be useful— in other words, the phenotype associated with the marker must be variable. DNA samples from affected families can be analyzed with genetic markers to follow the inheritance of specific DNA regions.

Describe the goals of the Human Genome Project

Genomics is the scientific effort to sequence, interpret, and compare whole genomes. Genomics provides a list of the genes present in an organism. Functional genomics looks at when those genes are expressed and how their products interact. HGP to complete the entire DNA sequence of humans.

How has our use of pedigrees helped to resolve whether a trait is discrete or quantitative? Autosomal of sex linked?

If neither parent has a dominant allele for one of the quantitative traits, but offspring shows up with dominant phenotype. Neither parents show it phenotypically but boys show up with it.

What is a gene family?

In eukaryotes, the major source of new genes is duplication of existing genes. Within a species, genes that are extremely similar to each other in structure and function are considered to be part of the same gene family. Genes that make up gene families are hypothesized to have arisen from a common ancestral sequence through gene duplication.

In truth, technically speaking, the terms dominance and recessive are descriptions of phenotypes, not of genes/genotypes, explain.

In genetics, the terms dominant and recessive identify only which phenotype is observed in individuals carrying two different genetic determinants for a given trait. Dominance and recessiveness determine which phenotype appears in an individual when two different alleles are present.

What is a ddNTP? How are they utilized in dideoxy sequencing

In the original technique, four separate reactions were performed, each containing all four dNTPs and one of the four ddNTPs. When the four reactions were separated, side by side, by gel electrophoresis, they revealed the DNA sequence. The current technique uses fluorescent markers for each ddNTP to simplify the DNA sequencing. This allows DNA to be sequenced with one dideoxy reaction instead of four.

What is RNA interference? hint-(miRNA's)

In the process of RNA interference, specific mRNAs are targeted by tiny, single-stranded RNA molecules called microRNAs. After binding to proteins called a RISC protein complex, these miRNAs bind to complementary sequences in the mRNA. Once part of an mRNA becomes double stranded in this way, specific proteins degrade the mRNA or prevent it from being translated into a polypeptide.

What is autosomal inheritance?

Inheritance of genes on non-sex chromosomes

How did a mutation and reciprocal crosses enable biologists, (Dr. Morgon), to determine that in fruit flies, eye color is a sex-linked trait. In your explanation, demonstrate knowledge of terms such as alleles, homozygous, heterozygous, and gene frequency vs. genotypic frequency.

Morgan identified red eyes as the wild type for eye color and white eyes as the mutation. He then mated a wild-type female fly with a mutant male and all of the F1 children had red eyes. When Morgan did the reciprocal cross all the F1 females had red eyes and all the F1 males had white eyes. This showed the relationship of eye color with the gender of the fly. Morgan proposed that a female fruit fly has two copies of the gene that specifies eye color because she has two X chromosomes. One of these chromosomes came from her female parent, the other from her male parent. A male, has only one copy of the eye-color gene because he has only one X chromosome, inherited from his mother.

What is Whole-Genome Sequencing and how are complete genomes sequenced?

Most genome sequencing projects use a whole-genome shotgun sequencing approach. In this process, the genome is broken up into a set of overlapping fragments that are sequenced, and these sequences are then put in order. Sonication (use of high-frequency sound waves) breaks a genome into pieces approximately 160 kilobases long. Each piece is inserted into a plasmid called a bacterial artificial chromosome (BAC). A BAC library is created by inserting each BAC into a different Escherichia coli cell. Colonies of each cell are allowed to grow, creating multiple copies of each BAC library. Each 160-kb DNA segment is broken into 1-kb segment.

If alleles at other loci in Mendel's pea plants had effected the expression of genes he tested, would he have been able to resolve his basic principles of hereidity? Explain

No, if we are talking about polygenic traits, he wouldn't be able to look at the hybrids and determine accurate phenotypic ratios

What is the relationship between histones and the nucleosome?

Nucleosomes are made up of DNA wrapped around histones. Chromatin are long chains of nucleosomes.

How is chromatin altered? What is acetylation and methylation?

One type of acetylation enzyme is called histone acetyl transferases (HATs). They add negatively charged acetyl groups to the positively charged lysine residues in histones. This acetylation reduces the positive charge on the histones, decondensing the chromatin and allowing gene expression. Enzymes called histone deacetylases (HDACs) then remove the acetyl groups from histones. This reverses the effects of acetylation and allows chromatin condensation.

Pedigree analysis is used extensively today to help resolve questions regarding the degree to which a certain disease might be inherited. Give some examples of how this could work.

Patterns of Inheritance: a. If a phenotype is due to an autosomal recessive allele, then i. Individuals with the trait must be homozygous ii. If the parents of an affect individual do not have the trait, then the parents are likely to be heterozygous for the trait/ carriers. b. When a trait is autosomal dominant, individuals who are homozygous or heterozygous for it must have the dominant phenotype. Any child with the trait must have a parent with this trait.

Define and give examples of Post-Transcriptional Control. For example, alternative splicing

Post-transcriptional control: 1) Splicing mRNAs in various ways-Introns are spliced out of primary RNA transcripts while it is still in the nucleus. During splicing, changes in gene expression are possible because selected exons may be removed from the primary transcript along with the introns. As a result, the same primary RNA transcript can yield more than one kind of mature, processed mRNA, consisting of different combinations of transcribed exons. This alternative splicing leads to production of different proteins. Alternative splicing is regulated by proteins that bind to the mRNAs in the nucleus and interact with the spliceosomes. 2) Altering the rate at which translation is initiated. 3) Modifying the life span of mRNAs and proteins after translation has occurred.

What are examples of Post-Translational Controls

Post-translational control: Chaperone proteins can regulate protein folding. Enzymes may modify proteins by adding carbohydrate groups or cleaving off certain amino acids. Proteins may be activated or deactivated by phosphorylation. Targeted protein destruction when ubiquitin tags are added to cylcin proteins and are recognized by a proteasome, which cuts the proteins into short segments.

What is Proteomics?

Proteomics is the large-scale study of protein function. Instead of studying individual proteins or how two proteins might interact, proteomics is based on studying all of the proteins present at once.

What is the relationship acknowledged between quantitative traits and polygenic inheritance?

Quantitative traits are polygenic traits: multiple genes make up the traits needed for a phenotype, you get a mix of polygenic/quantitative traits (gradient rather than yes or no) from your parents

How do chromosomes in prokaryotic cells differ from chromosomes in Eukaryotic cells? How are they similar?

Research shows that Pro DNA interacts with proteins that are organized similarly to nucleosomes, but nothing like the 30-nm fiber or higher order arrangements found in eukaryotic chromosomes has been found in prokaryotic chromosomes.

Define a single nucleotide polymorphism, (SNP). How are they used in genetic maps?

SNP are sites in DNA where some people in population have different bases, can be used as genetic markers. Single nucleotide polymorphisms, frequently called SNPs (pronounced "snips"), are the most common type of genetic variation among people. Each SNP represents a difference in a single DNA building block, called a nucleotide. For example, a SNP may replace the nucleotide cytosine (C) with the nucleotide thymine (T) in a certain stretch of DNA. SNPs occur normally throughout a person's DNA. They occur once in every 300 nucleotides on average, which means there are roughly 10 million SNPs in the human genome. Most commonly, these variations are found in the DNA between genes. They can act as biological markers, helping scientists locate genes that are associated with disease. When SNPs occur within a gene or in a regulatory region near a gene, they may play a more direct role in disease by affecting the gene's function.Most SNPs have no effect on health or development. Some of these genetic differences, however, have proven to be very important in the study of human health. Researchers have found SNPs that may help predict an individual's response to certain drugs, susceptibility to environmental factors such as toxins, and risk of developing particular diseases. SNPs can also be used to track the inheritance of disease genes within families. Future studies will work to identify SNPs associated with complex diseases such as heart disease, diabetes, and cancer.

Describe the surprising findings of the Human Genome Project with respect to the size of the human genome

Scientists do not know the function of more than half of the genes found in the human genome .Two recent discoveries are changing biologists' thinking about the human genome: Genes for miRNAs are much more common than previously thought. A much larger proportion of the genome is transcribed than previously thought. Many of these sequences are referred to as Transcripts of Unknown Function (TUFs) because their role in the cell is unknown.

what is catabolite repression?

System of gene control in some bacterial operons in which glucose is used preferentially and the metabolism of other sugars is repressed in the presence of glucose.

Explain how genetic markers can be used to detect abnormal alleles of a gene that has not yet been cloned.

The genetic marker must be polymorphic (many phenotypes). If a certain form of a marker and a disease are always inherited together (black hair and CF), then they are closely linked. Researchers must find a genetic marker that always occurs in affected individuals, but rarely in non-affected individuals.

Describe the polymerase chain reaction (PCR) and explain the advantages and limitations of this procedure

The polymerase chain reaction (PCR) is an in vitro DNA synthesis reaction in which a specific DNA sequence is replicated over and over again. This technique generates many identical copies of a particular DNA sequence. PCR is possible only when DNA sequence information surrounding the gene of interest is available, because PCR requires primers that match sequences on either side of the gene. One primer is complementary to a sequence on one strand upstream of the target DNA and the other primer is complementary to a sequence on the other strand downstream of the target. The primers will bind to single-stranded target DNA. A reaction mix containing dNTPs, a DNA template, copies of the two primers, and Taq polymerase. Denaturation - heating the mixture to 95°C separates the two strands of the DNA. Primer annealing - cooling the mixture allows the primers to bond, or anneal, to complementary sections of single-stranded target DNA. Extension - heating the mixture to 72°C causes the Taq polymerase to synthesize the complementary DNA strand from the dNTPs, starting at the primer. Because the complete genomes of a wide array of organisms have now been sequenced, researchers can find appropriate primer sequences to use in cloning almost any target gene by PCR.

Compare and Contrast Eukaryotic and Prokaryotic regulation of gene expression

There are four primary differences between gene expression in bacteria and eukaryotes: Packaging: Chromatin structure provides a mechanism of negative control in eukaryotes that does not exist in bacteria. Alternative splicing: Primary transcripts in eukaryotes must be spliced. This does not occur in bacteria. Complexity: Transcriptional control is much more complex in eukaryotes than in bacteria. Coordinated expression: In bacteria, genes may be organized into operons; such operons are rare in eukaryotes. (Slide 45)

When are "test crosses" utilized? How is it possible to observe a dominant phenotype and not then automatically know the exact genotype?

To determine the genotype of the dominant phenotyped organism. Could be Aa or AA.

Why did Mendel utilize the monohybid cross? How did its use enable him to develop his principle of segregation and a rebuttal to the ideas of blending inheritance and acquired characteristics?

To observe the resulting phenotype of the hybrid? The results showed that the traits did not blend together to form an intermediate phenotype, which proved the blending-inheritance hypothesis was false. Acquired characteristics: traits change during your lifetime, and you pass those down, wrong.

What are the two proteins E. coli needs for using Lactose? How are they utilized?

To use lactose, E. coli, must first transport the sugar into the cell. Once lactose is inside the cell =, the enzyme B-galactosidase catalyzes a reaction that breaks down the disaccharide into glucose and galactose. The glucose can go directly into the glycolytic pathways but other enzymes have to convert the galactose into a substance that can be processed by the glycolytic pathway.

What is gene linkage? How does it influence inheritance patterns?

When genes are located on the same chromosome. The closer they are to each other, the easier they both get inherited together.

Give examples of Functional Genomics

Whole-genome data can be used to answer fundamental questions about how organisms work. Large-scale analyses of gene expression are called functional genomics. Microassays: One of the basic tools of functional genomics is a DNA microarray. Microarrays, used to study gene expression, consist of a large number of single-stranded DNAs that are permanently affixed to a glass slide. mRNAs produced in two contrasting types of cells are isolated, and then cDNAs produced from these mRNAs are used to probe the microarray. Researchers can thus identify differences in which genes are expressed in the two cell types. A microarray allows researchers to study the expression of thousands of genes at a time, and to identify which sets of genes are expressed together under specific sets of conditions. (slides 46, 48, 49)

Explain the rationale for including a gene for antibiotic resistance and a gene that codes for a hydrolytic enzyme in the plasmid.

antibiotic resistance: agar medium kills the bacteria that did not take up a plasmid as they do not contain the antibiotic resistance + hydrolytic enzyme: prevents the recombinant bacteria from producing the proteins (such as beta-galactodsidase) required to hydrolyze a substance such as X-gal in the medium, thereby creating white colonies that are distinguishable from the blue colonies of non recombinant plasmid

What is a Positive control?

contains the variable for which you are testing; reacts positively and demonstrates the the test's ability to detect what you expect

Understand mechanisms of negative control. What is a repressor?

negative control is a way of regulating transcription that occurs when a regulatory protein called a repressor binds to DNA and shuts down transcription

What is a promoter-proximal element? Why are they necessary?

promoter proximal elements are regulatory sequences located close to the promoter and bind regulatory proteins. They are needed because they are unique to specific sets of genes, allowing eukaryotes to express certain genes but not others.

Why is it important that "pure lines" are established in genetic research?

pure lines are used in test crossing, and if two pure lines are crossed, we can tell by the hybrid which trait is dominant

What was Mendel attempting to find out by performing a dihybrid cross? What did he end up resolving?

to find out if his principle of segregation held true if individuals differ with respect to two traits, instead of just one or is a law of dependent assortment applied. Resolved that these genes were transferred in a process called principle of independent assortment.