Chapter 11, Chapter 15 Bio, bio quiz chapter 11, Biology Ch. 12 Mastering, BIO WEEK 14

activator structure

1. a DNA binding domain; which is a part of the proteins 3d structure that binds to DNA, 2. one or more activation domains; they bind other regulartory proteins or components of the transcription machinery facilitating a series of protein to protein interactions that result in transcription of a given gene

How the binding of activators to an enhancer located far from the promoter can influence transcription?

1. acitvator protens (which are specific transcription factors) bind to distal control elements grouped as enhancer in the DNA, this enhancer has three binding sites each called a distal control elements, 2. a DNA bending protein brings the bound activators closer to the promoter, general transcription factors, mediator proteins, and RNA poly 2 are nearby, 3. the activators bind to certain mediator proteins and general transcription factors helping them form an active transcription initiation complex on the promoter

noncoding RNAs

1. miRNA, 2. siRNAs, come from different precursors

why is trp operon not switched off permentaly if repressor molecules are rarely used?

1. the binding of repressor to operators is reversible, an operator alternates between two states: one with the repressor bound and one without, the relative duration of the repressor bound state is higher when more active repressor molecules are present, 2. the trp repressor like most regulatory proteins is an allosteric protein with two alternative shapes: active and inactive, the trp repressor is synthesized in an inactive form with little affinity for the trp operator, only if trytophan binds to the trp represser at an allosteric site does the repressor protein change to the active form that can attach to the operator turning the operon off

a typical human will express how much of its protein coding genes at a given time?

20 percent; highly differentiated cells such as muscle or nerve cells express an even smaller fraction of their genes

If an organism normally has 34 chromosomes, how many molecules of DNA should there be in the G1 phase of the cell cycle?

34 -There is one DNA molecule per chromosome

Translation of specific mRNAs may also be blocked by regulatory proteins that bind to the mRNA molecule, controlling the amount of protein produced. Often, polypeptides must be modified in some way to produce functional proteins. For example, a polypeptide might be cleaved into two or more polypeptide chains. Other molecules might be attached to the protein. Some proteins are then transported to specific destinations, where they carry out their functions.

A cell can get rid of abnormal or damaged proteins and limit the lifetime of functional proteins by breaking them down. Some proteins last months, others only hours or minutes. Selective breakdown enables the cell to keep its proteins in working order and adjust to changes in its environmentThis illustration summarizes the control of gene expression in a eukaryotic cell.

NUCLEAR TRANSPLANTATION

A cells fate - that is, the type of cell that it will ultimately become - is a function of differential gene expression and morphogenesis. The developmental potential of cells becomes restricted fairly early in normal development. A zygote has the ability to give rise to every cell type in the adult body, indicating that the genome contains instructions for all the structures and functions that will arise throughout the life cycle of an organism. Differentiated plant cells can be induced to generate all types of the plant's cells. Animal somatic cells cannot be fooled into acting like a zygote as easily as plant cells can; however, in a process known as nuclear transplantation, animal somatic cells can be induced to differentiate like a zygote. In nuclear transplantation, the nucleus of an unfertilized egg cell or zygote is replaced with the nucleus of a differentiated cell. No information is lost from the nucleus as it passes through the early stages of development. This fundamental principle of developmental biology is known as genomic equivalence. Furthermore, the cytoplasmic environment around the nucleus can modify its fate. If a mammalian embryo is to develop further, it must be implanted into the uterus of a surrogate mother. The resulting animal will be genetically identical to the donor of the nucleus - a "clone" of the donor. Reproductive cloning—the production of new individuals—has been demonstrated in many mammals, including sheep, mice, cats, cows, horses, mules, pigs, and dogs. Scientists have learned much from these experiments. One lesson learned is that in most nuclear transplantation studies, very few cloned embryos develop normally to birth and many of those exhibit defects. Additionally, cloned animals of the same species do not always look or behave identically. A stem cell is a relatively unspecialized cell that can both reproduce itself indefinitely and, under appropriate conditions, differentiate into specialized cells of one or more types. Thus, stem cells are able both to replenish their own population and to generate cells that travel down specific differentiation pathways. Many early animal embryos contain stem cells capable of giving rise to any type of differentiated embryonic cells. Embryonic stem cells can be isolated from early embryos at the blastula or blastocyst stage. If the major aim of nuclear transplantation is to produce embryonic stem cells to treat disease, the process is called therapeutic cloning. If stem cells were derived from an embryo formed by nuclear transplantation using an individual's own nuclei, the cells would be genetically identical and the problem of tissue rejection could be eliminated.

Gene Regulation in Eukaryotes

A eukaryotic cell may possess tens of thousands of genes. Different genes are activated at different times to cope with environmental changes. In addition, cell differentiation-- specialization for different jobs-- requires that specific genes be expressed in certain cells at certain times

biologists goal

A major goal of biologists is to learn how genes act together to produce and maintain a functioning organism; Large groups of genes are studied by a systems approach; Such approaches allow networks of expression across a genome to be identified

What is a Microarray?

A microarray is essentially, an ordered array of DNA or any nucleic acids. It's typically gridded out onto some kind of solid support, so that, basically in a very small area, let's say a microscope slide, you can put down every single gene in the genome, forty, fifty-thousand genes in that small area. And you can basically then, in a very quick hybridization experiment, if you label, let's say, different patients or different people's DNA, you can hybridize them on and basically measure, with fluorescent signal, how much of each DNA is binding to each part of the genome. So in basically one step, in a few hours or in twenty-four hours, you can assess the entire genome of an individual or a species for changes in copy number, for changes in expression, etc. So, essentially what it has done is given us the ability, rather than looking one gene at a time at specific things or a few genes at a time, to be able to look at the whole system of the genome in parallel. So it really has brought us into this area of genome systems biology.

Which of the following statements about proto-oncogenes is false?

A mutation in a tumor-suppressor gene can stop cell division immediately.

DIFFERENTIATION OF STEM CELLS

A stem cell is a relatively unspecialized cell that can both reproduce itself indefinitely and, under appropriate conditions, differentiate into specialized cells of one or more types. Thus, stem cells are able both to replenish their own population and to generate cells that travel down specific differentiation pathways. Many early animal embryos contain stem cells capable of giving rise to any type of differentiated embryonic cells. Embryonic stem cells can be isolated from early embryos at the blastula or blastocyst stage. The adult body also has adult stem cells, which are able to give rise to many, but not all, cell types. Scientists are learning to identify and isolate stem cells from various tissues and, in some cases, to grow them in culture. With the addition of specific growth factors, cultured stem cells from adult animals have been made to differentiate into multiple types of specialized cells. For example, bone marrow contains several types of adult stem cells, including one that can generate all the different kinds of blood cells and another that can differentiate into bone, cartilage, fat, muscle, and the linings of blood vessels. Even the adult brain contains stem cells that produce certain kinds of nerve cells. Embryonic stem cells are easier to grow than adult stem cells, can theoretically give rise to all types of cells in an organism, and offer more potential than adult stem cells for medical applications, at least for now. This technology may provide cells for the repair of damaged or diseased organs, such as insulin-producing pancreatic cells for people with diabetes or certain kinds of brain cells for people with Parkinson's disease or Huntington's disease.

A gene that can cause cancer will present in a single copy in a cell is called A.) Oncogene B.) enhancer Gene C.) carcinogen D.) Proto-oncogene E.) silencer gene

A.) Oncogene

Why don't the grafted hybrids produce apples with a blend of traits from the scion and the rootstock A.) The rootstock regulate gene expression in the scion but contributes no genetic information for fruit production B.) transplanted nuclei from scion cells regulate gene expression in the rootstock C.) The rootstock suppresses activation of the scion genes which alters fruit production D.) The LAC operon in the scion is the only regulator of gene expression in the hybrid E.) The rootstock is unable to perform photosynthesis and so can't produce fruit

A.) The rootstock regulate gene expression in the scion but contributes no genetic information for fruit production

A single cell the zygote can develop into an entirely new organism with many specialized cells. Which of the following statements about this process is false A.) additional genetic information for the formation of specialized cells is passed on to the developing embryo via placenta B.) The zygote contains all of the genetic information required for the development of many different cell types C.) only some of the genes in the zygote are expressed in all of its descendent cells D.)differentiation of the zygote into a multicellular organism results from the selection gene expression.

A.) additional genetic information for the formation of specialized cells is passed on to the developing embryo via placenta

The coding regions of a gene (The portions that are expressed as polypeptide sequences) are called A.) exons B.) Proto-oncogenes C.) introns D.) nucleosomes E.) redundant coding sections

A.) exons

To initiate a signal transduction pathway a signal binds to a receptor protein usually located in A.) plasma membrane B.) ER C.) cytoplasm D.) nucleus E.) cytosol

A.) plasma membrane

The LAC operon in E. coli A.) prevents lactose utilizing enzyme from being expressed when lactose is absent from the environment B.) regulates the rate of binary fission C.) allows the bacterium to resist antibiotics in the penicillin family D.) coordinates the production of tryptophan utilizing enzymes E.) uses activators to initiate the production of enzymes that break down lactose

A.) prevents lactose utilizing enzyme from being expressed when lactose is absent from the environment

A homeotic gene A.) serves as a master control gene that functions during embryonic development by controlling the develop mental fate of groups of cells B.) turns on the genes necessary for synthesis of proteins C) represses gene transcription and promotes mRNA translation D.) is found only in adult somatic cells E.) produces a product that controls the transcription of other genes

A.) serves as a master control gene that functions during embryonic development by controlling the develop mental fate of groups of cells

Mutations in the p53 gene can lead to cancer by A.) turning off the gene for a protein that inhibits cell division B.) increasing the production of growth hormones which trigger faster cell cycles C.) promoting the expression of mRNA that can interact with DNA resulting in new mutations D.) causing the production of excessive amounts of relay proteins E.) increasing the production of glycogen which nourishes the cell cycle

A.) turning off the gene for a protein that inhibits cell division

Yeast are able to communicate with each other A.) with signal transduction pathways B.) only if they can touch each other and have merged cell walls C.) with pseudopodia D.) only when a yeast cell has died and released its internal organelles in to the external environment E.) by close Cell to cell contact

A.) with signal transduction pathways

Which of the following statements regarding stem cells is false?

Adult, but not embryonic, stem cells can be grown in laboratory culture.

During which substage of mitosis do sister chromatids break apart and start moving to opposite poles of the cell?

Anaphase -Chromatids are pulled to opposite poles of the cell during anaphase, the fourth substage of mitosis

When lactose is present, it binds to the repressor and changes its shape.

As a result of this change, the repressor can no longer bind to the operator region. RNA polymerase can then bind to the promoter and transcribe the lac genes.

Which of the following is likely to occur in E. coli cells that are grown in skim milk A.) The TRP of operon and then LAC operon are both switched on B.) The TRP repressor is activated and the cells will produce lactose utilizing enzymes C.) The TRP operon is turned but the bacteria will not produce lactose utilizing enzymes D.) The LAC operon is shut off and the cells will not produce lactose utilizing enzymes E.) The TRP operon and the LAC operon are both switched off

B.) The TRP repressor is activated and the cells will produce lactose utilizing enzymes

Signal transduction pathways A.) are found strictly in multicellular organisms for cell to cell communication B.) are mechanisms of communication that involved in the ancient prokaryotes C.) originally evolved in vertebrates D.) first appeared in animals when primates began to walk upright E.) are limited for use in sexual identification

B.) are mechanisms of communication that involved in the ancient prokaryotes

Animal development is directed by A.) cell to cell signaling B.) cell to cell signaling and signal transduction pathways C.) cell receptors that detect transcription factors D.) Signal transduction pathways E.) The availability of certain key nutrients as cells divides

B.) cell to cell signaling and signal transduction pathways

The cloning of Dolly the sheep A.) revealed that cloud animals most resemble the egg donor B.) demonstrated that the nuclei from differentiated mammalian cells can retain their full genetic potential C.) revealed that cloned mammals most resemble the sperm donor D.) demonstrated that differentiated cells contain only a fraction of their full genetic potential E.) demonstrated for the first time the eggs are haploid and body cells are diploid

B.) demonstrated that the nuclei from differentiated mammalian cells can retain their full genetic potential

The development of colon cancer occurs slowly and is more prominent in the elderly then the young. This is most likely because A.) cancer cells have to wait until new blood cells grow into the area which takes much time B.) four or more somatic mutations must occur to give rise to the cancer which takes time C.) cancer cells don't have mitochondria so they grow slowly D.) cancer cells suppress the growth of each other in a tissue E.) most cancer mutations interfere with mitosis so cell division occurs more slowly

B.) four or more somatic mutations must occur to give rise to the cancer which takes time

The fact that the nucleus from an adult somatic cell cell can be used to create all of the cell types in a new organism demonstrates the development depends upon A.) the position of cells within an embryo B.) the control of gene expression C.) the deposition of materials in the extra cellular matrix D. The timing of mitosis and meiosis E.) the timing of meiosis and cell migrations

B.) the control of gene expression

The RNA transcript

Both exons (numbered 1-5) and introns (pink regions) are usually transcribed into RNA. Before RNA leaves the nucleus, the introns are removed and the exons are joined to produce a continuous coding sequence

Signal Pathways

Both stimulatory and inhibitory pathways regulate the cell cycle, commonly influencing transcription. The proteins encoded by many proto-oncogenes and tumor-suppressor genes are components of cell-signaling pathways. Cancer can result from aberrations in such pathways, which may be caused by mutations, either spontaneous or environmentally triggered. This example of a cell cycle-stimulating pathway is triggered by a growth factor that binds to its receptor on the plasma membrane. The signal is relayed to a G protein called ras. Like all G proteins, ras is active when GTP is bound to it. The ras protein passes the signal to a series of protein kinases. The last protein kinase activates a transcription activator that turns on one or more genes fro proteins that stimulate the cell cycle. If a mutation makes ras or any other pathway component abnormally active (hyperactive), excessive cell division and cancer may result. In this example of a cell cycle-inhibiting pathway, DNA damage is an intracellular signal that is passed via protein kinases and leads to activation of p53 (tumor suppressor gene). Activated p53 promotes transcription of the gene for a protein that inhibits the cell cycle. The resulting suppression of cell division ensures that the damaged DNA is not replicated. Mutations causing deficiencies in any pathway component can contribute to the development of cancer. Increased cell division, possibly leading to cancer can result if the cell cycle is over stimulated, or not inhibited when it normally would be.

Most differentiated cells retain A.) The ability to redifferentiate but then cannot return to their original no differentiated state B.) only a tiny fraction of their original set of genes but can regenerate lost genes as needed C.) A complete set of their genes and retain the ability to express those genes under certain circumstances D.) only a tiny fraction of their original set of genes E.) A complete set of their genes but lose the ability to express most of those genes

C.) A complete set of their genes and retain the ability to express those genes under certain circumstances

Adult stem cells have a limited therapeutic potential A.) because they lack a complete set of genes B.) because scientist have no reliable method of identification C.) because their developmental potential is limited to certain tissues D.) because they are fully differentiated E.) due to their excessive numbers in tissues

C.) because their developmental potential is limited to certain tissues

In female mammals, the inactive X chromosome in each cell A.) can be activated if mutations occur in the active X chromosome B.) is broken down and it's nucleotides are degraded and reused C.) becomes a bare body D.) is absorb and used in energy production E.) becomes a nucleotroph corpus

C.) becomes a barr body

MicroRNA or miRNA can be used by A.) researchers to artificially turn on gene expression B.) viruses to stop the production of new proteins C.) cells to prevent infections from double-stranded RNA viruses D.) researchers to induce the production of more mRNA E.) researchers to stimulate the production of DNA

C.) cells to prevent infections from double-stranded RNA viruses

Half the trees in an orchard were derived from rootstock A and half from rootstock B but all of the trees had the same scion. If the trees grafted onto rootstock A were infected by a parasite that causes blossom rot the trees grafted onto rootstock B A.) would be more likely to become infected since the pathogen would spread through the soil to the roots of other trees B.) would less likely to become infected because their grafted onto different rootstocks C.) would be very likely to become infected because the remaining scions are genetically identical to those that are already infected D.) only half of the remaining trees are likely to become infected because they're in a different location in the orchard E.) there's no way to determine the likelihood of infection since genetic variability gives all the trees different characteristics

C.) would be very likely to become infected because the remaining scions are genetically identical to those that are already infected

catabolite activator protein

CAP is the regulatory protein, is an activator

Connection: Causes of Cancer

Cancer can be caused by many different agents, called carcinogens. Some carcinogens are linked with cancers in specific parts of the body. Your personal lifestyle can greatly affect your exposure to carcinogens and therefore certain kinds of cancers. Drag the carcinogens on the right to the part of the body affected by these carcinogens.

Oncogenes TSGenes

Cancer is a set of diseases in which cells escape the control mechanisms that normally regulate cell growth and division. The gene regulation systems that go wrong during cancer are the very same systems that play important roles in embryonic development, the immune response, and other biological processes. The genes that normally regulate cell growth and division during the cell cycle include genes for growth factors, their receptors, and the intracellular molecules of signaling pathways. Mutations altering any of these genes in somatic cells can lead to cancer. Two kinds of genes are changed in many cancers - oncogenes and tumor suppressor genes. The agent of such changes can be random spontaneous mutations or environmental influences such as chemical carcinogens, X-rays, or certain viruses. Research led to the discovery of cancer-causing genes called oncogenes. The normal version of these cellular genes, called proto-oncogenes, code for proteins that stimulate normal cell growth and division and play essential functions in normal cells. A proto-oncogene becomes an oncogene following genetic changes that lead to an increase in the proto-oncogene's protein production or in the intrinsic activity of each protein molecule. These genetic changes include movement of DNA within the genome, amplification of the proto-oncogene, and point mutations in a control element or the proto-oncogene itself. Cancer cells frequently have chromosomes that have been broken and rejoined incorrectly. A fragment may be moved to a location near an active promoter or other control element. Movement of transposable elements may also place a more active promoter near a proto-oncogene, increasing its expression. Amplification increases the number of copies of the proto-oncogene in the cell. A point mutation in the promoter or enhancer of a proto-oncogene may increase its expression. A point mutation in the coding sequence may lead to translation of a protein that is more active or longer-lived. All of these mechanisms can lead to abnormal stimulation of the cell cycle, putting the cell on the path to malignancy. The normal products of tumor-suppressor genes inhibit cell division. Any decrease in the normal activity of a tumor-suppressor protein may contribute to cancer. Some tumor-suppressor proteins normally repair damaged DNA, preventing the accumulation of cancer-causing mutations. Other tumor-suppressor proteins control the adhesion of cells to each other or to an extracellular matrix, which is crucial for normal tissues and often absent in cancers. Still others are components of cell-signaling pathways that inhibit the cell cycle.

CELL COMMUNICATION

Cell-signaling systems appeared early in the evolution of life. Communication between cells is important for many unicellular organisms as well as multicellular organisms. Biologists have discovered universal mechanisms of cellular regulation involving the same small set of cell-signaling mechanisms. The ubiquity of these mechanisms provides additional evidence for the evolutionary relatedness of all life. Cells most often communicate by chemical signals, although signals may also take other forms. Pathway similarities suggest that ancestral signaling molecules evolved in prokaryotes and were modified later in eukaryotes. The cells of Saccharomyces cerevisiae, the yeast of bread, wine, and beer, identify potential mates by chemical signaling. There are two sexes, a and α, each of which secretes a specific signaling molecule, a factor and α factor, respectively. These factors each bind to receptor proteins on the other mating type. After the mating factors have bound to the receptors, the two cells grow toward each other and undergo other cellular changes. The two cells fuse, or mate, to form an a/α cell containing the genes of both cells. The cell-signaling process helps ensure that crucial activities occur in the right cells, at the right time, and in proper coordination with the other cells of the organism.

SIGNAL TRANSDUCTION PATHWAY

Cell-to-cell communication is absolutely essential for multicellular organisms given that cells must communicate to coordinate their activities. Multicellular organisms release signaling molecules that target other cells. The process by which a signal on a cell's surface is changed or transduced into a specific cellular response is a series of steps called a signal transduction pathway. The signal must be recognized by a specific receptor molecule, and the information it carries (the signal) must be changed into another form, or transduced, inside the cell, before the cell can respond. Ultimately, a signal transduction pathway leads to the regulation of one or more cellular activities such as open or close ion channels, activate kinase enzymes, phosphorylate channel proteins, or activate genes and induce protein synthesis. Cell signaling involves three stages: reception, transduction, and response. In reception, a chemical signal binds to a cellular protein, typically at the target cell's surface or inside the cell. Recognition occurs when the signal binds to a specific site on the receptor that is complementary in shape to the signal. In transduction, binding of the signaling molecule changes the receptor protein in some way, initiating the process of transduction. Transduction may occur in a single step but more often triggers a series of changes in a series of different molecules along a signal transduction pathway. The molecules in the pathway are called relay molecules. Multistep pathways also provide more opportunities for coordination and regulation than do simpler systems. In the third stage of cell signaling, the transduced signal finally triggers a specific cell response. The response may involve action in the nucleus or may occur in the cytoplasm. Many signaling pathways ultimately regulate protein synthesis, usually by turning specific genes on or off in the nucleus. Like an activated steroid receptor, the final activated molecule in a signaling pathway may function as a transcription factor. Often a transcription factor regulates several different genes. Binding of signal molecules to receptors must be reversible, allowing the receptors to return to their inactive state when the signal is released. As a result, the cell is soon ready to respond to a fresh signal.

Alternative RNA splicing

Cells can splice RNA in more than one way, producing different mRNA molecules. In these examples, one sequence contains exon #3 and the other contains exon #4, but not both. This produces more than one type of polypeptide from a single gene.

Remember what genes do—for the most part, genes make proteins. Gene expression is the overall process of genetic information flowing from DNA to RNA to proteins. In other words, gene expression is the means by which genotype controls phenotype. The control of gene expression—turning genes on and off—contributes to two important properties of cells:

Cells respond to changes in the internal and external environment by turning genes on and off, and 2. the cells within a multicellular organism become highly specialized with very specific structures and functions. Even though each kind of cell has the same genome as all the other kinds, they are different because they have different genes expressed.

Which of the following processes occurs when a salamander regenerates a lost limb?

Certain cells in the limb dedifferentiate, divide, and then redifferentiate to form a new limb

A signal outside a cell triggers changes in the transcription and translation inside the cell through the process of A.) post translational editing B.) X chromosome inactivation C.) protein breakdown D.) Signal transduction pathways E.) protein activation

D.) Signal transduction pathways

Which of the following statements about the problems created by cloning is false. A.) cloning endangered species may deemphasize the need to preserve critical natural habitats B.) cloning leads to malfunctions in gene regulation C.) cloning does not increase genetic diversity in the cloned species. D.) cloned animals live longer compared to naturally bred animals E.) cloned animals are less healthy than animals created by natural methods

D.) cloned animals live longer compared to naturally bred animals

Which of the following mammals has not yet been cloned and brought through the complete gestation cycle A.) cow B.) dog C.) pig D.) human E.) cat

D.) human

In this drawing of the LAC operon which molecule is an inactive repressor A.) molecule A B.) molecule B C.) molecule C D.) molecule D E.) molecule E

D.) molecule D.)

Why can some plants be cloned from a single cell A.) plant cells can produce genes to replace those lost during development B.) plant cells do not differentiate even when mature so any cell can grow into an entire plant C.) plant cells are capable of self renewal by utilizing cellular components from adjacent cells D.) plant cells can dedifferentiate and give rise to all of the specialized cells required to produce an entire plant E.) plant cells are capable to retrieve genes lost to the environment during development

D.) plant cells can dedifferentiate and give rise to all of the specialized cells required to produce an entire plant

The term gene expression refers to A.) fact that individuals of the same species have different phenotypes B.) flow of information from parent to offspring C.) fact that each individual of a species has a unique set of genes D.) process by which genetic information flows from genes to proteins E.) fact that certain genes are visible as dark strips on a chromosome

D.) process by which genetic information flows from genes to proteins

Which structure in this figure shows one complete nucleosome A.) structure A B.) structure B C.) structure C D.) structure D E.) structure E

D.) structure D

All of the following mechanisms are used to regulate protein production except

DNA editing.

Which of the following statements regarding DNA packing is false?

DNA packing tends to promote gene expression

PLANT CLONING

During development, cells become specialized in structure and function, undergoing cell differentiation. Because almost all cells in an organism have the same genome, differential gene expression results from differential gene regulation in different cell types. Scientists can now clone multicellular organisms from single cells. This is called organismal cloning to distinguish it from gene cloning and cell cloning, the division of an asexually reproducing cell into a collection of genetically identical cells. Organismal cloning produces one or more organisms genetically identical to the "parent" that donated the single cell. Cloning plants shows that differentiated cells may retain all of their genetic potential. In this experiment, a transverse section of carrot root is used to produce fragments which are cultured in nutrient medium. Stirring of the media shears off single cells. Single cells, free in the media, begin to divide and an embryonic plant develops The plantlet is cultured on agar medium and later is planted in soil. The result is a single somatic carrot cell developing into a mature carrot plant. Plant cloning is now used extensively in agriculture to reproduce plants that have valuable characteristics, such as the ability to resist a plant pathogen.

Which of the following permits a single gene to code for more than one polypeptide A.) retention of different introns in the final version of the different mRNA strands B.) addition of different types of caps and tails to the final version of the mRNA strand C.) protein degradation D.) genetic differentiation E.) Alternate RNA splicing

E.) Alternate RNA splicing

Which of the following processes occurs when a salamander regenerates a lost limb A.) A new salamander develops from the lost limb B.) The cell cycle is arrested and apoptosis begins C.) The homeotic genes of the regenerating cell turns off D.) oncogenes that cause accelerated cell division are turned on E.) certain cells in the limb de differentiate divide and then redifferentiate to form a new limb

E.) certain cells in the limb de differentiate divide and then redifferentiate to form a new limb

The tortoiseshell pattern on a cat A.) is a result of the alleles on the Y chromosome B.) usually occurs in males C.) occurs in males 25% of the time and in females 50% of the time D.) is the result of a homozygous recessive gene E.) results from X chromosome inactivation

E.) results from X chromosome inactivation

The basis of cellular differentiation is A.) The operon B.) Cellular specialization C.) cloning D.) mutation E.) selective gene expression

E.) selective gene expression

Which of the following mechanisms of controlling gene expression occurs outside the nucleus A.) RNA splicing B.) adding a cap and tail to RNA C.) DNA packing/unpacking D.) transcription E.) translation

E.) translation

precursor

Ecoli synthesizes the amino acid tryptophan from a precurser molecule in the multistep pathway, each reaction in the pathway is catalyzed by a specific enzyme, the five genes that code for the subunits of these enzymes are clustered together on the bacterial chromosome, a single promoter serves all 5 genes which together constitution a transcription unit; transcription gives rise to one long mRNA molecule that codes for the 5 polypeptides making up the enzyme in the trytophan pathway; the cell can translate this one mRNA into 5 separate polypeptides because the mRNA is punctuated with start and stop codons that signal where the coding sequence for each polypeptide begins and ends

True of False? Mitosis takes place during M phase, which is the longest phase of the cell cycle.

False -Mitosis does indeed take place during M phase, but M phase is the shortest phase of the cell cycle.

operon model

Gene expression in bacteria is controlled by a mechanism described as the operon model,

which of the following statements regarding RNA and proteins is false?

In eukaryotes, one gene controls the production of just one functioning protein.

RNA INTERFERENCE

In eukaryotes, the separation of transcription in the nucleus and translation in the cytoplasm provides possible points of regulation that do not exist in prokaryotes. A significant amount of the genome may be transcribed into non-protein-coding RNAs (or noncoding RNAs), including a variety of small RNAs. These discoveries suggest that there may be a large, diverse population of RNA molecules that play crucial roles in regulating gene expression in the cell. In the past few years, researchers have found small, single-stranded RNA molecules called microRNAs (miRNAs) that bind to complementary sequences in mRNA molecules miRNA associates with a protein complex and directs the complex to any mRNA molecules that have a complementary sequence. The miRNA-protein complex either degrades the target mRNA or blocks its translation. It is estimated that the expression of up to one-third of all human genes may be regulated by miRNAs. The phenomenon of inhibition of gene expression by RNA molecules is called RNA interference (RNAi).

DEVELOPMENTAL GENETICS

In the development of most multicellular organisms, a single-celled zygote gives rise to cells of many different types. Each type has a different structure and corresponding function. Cells of different types are organized into tissues, tissues into organs, organs into organ systems, and organ systems into the whole organism. Thus, the process of embryonic development must give rise not only to cells of different types but also to higher-level structures arranged in a particular way in three dimensions. As a zygote develops into an adult organism, its transformation results from three interrelated processes: cell division, cell differentiation, and morphogenesis. Through a succession of mitotic cell divisions, the zygote gives rise to a large number of cells. Cell division alone would produce only a great ball of identical cells. During development, cells become specialized in structure and function, undergoing cell differentiation. Different kinds of cells are organized into tissues and organs. The physical processes that give an organism its shape constitute morphogenesis, the "creation of form." One important source of information early in development is the egg's cytoplasm, which contains both RNA and proteins encoded by the mother's DNA. Cytoplasmic materials are distributed unevenly (as a gradient) in the unfertilized egg. The egg cell is surrounded by other cells that form a structure called the follicle within the mother's ovaries. The nurse cells shrink as they supply nutrients and mRNAs to the developing egg which grows larger. Substances are produced under the direction of maternal effect genes, also called egg-polarity genes, that are deposited in the unfertilized egg. These cytoplasmic determinants in the unfertilized egg provide positional information for two developmental axes (anterior-posterior and dorsal-ventral axis) before fertilization. Eventually, the mature egg fills the egg shell that is secreted by the follicle cells. The egg is fertilized within the mother and then laid. Embryonic development forms a larva, which goes through three stages. Pattern formation begins in the early embryo, when the major axes of an animal are established. Before specialized tissues and organs form, the relative positions of a bilaterally symmetrical animal's head and tail, right and left sides, and back and front are established. Genes known as homeotic genes control pattern formation in the late embryo, larva, and adult. Mutations in certain regulatory genes, homeotic genes, cause the misplacement of structures in an animal. These pictures contrast the head of a wild-type (normal) fruit fly, bearing a pair of small antennae, with that of a homeotic mutant, bearing a pair of legs in place of the antennae.

To which part of the centromere do mitotic spindle fibers attatch during prometaphase?

Kinetochore -The kinetochore is the region of the centromere on the sister chromatid to which the mitotic spindle attaches.

During which stage of mitosis are chromosomes lined up in the center of the cell?

Metaphase -Chromosomes held by spindle fibers are lined up in the middle of the cell during metaphase, the third and middle stage of mitosis

Several levels of DNA packing make up the compact chromosome seen in a metaphase cell. Even when a cell is not dividing, some of the DNA is folded tightly. The degree of DNA packing makes certain genes available or unavailable for transcription. Chromosomes consist of loops of supercoils, which are made up of tight helical fibers. These fibers are composed of nucleosomes, which consist of DNA wrapped around protein molecules. In the fiber, the DNA is unavailable for transcription. Click on the fiber to unpack the DNA and make it accessible for transcription.

Most of the fine-tuning of gene expression occurs at the transcription level-- making an RNA copy of a DNA sequence. Recall that to initiate transcription, an RNA polymerase must bind to the promoter region adjacent to a gene. This cannot occur without the help of specific protein transcription factors. Some transcription factors, called activators, bind to enhancer regions some distance from the gene. The DNA bends, bringing the activators closer to the gene, where the activators interact with other transcription factors and RNA polymerase to initiate transcription

The promoter contains short, specific nucleotide sequences that signal the start of a gene and is the site where RNA polymerase starts transcription.

Operators are regions of DNA that interact with regulatory proteins that control the transcription operons. Here's an analogy. A promoter is like a door knob, in that the promoters of many operons are similar. An operator is like the key hole in a door knob, in that each door is locked by only a specific key, which in this analogy is a specific regulatory protein.

A cell can rapidly adjust to environmental changes by regulating several processes that happen after transcription. In RNA processing, a cap and tail are added, introns removed, and remaining exons spliced together. Alternative splicing of RNA may create different mRNA molecules from the same primary RNA transcript.

Passage of mRNA through the nuclear envelope provides additional opportunities for control. The life span of mRNA molecules helps determine how much of a protein is made. Enzymes attack mRNA, and its components are recycled. Depending on its ability to resist this breakdown, a eukaryotic mRNA molecule may last from hours to weeks. The longer an mRNA lasts, the more protein can be made.

Which of the following events would cause the cell cycle to arrest?

Poor nutrient conditions -Poor nutrient conditions would arrest the cell cycle at the G1 checkpoint.

Chromosomes become visible during _____.

Prophase -During prophase, the chromatin fibers become discrete chromosomes.

rna molecules dictating

RNA activity; A significant amount of the genome may be transcribed into noncoding RNAs (ncRNAs), Noncoding RNAs regulate gene expression at several points

structure of miRNA

RNA dictating RNA being made: is a single stranded RNA of about 22 nucleotides that forms a complex with one or more proteins, the miRNA allows the complex to bind any mRNA molecules with 7-8 nucleotides of complementary sequences, the mRNA protein complex then either degrades the target mRNA (if the miRNA and mRNA bases are complementary along all their length then the mRNA is degraded) or blocks its transcription (if the match is less complete then translation is blocked because it don't let the ribosomesattach to it)

RNA interference

RNAi, the blocking of gene expressoion by siRNAs, it is used in the lab as a means of dialing specific genes to investigate their function (1- miRNA. Imperfect base pairing between the small RNA and the target. This complex sorts the RNA to p-bodies (processing bodies) where other proteins join in. The mRNA is either destroyed or stored. 2- siRNA. Perfect base pairing. The mRNA is destroyed and that's it)

reverse transcriptase-polymerase chain reaction

RT-PCR, Another widely used method for comparing the amounts of specific mRNAs in several different samples is reverse transcriptase-polymerase chain reaction (RT-PCR), its a protein that will take RNA into DNA; 1. reverse transcriptiontase is added to a test tube containing mRNA isolated fro containing mRNA isolated from a certain type of cell, 2.reverse transcriptase makes the first DNA strand using the mRNA as a template and a stretch of thymine deoxyribose nucleotides (dTs) as a DNA primer, 3. mRNA is degraded by another enzyme, 4. DNA polymerase seynthesisizes the second strand using a primer in the reaction picture (several options exist for primers), 5. the result is cDNA which carries the complete coding sequence of the gene but no introns

The copying of chromosomes occurs during which of the following phrases of the cell cycle?

S phase -Chromosomes must undergo replication before mitosis can occur; this copying occurs during the S phase

Which term describes two recently replicated DNA strands that are joined together just before cell division?

Sister chromatids -Sister chromatids are the two strands of a recently replicated chromosome that will be split apart during cell division.

What's on a microarray, Patrick Brown

So this is how we represent the human genome in a microarray. It, as you can see there are about thirty thousand spots representing roughly the thirty thousand genes that we currently recognize in the human genome, and this gives us a way to, whenever we look at a cell or a tissue sample, to recognize which genes are being used and how they're being used in a particular cell or a tissue or a process.

Which stage of mitosis is characterized by the disintegration of mitotic spindles and the formation of two new nuclear membranes?

Telophase -the mitotic spindles disintegrate and a nuclear envelope begins to form around each set of chromosomes during telophase, the last substage of mitosis

For the first several divisions of early frog embryos, cells proceed directly from the M phase to the S phase and back to M without gaps. Which of the following is likely to be true about dividing cells in early frog embryos?

The cells get smaller with each generation. -Without gap phases, the cells have no opportunity to grow

Exons and Introns: DNA coding and non-coding regions

The coding sequence for most eukaryotic polypeptides is not continuous. The coding regions (exons) are separated by non-coding regions (introns).

nucleic acid probe

The complementary molecule a short single-stranded nucleic acid (that can be DNA or RNA) called a nucleic acid probe, different probes can be labeled with diff flupresscent dyes (it will attach to the mRNA)

PROTEIN ACTIVATION

The final opportunity for controlling gene expression in eukaryotic cells occurs after translation. Often, eukaryotic polypeptides must be processed to yield functional protein molecules. For example, insulin is a protein hormone made up of two peptide chains connected at two locations by disulfide bridges (bonds). This is the form of insulin released into the bloodstream and acts on target cells. However, insulin is synthesized in beta cells on the endoplasmic reticulum as a much larger, single peptide chain called proinsulin. During late processing, this long peptide folds as a result of formation of disulfide bridges During packaging in the Golgi apparatus, enzymes convert proinsulin to insulin by cleaving the long chain at two locations, splitting the original single chain into two pieces.

The regulatory gene of the lac operon produces an mRNA that produces a repressor protein, which can bind to the operator of the lac operon.

The general term for the product of a regulatory gene is a regulatory protein. The Lac regulatory protein is called a repressor because it keeps RNA polymerase from transcribing the structural genes. Thus the repressor inhibits transcription of the lac operon

DNA Microarray

The grid you can see in this microarray slide is actually composed of 30,000 individual DNA dots, each targeted to match a specific human gene. In order to work out which genes are being expressed, messenger RNA is first extracted from the cell sample and copied back to DNA using an enzyme. This DNA, called cDNA, is complementary to the target gene, so we'll associate with it, or hybridize with it, on the slide. After labeling with a fluorescent dye, the cDNA is washed over the slide. The genes currently active in the cell can then be identified by the level of the fluorescence and the color of the spots.

Which of the following statements about fruit fly development is false?

The location of the head and tail ends of the egg is primarily determined by the location of sperm entry during fertilization

In 1961, Francois Jacob and Jacques Monod proposed the operon model of gene regulation in bacteria

The model was based on their study of the genes in E. coli that code for enzymes that affect the breakdown of lactose. Because of the pioneering work of Jacob and Monod, the lac operon is typically used to illustrate gene regulation in bacteria. Gene regulation in eukaryotes is quite different

Which event does not take place before the start of mitosis?

The nuclear envelope disintegrates -this event takes place during mitosis

operator

The regulatory "switch" is a segment of DNA called an operator, it is positioned within the promoter or in some cases between the promoter and the enzyme coding genes, the operator controls the access of RNA polymerase to the genes, is the operons switch for controlling transcription

regulatory gene

The repressor is the protein product of a separate regulatory gene, it is usually located some distance away from the trp operon and has its own promoter, regulatory genes are expressed continously although at a low rate

Which of the following is a function of the S phase in the cell cycle?

The synthesis of sister chromatids -DNA replication occurs during S phase and results in two sister chromatids for each original chromosome

Colon Cancer

There are many oncogenes and tumor suppressor genes, some of which act only in certain cells at certain times. Therefore, a complex sequence of events must occur before a normal cell becomes malignant. More than two mutations are usually needed for full-blown cancer. To transform a normal colon epithelial cell into a cancer cell takes multiple mutations; actually at least five genes must be mutated in a single cell to produce metastatic colon cancer. At least four tumor suppressor genes and one oncogene must be mutated in sequence for an epithelial cell in a colon to become metastatic. Although the occurrence of all these events in a single cell might appear unlikely, remember that the colon has millions of cells, that the cells giving rise to colon epithelial cells are constantly dividing, and that these changes take place over many years of exposure to natural and synthetic carcinogens as well as spontaneous mutations. In colon cancer, loss of normal tumor suppressor gene APC helps to initiate the formation of a polyp (small growth) on the colon wall. A benign precancerous tumor grows in addition to the activation of oncogene ras. A class II adenoma (benign) grows. After the loss of tumor suppressor gene DCC, a class III adenoma (benign) grows. Upon the loss of the tumor suppressor gene p53, a carcinoma (malignant) develops. Other changes such as loss of anti-metastisis gene occur and the cancer metastasizes (spreads to other tissues). Other mutation sequences can also lead to colon cancer. The characterization of the molecular changes in tumor cells has opened up the possibility of genetic diagnosis and screening for cancer. It is also possible to detect early in life whether an individual has inherited a mutant tumor suppressor gene. A person who inherits mutated copies of the tumor suppressor involved in colon cancer, for example, normally would have high probability of developing this cancer by age 40. Surgical removal of the colon would prevent a metastatic tumor from arising. Ongoing research has resulted in the development of increasingly accurate diagnostic tests and a better understanding of various genetic diseases at the molecular level. This knowledge is now being applies to develop new treatments for genetic diseases.

x chromosome inactivation

This calico cat is heterozygous for alleles of a coat color gene that produce either dark fur or orange fur. This gene is on the X chromosome, so the different colored fur is due to inactivation of one X chromosome. The patchy distribution and white color is due to a second gene that is epistatic to the coat color gene and thus masks the effects. Epistasis is the interaction between the genes at two or more loci, so that the phenotype differs from what would be expected if the loci were expressed independently.Which X chromosome is inactivated in females varies randomly from cell to cell. The inactivated X chromosome becomes highly condensed, making it visible as an intensely stained Barr body. If a female is heterozygous for a sex-linked trait, some of her cells will express one allele and some cells express the other allele. These heterozygous females are referred to as genetic mosaics. Although males have only one copy of the X chromosome, and females have two, females do not produce twice as much of the proteins encoded by genes on the X chromosome. Instead, one of the X chromosomes in females is inactivated early in embryonic development, shortly after the embryo's sex is determined. This inactivation is an example of dosage compensation, which ensures an equal expression from the sex chromosomes despite a differing number of sex chromosomes in males and females.The dark fur and orange fur are due to heterozygosity for a gene on the X chromosome that determines pigment color. One allele results in dark pigment expression and the second allele results in orange pigment expression. Which of these colors is expressed in any particular cell is due to inactivation of one X chromosome - if the chromosome with the dark allele is inactivated, the fur will be orange, and vice versa

Review: Gene Regulation in Eukaryotes

This figure highlights the multiple points where eukaryotic gene expression can be controlled. Select the correct process at each control point from the pull-down menus.

mechanisms of post transcriptional regulation

Transcription alone does not account for gene expression, Regulatory mechanisms can operate at various stages after transcription, Such mechanisms allow a cell to fine-tune gene expression rapidly in response to environmental changes

True of false? The M phase is characterized by the replication and division of a cell's chromosomes

True -Correct: Cells replicate their chromosomes during the S phase and divide partition their chromosomes during the M phase

Making a DNA Microarray, Patrick Brown

We built a very simple robot that used a very simple and ancient technology, the technology of the fountain pen, and what the robot does is it takes a set of fountain pens and dips them in each of these little ink wells in this 96-well plate, and the ink in these ink wells is the DNA that represents a human gene. Each well represents a different human gene. The pens dip into the wells and then they move over and print the DNA ink in a nice array on a little microscope slide like this and they repeat that process over and over again from hundreds of these plates, finally producing an array that represents about thirty thousand different human genes. And then we can use these microarrays in a very simple experimental procedure that allows us, that basically causes the spots to light up whenever the genome in a particular cell or tissue sample uses one of these genes, one of these words, in the script that it's writing

Using DNA Microarrays To Study Cancer, Patrick Brown

Well we knew that differences in the gene expression program were largely responsible for the differences in the appearance and the behavior of the normal cells in our body, say a brain cell compared to a liver cell. And so it seemed natural that by looking systematically at the gene expression program in cancer cells, we would be able to get a better understanding of why those cells are different from their normal counterpart and why a breast cancer in one woman looks and behaves differently from a breast cancer in another woman

An operon is a cluster of bacterial genes along with an adjacent promoter that controls the transcription of those genes.

When the genes in an operon are transcribed, a single mRNA is produced for all the genes in that operon.

Why we developed the microarray, Patrick Brown

When we started developing the microarray technology it was to enable a new method for relating sequence differences in genes to complex traits in people, that was the idea. When we began doing experiments we realized that the microarrays could be used to characterize essentially any property of a gene on a genome-wide basis, to look at the whole genome, all the genes in the genome and not only look at things like heritable differences in sequences but look at dynamic behavior of the genes.

repressor active

a activated repressor protein is one that gets bound to by a corereepressor which activates the repressor and makes it bind to the operon blocking transcription

Most differentiated cells retain

a complete set of their genes, and retain the ability to express those genes under certain circumstances.

combinational control of gene activation

a dozen or so short nucleotide sequences appear again and again in the control elements for different genes; each enhancer is composed of about 10 control elements and each of which can bind only one to two specific transcription factors; A particular combination of control elements in an enhancer associatwed with a gene rather than the presence of a single unique control element is important in regulating transcription of the gene, A particular combination of control elements can activate transcription only when the appropriate activator proteins are present, need that activators to work

how microRNAs came about

a long RNA precursor is processed by cellular enzymes into an miRNA

activator

a protein that binds to DNA and stimulates transcription of a gene

repressor specificifty

a repressor protein is specific for the operator of a particular operon (ex: the repressor that switches off the trp operon by binding to the trp operator has no effect on other operons in the E coli genome)

The expression of the tryptophan operon is controlled by

a repressor that is active when it binds to tryptophan.

the genome codes for

a significant amount of nonprotein coding RNAs/noncoding RNAs, small RNAs, and longer RNA transcripts

corepessor

a small molecule that cooperates with the repressor protein to switch an operon off (ex: tryptophan functions as the corepressor in the trp operon system; as tryptophan accumulates more tryptophan molecules associate with trp repressor molecules which can then bind to the trp operator and shuts down production of the tryptophan pathway enzymes, if the cells trytophan level drops transcription of the operons genes resumes)

inducer

a specific small molecule called an inducer inactivates the repressor

cyclic AMP

accumulates when glucose is scarce, is the small molecule that binds to the allestetic regulatory protein called CAP and activates it

Proteins that bind to DNA and turn on operons by making it easier for RNA polymerase to bind to a promoter are called

activators.

genome

all cells in an org contain identical genome; therefore the differences between cell types is not due to different genes being present but due to differential gene expression

Which of the following permits a single gene to code for more than one polypeptide?

alternative RNA splicing

how bacteria tune their metabolism to changing environment

an individual Ecoli living the the erratic environment of a human colon depedenent on nutrients for its whimsical eating habits of the hosts; so if the environment is lacking the amino acid tryptophan which the bacterium needs to survive then the cell responds by activating a metabolic pathway to make tryptophan from anotherr compounds; but once a human eats tryptophan then the bacterial stops producing tryptophan thus avoiding wasting its resources

allolactose

an isomer of lactose formed in small amounts from lactose that enters the cell

Centromeres divide and sister chromatids become full-fledged chromosomes during _____.

anaphase -During anaphase, sister chromatids separate and daughter chromosomes migrate to opposite poles.

histone acetylation

appears to promote transcription by opening up the chromatin structure; the amino acids in the N terminus tails of histones are accessible for chemical modification such as addition of acetyl groups, a region of chromatin in which nuleosomes are unacetalted forms a compact structure in which DNA is not transcribed while highly acetylated nucleosome cause the chromosome to be less compact and the DNA accessible for transcriptipn

coexpressed eukaryotic genes

are genes coding for enzymes of a metabolic pathway are typically scattered over different chromosomes; so to coordinate gene expression it depends on the association of a specific combination of control elements with every gene of a dispersed group

enzymes that modify chromatin structure

are integral part of the eukaryotic cells machinery for regulating transcription

proximal control elements

are located close to the promoter

enzymes for trytophan synthesis

are said to be repressible; An enzyme whose production is generally continuous but can be halted if a particular substance is present in concentrations greater than normal

methylation will

be inherited

more gene control for eukaryote vs prokaryote

because eukaryotic cell structure is more complex

don't want rna floating around in cell

because it will make the same proteins

In female mammals, the inactive X chromosome in each cell

becomes a Barr body

lactose metabolism

begins with the hydrolysis of the disaccharide into its component monosaccharides; glucose and galactose, this reaction is catalyzed by the enzyme B-galactosidase

Silencers are sites in DNA that

bind repressor proteins to inhibit the start of transcription.

mediator proteins

bind to general transcription factors which then assemble the transcription initiation complex

protein mediated bending of the DNA

brings the bound activator in contact with a group of mediator proteins which in turn interact with proteins at the promoter (bending of the DNA by a protein enables enhancers to influence a promoter hundreds or thousands of nucleotides away)

how does the operator switch work?

by itself the trp operon is turned on; RNA polymerase can bind to the promoter and transcribe the genes of the operan, the operon can be switched off by a protein called the trp repressor

complemtary DNA

cDNA, RT-PCR relies on the activity of reverse transcriptase, which can synthesize adouble stranded DNA copy of an mRNA

eukaryotes rate og gene expression

can be increased or decreased by the binding of specific transcription factors either activators or repressors to the control elements on enhancers

specific transcription factors that function as repressors

can inhibit gene expression in several different ways; some repressors bind directly to control element DNA (in enhancers or elsewhere) blocking activator bind or in some cases turning off transcription even when activators are bound, or some repressors block the binding of activators to proteins that allow the activator to bind to DNA

Animal development is directed by

cell-to-cell signaling and signal transduction pathways.

miRNA can be used by

cells to prevent infections from double-stranded RNA viruses.

Which of these is NOT a carcinogen?

cigarette smoke, fat, UV light, testosterone, all of the above are carcinogens -all of these substances can cause cancer

lacY

codes for a permease the membrane protein that transports lactose into the cell

lacA

codes for an enzyme called transacetylase whose function in lactose metabolism is still undefined

central dogma

concept that cells are governed by a cellular chain of command.

DNA microarray assays/chip

consists of tiny amounts (Chop it up) of a large number of single stranded DNA fragments representing different genes fixed to a glass slide in a tightly spaced array or grid; these garments should represent all the genes in the genome of an org, used for genome wide studies

RNA processing

control splicing: happens in the nucleus, it ends up exporting mature RNA to the cytoplasm provide opportunities for regulation gene expression that are not available in prokaryotes; one example of regulation at the RNA processing level is alternative RNA splicing; which different mRNA molecules are produced from the same primary transcript depending on whih RNA segments are treated as eons and which are treated as introns; regulatory proteins specific to a cell control the intron exon choices by binding to RNA sequence within the primary transcript (ex: the troponin T gene can be spiced in more than one way generating 2 different mRNA molecule that are translated into different but related muscle protein)(ex: other genes offer possibilities for far greater number of products like a gene in drosophila with enough alternative spliced eons to generate about 19,000 membrane proteins with different cellular domain (at least 17,500 which is 94 percent of the alternative mRNAs are actually synthesized; this is because the developing nerve cells apeat yo synthesize a unique form of the protein to act as identification badge on the cell surface), RNA splicing expands the repertoire of a eukaryotic genome; its proposed thats why humans have low number of genes is because 90 percent of the human protein coding genes undergo alternative splicing

eukaryotes precise control of transcription

depends largely on the binding of activators to DNA controll elements

function of any cell

depends on what appropriate set go genes are being expressed; the transcription factors of a cell must locate the right genes at the right time; when gene expression proceeds abnormally series imbalances and diseases including cancer can arise

small interfering RNAs

dictates it will be read, degraded, and translated: siRNAs, are similar in size and function to miRNAs because both can associate with the same proteins and produce similar results, the distinction between miRNA and siRNAs is based on subtle difference in the structure of their double stranded RNA precurosr molecules; if researches inject siRNA precursor molecule into a cell the cells machinery can process them into siRNAs that turn off expression of genes with related sequences

transcription control eukaryotes

different cells make different proteins because different activators were available; transcription don't use operator site but use transcription factors and enhancers that bind to it; so we can have diff cells to have diff proteins to bind at different sites to produce different things (Unlike the genes of a prokaryotic operon, each of the co-expressed eukaryotic genes has a promoter and control elements These genes can be scattered over different chromosomes, but each has the same combination of control elements Copies of the activators recognize specific control elements and promote simultaneous transcription of the genes)

chromatin modification

does not entail a change in the DNA sequence, it is passed along to future generation of cells

in situ hybridization

each molecule is labeled during synthesis with a florescent tag so we can follow it, a solution with the probe is applied to the embryos which allows probe molecules to hydribize specifically to any complementary sequences on this many mRNAS in the embryonic cell that are transcribing the gene, this technique alloqes us to see th mRNA in place or in situ in the intact organism

gene expression in a eukaryotic cell

each stage is a potential control point which gene expression can be turned on or off, accelerated, or slowed down: 1. chromatin modification: DNA unpacking involving histone acetylation and DNA demethylation, 2. transcription, 3. RNA processing, 4. Transport to cytoplasm, 5. translation, 6. protein processing such as cleavage and chemical modification; 6b. degradation of mRNA, 7. transport to cellular destination; 7.b digression of protein

general transcription factors

essential for transcription of all protein coding genes, only a few of these bind a DNA sequence within the promoter (like TATA box), the others primarly bind proteins including each other and RNA polymerase II; protein to protein interaction is crucial to the initiation of eukaryotic transcription because only when the complete initiation complex has been assembled can the polymerase begin to move along the DNA template strand producing a comp strand of RNA

The coding regions of a gene (the portions that are expressed as polypeptide sequences) are called

exons.

___ is a carcinogen that promotes colon cancer

fat -a diet high in fat increases the risk of both colon and breast cancer

positive control

gene regulation is said to be positive control only when a regulatory protein interacts directly with the genome to switch transcription on

distal control elements

groupings of which are called enhancers, may be thousands of nucleotides upstream or downstream of a gene or even within an intron, a given gene may have multiple enhancers and each active at a different time or in a different cell type or location in the organism; each enhancer is generally associated with only that gene and no other

natural selection (bacteria)

has facored bacteria that express only the genes whose products are needed by the cell (ex: bacterial cell that can conserve resources and energy have selective advantage over cells unable to do so)

icily growing in absent of lactose

has only a few of the B-galactosidase enzyme but if lactose was added to the environment the enzymes would increase a thousandfold within about 15 minutes

chemical modifications to hsitones

histones are the proteins which the DNA is wrapped in nucleosomes, chemical modifications to histones play a direct role in the regulation of gene transcription; the N terminus of each histone molecule in a nucleosome protrutdes outward from the nucleosome, these histone tails are accessible to various modifying enzymes that catalyze the additional or remove of a specific chemical groups such as acetyl (-COCH3), methyl, and phosphate groups; acetyl causes DNA to be more transcribed while methyl doesn't: while addition of methyl groups can lead to codensation of chromatin and reduced transcription

how many transcription activators are found n eukaryotes

hundreds

regulation of gene expression in eukaryotes improtant

important for specilization of multicellular organisms; because these orgs are made up of different types of cells with distinct roles and to perform theses different roles each cell type must maintain a specific program of gene expression in which certain genes are expressed and others are not

How does the eukaryotic cell deal with a group of genes related function that need to be turned on or off at the same time?

in bacteria it is the coordinately controlled genes that often cluster in an operon is regulated by a single promoter and transcribed into a single mRNA molecule; thus genes are expressed together and the encoded proteiens are produced concurrently; this hasn't been found in eukaryotes, instead they have co expressed genes

lac operon

includes three genes: one for B-galactosidase and two other genes coding for enzymes that function in lactose utilization

activators and repressors

infleucne transcription directly, also some act indirectly by affecting chromatin structure; (ex: some activators recruit proteins that acetylate histones near the promoters of specific genes thus promoting transcription, some repressors recruit proteins that remove acetyl groups from histones leading to reduced transcription (silencing)); the recruitment of proteins that modify chromatin seems to be the most common mechanism of repression in eukaryotes

epigenetic inheritance

inheritance of traits transmitted by mechanisms not directly involving the nucleotide sequence is called epigenetic inheritance, histone acetylation is a type of that, unlike mutations in DNA which are permiant the modification to the chromatin can be reversed, is a big reason in gene regulation (ex: might help explain why one twin acquires a genetically based disease but the other does not despite their identical genomes, or alterations in normal patters of DNA methylation are seen in some cancers where the alterations are associated with inappropriate gene expression)

Nucleoli are present during _____.

interphase -Nucleoli are present during interphase

During _____ the cell grows and replicates both its organelles and its chromosomes.

interphase -these are the events of interphase

bacteria regulation of transcription intiation

involves proteins that bind to DNA (repressors or activators) that either facilitate or inhibit binding of RNA polymerase

regulation of both the trp and lac operons

involves the negative control of genes because the operons are switched off by the active form of the repressor protein (allolactose induces enzyme synthesis not by acting directly on the genome but by freezing the lac operon from the negative effect of the represser)

repressor

is a protein that turns off the operan, the repressor binds to the operator and blocks attachment of RNA polymerase to the promoter preventing transcription of the genes

MyoD

is a protein transcription factor, made up of two subunits with extensive regions of alpha helix, each subunit has one DNA binding domain and one activation domain; the activation domain includes binding sites for the other subunit and other proteins, is involved in muscle development in vertebrate embryos

DNA mytgkation

is a set of enzymes that methylate certain bases in the DNA itself usually cytosine (not just methylate the tails of histone proteins but the actual DNA bases)

lac repressor

is active by itself binding to the operator and switching the lac operon off; for the lac operon the inducer is allolactose; so when the absence of lactose (hence alloalatose) the lac repressor is in its active configuration (nothing blinded to it) and the genes of the lac operon are silenced, if lactose is added to the cells surroundings allolactose binds to the lac repressor and alters it conformation nullyinfying the repressors ability to attach to the operator

reverse transcriptase

is an enzyme that is slated from a type of virus called retrovirus, it is an enzyme that turns mRNA into a double stranded DNAs, synthesize a comp dna copy of an mRNA thus making a reverse transcript

common control point for gene expression

is at transcription for both eukaryotes and prokaryotes: regulation at this stage often occurs i response to signals coming from outside the cell such as hormones or other signaling molecules

gene for B galactosidase

is called lacZ, is part of the lac operon

ncRNAs

is known to occur at several points in the pathway of gene expression including mRNA translation and chromatin modification

PCR

is next step and is a way to make many copies of one specific stretch of double stranded DNA using primers that hybridize to the opposite ends of the region of interests and then run through gel electrophoresis to see if you have it again

DNA of eukaryotic cells

is packaged with proteins in an elaborate complex known as chromatin which is the basic unit of which is the nucleosome; the structural organization of chromatin not only packs a cells dna into a compact form that fits inside the nucleus but also helps regulate gene expression in several ways and all catalyzed by enzymes: 1. The location of a gene promoter relative to nucleosomes and to the sites where the DNA attaches to the chromosome scaffold or nuclear lamina attachment sites can influence gene transcription (whether its transcribed or not), 2. Genes within highly condensed heterochromatin are usually not expressed, 3. Chemical modifications to histone proteins and DNA of chromatin can influence both chromatin structure and gene expression

key advantage of grouping genes of related function into one transcription unit

is that a single on off switch can control the whole cluster of functionally related genes; these genes are coordinately controlled (ex: when Ecoli must make tryptophan for itself because the nutrient medium lacks this amino acid all the enzymes for the metabolic pathway are synthesized at one time)

operon

is the entire stretch of DNA that includes the operator, the promoter, and the genes that they control (ex: is the trip operon which includes the promoter, operator, trpE, trpD, trpC, trpB, and trpA)

protein processing and degradtion

is the final opportunity to control gene expression after translation, eukaryotic polypeptides must be processed to yield functional protein molecules (ex: cleavage of the initial insulin polypeptide forms the active hormone, or proteins undergo chemical modification to make them functional), regulatory proteins are commonly activated or inactivated by the reversible addition of phosphate groups and proteins destine for the surface of animal cells acquire sugars; cell surface proteins and many others must be transported to target destinations in the cell in order to function) regulation might occur at any of the steps involved in modygiyinh or transporting a protein, also the length of time a protein functions n the cell is strickly regulated by means of selective degradation; many proteins such as the cyclins involved in regulating the cell cycle must be relatively short lived if the cell is to function properly; to make a particular protein for destruction the cell commonly attaches molecules of a small protein called ubiquitin to the protein which triggers its destruction by protein complexes in the cell

How does the Ecoli cell sense the glucose concentration and relay this information to the genome?

is the interaction of an allosteric regulatory protein with a small organic molecule (cyclic AMP) which accumulate when glucose is scarce

lacl

is the regulatory gene; the gene for the allosteric repressor called the lac repressor, is located outside the operon happens to be adjacent to the operon which is an unusual situation

lac transcription unit

is under the command of one main operator and promoter

inducible operan

is usually off but can be stimulated/induced when a specific small molecule interacts with a regulatory protein, lac operon is induced

CAP (not with lac)

it helps regulate other operons that encode enzymes used in catabolic pathways (could effect the expression of more than 100 genes in Ecoli), when glucose is plentiful CAP is inactive and the synthesis of enzymes that catabolize compounds other than glucose slows down; the ability to catabolize other compounds such as lactose enables a cell deprived of glucose to survive

what is methylated?

it occurs in most plants animals and fungi; 1. long stretches of inactive DNA (more than one gene) such as that of inactivated mammalian X chromosome are generally more methylated than regions of actively transcribed DNA (there are exceptions), 2. smaller scare individual genes are usually more heavily methylated in cells in which they are not expressed; removal of the extra methyl groups can turn on some of these genes

once a gene is methylated

it usually stays that way through successive cell divisions in a given individual; at DNA sites where one strand is already methylated enzymes methylate the correct daughter strand after each round of DNA replication so this way methylation patterns can be inherited

DNA microarray assays

mRNAs from cells of interest are isolated and made into cDNAs labeled with fluorescent molecules, then cDNAs are labeled with fluorescent molecules and then allowed to hybridize to a microarray slide, the cDNAs from two samples are labeled with molecules tht emit different colors and teested on the same microrarray, this identifies the subset of genes i

two ways to regulate the dna

methylate; doesn't allow for bible to for and stops rna making it or aceyltate it (for transcription or dna replication)

microRNAs

miRNAS, small single stranded RNA molecules, they are capable of binding to complementary sequences in mRNA molecules

biologists driven to understand any types of cells

must first try to discover which genes are expressed by the cells of interest; to do this one must identify the mRNAs being made

dual control (lac)

negative control by the lac repressor and positive control by CAP: the state of the lac repressor with or without bound allolactose determines whether or not transpiration of the lac operon genes occur at all, the state of CAP with or without bound cAMP controls the rate of transcription if the operon is repressor free (like on and off switch and volume control; on and yes cAMP then high volume and on and no cAMP is low volume)

metabolic control

occurs on two levels: 1. cells can adjust the activity of enzymes already present; it is a fast response which relies on the sensitivity of many enzymes to chemical cues that increase or decrease their catalytic acitivty (ex: the activity of the first enzyme in the tryptophan synthesis pathway is inhibited by the pathways end product; thus if trytopan accumulates in a cell it shuts down the synthesis of more tryptophan by inhibiting enzyme activity), this is feedback inhibition; it allows a cell to adapt to short term fluctuations in the supply of a substance it needs (happens in anabolic/biosynthetic pathways); An enzyme inhibitor is a molecule that binds to an enzyme and decreases its activity. , 2. cells can adjust the production level of certain enzymes; they can regulate the expressions of the genes encoding the enzymes (ex: the environment provides all the tyroptophan the cell needs then the cells stop making the enzymes that catalyze synthesis of tryotphan), in this care the control of enzymes production occurs at the level of transcription because the it turns off the synthesis of mRNA coding for these enzymes, many genes in the bacterial genome are switched on or off by changes in the metabolic status of the cell

eukaryote

one promoter and one gene and control elements

active shape (POS AND NEG)

pos: helps switch transcription on, neg: helps turns transcription off

The lac operon in E. coli

prevents lactose-utilizing enzymes from being expressed when lactose is absent from the environment

regulation of genes

prokaryotes and eukaryotes at all times must regulate which genes are expressed; both unicellular organisms and the cells of multicellular organisms must continually tuen genes on and off in response to signals from their external and internal environments

Spindle fibers attach to kinetochores during _____.

prometaphase -attachment of spindle fibers to kinetochores is one of the events of prometaphase

regulate prokaryotes

proteins or regulate transcription

chromatin modifying enzymes

provide initial control of gene expression by making a region of DNA either more or less able to bind the transcription machinery; once a chromatin of a gene is optimally modified for expression the initiation of transcription is the next major step at which gene expression is regulated

silencing

reduced transcription

enzymes of the lactose pathway

referred to as inducible enzymes because their synthesis is induced by a chemical signal (allactose)

initiation of translation

regulation for translation occurs most commonly at the initiation stage; 1. for some mRNAs the initiation of translation can be blocked by regulatory proteins that bind to specific sequences or structures within the 5' or 3' UTR preventing the attachment of the ribosome, 2. a different mechanism for blocking translation is seen in a varierty of mRNAs present in the eggs of many organisms; initially these stored mRNAs lack poly A tails of sufficent elgnth to allow translation initiation but at appropriate time during embryonic development a cytoplasmic enzymes adds more adenine (A) nucleotides prompting translation to begin, 3. tranlastion of all mRNAs in a cell may be regulated simultaneously; in eukaryotic cell such global control involves the activation or inactivation of one or more of the protein factors required to initiate translation (For example: translation initiation factors are simultaneously activated in an egg following fertilization)

Both prokaryotic and eukaryotic cells use ________ to turn certain genes on or off.

regulatory proteins

RNA splicing involves the

removal of introns from the molecule

repressible enzymes

repressible enzymes typicaly function in anabolic pathways which synthesize essential end products from raw materials (precursors); by suspending production of an end product when it is already present in suffiencent quantities the cell can allocate its organic precursors and energy for other uses

control elelments

segments of noncoding DNA having particular nucleotide sequences that serve as binding sites for the proteins called transcription factors which in turn regulate transcription, control elements on the DNA and the transcription factors they bind are critical to the precise regulation of gene expression seen in different types of cells

The basis of cellular differentiation is

selective gene expression.

A homeotic gene

serves as a master control gene that functions during embryonic development by controlling the developmental fate of groups of cells.

lac

short for lactose; the disaccharide lactose/milk sugar is available to Ecoli in the human colon if the host drinks milk

A signal outside a cell triggers changes in the transcription and translation inside the cell through the process of

signal transduction pathways.

specific transcription factors

specific transcription factors and the interaction of control elements with these proteins can cause high levels or transcription of particular genes at appropriate time and place

Cytokinesis often, but not always, accompanies _____.

telophase -Cytokinesis often, but not always accompanies telophase.

nucleic acid hybridization

the base pairing of one strand of a nucleic acid to the complet\mentary sequence of another strand

if the amount of glucose in the cell increases (pos control)

the cAMP concentration falls and without cAMP the CAP detaches from the operon, because CAP is inactive RNA polymerase binds less efficiently to the promoter and transcription of the lac operon proceeds at only a low level even in the presence of lactose; thus lac operon is under dual control: negative control by the lac repressor and positive control by CAP

differential gene expression

the expression of different genes by cells with the same genome

mRNA degration

the life span of mRNA molecules in the cytoplasm is important in determining the pattern of protein synthesis in a cell; bacterial mRNA molecules degrade by enzymes a few minutes of their synthesis (also no cap so degraded); this short life span of mRNAs is one reason bacteria can change their patterns of protein synthesis so quickly in response to environmental changes (like the lac and trp operon thing), eukaryotes: mRNA survive for hours, days, and even weeks because of the poly-A-tails; the 200 RNAs on the cap allows for it to survive for a period of time; so depending in how man A's i put on determines how long until degradtion; this is regulation by determining how many A's to put it on; regulate how often the mRNA is available to be read by a ribosome; the more times its read the more protein is produced; Nucleotide sequences that influence the life span of mRNA in eukaryotes reside in the untranslated region (UTR) at the 3 end of the molecule (ex: the mRNAs for the hemoglobinpolypeptides in developing red blood cells are unusually stable and these long lived mRNAs are translated repedeatly in the cells)

During _____ both the contents of the nucleus and the cytoplasm are divided

the mitotic phase -the mitotic phase encompasses both mitosis and cytokinesis

Enhancers are

the site on DNA to which activators bind

if glucose is scare (pos control)

then high levels of cAMP accumulate and then when cAMP binds to this regulatory protein CAP assumes its active shape and can attach to a specific site at the upstream end of the lac promoter, this attachment increases the affinity of RNA polymerase for the promoter which is actually rather low even when no repressor is bound to the operator, by facukitung the binding of RNA polymerase to the promoter and thereby increasing the rate of transcription the attachment of CAP to the promoter directly stimulate gene expression; therefore this mechanism qualifies as positive regulation

The carcinogen known to cause the most cases of cancer is

tobacco.

A gene operon consists of

transcribed genes, an operator, and a promoter.

respressible operon

transcription is usually on but can be inhibited/repressed when a specific molecule (tryptophan) binds allosterically to a regfulatory protein, trp operon is said to be a repressible operan

example of how genes expression can respond to changes in the cells internal and external environment

trp operon

During prophase a homologous pair of chromosomes consists of _____.

two chromosomes and four chromatids. -at this point each of the chromosomes consists of two chromatids.

why use this reverse transcriptase-polymerase chain reaction process?`

uses mRNA as the template for the first strand and DNA is made in vitro, to stick human DNA into prokaryotes because no introns

inducible enzymes

usually function in catabolic pathways' which break down a nutrient to simpler molecules, by producing the approtiopte enzymes only when the nutrient is available the cell avoids wasting energy and precursors making proteins that are not needed

glucose and lactose ecoli

when both present in the environment ecoli uses glucose because the enzymes for glucose breakdown in glycolysis are continually present, only when lactose is present and glucose is in short supply does E coli use lactose as an energy source and only then does it synthesize appreciable quantities of the enzymes for lactose breakdown

without a bound repressor

without a bound repressor the lac operates is transcribed into mRNA for the lactose utilizying enzymes