Test 18 - Chapter 18

What is the basic unit of chromatin?

Chromatin is a complex where the DNA of eukaryotic cells is packaged. The basic unit of chromatin is a nucleosome

Define embryonic lethals

Mutations with phenotypes causing death at the embryonic or larval stage.

What is the role of ncRNA with X chromosomes?

ncRNAs inactivate X chromosomes, which prevents expression of genes located on one of the X chromosomes.

What was the order of evolution of ncRNAs?

siRNAs, miRNAs, piRNAs (only found in animals)

Define repressible enzyme and give an example

Enzyme where synthesis is repressed by a chemical signal (ex: tryptophan pathway enzymes)

Describe how the binding of activators to an enhancer located far from the promoter can influence transcription

1. Activator proteins bind to distal control elements grouped as an enhancer in the DNA. 2. A DNA-bending protein brings the bound activators closer to the promoter. General transcription factors, mediator proteins, and RN polymerase 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.

Describe the process of gene expression (key stages and regulation processes)

1. Chromatin - Chromatin Modification: DNA unpacking 2. DNA - Gene available for transcription - Transcription 3. RNA Primary Transcript - RNA Processing 4. mRNA with tail and cap - Transport to cytoplasm 5. mRNA in cytoplasm - Translation 6. Polypeptide - Protein processing 7. Active protein - Transport to cellular destination

Describe the lac operon

1. Contains genes that code for enzymes that function in the use of lactose, such as beta galactosidase - these genes are lacZ, Y, A - this is the transcription unit 2. Operator 3. Promoter

Two structural domains in activator proteins

1. DNA-binding domain, where the protein binds to DNA 2. Activation domain, which binds to other regulatory proteins or components of the transcription machinery, facilitating a series of protein-protein interactions that result in enhanced transcription of a gene

What is the rest of the genome (some of which is transcribed into nontranslated RNA) made of/made into?

1. Introns 2. non-protein-coding RNAs, noncoding RNAs or ncRNAs

What are specialists at making tissue-specific proteins?

Differentiated cells

What is the length of the time each protein functions in the cell regulated by?

Selective degradation

Why was bicoid research groundbreaking?

1. It led to the identification of a specific protein required for pattern formation 2. Increased understanding of mother's role in embryonic development 3. Gradient of morphogens can determine polarity and position is a developmental concept

Four types of breast cancer, descriptions, and how they can be treated

1. Luminal A - overexpresses ER and PR, lacks HER2 2. Luminal B - same as luminal A 3. HER2 - overxpresses HER2, lacks ER and PR 4. Basal-like - does not express ER, PR, or HER2 Tamoxifen can help treated Luminal A and B; HER2 with herceptin

What were three reasons their project was difficult?

1. Many genes affect segmentation 2. Embryonic lethals affect development but can't be bred for study; this was fixed by looking for recessive mutations in genetic carriers 3. Cytoplasmic determinants influence axis formation, so mother and embryonic genes had to be studied

How is the lac operon under dual control?

1. Negative control by the lac repressor, as its active form switches off transcription 2. Positive control by CAP, as its active form switches on transcription

Describe the growth of cancer

1. Normal cells - loss of tumor suppressor genes 2. Polyp, small benign growth - activation of oncogene, loss of tumor suppressor gene 3. Larger benign growth, adenoma - loss of tumor suppressor gene and additional mutations 4. Malignant tumor, carcinoma

Describe how point mutations within the genome causes proto-oncogenes to become oncogenes

1. Point mutations in the promoter or an enhancer that controls a proto-oncogene causes an increase in its expression 2. Point mutation in the coding sequence changes the protein product to one that is more active or resistant to degradation

How do siRNAs cause the re-forming of heterochromatin at the centromere?

1. RNA transcripts are produced from centromeric DNA 2. Each RNA transcript is used as a template by an enzyme that syntheizes a complementary strand, forming double-stranded RNA 3. The double stranded RNA is processed into shot, single stranded siRNAs that associate with proteins, forming siRNA protein complexes 4. These complexes bind the RNA transcripts being produced from the centromeric DNA 5. Proteins in the siRNA-protein complexes recruit enzymes that modify the histones within the chromatin and initiate condensation 6. This results in the formation of heterochromatin at the centromere

How do specific transcription factors that function as repressors inhibit gene expression?

1. Repressors bind directly to control element DNA (such as at enhancers), blocking activator binding 2. Repressors interfere with the activator so it can't bind to the DNA

If regulatory genes are expressed continuously, why aren't operons switched off permanently (ex: trp regulatory gene always expressed to make repressors, but trp operons are always on)

1. The binding of repressors to operators is reversible. This is because operators alternate between two states; bound and unbound repressors. When there are more repressor molecules, the length of the repressor-bound state increases. When there are less, the length of the repressor-bound, active state decreases 2. Repressors are allosteric proteins with two shapes, one active and one inactive. The repressor is synthesized in the inactive form, which has low affinity for the operator. Only when specific molecules (such as tryptophan) binds to the repressor at an allosteric site does the repressor change shape and become active, which attaches to the operator and turns the operon off

How does destruction of a protein occur?

1. The cell attaches molecules of a small protein called ubiquitin to the protein 2. Protein complexes called proteasomes recognize the ubiquitin tagged proteins and degrade them

Describe the life cycle of the Drosophila egg

1. The egg develops in the female's ovary, surrounded by ovarian cells called nurse cells and follicle cells, which support the egg with nutrients, mRNAs, and other substances needed for development and the shell 2. After fertilization and laying of the egg, embryonic development results in the formation of a segmented larva, which goes through three larval stages 3. The fly parva forms a pupa from which it metamorphoses into an adult fly

In addition to packing DNA in a compact form that fits inside the nucleus, how does the organization of chromatin help regulate gene expression?

1. The location of a gene promoter (relative to the nucleosomes and where DNA attaches to the scaffold) can affect whether the gene is transcribed 2. Genes within heterochromatin (condensed) usually are not expressed 3. Certain chemical modifications to histone proteins and the DNA of chromatin can influence both chromatin structure and gene expression

Describe and contrast trp and lac operons

1. Trp operon: The operon is on as default. Tryptophan is absent, the repressor is inactive, and transcription occurs. However, when the product accumulates, it inhibits its own production by binding to the repressor, which becomes active. Then, the repressor binds to the operator, blocking transcription. (Default off inactive no binding, changed is on active binding) 2. Lac operon: The operon is off as default. Lactose is absent, the repressor is active, and transcription does not occur. However, when lactose is present, allolactase binds to the repressor and inactivates it, causing transcription to occur. (Default on active no binding, changed is off inactive binding)

Describe Epstein-Barr virus and other viruses that cause cancer

A virus that causes mononucleosis that causes cancer in humans (such as Burkitt's lymphoma). Papillomaviruses cause cervix cancer and HTLV-1 causes a type of leukemia cancer.

Usually, how many control elements are enhancers composed of?

10 control elements, which can only bind 1 or 2 specific transcription factors

Describe the body of flies and arthropods

3 major body parts: the head, the thorax (the mid body form which the legs and wings extend), and the abdomen

What is the Ras protein, encoded by the ras gene?

A G protein that relays a signal from a growth factor receptor on the plasma membrane to a cascade of protein kinases; the cellular response at the end is the synthesis of a protein that stimulates the cell cycle. These pathways are usually stimulated by growth factors.

Define transcription initiation complex

A cluster of proteins that assembles on the promoter sequence at the upstream end of the gene

Define corepressor and give an example

A corepressor is a small molecule that cooperates with a repressor protein to switch an operon off. An example is tryptophan, as when it accumulates, more molecules associate with repressor molecules, which then bind to the trp operator and shut down production of the tryptophan pathway enzymes. If tryptophan level drops, transcription continues.

Define maternal effect genes

A gene that, when mutant in the mother, results in a mutant phenotype in the offspring, regardless of the offspring's own genotype

Define bicoid

A gene where an embryo/larva whose mother has two mutant bicoid alleles lacks the front half of its body and has two structures at both ends.

How are miRNAs produced? What happens after miRNA is produced?

A longer RNA precursor is processed by cellular enzymes into an miRNA. This miRNA then forms a complex with one or more proteins.

What did Jacob and Monod propose?

A mechanism for the control of gene expression in bacteria known as the operon model

What switches off the tryp operon, and operons in general?

A protein called the (trp) repressor. Repressors are specific for the operator of a specific operon.

Define activator protein

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

Define repressor

A protein that binds to the operator and blocks attachment of RNA polymerase to the promoter, preventing transcription of the genes

What happens after transcription initiation complexes assemble on the gene?

A protein, RNA polymerase 2, begins to transcribe the gene, synthesizing a primary RNA transcript.

Define regulatory gene

A regulatory gene is the gene that codes for the protein product of a repressor (called trp R for tryptophan)

Define repressible operon and give an example

A repressible operon is an operon where transcription is usually on but can be inhibited when a specific small molecule binds allosterically to a regulatory protein. An example is the tryptophan operon, which is usually on but can be inhibited when tryptophan binds to the repressor protein.

What is an advantage of grouping genes of related function into one transcription unit?

A single on/off switch can control the entire cluster of related-function genes, and the genes are coordinately controlled.

Define inducer

A small molecule that binds to the repressor to make it inactive, preventing it from binding to the operon and resulting in activated gene expression

What are anableps anableps? Describe one of their characteristics.

A species of fish known as "four eyes" that glides through freshwater lakes and ponds in Central/South America with the upper half of each eye protruding from the water. The upper half of each eye is well-suited for aerial vision and the lower half for aquatic vision. This is because the cells of the two parts of each eye express a slightly different set of genes involved in vision, even though the two groups of cells are similar with identical genomes.

What is the p53 gene? What happens when a mutation occurs?

A tumor suppressor gene. The protein it encodes is a specific transcription factor that promotes the synthesis of cell-cycle inhibiting proteins. A mutation causes excessive cell growth and cancer.

What is APC, adenomatous polypsis coli?

A tumor-suppressor gene. It helps regulate cell migration and adhesion. It is mutated in many types of cancers.

Define piwi-associated RNAs (piRNAs), how they are made, and their role

A type of ncRNA processed from a longer, single-stranded RNA precursor. It induces formation of heterochromatin, blocking expression of some parasitic DNA elements in the genome known as transposons. It also establishes proper methylation patterns in the genome during gamete formation

How much of non-protein-coding DNA consists of genes for RNAs such as rRNAs and tRNAs?

A very small fraction as well

How much of the genome does protein-coding DNA account for?

A very small fraction of the genome

For the lac operon, what is the inducer?

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

Which cells of an organism contain an identical genome?

Almost all cells in a multicellular organism

What is the catabolic activator protein (CAP)?

An activator protein to which cAMP binds to

Define inducible operon and give an example

An inducible operon is one that is usually off but can be stimulated when a specific small molecule interacts with a regulatory protein. An example is the lac operon (lactose)

Where do repressible enzymes usually function? How do they help cell preserve energy?

Anabolic pathways, which synthesize end products from precursors. By suspending production of an end product when it's already present, the cell can allocate its energy for other uses.

Where does the regulation of translation typically occur?

At the initiation stage

Which bacterial cells have a selective advantage over other cells? As a result, what does natural selection favor?

Bacterial cells that conserve resources and energy have a selective advantage over cells that are unable to do so. Therefore, natural selection favors bacteria that express only the genes that are needed by cells.

Why does cancer increase with age?

Because more than one mutation is needed to produce changes, and over one's life time, more mutations occur.

Describe liver cells and lens cells and why they create different proteins even though they have the same gene

Both liver and lens cells have the genes for making the proteins albumin and crystallin, but only liver cells make albumin (blood protein) and lens cells crystallin (main protein of the lens of the eye). This is because specific transcription factors in the cell determine which genes are expresses. Each enhancer for each protein have a unique combination of control elements. The activator proteins required for the albumin gene are only in liver cells, where the activator proteins for crystallin are only in lens cell.

What does protein-mediated bending of the DNA bring together?

Bound activators at the distal elements of the enhancer in contact with the group of mediator proteins, which interacts with proteins at the promoter. This helps assemble and position the initiation complex on the promoter.

How does CAP stimulate gene expression?

By facilitating the attachment of RNA polymerase to the promoter and therefore increasing the rate of transcription

How do 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

For some mRNAs, how can the initiation of translation be blocked?

By regulatory proteins that bind to specific sequences/structures within the untranslated region (UTR) at the 5' or 3' end, preventing the attachment of ribosomes.

How can the rate of gene expression be increased/decreased?

By the binding of specific transcription factors, either activators or repressors, to the control elements of enhancers.

When glucose is present, what occurs?

CAP is inactive and the synthesis of enzymes that catabolize compounds other than glucose slows down.

Define oncogene

Cancer-causing genes (present in viruses)

Where do inducible enzymes usually function? How do they help cells preserve energy?

Catabolic pathways, which break down a nutrient to simpler molecules. By producing the appropriate enzymes only when the nutrient is available, the cell avoids wasting energy and precursors making unneeded proteins.

Three processes of embryonic development

Cell division, cell differentiation, morphogenesis

The proteins encoded by many proto-oncogenes and tumor-supressor genes are components of what?

Cell signaling pathways

Describe the first level of metabolic control

Cells can adjust the activity of enzymes already present. This response depends on the sensitivity of enzymes to chemical cues that increase or decrease their catalytic activity. The activity of the first enzyme in the pathway is inhibited by the pathway's end product, and excessive production of a specific substance shuts down substance of more of it. This is called feedback inhibition and is typical in anabolic pathways, which helps cells adapt to fluctuations in the supply of substances it needs.

Describe the second level of metabolic control

Cells can adjust the production level of certain enzymes and regulate the expression of the gene encoding for these enzymes. If a substance is already provided by the environment, the cell will stop making the enzymes that catalyze the synthesis of this particular substance. Enzyme production can be controlled at the level of transcription (synthesis of mRNA coding for these enzymes). However, genes are typically switched on or off by changes in the metabolic status of the cell.

In embryonic development, what does a fertilized egg/zygote give rise to?

Cells of many different types, each with a different structure and corresponding function. These different types of cells are organized into higher-level structures arranged in a particular 3D way.

Define myoblasts

Cells that have committed to becoming muscle cells after determination. Myoblasts churn out muscle specific proteins and fuse to form mature skeletal muscle cells.

What does the activity of a cell, such as during development, depend on?

Cellular behavior; changes in shape, motility, and cell characteristics; the genes it expresses and the proteins it produces

What does coordinate control of dispersed genes in a eukaryotic cell often occur due to? Give an example.

Chemical signals from outside the cell. For example, steroid hormones enter cells and binds to an intracellular receptor protein, forming a hormone-receptor complex that serves as a transcription activator. Every gene whose transcription is stimulated by a particular steroid hormone has a control element recognized by this hormone-receptor complex.

Define enhancer

Groups of distal control elements

Describe how movement of DNA within the genome causes proto-oncogenes to become oncogenes

Chromosomes can be translocated. If a translocated proto-oncogene ends up near an active promoter/control element, its transcription may increase, making it an oncogene.

What provides positional information for the placement of these axes before fertilization?

Cytoplasmic determinants that are localized in the unfertiliized egg

How is the p53 gene activated?

DNA damage that is an intracellular signal passed on that leads to the activation of this gene

What causes cancer development?

DNA methylation and histone modification patterns that are altered, as well as miRNAs.

Define genomic imprinting and give an example

Differential expression of a gene depending on whether it was inherited from the male or female parent.

Where does E. coli live and what does it depend on for its nutrients?

E. coli lives in the human colon. E. coli depends for its nutrients on the eating habits of its host.

Describe skeletal muscle cells

Each cell is a long fiber containing many nuclei within a single plasma membrane. They have high concentrations of muscle-specific versions of the contractile proteins myosin and actin, and membrane receptor proteins that detect signals from nerve cells

What is another name for maternal effect genes and why?

Egg-polarity genes, because they control the orientation/polarity of the egg and that of the organism

What does RNA processing include?

Enzymatic addition of a 5' cap and poly A tail, as well as the splicing of introns to yield a mature mRNA.

Define inducible enzyme and give an example

Enzymes where their synthesis is induced by a chemical signal (ex: enzymes of the lactose pathway, because allolactase makes the repressor inactive and causes transcription)

Describe protein processing and degradation after translation, the final way to control gene expression

Eukaryotic polypeptides processed to yield functional proteins: 1. Cleavage of polypeptides (such as insulin cleavage forms the active hormone) 2. Chemical modifications 3. Regulatory proteins are usually activated/inactivated by the reversible addition of phosphate groups 4. Proteins destined for the surface of animal cells acquire sugars 5. Cell-surface proteins transported to target destinations in the cell to function

In all organisms, where is gene expression commonly controlled, and how?

Gene expression is commonly controlled at transcription, and commonly equated with transcription for both bacteria and eukaryotes. Regulation occurs in response to signals coming from outside the cells, such as hormones and signaling molecules.

Since all cells in an organism have the same genome, what does differential gene expression result from?

Genes being regulated differently in each type

What are the genes that normally regulate cell growth and division during the cell cycle?

Genes for growth factors, receptors, and intracellular molecules of signaling pathways

Define homeotic genes

Genes that control pattern formation in the late embryo, larva, and the adult; they direct developmental processes

Define tumor supressor genes

Genes whose normal products inhibit cell division; the proteins they encode help prevent uncontrolled cell growth (mutations in these contribute to cancer)

Define master regulatory genes

Genes whose protein products commit the cells to become cells with specific functions during determination

When glucose and lactose are both present, what does E. coli prefer? Why?

Glucose. This is because the enzymes for glucose breakdown in glycolysis are continually present.

Define morphogen gradient hypothesis

Gradients of substances called morphogens establish an embryo's axes and other features of its form

What did Lewis do?

He showed the value of the genetic approach to studying embryonic development in Drosophila. He studied mutant flies with developmental defects that led to extra wings/legs, located these mutations on a genetic map, and connected developmental abnormalities to specific genes. This research supported the idea that genes direct developmental processes.

Define anterior-posterior, dorsal-ventral, right-left axis

Head to tail, back to belly, right left axes

When is lactose available to E. coli in the human colon?

If the host drinks milk

What happens when the mRNA or protein products of maternal effect genes are placed in the egg?

If the mother has a mutation, she makes a defective gene product or none at all, and the eggs become defective. When they are fertilized, they fail to develop properly.

What other functions does CAP have?

In addition to regulating the lac operon, it also regulates other operons that encode enzymes used in catabolic pathways, such as other genes in E. coli.

Where does pattern formation in animals begin? How?

In the early embryo, when the major axes of an animal are established. The relative positions of head/tail, right/left sides, and back/front are set up before organs appear

Where are the nucleotide sequences that affect how long an mRNA remains intact found?

In the untranslated region (UTR) at the 3' end of the molecule.

Which genes are typically more heavily methylated? What happens when these methyl groups are removed?

Individual genes are more methylated in the cells where they are not expressed. When these methyl groups are removed, some of the genes can be turned on.

How does cancer run in families?

Individuals that inherit oncogenes or mutant alleles are closer to accumulating the mutations necessary for cancer to develop

How does extra levels of gene regulation affect regulation?

It allows for a higher degree of complexity to form. This has led some scientists to believe that an increase in the number of different miRNAs has allowed complexity to increase over time (due to the versatility of miRNA regulation)

What is one unique function of myoD?

It can change some fully differentiated non-muscle cells into muscle cells. It doesn't work on all kinds of cells because activation of the muscle-specific genes is not solely dependent on myoD but requires a particular combination of regulatory proteins, some of which are lacking in cells.

What is the myoD master regulatory gene?

It encodes myoD protein, a transcription factor that binds to specific control elements in the enhancers of various target genes and stimulates their expression. Some target genes encode muscle specific transcription factors, as well as the expression of the myoD gene itself (positive feedback that helps maintain the differentiated cell state). Genes activated by myoD have enhancer control elements recogniezed by myoD and are coordinately controlled. The secondary transcription factors that activate the genes for proteins that give skeletal muscle cells their unique properties.

How does RNA splicing contribute to the possibilities of a genome?

It expands the number of possible proteins. (It accounts for why the number of low human genes can account for the complex form and large number of proteins in humans, as most human genes have multiple exons that undergo alternative splicing.)

Describe how amplification within the genome causes proto-oncogenes to become oncogenes

It increases the number of copies of the proto-oncogene in the cell through repeated duplication

In what pathway does E. coli synthesize the amino acid tryptophan?

It is synthesized from a precursor molecule in a three step pathway. Each reaction in the pathway is catalyzed by a specific enzyme, and five genes code for the subunits of these enzymes, which are clustered together on the bacterial chromosome.

What happens after the fly embryo grows?

It reaches a point where the embryonic program of gene expression takes over, and maternal mRNA is destroyed. Later, positional information encoded by the embryo's genes establishes a number of specific segments/shapes and triggers the formation of segment structures.

Which regions of DNA are more methylated?

Long stretches of inactive DNA (such as inactivated mammalian X chromosomes) are typically more methylated than regions of actively transcribed DNA.

Define transcription factories

Loops from the same and different chromosomes that associate with each other, which have many RNA polymerase and transcription proteins, typically specialized for a common function.

What does the interaction of general transcription factors and RNA polymerase 2 within a promoter lead to?

Low rates of initiation and production of few RNA transcripts

Which scientist determined the gene of breast cancer, and what is this gene?

Mary-Claire King. Tte mutation in the gene BRCA-1 and BRCA-2 often result in breast cancer. These genes are tumor suppressor genes because they protect against breast cancer as wild-types. They both function in the cell's DNA damage repair pathway. BRCA2 helps repair breaks in both strands of DNA.

Define cytoplasmic determinants

Maternal substances in the egg that influence the course of early development

How do methylation patterns relate to genomic imprinting?

Methylation patterns are maintained through successive generations, where methylation permanently regulates expression of either the maternal or paternal allele of particular genes during development.

After fertilization, what occurs to the zygote and its cytoplasm?

Mitotic divisions distribute the zygote's cytoplasm into separate cells. The nuclei of these cells may be exposed to different cytoplasmic determinants. The combination of cytoplasmic determinants helps determine its developmental fate by regulating expression of the cell's genes during the course of cell differentiation.

Are chromatin modifications reversible? What about mutations?

Mutations in the DNA are permanent changes, where modifications to the chromatin can be reversed, such as DNA methylation being erased and reestablished during gamete formation.

In eukaryotes, are groups of genes with related function that need to be turned off/on at the same time grouped together in an operon like in bacteria?

No, operons are not in eukaryotes. (In bacteria, coordinately controlled genes are typically clustered into an operon, which is regulated by a single promoter and transcribed into a single mRNA molecule. This causes the genes to be expressed together and the encoded proteins produced at the same time).

In interphase, do chromosomes in the nucleus occupy a distinct territory?

No, the chromosomes are not completely isolated. Some regions of chromosomes cross-link and associate with each other during interphase.

What is the differences in cell types due to?

Not due to different genes being present, but to differential gene expression

How do proto-oncogenes become oncogenes?

Oncogene arises from genetic changes that leads to either an increase in the amount of the proto-oncogene's protein product or the activity of each protein molecule. The three main categories are movement of DNA within the genome, amplification of a proto-oncogene, and point mutations in a control element or within the gene

When does E. coli use lactose as an energy source?

Only when lactose is present and glucose is low. This causes the synthesis of enzymes for lactose breakdown.

Define body plan

Overall 3d arrangement of an organism

What type of gene regulation is the CAP mechanism?

Positive gene regulation, because a regulatory protein interacting with the gene switches transcription on.

Define tissue-specific proteins

Proteins that are only found in a specific cell type and give the cell its characteristic structure and function.

What does the regulation of transcription initiation include?

Proteins that bind to DNA and either facilitate or inhibit binding of RNA polymerase

Define proximal control elements and distal control elements

Proximal control elements are located close to the promoter; distal control elements are located thousands of nucleotides upstream/downstream of a gene or within an intron and further away from the promoter

In eukaryotes, what provides opportunities for regulating gene expression right after transcription?

RNA processing in the nucleus and the export of mature RNA to the cytoplasm

Define small interfering RNAs (siRNAs)

RNAs that are similar in size and function to miRNAs, as they both associate with the same proteins and produce similar results (degrade mRNA or block translation).

Define microRNA

Small single-stranded RNA molecules that are capable of binding to complementary sequences in mRNA molecules.

What is essential for cell specialization in multicellular organisms, which are made up of different types of cells? How do cells perform their own distinct roles and carry out their own functions?

Regulation of gene expression. Cells perform their own distinct roles by maintaining a specific program of gene expression where certain genes are expressed and others are not (the subset of genes expressed in the cells of each type is unique)

What controls intron-exon choices and how?

Regulatory proteins specific to a specific cell type control intron-exon choices by binding to regulatory sequences within the primary transcript

Define control elements

Segments of noncoding DNA that serve as binding sites for transcription factor proteins that regulate transcription.

The product of the mother's bicoid gene is essential for what?

Setting up the anterior end of the fly and is concentrated at the anterior end of the embryo.

At what points do regulation by small and large ncRNAs occur?

Several points in the pathway of gene expression, including mRNA translation and chromatin modification

How do signaling molecules cause coordinate control of gene expression?

Signaling molecules, such as nonsteroid hormones and growth factors, bind to receptors on a cell's surface and never actually enter the cell. This triggers gene expression by causing signal transduction pathway that leads to activation of particular transcription activators or repressors. Genes with the same sets of control elements are activated by the same chemicals.

What are the most influential signals from the egg's cellular environment? Describe them.

Signals on a cell from other embryonic cells in the vicinity, including contact with cell-surface molecules on neighboring cells and the binding of growth factors secreted by neighboring cells. These signals cause changes in target cells, which is called induction. The molecules that convey the signals within the target cell are cell-surface receptors and other signaling pathway proteins. These signaling molecules send a cell down a specific developmental path by causing changes in gene expression, causing differentiation.

Where do general transcription factors bind?

Some bind to a DNA sequence such as the TATA box within the promoter. However, transcription factors usually bind to proteins, such as other transcription factors and RNA polymerase 2.

How did the RNAi pathway evolve?

Some viruses have double-stranded RNA genomes. Since the RNAi pathway processes double stranded RNAs into items that can destroy related RNAs, this pathway might have evolved as a natural defense against virus infection. However, since RNAi can also affect the expression of non-viral genes may reflect a different evolutionary origin.

Define pattern formation

Spatial organization where the tissues and organs of an organism are in their characteristic places

What are some causes of cancer?

Spontaneous mutations, carcinogens, X rays, radiation, viruses

What occurs when cyclic AMP binds to CAP?

The CAP is originally inactive, but when cyclic AMP binds to CAP because glucose levels are low, CAP becomes active and can attach to a specific site on the lac promoter. This increases the affinity of RNA polymerase to bind to the promoter (which is sometimes low even when repressors aren't bound to operators).

How is the N-terminus of each histone molecule positioned in a nucleosome? What does this allow for?

The N-terminus of each histone molecule in a nucleosome protrudes outward from the nucleosome. These tails are accessible to enzymes that catalyze the addition or removal of specific chemical groups (acetyl, methyl, phosphate)

What does global control usually involve?

The activation or inactivation of one or more protein factors required to initiate translation, resulting in protein synthesis from the mRNAs (translation initiation factors triggered)

What is the expression of a protein-coding gene measured by?

The amount of functional protein a cell makes. It is not just transcription, as much happens between the synthesis of the RNA transcript and the activity of the protein in the cell. Many regulatory mechanisms operate after transcription, fine tuning gene expression in response to environmental changes.

What changes usually occur for a cell to become fully cancerous?

The appearance of at least one active oncogene and the mutation or loss of several tumor suppressor genes. Also, both alleles typically must be affected because mutant alleles are usually recessive.

To initiate transcription, what does RNA polymerase require?

The assistance of transcription factors, which first bind to control elements

In eukaryotes, what does coordinate gene expression depend on?

The association of a specific combination of control elements with every gene of a dispersed groups. Activator proteins that recognize these control elements bind to them, promoting simultaneous transcription of the genes no matter where they are in the genome.

In eukaryotes, what does the precise control of transcription depend on?

The binding of activators to DNA control elements

Define RNA interference (RNAi)

The blocking of gene expression by siRNA

If the environment that E. coli lives in lacks the amino acid tryptophan, which it needs to survive, how does the bacteria react? What happens if the host eats a tryptophan rich meal? What does this demonstrate?

The cell responds by activating a metabolic pathway that makes tryptophan from another compound. If the host eats a tryptophan rich meal, the bacteria stops producing tryptophan, which helps it avoid wasting resources to produce a substance already available. This demonstrates that bacteria can change their metabolism based on their environments

What is in the egg's cytoplasm?

The cytoplasm contains RNA, proteins encoded by the mother's DNA, mRNA, organelles, and other substances.

What is the first source of information that influences early development?

The egg's cytoplasm

What is the second source of information that influences development?

The environment around a particular cell.

Define differential gene expression

The expression of different genes by cells with the same genome

What is the outcome of determination, or observable cell differentiation, marked by?

The expression of genes for tissue-specific proteins

How do the types of breast cancer differ?

The four types of breast cancer differ in their expression of three signal receptors involved in regulating cell growth and division. These signal receptors are HER2 (receptor tyrosine kinase), Progesterone receptor (PR), Estrogen receptor alpha (ERalpha). The absence of excess expression can cause incorrect signaling, division, and cancer.

Define epigenetic inheritance and give an example

The inheritance of traits transmitted by mechanisms not involving the nucleotide sequence itself (such as chromatin modifications)

After the chromatin of a gene is optimally modified for expression, what is the next major step at which gene expression is regulated?

The initiation of transcription

What do high levels of transcription of particular genes depend on?

The interaction of control elements with another set of proteins, called specific transcription factors

What is a hallmark of prokaryotic and eukaryotic cells?

The intricate and precise regulation of gene expression

When is the lac repressor active and inactive?

The lac repressor is active by itself and binds to the operator to switch the lac operon off, which is why the lac operon is usually off. The lac repressor becomes inactive when an inducer binds to it, and it can't bind to the operon, causing transcription to occur

How is the pattern of protein synthesis determined by?

The life span of mRNA moleculse in the cytoplasm

How do chromosomes associate during interphase?

The loops of chromatin extend from individual chromosomal territories into specific sites in the nucleus. Different loops from the same chromosome and loops from other chromosomes may congregate in sites, some of which are rich in RNA polymerases and other transcription-associated proteins.

What occurs if the miRNA binds to a target mRNA that are complementary all along their length? What occurs if the miRNA to mRNA match is less complete?

The mRNA is degraded; translation is blocked

What coordinates cell differentiation during embryonic development?

The materials placed into the egg by the mother set up a sequential program of gene regulation that is carried out as cells divide

Define positional information, how they are provided, and what they do

The molecular cues that control pattern formation; provided by cytoplasmic determinants and inductive signals. They tell a cell its location relative to the body axes and to neighboring cells.

Define proto-oncogenes

The normal versions of cellular genes that are the counterparts of viral oncogenes; they code for proteins that stimulate normal cell growth n=and division

Where is the operator located?

The operator is positioned within the promoter, and sometimes between the promoter and the enzyme-coding genes.

Define operon

The operator, the promoter, and the genes they control (the DNA required for enzyme production for a specific pathway) (Ex: trp operon codes for enzymes in a tryptophan pathway)

What is the distinction between miRNAs and siRNAs based on?

The subtle differences in the structure of miRNA and siRNA precursors, which in both cases are double-stranded RNA molecules.

What are other functions of p53 gene?

The p53 protein functions as an activator for other genes. It activates p21. It also activates expression of a group of miRNAs, which can inhibit the cell cycle. It can also turn on genes involved in DNA repair. It also activates suicide genes for apoptosis. All of these functions prevent a cell from passing on mutations due to DNA damage.

Define morphogenesis

The physical processes that give an organism its shape; the development of the form of an organism and its structures

Define determination

The point at which an embryonic cell is irreversibly committed to becoming a particular cell type. (After determination, the cell can be placed into another location and it will still differentiate into the cell type that is its normal fate)

What occurs after the complete initiation complex assembles?

The polymerase can begin to move along the DNA template strand to produce a complementary strand of RNA.

Define cel differentiation

The process by which cells become specialized in structure and function (these different kinds of cells are then organized into tissues and organs in a particular 3d arrangement)

What does the relocation of particular genes from their chromosomal territories to transcription factories be a part of?

The process of readying genes for transcription

What occurs when there are mutations in the ras gene?

The production of a hyperactive Ras protein that triggers the cascade, even without the presence of a growth factor, resulting in increased cell division.

Define histone

The protein around which the DNA is wrapped in nucleosomes

Where is the regulatory gene located? Are they usually expressed?

The regulatory gene is located away from the operon and has its own promoter. Regulatory genes are expressed continuously.

What codes for the allosteric repressor protein that switches off the lac operon by binding to the operator?

The regulatory gene, lac I, located outside the operon

What are the gene regulation systems that go wrong during cancer (disease where cells escape the control mechanisms that normally limit their growth)?

The same systems that play roles in embryonic development, immune response, and other biological processes

Define operator

The segment of DNA that turns genes on or off. It controls the access of RNA polymerase to genes.

What is important in regulating transcription of a gene in terms of control elements?

The specific combination of control elements in an enhancer of a gene, rather than the presence of a single unique control element, is important in regulating transcription of a gene.

What does the state of the lac repressor determine? What about CAP?

The state of the lac repressor (with or without bound allolactose) determines whether or not transcription of the lac operon's genes occurs at all. The state of CAP (with or without bound cAMP) controls the rate of transcription if the operon is repressor-free.

Is the tryp operon usually on?

The trp operon is turned on, and RNA polymerase can bind to the promoter and transcribe the genes of the operon

How many nucleotide sequences are found in control elements?

There are only around a dozen nucleotide sequences that appear again and again in the control elements of different genes. This number is relatively small, considering the great number of genes that must be regulated.

Where are the genes that code for the enzymes of the tryptophan metabolic pathway present?

These genes are clustered together on the bacterial chromosome, and a single promoter (site where RNA polymerase binds to DNA and begins transcription) serves all five genes, which make up one transcription unit.

In addition to influencing transcription directly, how do other activators and repressors act?

They act indirectly by affecting chromatin structure. 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.)

What is the lifespan of bacterial mRNA molecules?

They are typically degraded by enzymes within a few minutes of their synthesis. This short lifespan of mRNA molecules is why bacteria can change their patterns of protein synthesis so quickly in response to the environment.

What is the lifespan of eukaryotic mRNA molecules?

They can survive for hours/days/weeks. This results in repeated translation of mRNAs into proteins.

How did scientists determine if the Bicoid product is a morphogen that determines the anterior end of a fly?

They determined that the bicoid mRNA is highly concentrated at the anterior end, and when the egg is fertilized, the mRNA is translated into protein. This protein then diffuses across the anterior end towards the posterior, resulting in a a gradient of protein with the highest concentration at the anterior end.

From what embryonic precursor cells do muscle cells develop?

They develop from precursors that have the potential to develop into a number of cell types, but particular conditions commit them to becoming muscle cells

How did Nusslein-Volhard and Wieschaus determine the segmentation genes?

They exposed flies to a mutagenic chemical that affected the flies' gametes. They mated the mutagenized flies and scanned their descendants for dead embryos or larva with abnormal defects. Using this approach, they mapped genes essential for pattern formation during embryonic development. These were later grouped by function and mapped, resulting in understanding of pattern formation in these flies.

What is the role of ncRNAs?

They help regulate gene expression and are crucial to it

How do viruses cause cancer?

They interfere with gene regulation, as they integrate their genetic material into the DNA of a cell. They can donate oncogenes, disrupt tumor-suppressor genes, or convert a proto-oncogene into an oncogene. Some viruses produce proteins that inactivate tumor suppressor proteins.

In the S phase of the cell cycle, what must occur to the centromere regions of DNA?

They must be loosened for chromosomal replication and then re-condensed into heterochromatin in preparation for mitosis

What must be the life span of some proteins for the cell to function?

They must be short lived (such as the cyclins involved in regulating the cell cycle)

How do ncRNAs affect chromatin structure?

They remodel chromatin structure, such as during the formation of heterochromatin at the centromere.

What is the function of tumor supressor genes?

They repair damaged DNA (prevents the cell from accumulating mutations); control the adhesion of cells to each other or the matrix, as proper anchorage is important in normal tissues; or are components of cell-signaling pathways that inhibit the cell cycle

What did Nusslein-Volhard and Wieschaus do?

They wanted to identify all the genes that affect segment formation in Drosophila.

What does the miRNA allow the complex to do?

To bind to any RNA molecule with at least 7-8 nucleotides of complementary sequence

What does transcription of this specific segment of enzyme-coding genes give ride to? How are multiple polypeptides created?

Transcription creates one long mRNA molecule that codes for the 5 polypeptides that make up the enzymes in the tryptophan pathway (trypA, B, C, D, E). Multiple polypeptides are created because the mRNA contains start and stop codons that signal where the sequence for each polypeptide is.

Define general transcription factors

Transcription factors that are essential for the transcription of all protein-coding genes

What is the most common method of differentiation regulation?

Transcription, which maintains proper gene expression

Define global control

When translation of all the mRNAs in a cell are regulated simultaneously

How is the entire inactivated chromosome condensed?

Transcripts of the XIST gene located on the inactivated chromosome bind back to and coat the chromosome, and this binding leads leads to condensation of the entire chromosome into heterochromatin.

What does the troponin T gene code for?

Two different related muscle proteins

How many genes do typical human cells express? What about highly differentiated cells (muscle/nerve cells)?

Typical human cells express around 20% of their genes, but highly differentiated cells express an extremely small fraction

How are co-expressed eukaryotic genes found in eukaryotes?

Typically, they are scattered over different chromosomes

Define tumor viruses

Viruses that cause cancer in animals

Define DNA methylation

When a set of enzymes (different from those that methylate histone tails of histone proteins) methylate specific bases in DNA, such as cytosine.

Define histone acetylation and its effects

When acetyl groups are added to histone tails. This promotes transcription by opening up chromatin structure

Define alternative RNA splicing (regulation at the RNA-processing level)

When different mRNA molecules are produced from the same primary transcript, depending on which RNA segments are treated as introns and exons

When lactose is present, is the repressor active or inactive? What about when lactose is absent?

When lactose is present, allolactase binds to the repressor and it becomes inactive because it changes shape, causing the lac operon to be actively transcribed. When lactose is not present, the lac repressor is in its active shape and the genes of the lac operon are silenced.

Define histone methylation

When methyl groups are added to histone tails. This leads to the condensation of chromatin and reduces transcription.

Define negative gene regulation

When operons are switched off by the active form of the repressor protein

Define positive gene regulation

When operons are switched on when the regulatory protein interacts directly with the genome.

Each combination of control elements can activate transcription only when what?

When the appropriate activator proteins are present, which may occur at a precise time or in a particular cell type.

Define cell division

When the zygote gives rise to a large number of cells

What do epigenetic variations help explain?

Why one identical twin has a particular disease, abnormal DNA methylation patterns cause cancer due to inappropriate gene expression, etc.

How does lactose metabolism begin?

With the hydrolysis of the lactose disaccharide into its monosaccharides glucose and galactose, which is catalyzed by the enzyme beta-galactosidase (typically not present when no lactose is present; amount of this enzyme increases when more lactose is present)

Can genes have multiple enhancers?

Yes, genes can have multiple enhancers, each active at a different time/different cell type. However, each enhancer is usually associated with only one gene and no others.

After methylation, do genes stay methylated after cell divisions?

Yes, once methylated, genes usually stay that way through successive cell divisions. At DNA sites where one strand is already methylated, enzymes methylate the correct daughter strand after each DNA replication. Therefore, methylation patterns are passed on.

Define p21 gene

a gene whose product halts the cell cycle by binding to cyclin-dependent kinases, allowing time for the cell to repair the DNA

If the amount of glucose in the cell increases, how does cAMP concentration change? What effect does this create on CAP?

cAMP concentration falls. This causes CAP to become inactive and detach from the operon. Since CAP is inactive, RNA polymerase binds less efficiently to the promoter, and transcription of the lac operon proceeds at a low level, even if lactose is present.

When is cyclic AMP present?

cyclic AMP is a small organic molecule that accumulates when glucose is scarce.

What is the first evidence of differentiation? What about later steps?

mRNAs for tissue-specific proteins. Later on, differentiation is observable with changes in cellular structure, and different sets of genes are expressed.