Chp. 18 BIO 108

How does a repressible operon function?

A repressible operon is one that is usually on; binding of a repressor to the operator shuts off transcription.

What information about genomic equivalency was gleamed from the work of Briggs, King and Gurdon?

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What type of operon is the lac operon?

An inducible operon

Why do cancers run in some families?

The fact that multiple genetic changes are required to produce a cancer cell Individuals who inherit a mutant oncogene or tumor-suppressor allele have an increased risk of developing certain types of cancer. For example, mutations in the BRCA1 or BRCA2 gene occur in at least 50% of inherited breast cancers. A woman who inherits one mutant BRCA1 allele has a 60% probability of developing breast cancer by age 50

What is meant by the term "epigenetic inheritance"?

The inheritance of traits transmitted by mechanisms not directly involving the nucleotide sequence is called epigenetic inheritance.

What activates the activator in the lac pathway?

When glucose (a preferred food source of E. coli ) is scarce, the lac operon is activated by the binding of CAP. CAP is converted to its active shape by the binding of a small organic molecule cAMP.

Is the trp operon a repressible operon?

Yes

Repressible enzymes usually function in _____ pathways.

anabolic

What factors regulate chromatin structure?

histone acetylation, The addition of methyl groups, A.A. phosphorylation

In what ways does lac differ from the trp operon?

o Trp is different from the lac operon because the trp repressor is inactive by itself and requires trp as a corepressor in order to bind to the operator. Also, the enzymes for tryptophan synthess are repressible enzymes, generally function in anabolic pathways, which synthesize end products from raw materials (precursors). Lac has inducible enzymes that function in catabolic pathways.

What information about genomic equivalency was gleamed from the work of Steward and colleagues? Briggs, King and Gurdon?

whether a differentiated cell can generate a whole organism. A totipotent cell is one that can generate a complete new organism. Cloning is using one or more somatic cells from a multicellular organism to make a genetically identical individual.

Explain the combinatorial approach to gene activation.

1. Activator proteins bind to distal control elements grouped as an enhaner in the DNA. This enhancer has three binding sites, each called a distal control element. 2. A DNA-bending protein brings the bound activators closer to the promoter. General transcription factos, mediator proteins, and RNA polymerase 2 are nearby. 3. The activators bind to certain mediator proteins and general transcriptin factors, helping them form an active transcriptino initiation complex on the promoter.

The lac operon contains genes coding for enzymes in what?

Hydrolysis and metabolism of lactose

What is meant by the terms "positive regulation"?

Some operons are also subject to positive control through a stimulatory activator protein, such as catabolite activator protein (CAP).

How can a mutation in the Ras protein lead to cancer?

The Ras protein, encoded by the ras gene, is a G protein that relays a signal from a growth factor receptor to a cascade of protein kinases. Many ras oncogenes have a mutation that leads to a hyperactive Ras protein that issues signals on its own, resulting in excessive cell division. Mutations in ras occur in about 30% of human cancers.

Some distal control elements (enhancers) are located thousands of nucleotides away from the promoter region. How is it that these enhancers can influence events occurring at the promoter?

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What are the two major ways that morphogenesis differs between animals and plants?

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What is a stem cell? What is the difference between an embryonic and adult stem cell?

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Why do only a small percentage of cloned embryos develop normally to birth?

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Histone modification with A.A. phosphorylation

A.A. phosphorylation next to a methylated A.A. can have the opposite effect.

What is the difference between a "general transcription factor" and a "specific transcription factor"?

An activator (specific transcription factor) is a protein that binds to an enhancer and stimulates transcription of a gene. High levels of transcription of particular genes require another set of proteins To initiate transcription, eukaryotic RNA polymerase requires the assistance of proteins called transcription factors. Since these are required for the transcription of all protein encoding genes they are called general transcription factors.

How does an inducible operon function?

An inducible operon is one that is usually off; a small molecule called an inducer inactivates the repressor and turns on transcription.

Is the trp pathway a catabolic or anabolic pathway?

Anabolic

In which types of cells would you find it?

Bacteria

Know the role of miRNAs in the regulation of gene expression. What is "dicer" and how does it work?

Capable of binding to complementary sequences in mRNA molecules. 1. An enzyme cuts each hairpin from the primary miRNA transcript. 2.A second enzyme, called DICER, trims the loop and the single-stranded ends from the hairpin, cutting at the arrows. 3. One strand of the double-stranded RNA is degraded; the other strand (miRNA) then forms a complex with one or more proetins. 4. The miRNA in the complex can bind to any targed mRNA that contains at least 7 bases of complementary sequence. 5. If miRNA and mRNA bases are complementary all along their length, the mRNA is degrades. If the match is less complete, translation is blocked

A eukaryotic genome has fewer genes than would be predicted based upon the number of known gene products. How is this finding tied into the phenomenon of "alternative RNA splicing"?

Human genes that have multiple exons probably undergo alternative splicing. The extent of alternative splicing greatly mutiplies the number of possible human proteins. In alternative RNA splicing, different mRNA molecules are produced from the same primary transcript, depending on which RNA segments are treated as exons and which as introns.

What are some examples of gene inactivation by DNA methylation that we have previously discussed in class?

In genomic imprinting, methylation turns off either the maternal or paternal alleles of certain genes at the start of development.

How is the modification of chromatin structure related to transcriptional regulation?

In histone acetylation, acetyl groups (-COCH3) are attached to positively charged lysines in histone tails. This process appears to loosen chromatin structure, thereby promoting the initiation of transcription.

Know the effects of histone acetylation and methylation on chromatin structure.

In histone acetylation, acetyl groups (-COCH3) are attached to positively charged lysines in histone tails. This process appears to loosen chromatin structure, thereby promoting the initiation of transcription. . The addition of methyl groups (-CH3) can lead to condensation of the chromatin

What types of alterations at the DNA level of a gene can lead to cancer?

Interference with Normal Cell-Signaling Pathways Increased cell division, possibly leading to cancer, can result if the cell cycle is overstimulated as in (a) or not inhibited when it normally would be as in (b). More than one somatic mutation is generally needed to produce a full-fledged cancer cell. About a half dozen DNA changes must occur for a cell to become fully cancerous. These changes usually include at least one active oncogene and mutation or loss of several tumor-suppressor genes.

How is mRNA degradation controlled?

Nucleotide sequences affect how long an mRNA remains intact, found in the untranslated region (UTR) at the 3' and 4' end of the molecule.

What is the difference between a proto-oncogene and an oncogene?

Oncogenes are cancer-causing genes. Proto-oncogenes are normal cellular genes that code for proteins that stimulate normal cell growth and division. A change in DNA that makes a proto-oncogene excessively active converts it to an oncogene, which may promote excessive cell division and cancer.

What is meant by the terms "negative regulation"?

Regulation of the trp and lac operons involves negative control of genes because operons are switched off by the active form of the repressor.

Know the different levels of DNA compaction in the cell.

Smallest to largest DNA (2nm), Histones (100 A.A. each), Nucleosomes (10nm fiber), 30 nm fiber, Looped domains (300nm), Metaphase chromosome (700nm).

Histone modification with methyl groups

The addition of methyl groups (-CH3) attached to A.A. in histone tails can lead to condensation of the chromatin.

What role does the chromosomal scaffold protein play?

The location of a gene's promoter relative to nucleosomes and to the sites where the DNA attaches to the chromosome scaffold or nuclear lamina can affect whether the gene is transcribed.

What is a tumor-suppressor gene and how does it work?

The p53 gene encodes a tumor-suppressor protein that is a specific transcription factor that promotes synthesis of cell cycle-inhibiting proteins (allowing time for DNA repair). Named for its 53,000-dalton protein product, the p53 gene is often called the "guardian angel of the genome". Can turn on genes directly involved in DNA repair or activate "suicide" genes if damage is irreparable. Mutations that knock out the p53 gene can lead to excessive cell growth and cancer. Mutations in p53 occur in more than 50% of human cancers.

What is the p53-tumor suppressor gene and how does it work?

The p53 gene encodes a tumor-suppressor protein that is a specific transcription factor that promotes synthesis of cell cycle-inhibiting proteins (allowing time for DNA repair). Can turn on genes directly involved in DNA repair or activate "suicide" genes if damage is irreparable. Mutations that knock out the p53 gene can lead to excessive cell growth and cancer. Mutations in p53 occur in more than 50% of human cancers.

What are histone proteins and how do they bind DNA?

They are responsible for the first level of DNA packing in chromatin. More than a fifth of a histone's amino acids are positively charged (lys and arg) and bind tightly to the negatively charged DNA.

How does the combinatorial approach to gene activation work to coordinately control genes in a metabolic pathway that are not clustered together as in a prokaryotic operon?

Unlike the genes of a prokaryotic operon, coordinately controlled eukaryotic genes each have a promoter and control elements. The same regulatory sequences are common to all the genes of a group, enabling recognition by the same specific transcription factors.

Histone modification with acetylation

acetyl groups (-COCH3) are attached to positively charged lysines in histone tails. This process appears to loosen chromatin structure, thereby promoting the initiation of transcription. A.A. phosphorylation next to a methylated A.A. can have the opposite effect.

Which types of genes are generally associated with cancer?

are genes for: (1) Growth factors (2) Growth factor receptors (3) Intracellular molecules of signaling pathways Mutations altering any of these genes in somatic cells can lead to cancer.

Inducible enzymes usually function in ______ pathways.

catabolic

What is the "activator" in the lac pathway?

catabolite activator protein (CAP)

What is meant when they say the lac operon is under dual control?

negative control by the lac repressor and positive control by CAP. The state of the lac repressor determines whether or not transcription of the lac operon's genes occurs at all; the state of CAP controls the rate of transcription if the promoter is repressor-free. It is as the operon has both an on-off switch and a volume control.

How does positive regulation work with respect to the lac operon?

o E. Coli uses glucose as an energy source when it's present, it only uses lactose when glucose is scarce. o Mechinism depends on the interaction of an allosteric regulatory preotein with a small organic molecule, in this case cyclic AMP (cAMP). o cAMP accumulates when glucose is scarce. o o Regulatory protein called, catabolite activator protein (CAP), is an activator, a protein that binds to DNA and stimulates transcription of a gene. o When cAMP binds to CAP, CAP assumes its active shape and can attach to a specific site at the upstream end of the lac promoter. o This attatchement increases the affinity of RNA polymerase for the promote. o By facilitating the binding of RNA polymerase to the promoter and increasing the rate of transcription, the attachment of CAP to the promoter directly stimulates gene expression. Resulting in positive regulation. o If the glucose increases, cAMP decreases. o W/O cAMP, CAP detaches from the operon. o B/c CAP is inactive, RNA polymerase bins less efficiently to thr promoter and transcription of the lac operon proceeds at only a low level. Even in the presence of lactose. o CAP also helps regulate other operons that encode enzymes used in catabolic pathways o When glucose is plentiful and CAP in inactive, the synthesis of enzymes that cataboliz compounds other than glucose generally slows down. o The ability to catabolize other compounds, such as lactose, enables a cell deprived of glucose to survive.

How does the trp operon function?

o If the trp level drops, transcription of the operon's genes resumes. RNA polymerase can bind to the promoter and transcribe the genes of the operon. The operon can be switched off by a protein called the trp repressor. The repressor binds to the operator and blocks attachment of RNA polymerase to the promoter, preventing transcription of the genes. The trp repressor is an allosteric protein, with 2 alternative shapes of active and inactive. Trp repressor is synthesized in an inactive form with little affinity for the trp operator. Trp repressor only becomes active if it binds to the trp at an allosteric site, turning to operon off.

How does the lac operon function?

o Lactose metabolism: o Begins with hydrolysis of the disaccharide into its component monosaccharides, glucose and galactose, a reaction catalyzed by the enzyme B-galactosidase. o B-galactosidase is part of the lac operon, includes two other genes coding for enzymes that function in lactose utilization. o The entire transcription unit is under the command of one main operator and promoter. o Regulatory gene, lacI, located outside the operson, codes for an allosteric repressor protein that can switch off the lac operon by binding to the operator. o The lac repressor is active by itself, binding to the operator and switching the lac operon off. o A specific small molecule, inducer, inactivates the repressor. o For the lac operon, the inducer is allolactose, an isomer of lactose formed in small amounts from lactose that enters the cell. o In the absence of lactose ( and allolactose), the lac repressor is in tis active configuration, and the genes of the lac operon are silenced. o If lactose is added to the cell's surrounding, allolactose binds to the lac repressor and alters its conformation, nullifying the repressor's ability to attach to the operator. o Without bound repressor, the lac operon is transcribed into mRNA for the lactose-utilizing enzymes.

What is DNA methylation and what does it do?

the addition of methyl groups to certain bases in DNA, is associated with reduced transcription in some species. In some species, DNA methylation causes long-term inactivation of genes in cellular differentiation.