bio11

inducers

(1) A compound that stimulates the synthesis of a protein. (2) In embryonic development, a substance that causes a group of target cells to differentiate in a particular way.

What is the lac operon? How does it work?

(1) The lac operon is an operon that encodes the three lactose-metabolizing enzymes in E. coli. It is very efficient, but its activity can be reduced when enzymes are not needed. - It contains a DNA sequence called an operator (lives near promoter) and controls transcription of lac genes. - The lac operon is not transcribed at high levels unless a B-galactoside (lactose) is the predominant sugar available in the cell's environment. Repressor proteins bind to the operator, preventing RNA polymerase from binding (no transcription) until lactose is present. When lactose is present, the repressor detaches from the RNA polymerase to bind to the promoter and begin lac gene transcription.

What are sigma factors?

(Specific to prokaryotes) A protein that binds to RNA polymerase, allowing the complex to bind to and stimulate the transcription of a specific class of genes (e.g. those involved in sporulation). Sigma factors can direct RNA polymerase to specific promoters.

structural genes

A gene that encodes the primary structure of a protein not involved in the regulation of gene expression.

operon

A genetic unit of transcription, typically consisting of several structural genes that are transcribed together.

chromatin remodeling

A mechanism for epigenetic gene regulation by the alteration of chromatin structure.

Explain the e. coli example and how it applies to this lesson?

Example: Escherichia coli normally inhabits human intestines. It must adjust to sudden changes in environment by changing the transcription of its genes. Three proteins are involved in the uptake and metabolism of lactose by E. Coli: - B-galactoside permease (carrier protein in the bacterial cell membrane that moves sugar into the cell) - B-galactosidase (enzyme that hydrolyzes lactose to glucose and galactose) - B-galactoside transacetylase (Transfers acetyl groups from acetyl CoA to certain B-galactosides. Its role in metabolizing lactose is not clear) E Coli's lactose-metabolizing proteins are encoded by inducible genes.

constitutive genes

Genes that expressed all of the time.

histone deacetylases

In chromatin remodeling, an enzyme that removes acetyl groups from the tails of histone proteins.

histone deacetylase

In chromatin remodeling, an enzyme that removes acetyl groups from the tails of histone proteins. (Contrast with histone acetyltransferases

Explain the example of the amino acid tryptophan and how it is relevant to corepressors.

In the book, it looks at the operon whose structura genes catalyze the synthesis of the amino acid tryptophan. *Precursor molecules >>> Five enzyme-catalyzed reactions >>> Tryptophan When tryptophan is present in adequate concentrations, it is energy-efficient for the cell to stop making the enzymes for tryptophan synthesis *Tryptophan itself functions as a corepressor. - Tryptophan binds to the repressor of the trp operon, causing the repressor to bind to the trp operator to prevent transcription of the enzymes in the pathway.

proteasome

In the eukaryotic cytoplasm, a huge protein structure that binds to and digests cellular proteins that have been tagged by ubiquitin.

Using NFAT (nuclear factors of activated T cells) as an example, describe how a specific nucleotide sequence in DNA is recognized by transcription factors.

NFAT's are a group of transcription factors that control the expression of genes essential for the immune response. 1) NFAT proteins bind to a 12-bp recognition sequence near the promoters of these genes. (CGAGGAAAATTG) 2) Note: There are atoms in DNA bases that can be hydrogen bound, but aren't part of base pairing. 2a) NFAT and DNA bind by these interactions between the rings in DNA bases and some amino R groups in the NFAT proteins. 3) NFAT and the DNA have an induced fit between each other for enzyme-substrate reactions. The protein will undergo a conformational change after binding begins. 4) The base sequence of a binding site on DNA determines the arrangement of chemical groups available for hydrogen bonding and hydrophobic interactions with DNA-binding proteins. (This is the basis of specificity of DNA-protein interactions)

What happens during positive regulation?

The binding of an activator stimulates transcription.

genomic imprinting

The form of a gene's expression is determined by parental source (i.e., whether the gene is inherited from the male or female parent).

What types of chromatin are present in DNA? What differentiates them?

Two kinds of chromatin can be distinguished in the stained interphase nucleus: Euchromatin and heterochromatin. 1) Euchromatin appears diffuse and stains lightly. It contains the DNA that is transcribed into mRNA. 2) Heterochromatin is condensed and stains darkly. If you find this in a gene, this means it will generally not be transcribed.

lac operon

a gene system whose operator gene and three structural genes control lactose metabolism in E. coli; example of an inducible operon

alternative splicing

a process for generating different mature mRNAs from a single gene by splicing together different sets of exons during RNA processing

beta galactosidase

an enzyme that hydrolyzes lactose to glucose and galactose.

What does differentiation mean to the expression of transcription factors?

- During the development of a complex organism from egg to adult, cells become more and more differentiated (a.k.a specialized). - Virtually all differentiated cells contain the entire genome. Their specific characteristics arise from differential gene expression.

What are two examples of how alternative splicing can be a deliberate mechanism for generating a family of different proteins + different activities/functions from a single gene?

1) HIV's genome encodes nine proteins, but is transcribed by a single pre-mRNA. Most of the proteins are then generated by alternative splicing of this pre-mRNA. 2) Drosophilia fruit fly sex is determined by the Sxl gene. The gene has four exons. In the female embryo, splicing generates two active forms of the Sxl protein, containing 1-2 and 1-2-4 exons. The male embryo, however, contains 1-2-3-4 and is inactive.

What is histone deacetylase? What other ways can histone be modified? Are they reversible?

A class of chromatin remodeling proteins that can remove the acetyl groups from histones and "repress" transcription. Histones can also be: 1) methylated (add methyl group), which can contribute to activation/repression of gene expression depending on the lysine that is messed with. 2) phosphorylated (add phosphate group), which is involved in chromosome condensation during mitosis and meiosis. Both alternate actions are reversible, so transcription activity in a eukaryotic gene may be determined by varying patterns of histone modification.

What is an operon?

A cluster of genes with a single promoter.

inducer

A compound that stimulates the synthesis of a protein.

operon

A genetic unit of transcription, typically consisting of several structural genes that are transcribed together; the operon contains at least two control regions: the promoter and the operator

corepressor

A molecule that binds to a bacterial repressor protein, altering its shape so that it binds to the operator sequence in DNA and prevents its transcription.

What is a corepressor?

A molecule that that binds to the repressor, causing it to change shape and bind to the operator, inhibiting transcription. Repressible operons bind to the DNA only in the presence of a corepressor. Note: A repressible operon is switched off when its repressor is bound to its operator.

alternative splicing

A process for generating different mature mRNAs from a single gene by splicing together different sets of exons during RNA processing.

repressor

A protein encoded by a regulatory gene that can bind to a promoter and prevent transcription of the associated gene.

translational repressor

A protein that blocks translation by binding to mRNAs and preventing their attachment to the ribosome.

What happens during negative regulation?

A repressor binds a specific site in or near the promoter to prevent transcription.

What is an operator?

A repressor-binding site that can bind very tightly with a repressor protein. Repressors bound by operators (?) play different roles: - An inducible operon is turned off unless needed. - A repressible operon is turned on unless needed.

ubiquitin

A small protein that is covalently linked to other cellular proteins identified for breakdown by the proteosome.

microRNA (miRNA)

A small, noncoding RNA molecule, typically about 21 bases long, that binds to mRNA to inhibit its translation.

How is a structural gene different from other genes?

A structural gene is any gene that encodes a protein that is not directly involved in gene regulation. The three genes that encode the lactose-metabolizing enzymes of E. Coli are structural genes.

activator

A transcription factor that stimulates transcription when it binds to a gene's promoter.

What is histone acetyltransferase?

A variety of transcription factors and RNA polymerases that can bind to enzymes. These enzymes add acetyl groups to positively charged amino acids and neutralize their charges.

TATA box

An eight-base-pair sequence, found about 25 base pairs before the starting point for transcription in many eukaryotic promoters, that binds a transcription factor and thus helps initiate transcription.

DNA methyltransferase

An enzyme that catalyzes the methylation of DNA.

maintenance methylase

An enzyme that catalyzes the methylation of the new DNA strand when DNA is replicated.

demethylase

An enzyme that catalyzes the removal of the methyl group from cytosine, reversing DNA methylation.

maintenance methyltransferase

An enzyme that transfers methyl groups to DNA after DNA replication.

histone

Any one of a group of proteins forming the core of a nucleosome, the structural unit of a eukaryotic chromosome.

Explain the process of chromatin remodeling.

Chromatin remodeling is a mechanism for epigenetic gene regulation by the alteration of chromatin structure. 1) Large amounts of DNA are packed within the nucleus in the form of nucleosomes (the basic unit of DNA packaging). Nucleosomes are wrapped around histone proteins. 2) Each histone protein has a tail of 20 amino aids on its N terminus (positively charged AAs like lysine). Nucleosomes can make DNA physically inaccessible to RNA polymerase via a strong ionic attraction between the positively charged histone protein and DNA.

CpG islands

DNA regions rich in C residues adjacent to G residues. Especially abundant in promoters, these regions are where methylation of cytosine usually occurs.

What are enhancers?

DNA sequences that bind activators.

What are silencers?

DNA sequences that bind repressors.

What catalyzes the removal of methyl groups from cytosine?

Demethylase. We don't know how it does it fully, sadly.

How does DNA methylation affect transcription? What kind of mechanism is DNA methylation?

Depending on the organism, 1-5% of cytosines in DNA are modified by methylation to create 5-methylcytosine. 1) Methylation of cytosine is catalyzed by DNA methyltransferase. A vast majority of the CpG sites are methylated EXCEPT for the ones near active promoters. 2) DNA methylation is usually a stable, long-term silencing mechanism. Note: In mammals, DNA methylation occurs mostly with cytosines adjacent to guanine.

histone acetyltransferase

Enzymes involved in chromatin remodeling. Add acetyl groups to the tail regions of histone proteins.

histone acetyltransferases

Enzymes involved in chromatin remodeling. Add acetyl groups to the tail regions of histone proteins.

inducible genes

Genes that are expressed only when their products are needed.

general transcription factors

In eukaryotes, transcription factors that bind to the promoters of most protein-coding genes and are required for their expression.

general transcription factors

In eukaryotes, transcription factors that bind to the promoters of most protein-coding genes and are required for their expression. Distinct from transcription factors that have specific regulatory effects only at certain promoters or classes of promoters.

How does genomic imprinting occur in DNA methylation?

In mammals, specific patterns of methylation develop for each sex during gamete formation in two stages: Stage 1) The existing methyl group is removed from the 5'-methylcytosines by a demethylase Stage 2) A DNA methylase adds methyl groups to a new set of cytosines. When the gametes form, they carry this new pattern of methylation. Genomic imprinting: When the offspring would inherit a maternal gene that is transcriptionally inactive (methylated) and a paternal gene that is transcriptionally inactive (unmethylated).

sigma factors

In prokaryotes, a protein that binds to RNA polymerase, allowing the complex to bind to and stimulate the transcription of a specific class of genes (e.g., those involved in sporulation).

co-repressor

In the regulation of bacterial operons, a molecule that binds to the repressor, causing it to change shape and bind to the operator, thereby inhibiting transcription.

What are inducers and what are they activated by?

Inducers are compounds that stimulate the transcription of specific genes. They are activated by inducers called inducible genes. Note: Some other genes are expressed at a constant rate (constitutive genes)

Explain the difference between inducible systems and repressible systems.

Inducible Systems: The substrate oof the metabolic pathway (the inducer) interacts with a transcription factor (repressor), renderig the repressor incapable of binding to the operator and thus allowing transcription. Repressible Systems: A product of a metabolic pathway (the corepressor) binds to the repressor protein, which is then able to bind to the operator and block transcription.

How does maintenance methyltransferase work? When does it occur?

Maintenance methyltransferase catalyzes the formation of 5-methylcytosine in the new DNA strands. Maintenance methyltransferase occurs when DNA synthesis occurs.

Methylation patterns are stable and are passed on from generation to generation. How would monozygotic twins show how these patterns can be changed?

Monozygotic twins come from a single fertilized egg that divides to produce two separate cells. At around 3 years, the DNA methylation patterns in their tissue are virtually identical. However, by age 50, their patterns are different and the genes expressed are different. This difference by late age indicates that environment plays an important role in epigenetic modifications. Twins make that point evident. Things like tobacco smokes, stress, or dietary components can affect DNA methylation patterns.

How do transcription factors coordinate the expression of sets of genes? Describe how the plant example from the textboook illustrates the function of transcription factors.

Note: Prokaryotes coordinate gene regulation by arranging them in an operon. They also use sigma factors to guide RNA polymerase to specific classes of promoters. Eukaryotes will use sigma factors to coordinate genes that may be far apart, even on different chromosomes. Coordination via sigma factors is used by organisms to respond to stress. example: Stress response: Plants simultaneously synthesizes numerous proteins whose genes are scattered throughout the genome in response to drought). 1) In order to coordinate expression, each of the genes of the plant has a specific regulatory sequence near its promoter (plant sequence = dehydration response element). 2) In response to drought, a transcription factor changes so that it binds to this element and stimulates mRNA synthesis. The DRE helps conserve the plant's water or protect against non-ideal conditions (salt, heat, cold).

How do microRNAs act as important regulators of gene expression?

Originally, scientists believed that small portions leftover from the encoding of ribosomal RNA and transfer RNA was junk that was noncoding. This "junk" turned out to be microRNA, which was found in the worm Caenorhabditis elegans. - miRNAs are about 22 nucleotides long and have dozens of mRNA targets. - They are transcribed as longer precursors that fold into double-stranded RNA molecules, which are then processed through a series of steps into a single-stranded miRNAs. - A protein complex guides the miRNA to its target mRNA, where translation is inhibited and mRNA is degraded. ANSWER TO ACTUAL QUESTION: The conservation properties of the gene-silencing mechanism of miRNA indicates its biological importance as a regulator of gene expression.

How do prokaryotes conserve energy in regulating gene transcription?

Prokaryotes conserve energy and resources by making certain proteins only when they are needed (given that they can live in environments that can change abruptly).

The concentration of proteins cannot be determined simply by the quantity of mRNA. Factors acting AFTER mRNA is made must be the determinant for the concentration of proteins. What are three known ways in which translation of mRNA can be regulated?

Protein concentration is determined by factors acting AFTER mRNA is made. There are three known ways in which the translation of mRNA can be regulated. 1) Inhibition of translation with miRNAs. 2) Modification of the 5' cap: mRNA usually has a modified GTP on its 5' end. An mRNA that is capped with an unmodified GTP is not translated. 3) Translational repressor proteins: Proteins like these are used to block translation by binding to mRNAs and preventing them from attaching to the ribosome. Example: For mammals, the translation rate of the protein ferritin is increased rapidly when the level of free iron ions increases in the cell in order to protect the body from excess iron toxicity. When ferritin mRNA levels are constant but iron levels are low, a translational repressor binds to the ferritin mRNA and prevents its tranlsation. Excess iron binds to the repressor, altering the 3D structure so that it detaches from the mRNA and allows translation of the mRNA to proceed again.

How is protein stability regulated?

Protein content in any cell is a function of both protein synthesis and protein degradation. 1) Proteins can be targeted for destruction by a chain of events begun by the 76 AA protein ubiquitin binding to a lysine residue to the protein that gon' get ganked. 2) Ubiquitin don't like this protein's shit so he call his other ubiq- homies to tag on him to form a polyubiquitin chain. This complex of ubiquitin and protein takes the foo out back and they bind to a huge protein complex called a proteasome. 3) At the proteasome, the polyubiquitin chain is removed and ATP is used to mess up the protein's fold structure. This foo gets peppered. Three different proteases then digest the protein into small peptides and amino acids.

transcription factors

Proteins that assemble on a eukaryotic chromosome, allowing RNA polymerase II to perform transcription.

What is the polymerase that transcribes protein-coding? Can it bind to the promoter and initiate transcription? If not, why?

RNA Polymerase II. No it cannot bind and initiate transcription "by itself." It requires several general transcription factors to have bound to the core promoter before it can.

How do DNA methylation patterns in male gametes differ from female gametes? Genomic imprinting patterns?

The male sperm differs from the female egg ab about 200 genes in the mammalian genome. DNA methylation: A given gene in this group may be methylated in eggs, but unmethylated in sperm. Genomic Imprinting: Males and females may be the same "genetically," but they differ "epigenetically."

operator

The region of an operon that acts as the binding site for the repressor.

Why is the repressor protein key to regulatory systems in E. Coli?

The repressor is always present in the cell in adequate amounts to occupy the operator and keep the operon turned off. The repressor has a recognition site for the DNA sequence in the operator and it binds very tightly. It also has an allosteric binding site for the inducer. When the inducer (allolactose) binds to a repressor, the repressor changes shape so that it can no longer bind DNA.

epigenetic

The scientific study of changes in the expression of a gene or set of genes that occur without change in the DNA sequence.

What is an example of heterochromatin in action?

The x-chromosome of female mammals. A normal female has two X chromosomes, whereas a normal male has an X and a Y. In an early female embryo, one copy of X becomes heterochromatic and transcriptionally inactive in each cell. The same cell remains inactive in all of that cell's descendants. The choice of which X to inactivate is random.

microRNA

a small noncoding RNA molecule, typically about 21 base pairs long, that binds to mRNA to inhibit its translation

trp operon

an example of a repressible operon(production of tryptophan)

Constitutive genes

genes that are expressed all the time

inducible genes

genes that are expressed only when their proteins are needed by the cell

epigenetics

the study of changes in the expression of a gene or set of genes that occur without change in the DNA sequence

beta galactoside transacetylase

transfers acetyl groups from acetyl CoA to certain β-galactosides. Its role in the metabolism of lactose is not clear.