Chapter 18: Regulation of Gene Expression***

What are the two main ways of controlling metabolism in bacterial cells?

1. adjust activity of present enzymes 2. adjust production level of an enzyme

what percentage of the genes of a typical human cell is expressed at any given time?

20%, but highly differentiated cells like muscle or nerve cells express even less. Cells of the immune system have a different genome

What is a promoter?

A site where RNA polymerase can bind to DNA and begin transcription.

What occurs in cell differentiation and morphogenesis?

Cell differentiation is when specialized structures and functions are achieved. Morphogenesis is the arrangement of cells to make organs/shapes

What is controlled by homeotic genes?

Control pattern formation in lat embryo, larva, and adult drosophilia

What is genomic imprinting and how is it maintained? Give an example discussed earlier in human genetics.**

It is an example of epigenetics. Methylation patterns are passed down paternally or maternally. Methylation controls the expression of genes

In prokaryotes, functionally related genes are usually clustered in a single operon. What has been found to be the case in eukaryotes?

Operons that works like that have not been found in eukaryotic cells, related genes are scattered throughout the genome

What happens when a repressor is bound to the operator?

RNA polymerase cannot bind to the promoter. The operator is switched off

Compare and contrast the lac operon and the trip operon.

The lac operon is inducible and the trip operon is repressible. They both have an operator, promoter, and regulatory gene. The trip repressor is inactive alone and needs a corepressor. The lac is active by itself and need an inducer to inactivate.

What is the operator? What does it do>

The operator is the "on switch" for gene regulation. it is positioned within the promoter or between the promoter and enzyme coding genes. It controls the access of RNA polymerase to the genes.

What makes the barr body in mammals inactive?

The x chromosome is inactivated by heavy methylation, this results in it not being expressed

How can both repressible and inducible operons be negative regulators?

They both involve operators being switched on and off by a repressive protein.

How are siRNA and mRNA different?

They form from different precursors.

What are two types of activators present two create cell differentiation? What do they do

a. distribution of cytoplasmic determinants, the maternal substances in the egg that influence development. They are spread unevenly in cytoplasm, cells take up cytoplasm and are exposed to different determinants. b. different inductive signals, communication between embryonic cells with cell surface molecules, like growth factors, proteins are expressed that cause changes in cells.

What effect does phosphorylation have on chromatin?

The addition of a phosphate group next to a methylated amino acid can loosen chromatin

What three processes lead to the transformation of a zygote into an organism?

cell division, cell differentiation, morphogenesis

What would occur if the repressor of an inducible operon were mutated so it could not bind to the operon?

continous transcription of the operons genes

What are maternal affect genes and what else are they referred to as?

encode for cytoplasmic determinants. also called egg polarity genes because they control the orientation of the egg and consequently the fly

Muscle cells vary from nerve cells mostly because ____

express different genes (cell differentiation/expression)

Where are nucleotides found that influence the lifespan of mRNA in eukaryotes?

in the untranslated region of the molecules (UTR) at the 3' end.

Inducible enzymes usually function in what type of pathways? Repressible enzymes?

inducible enzymes usually function in catabolic pathways, their activity is induced by a chemical signal. repressible enzymes usually function in anabolic pathways, their synthesis is repressed by high levels of the end product.

Noncoding RNAs influence gene expression at what two points?

mRNA translation and chromatin configuration.

Explain the two modes of action of microRNA's **

miRNA has a double stranded hairpin structure. 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 3. One of the strands is degraded, the other forms a complex with one or more proteins 4. binds to target mRNA, containing at least 7 complimentary bases and blocks translation

What is the common control point of gene expression for all organisms?

at transcription

What new type of RNA has been discovered? What is there role?

non coding RNA, play a role in gene expression regulation.

What is DNA methylation? What role may it play in gene expression?**

The methylation of certain bases in DNA usually cytosine, is the addition of a methyl group (-CH3). it reduces the expression

Explain why CAP binding and stimulation of gene expression is positive regulation.

It is a regulatory protein that directly interacts with the genome.

Describe how enhancers and activators interact with transcription factors to affect gene expression

1. activator proteins ind to distal control elements grouped as an enhancer. The enhancer has 3 binding sites, each a distal control element. 2. A DNA bending protein brings the bound activators closer to the promoter. General transcription factors, mediator proteins, and RNA polymerase II are nearby. 3. Activators bind to certain mediator proteins and general transcription factors, helping form active transcription initiation complex.

What are three mechanisms for converting a porto-oncogene to an oncogene?

1. movement of DNA within genome 2. amplification of porto-oncogene 3. point mutation in control element of photo-oncogene

Operons have not been found in eukaryotic cells, and the genes coding for the enzymes of a particular metabolic pathway are often scattered over different chromosomes. What is a plausible mechanism for the coordination of gene expression?

A specific combination of control elements often respond to the same chemical signal, activating varying genes throughout the genome.

What two effects can miRNA have on mRNA?

Can degrade it or simply block translation.

How does a repressor protein work?

It binds to the operator and blocks the attachment of RNA polymerase to the promoter. It is specific the operator of a certain operon.

If a particular operon encodes enzymes for making an essential amino acid and is regulated like the trp operon, then the amino acid acts as a ____

corepressor

What mechanism is involved in the beginning of tumor growth? Discuss oncogenes and proto oncogenes

proto oncogenes are the normal genes responsible for cell growth and division. oncogenes are the cancer causing version that are overexposed proto oncogenes.

What is an operon?

the operator, promoter, and genes they control

Cell differentiation always involves ___

the production of tissue specific proteins, such as muscle actin

How are proteins targeted for degradation?

A small protein called ubiquitin is attached to mark for destruction. Then proteasomes, giant protein complexes, destroy proteins. Mutations in this process can lead to cancer.

What occurs in histone acetylation? How does it affect gene expression?

Acetyl groups (-COCH3) are attached to lysine in histone tails. This neutralizes the lysine positive charge. Histone tails no longer bind to neighboring nucleosomes which causes the chromatin to have a looser structure and be accessed for transcription easier.

How can proteins be activated, processed, and degraded? Give an example of each process

Cleavage of insulin activates it, chemical modifcation such as addition of phosphate groups or sugars if they are destined for the surface of animal cells, selective degradation such as cyclins.

In though all cells of an organism have the same genes, there is differential gene expression. What does this mean?

Different types of cells occur because different parts of the genome they share are expressed.

Feedback inhibition is a recurring mechanism throughout biological systems. In the case of E coli regulating tryptophan synthesis, is it positive or negative inhibition? explain.

E coli is negative inhibition. meaning that it involves an operon being switch off by active form of repressor protein. Positive regulation is when the regulatory protein interacts directly with the genome.

All genes are not "on" all the time. Using the metabolic needs of E.coli, explain why not.

E coli regulate their gene expression to save or reserve resources when the environment is giving them what they need. E coli feed on tryptophan, they produce it when tryptophan is low in their environment and they halt the production when it is abundant in their environment.

Gene expression can be regulated my modifications of the chromatin. Distinguish between heterochromatin and euchromatin.

Heterochromatin is highly condensed and usually not expressed. Euchromatin is lightly packed and generally expressed.

Posttranscriptional control includes regulation of mRNA degradation. Explain how this effects translation.

It affects how long mRNA lasts in the cell, which in turn affects how many times the mRNA is translated (affecting the magnitude of protein production)

What is CAP? How does it work?**

It is a regulatory protein, an activator. "Catabolite activator protein". It binds to DNA and stimulates the transcription of a gene. Cyclic Amp (cAMP) binds to CAO to induce its active shape. This increases affinity of RNA polymerase to promoter. Enzyme to break dow alternative source of energy is produced. (like lactose in E. coli)

What process ensures that all the tissues and organs of an organism are in their characteristic places? Where'd do the molecules cues that control this process arise?

Pattern formation. positional information is provided for by cytoplasmic determinants and inductive signals. also from homeotic genes

Distinguish between inducible and repressible operons. Describe one example of each type. ***

Repressible operons are like the trp operon, they are usually on but can be switch off by a small molecule binding allosterically to a regulatory protein. An inducible operon is usually off but can be induced by the interaction of a small molecule and regulator. the lac operon is inducible.

List the three components of an operon and explain the role of each one

The operator is the on/off switch and controls what attaches to the promoter. The promoter allows transcription to begin when RNA polymerase attaches to it. The genes are responsible for coding for the correct protein (enzyme) production.

What are regulatory genes?

They code for regulatory proteins aka repressor proteins, they are located some distance from the operon the operon and have their own promoter. They are expressed continually but at a low rate.

What is APC?

adenomatous polyposis coli (APC). it is a tumor supressor gene. mutations to this gene are common in individuals with colorectal cancer

Explain what is meant by epigenetic inheritance, and give an example of epigenetic changes discussed in the text or in class.

inheritance of traits transmitted by mechanisms not directly involving the nucleotide sequence. for example the "lick your rat" lab, schizophrenia in twins, or cancer

How can alternative RNA splicing result in different proteins derived from the same initial RNA transcript?

introns/exons are read and chosen differently. Original RNA is spliced differently producing varying mRNA. reading frame is different.

What is needed for eukaryotic transcription to begin?

many need control elements to interact with specific transcription factors. General transcription factors are absolutely necessary for all transcription and for RNA polymerase to initiate transcription.

Absence of bicoid mRNA from a Drosophila egg leads to the absence of anterior larval body parts and mirror image duplication of body parts. This is evidence that the product of the bicoid gene ____`

normally leads to formation of head structures

What is the ras gene? What do mutations to this gene cause?

ras is a proto oncogene, mutation can lead to production of a hyperactive Ras protein and increased cell division

What is meant by determination? Explain what this means within an embryonic cell.

the events that lead to observable changes and differentiation in embryonic cells. Irreversible, becomes a certain type of cell. Involves tissue specific proteins

What is RNA interference?

the inhibition of gene expression by RNA molecules. RNA molecules in a cell are destroyed if they have a sequence complimentary to that of an introduced double stranded RNA. caused by small interfering RNA, siRNA.

What is a well known example of a tumor suppressor gene? explain its function

the p53 gene, is mutated in more than 50% of human cancer. It activates p21 which halts the cell cycle by binding to cyclin dependent kinases. It activates miRNAs that inhibit the cell cycle, it is responsible for DNA repair. It also activates apoptosis in cells with irreparable DNA

Within a cell, the amount of protein made using a given mRNA molecule depends partly on___

the rate at which the mRNA is degraded

How do activators stimulate transcription?

they bind to the enhancer. They have two domains, one that binds DNA and a second that activates transcription. bound activators facilitate a sequence of protein to protein interactions that result in transcription

The functioning of enhancers is an example of ____

transcriptional control of gene expression

What can mutations in homeotic genes lead to?

transformation in the identity of entire body parts

Describe the relationship between glucose supply, cAMP, and CAP.

when glucose supply gets low, cAMP accumulates, cAMP binds to CAP which makes it its active shape and it binds to DNA increasing affinity of RNA polymerase to attach to promoter