Chapter 18

when does e. coli use lactose as an energy source

when lactose is present and glucose is in short supply (it'll only use lactose if necessary it prefers glucose)

what is the role of the represor

binds to the operator, preventing transcription, often by preventing RNA Pol from binding. they're specific to their operon

histone acetylation

the attachment of acetyl groups to certain amino acids of histone proteins

how do specific transcription factors that function as repressors inhibit gene expression

-binding directly to control element DNA -blocking activator binding -interfering with the activator itself so it can't bind with the DNA -indirectly affecting chromatin structure by recruiting 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, called silencing

What are the two main ways of controlling metabolism in bacterial cells? Which is a short-term response, and which is a long-term response?

1. cells can adjust the activity of enzymes already present through feedback inhibition 2. cells can adjust the production level of certain enzymes aka regulate the expression of the genes encoding the enzymes

Explain how this repressible operon can be turned off. Figure 18.3(b) in the text will help.

A corepressor can bind to the repressor, turning it on. It then binds to the operator.

cytoplasmic determinant

A maternal substance, such as a protein or RNA, that when placed into an egg influences the course of early development by regulating the expression of genes that affect the developmental fate of cells.

control elements

A segment of noncoding DNA that helps regulate transcription of a gene by serving as a binding site for a transcription factor. Multiple control elements are present in a eukaryotic gene's enhancer

inducer

A specific small molecule that binds to a bacterial repressor protein and changes the repressor's shape so that it cannot bind to an operator, thus switching an operon on.

how does histone acetylation affect gene expression

Acetylation of histone tails promotes loose chromatin structure that permits transcription. Highly acetylated=less condensed

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

Cell division, Cell differentiation, morphogenesis

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

Different segments are treated as exons and introns.

Feedback inhibition is a recurring mechanism throughout biological systems. Is the regulation of tryptophan synthesis by E. coli achieved by positive or negative feedback? Explain your choice.

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.

What are general transcription factors, and how do they function?

General transcription factors are essential for the transcription of all protein coded-genes. A few transcription factors bind to the DNA sequence, but may also bind to proteins, including other transcription factors as well as RNA polymerase II.

epigenetic inheritance

Inheritance of traits transmitted by mechanisms not directly involving the nucleotide sequence.

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 involving the nucleotide sequence itself. Children in WWII who were born at a time when food was scarce were more likely to develop health problems.

histone tails

N-terminus of each histone protein in a nucleosome protrudes outward from the nucleosome

What are the respective roles of distal and proximal control elements?

Proximal means near distal means far (from the promoter). Distal control elements can be grouped together as enhancers. Proximal control elements are close to the promoter.

what happens when an operon is turned on

RNA polymerase can bind to promoter and start transcribing genes of the operon

It is now known that much of the RNA that is transcribed is not translated into protein. These RNAs are called noncoding RNAs. Read carefully to discern a crucial role played by these ncRNAs. What is this role?

Regulate mRNAs and cause remodeling of chromatin structure.

Distinguish between inducible and repressible operons and describe one example of each type of operon.

Repressible - its transcription is usually on but can be inhibited (tryptophan) Inducible - its transcription is usually off but can be stimulated (lactose)

How can the rate of gene expression be modified by specific transcription factors (activators or repressors)?

The interaction of general transcription factors and RNA polymerase II with a promoter usually leads to a low rate of initiation and production of few RNA transcripts from genes that are not expressed at significant levels all the time or in all cells. Specific transcription factors help determine when high levels of transcription of these genes will be and where.

determination

The progressive restriction of developmental potential in which the possible fate of each cell becomes more limited as an embryo develops. At the end of determination, a cell is committed to its fate.

What is the fundamental difference between the repressor protein in a repressible operon versus the repressor protein in an inducible operon?

The trp repressor protein is inactive by itself and requires tryptophan as a corepressor in order to bind to the operator. The lac repressor is active by itself, binding to the operator and switching the lac operon off. An inducer is required to inactivate the repressor.

regulatory genes

a gene that codes for a protein, such as a repressor, that controls the transcription of another gene or group of genes

corepressor

a small molecule that binds to a bacterial repressor protein and changes the protein's shape, allowing it to bind to the operator and switch an operon off

microRNA (miRNA)

a small, single-stranded RNA molecule, generated from a double-stranded RNA precursor; the miRNA associates with one or more proteins in a complex that can degrade or prevent translation of an mRNA with a complementary sequence

alternative RNA splicing

a type of eukaryotic gene regulation at the RNA-processing level in which different mRNA molecules are produced from the same primary transcript, depending on which RNA segments are treated as exons and which as introns

operon

a unit of genetic function found in bacteria and phages, consisting of a promoter, an operator, and a coordinately regulated cluster of genes whose products function in a common pathway

long noncoding RNA (lncRNA)

an RNA between 200 and hundreds of thousands of nucleotides in length that does not code for protein but is expressed at significant levels

Given access to both glucose and lactose, E. coli will use the glucose. Describe the relationship between glucose supply, cAMP, and CRP.

cAMP accumulates when glucose is scarce. When cAMP binds to CRP is assumes its active shape and can attach to a specific site at the upstream end of the lac promoter, which increases the affinity of RNA polymerase for the lac promoter.

control of gene expression video

done

figure 18.11

done

figure 18.15

done

inducible enzymes

enzymes of the lactose pathway their synthesis is induced by a chemical signal

operator

in bacterial and phage, DNA, a sequence of nucleotides near the start of an operon to which an active repressor can attach. The binding of the repressor prevents RNA polymerase from attaching to the promoter and transcribing the genes of the operon

what happens when lactose with present near a lac operon

it binds to the repressor and changes its shape, keeping the repressor from binding to the operator

repressible operon

its transcription is usually on but it can be inhibited when a specific small molecule binds allosterically to a regulatory protein

heterochromatin

more densely arranged than euchromatin, genes not expressed

how is the lac operon under dual control

negative control by the lac repressor and positive control by CRP

Poly-A signal sequence

on last exon downstream on the poly-a signal sequence side transcribed into an RNA sequence that signals where the transcript is cleaved and the poly-a tail added. transcription can continue beyond the poly-a tail before terminating

negative control of genes

operons are switched off by the active form of their respective repressor protein

chromatin

package where DNA of eukaryotic cells is

is the CRP thing positive or negative regulation

positive

what's the purpose of histone acetylation

promotes transcription by opening up chromatin structure

proximal control elements vs distal control elements

proximal - close to promoter distal - groupings called enhancers that are far upstream or downstream of the gene or even within an intron

what bases are most often used in dna methylation

rather than modifying histone proteins, a different set of enzymes can methylate the DNA itself on certain bases, usually cytosine

how does repressor turn on and off

repressor is an allosteric protein - inactive until molecule binds to repressor @ allosteric site binding of repressors to operators is reversible repressor bound state is higher w/more active repressor molecules

where does the corepressor bind to

repressor which binds to mRNA

promoter

site where RNA polymerase can bind to DNA and begin transcription

chromosome conformation capture

techniques that help cross-link and identify regions of chromosomes associated with each other during interphase

What is differential gene expression?

the expression of different genes by cells with the same genome. The uniquely expressed genes allow cells to carry out their specific function.

differential gene expression

the expression of different sets of genes by cells with the same genome

DNA methylation

the presence of methyl groups on the DNA bases (usually cytosine) of plants, animals, and fungi. (the term also refers to the process of adding methyl groups to DNA bases)

differentiation

the process by which a cell or group of cells becomes specialized in structure and function

positive control of genes

when a regulatory protein interacts directly with the genome to increase transcription

what happens when cAMP binds to the regulatory protein

CRP (cAMP receptor protein) assumes its active shape and can attach to a specific site at the upstream end of the lac promoter this increases the affinity of RNA polymerase for the lac promoter

general vs specific transcription factors

General transcription factors are essential for the transcription of all protein coding genes. Specific transcription factors are only needed for the transcription of specific genes.

Explain why CRP binding and stimulation of gene expression is positive regulation. What is the role of the activator?

It facilitates the binding of RNA polymerase to the promoter and thereby increases the rate of transcription of the lac operon, the attachment of CRP to the promoter directly stimulates gene expression.

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

One third to one half

All genes are not "on" all the time. Using the metabolic needs of E. coli, explain how this conserves energy resources.

The cell only activates the metabolic pathway to create what's missing. Therefore, it avoids wasting resources to produce a substance that is readily available from the surrounding solution.

Post-transcriptional control includes regulation of mRNA degradation. Explain how this affects translation.

The length of time each protein functions in the cell is strictly regulated by selective degradation. The lifespan of an mRNA molecule determines how much mRNA is made.

The old view that the nuclear contents are like a bowl of chromosomal spaghetti has been replaced with a much more structured vision of chromosomal arrangement. Using Figure 18.13 in your text, explain the current understanding of chromosomal arrangement.

Unexpressed genes are located in the outer edges of the nucleus, while those that are being expressed are found in its interior region.

RNA interference (RNAi)

a mechanism for silencing the expression of specific genes; in RNAi, double-stranded RNA molecules that match the sequence of a particular gene are processed into siRNAs that either block translation or trigger the degradation of the gene's messenger RNA; this happens naturally in some cells, and can be carried out in laboratory experiments as well

induction

a process in which a group of cells or tissues influences the development of another group through close-range interactions

activator

a protein that binds to DNA and stimulates gene transcription. in prokaryotes, activators bind in or near the promoter; in eukaryotes, activators generally bind to control elements in enhancers

repressor

a protein that inhibits gene transcription. In prokaryotes, repressors bind to the DNA in or near the promoter. In Eukaryotes, repressors may bind to control elements within enhancers, to activators, or to other proteins in a way that blocks activators from binding to DNA

enhancers

a segment of eukaryotic DNA containing multiple control elements, usually located far from the gene whose transcription it regulates

coordinately controlled

a whole cluster of functionally related genes can be turned on and off because they are in one transcription unit

To demonstrate you understand how the lac and trp operon work, let's assume a human host has had a meal of turkey (rich in the amino acid tryptophan) and washed it down with milk. Explain your answer to each of the following: a. Will the trp operon of E. coli in the gut of the human be active? b. Will the lac operon of E. coli in the gut of the human be active?

a. no it'll be saving energy b. yes because lactose is available

what is cAMP

an activator

nucleosome

basic unit of chromatin

transcription initiation complex

cluster of proteins that assembles on the promoter sequence at the "upstream" end of the gene RNA polymerase II is one of the proteins

cyclic AMP (cAMP)

cyclic adenoside monophosphate, named because of its ring structure, is a common chemical signal that has a diversity of roles, including as a second messenger in many eukaryotic cells, and as a regulator of some bacterial operons

what are the two types of structural domains that are commonly found in a large number of transcription activators

dna-binding domain - a part of the protein's 3d structure that binds to dna activation domains - bind other regulatory proteins or components of the transcription machinery, facilitating a series of protein-protein interactions that result in enhanced transcription of a given gene

what type of cells have lac and trp operons

e. coli

what does the regulator gene do

encodes repressor protein separate from operon has its own promotor gene is expressed continuously (regulator is only activated sometimes tho)

zygote

fertilized egg

coordinate control of dispersed genes

genes that are scattered over different chromosomes. Transcription activators in the nucleus that recognize the control elements bind to them, promoting simultaneous transcription of the genes, no matter where they are in the genome often occurs in response to chemical signals from outside the cell, like steroid hormones signaling molecules can activate it by binding to receptors on a cell's surface and and triggering signal transduction pathways that activate particular transcription factors

coordinately controlled genes

genes who have related functions and are turned on and off together. often clustered into an operon

genomic imprinting

in mammals, where methylation permanently regulates expression of either the maternal or paternal allele of particular genes at the start of development

where it the operator

in promotor or between promotor and enzyme-coding genes

piwi-interacting RNA (piRNA)

include information about heterochromatin, blocking expression of some parasitic DNA elements in the genome known as transposons

how does the e. coli cell sense the glucose concentration and relay this information to the lac operon

interaction of an allosteric regulatory protein cyclic AMP (cAMP) which accumulates when glucose is scarce.

what its the operator's role

on/off switch for cluster of similar genes in one transcription unit. it controls the access of RNA polymerase to the genes

small interfering RNA (siRNA)

one of multiple small, single-stranded RNA molecules generated by cellular machinery from a long, linear, double-stranded RNA molecule; the siRNA associates with one or more proteins in a complex that can degrade or prevent translation of an mRNA with a complementary sequence

mediator proteins

protein mediated bending of the DNA brings the bound activators into contact with the group of mediator proteins, which in turn interact with general transcription factors at the promoter. this helps assemble and position the initiation complex on the promoter

how does selective degradation determine the length of time each protein functions in the cell

some proteins must be short lived for the cell to function properly to mark a protein for destruction, the cell commonly attaches molecules of a protein called uniquitin to a protein giant protein complexes called proteasomes than recognize the uniquitin tagged proteins and degrade them

where does histone acetylation happen

the addition of acetyl group to an amino acid in a histone tail

how are siRNAs and RNAi related

the blocking of gene expression by siRNAs, referred to as RNAi, is used in the lab to disable specific genes to investigate their function

morphogenesis

the development of the form of an organism and its structures

epigenetics

the study of the inheritance of traits transmitted by mechanisms that do not involve the nucleotide sequence

what do the enzymes encoded by the lac operon do

they break down the lactose, freeing the repressor to bind to the operator again

where is gene expression commonly controlled

transcription; regulation at this stage often occurs in response to signals coming from outside the cell, such as hormones or other signaling molecules

repressible enzymes

tryptophan synthesis generally function in anabolic pathways, which synthesize the essential end product from raw materials (precursors) by suspending production of an end product when it is already present in sufficient quantity, the cell an allocate its organic precursors and energy for other uses

feedback inhibition

typical of anabolic (biosynthetic) pathways, allows a cell to adapt to short-term fluctuations in the supply of a substance it needs

inducible operon

usually off but can be stimulated to be on when a specific small molecule interacts with a different regulatory protein (lactose operon)

silencing

when repressors recruit proteins that remove acetyl groups from histones, leading to reduced transcription

euchromatin

whether or not a gene is transcribed is affected by the location of nucleosomes along a gene's promoter and also the sites where the DNA attaches to the protein scaffolding of the chromosome