BIOL 190: Chapter 12

proteins, necessary

Living organisms benefit from gene regulation because it conserves energy; ______that are encoded by genes will be produced only when they are ______

free region

Many eukaryotic genes are flanked by a nucleosome-________ , which is a site that is missing nucleosomes.

a. activators: proteins that bin to DNA and increase transcription b. enhancers: DNA sequences that increase transcription c. repressors: proteins that bind to DNA and inhibit transcription d. silencers: DNA sequences that prevent transcription

Match each term with the correct description. a. activators b. enhancers c. repressors d. silencers

histone

The acetylation of ______proteins can loosen chromatin packing.

A cluster of genes under the transcriptional control of a single promoter

What is an operon?

operon

A cluster of genes that are part of a single transcription unit that is under the control of a single promoter is referred to as a(n)

of 4 globin subunits

A functional hemoglobin protein is composed of______

(a) to respond to environmental changes (b) to make proteins in specific cell types (c) to make proteins at specific stages of development

A reason for gene regulation is

transcription factors that exert positive control and increase transcription

Activators are (BACTERIA)

recruiting the GTF to the TATA box.

An activator can affect the function of a GTF by:

TFIID

An activator can improve the ability of Blank______ to bind to the TATA box on the DNA.

CAP site

An activator protein recognizes the Blank______ of the lac operon.

Translation Transcription Processing of mRNA Post-translation

Control of gene expression takes place at what levels in eukaryotes? Multiple select question.

genes

Different cell types, such as skin cells and nerve cells, have different morphologies because ________are expressed and regulated in different ways in different cells.

different globin genes are expressed at different developmental stages.

During mammalian development:

chaperone; deacetylated

During transcription, evicted histones are then reassembled by Blank______ proteins and placed back on the DNA behind the moving RNA polymerase II. These histones may be Blank______ so they bind more tightly to the DNA. Multiple choice question.

a. Transcription: control of synthesis of mRNA from a gene b. RNA processing: regulation of splicing of mRNA c. Translation: regulation of protein synthesis d. Post-translation: regulation of the amount or function of a protein that has already been synthesized

Eukaryotes can regulate gene expression in several ways. Match each level of regulation with the correct description. a. Transcription b. RNA processing c. Translation d. Post-translation

blocks, relieves

Glucose _____ activation of the lac operon; lactose _____repression of the lac operon. What happens when there is high lactose and high glucose? High lactose and low glucose? Low lactose and high glucose? Low lactose and low glucose? (BACTERIA)

Proteins that metabolize molecules such as small sugars are produced only when those sugars are available in the environment.

How can gene regulation conserve energy?

-When lactose is present, the lac repressor protein does not bind to the operator site and transcription can occur. -When lactose is present, transcription of the lac operon is high.

How does the presence of lactose in the cell influence the transcription of the lac operon?

inhibits

In eukaryotes, DNA methylation usually ________gene transcription.

False

Methylation of DNA near the promoter a eukaryotic gene tends to activate transcription of the gene.

regulation of RNA processing

Regulation of prokaryotic gene expression typically involves all of the following mechanisms except Blank______.

promoter

Regulatory transcription factors influence the expression of genes by binding directly to DNA at or near the _______site and affect the rate of transcription.

transcription factors that exert negative control and decrease transcription

Repressors are (BACTERIA)

1. factors 2. negative 3. activators 4. positive

Repressors are regulatory transcription ______that bind to the DNA and decrease the rate of transcription. This is a form of regulation called_____ control. On the other hand, ______bind to the DNA and increase the rate of transcription, a form of regulation termed ______control.

chromatin, histone

The binding of general transcription factors and RNA polymerase II to the core promoter is facilitated by the actions of_________ -remodeling complexes and__________ -modifying enzymes. This allows the formation of a preinitiation complex.

positive

The catabolite activator protein (CAP) is involved in Blank______ control of the lac operon.

TATA, transcriptional

The core promoter of a eukaryotic gene typically includes the ______box and the______ start site.

CAP

The lac operon is also under positive control by an activator protein called what?

RNA polymerase

The lac repressor protein prevents the enzyme _______ ________from transcribing the genes in the lac operon.

operator

The lacO site of the lac operon is called the________ and is the site where the repressor protein binds.

iron regulatory protein

The mRNA encoding ferritin is controlled by an RNA-binding protein called the Blank______.

express different genes.

The morphologies of different cell types, such as skin cells and nerve cells, is strikingly different. This is due to the fact that the cells:

transcription

The most common point of gene regulation in bacteria is

GLUCOSE, A DECREASE

The presence of ___ in the environment of E. coli prevents CAP from binding to the DNA, resulting in ___ in transcription of the lac operon.

expression

The process in which the information in a gene is made into a functional gene product, such as an RNA molecule or a protein, is termed gene .

alternative splicing

The process whereby different mature mRNAs can be made from the transcript of a single gene is called_____ _______

When the concentration of lactose is low in the cell

Under what conditions does the lac repressor bind to the operator of the lac operon and prevent transcription?

Proteins that bind to DNA and affect the transcription of one or more genes

What are regulatory transcription factors?

-•Cell differentiation is the process by which cells become specialized into particular types -The skeletal muscle cell, neuron, and skin cell shown below all contain the same genome, however the proteome of each cell is quite different due to gene regulation -Both the types of proteins as well as the amount of particular proteins are important differences between cell types

What is cell differentiation? What are some examples?

-refers to the ability of cells to control the expression of their genes -Most genes are regulated to ensure proteins are produced at the correct time and in the correct amount -Regulation conserves energy by producing only what is needed -Many proteins regulate gene expression through binding to DNA

What is gene regulation? Why does it occur? How does it occur?

the epsilon (ε)- and zeta (ζ)-globin

•During the embryonic stage,___________genes are "turned on"

a site on a chromosome that is missing nucleosomes.

A nucleosome-free region (NFR) is:

•Eukaryotic regulation of transcription involves some of the same principles as prokaryotic regulation (Activator and repressor proteins influence the ability of RNA polymerase to initiate transcription; small effector molecules may participate in regulation) -Eukaryotic regulation differs in many important ways (Genes are almost always organized individually (not in operons)) (Regulation tends to be more intricate) Most eukaryotic genes are under combinatorial control, where expression is regulated by the combination of many factors

How does eukaryotic regulation differ? What are most eukaryotic genes under?

A repressor can prevent binding of TFIID to the TATA box. A repressor can inhibit assembly of the pre-initiation complex.

Identify the two ways that a repressor can interact with a GTF to inhibit transcription.

an operon, a polycistronic

In bacteria, the unit of DNA that contains multiple genes under the control of a single promoter is called ___. The mRNA produced from this unit is referred to as ___ mRNA.

general

In order to initiate transcription, RNA polymerase II must associate with proteins known as Blank______ transcription factors at the TATA box of the core promoter.

true

Repressors can prevent TFIID from binding to the TATA box.

transcription

Small effector molecules bind to regulatory_______ factors and cause conformational changes that influence their ability to bind to DNA.

gene expression.

The production of the functional product of a gene is called:

iron regulatory element

The protein IRP binds to a site within the ferritin mRNA known as the _______ _______ ________

the lac operator

The transcription of the lac operon genes is inhibited when the lac repressor protein binds to Blank______.

•Some genes have relatively constant levels of expression; such constitutive genes frequently encode proteins that are constantly required (like enzymes for carbohydrate metabolism)

What are constitutive genes?

-proteins that bind to regulatory sequences in DNA, are frequently used to change levels of gene expression

What are regulatory transcription factors? (BACTERIA)

Molecules that bind to transcription factors and change their conformation

What are small effector molecules?

-transcriptional regulation also involves small effector molecules -Small effector molecules bind repressors or activators, causing a change in their conformation and function

What are small effector molecules? (BACTERIA)

Promoter lacA lacY lacZ

What are the basic components of the lac operon?

Transcriptional start site TATA box

What are the two components of the core promoter in eukaryotes?

Expression of genes at appropriate times The conservation of energy

What are two major benefits of gene regulation?

Gene regulation ensures that the correct hemoglobin protein is produced at the right time in development

What does gene regulation in eukaryotics ensure?

-An operon is a cluster of genes that is under transcriptional control of one promoter; operons are found in bacterial chromosomes -An operon allows the coordinated regulation of a group of genes with a common function; transcription produces a polycistronic mRNA that encodes more than one polypeptide -In E. coli, the lac operon contains genes for lactose metabolism

What is an operon? What does it do? What does it do in E.coli?

The sequence of nucleotides that is recognized by an activator protein

What is the CAP site for the lac operon?

Bacteria can coordinate the expression of multiple genes in the same biological pathway.

What is the advantage of operon organization in bacteria?

They cause a change in the locations and/or compositions of nucleosomes.

What is the function of chromatin-remodeling complexes?

GTFs and RNA polymerase come together at the core promoter for the initiation of transcription.

What is the function of general transcription factors (GTFs) in the initiation of transcription?

The TATA box determines the starting point of transcription.

What is the role of the TATA box?

transport of RNA out of the nucleus

What level of regulation do eukaryotes possess that prokaryotes do not?

it forms noncovalent bonds with functional groups on the nitrogenous bases.

When a transcription factor interacts with DNA (BACTERA)

𝛾-globin gene beta (β)-globin gene

At birth, the ______ is "turned off" and the______is "turned on"

alpha (α)- and gamma (𝛾)-globin genes

At the fetal stage, the embryonic genes are "turned off" and the_______are "turned on"

operator

In the lac operon, the Blank______ is the DNA sequence at which the lac repressor binds.

a. lacZ: gene that encodes β-galactosidase b. lacY: gene that encodes lactose permease c. lacA: gene that encodes galactose transacetylase d. lacO: regulatory sequence that provides a binding site for a repressor protein e. lacP: promoter for the lac operon genes f. CAP site: regulatory sequence that is recognized by an activator protein

Match each component of the lac operon with the correct description. a. lacZ b. lacY c. lacA d. lacO e. lacP f. CAP site

coordinate the regulation of genes with related functions

Operons enable bacteria to ______.

chromatin-remodeling

Proteins that use energy from ATP hydrolysis to change the locations and compositions of nucleosomes are called ATP-dependent_________ - complexes.

1.Activators - activator proteins stimulate RNA polymerase to initiate transcription 2.Repressors - repressor proteins inhibit RNA polymerase from initiating transcription 3.Modulation - small effector molecules, protein-protein interactions, and covalent modifications can modulate activators and repressors 4.Chromatin structure - activator proteins promote loosening up of the region in the chromosome where a gene is located, making it easier for RNA polymerase to transcribe the gene 5.DNA Methylation - usually inhibits transcription, either by blocking an activator protein or by recruiting proteins that inhibit transcription

What does combinatorial control of transcription involve? There is 5 describe each.

binds to the iron regulatory element and blocks translation of ferritin.

When iron levels are low, the iron regulatory protein:

The TATA box determines the precise starting point for transcription. The TATA box is a sequence upstream of the transcriptional start site.

Which of the following describe the TATA box?

Silencers Enhancers

Which of the following elements are DNA sequences that regulate gene transcription?

Loosening of chromatin structure Binding of an activator protein to DNA

Which of the following factors help to increase transcription levels in eukaryotes?

Alternative splicing

Which of the following is a form of gene regulation in which a eukaryotic pre-mRNA can be processed to produce more than one mature RNA? Multiple choice question.

Different globin genes are expressed in the embryo, fetus, and adult.

Which of the following is an example of developmental gene regulation in mammals?

Acetylated histone proteins do not bind as tightly to the DNA, which aids in transcription.

Which of the following statements about histone acetylation is TRUE?

-One or more activator proteins may be involved in transcriptional regulation. -One or more repressor proteins may be involved in transcriptional regulation. -DNA methylation usually inhibits transcription.

At the level of transcription, there are several common factors that contribute to combinatorial control. What are they?

Post-translation Transcription Translation

At what levels does gene regulation occur in prokaryotes?

-The bacterium Escherichia coli can use many types of sugars as food sources, which increases its chances of survival -In order to utilize lactose, E. coli cells need a transporter and an enzyme that catalyzes the breakdown of lactose When lactose is not present, the cell makes very little of these proteins However, when lactose becomes available gene regulation directs increased expression of these proteins

How do bacteria regulate genes in response to changes in their environment? Explain how E.coli utilizes lactose.

a. Negative control: a repressor protein binds to DNA and blocks transcription b. Positive control: an activator protein binds to DNA and activates transcription c. Induction: a small effector molecule activates transcription d. Repression: a small effector molecule prevents transcription

Match each mechanism for the regulation of gene expression with the proper description. Negative control Positive control Induction Repression

-Regulation of the lac operon allows E. coli to conserve energy, making proteins for lactose utilization only when needed -The lac operon is inducible (normally "off", turned "on" as needed) and allolactose is an inducer (effector that increases transcription)

What does regulation of the lac operon allow E. coli to do? What is the lac operon usually described as? What is allolactose described as? (BACTERIA)

-•The lac operon includes the promoter (lacP), three structural genes (lacZ, lacY, lacA), the operator (lacO) which is a repressor binding site, and the CAP site which is an activator binding site

What does the lac operon include? (BACTERIA)

-•The lacI gene encodes the lac repressor, and it is constitutively expressed at a low level -In the absence of lactose, the lac repressor binds the operator and prevents RNA polymerase from transcribing the structural genes

What does the lacl gene encode? What does the lac repressor do? (BACTERIA)

-•For multicellular organisms that progress through developmental stages, certain genes are expressed at particular stages -•For example, the expression of hemoglobin subunits changes during embryonic, fetal, and newborn developmental stages -Embryonic and fetal forms of hemoglobin have a higher affinity for oxygen than adult hemoglobin, which allows the developing offspring to take oxygen from the maternal bloodstream

How does eukaryotic gene regulation enable multicellular organisms to proceed through developmental stages? Name an example.

genes

So that the proteins they specify are produced at appropriate times and in specific amounts, most_______ in all species are regulated.

it would be expressed in the presence or absence of lactose in the environment

Suppose that a mutation in the lacI gene prevented the lac repressor from being made. How would this mutation affect the expression of the lac operon?

-For protein-encoding genes in bacteria, gene expression can be regulated during transcription, translation, or post-translation (ex: feedback inhibition of enzymes)

When can gene expression be regulated for protein-encoding genes in bacteria?

-For protein-encoding genes in eukaryotes, gene expression can be regulated during transcription, RNA modification, translation, or post-translation

When can gene expression be regulated for protein-encoding genes in eukaryotes?

IRE; iron

When the IRP is bound to Blank______, translation is blocked; when the IRP is bound to Blank______, translation proceeds.

cAMP, promoter

When_____ binds to CAP, the resulting complex binds to the CAP site near the lac _______. This causes a bend in the DNA that enhances the ability of RNA polymerase to bind, and so the transcription rate is increased.

1. A small amount of lactose is transported into the cytoplasm via lactose permease, and some is converted to allolactose by the β-galactosidase enzyme 2.Allolactose levels rise and allolactose (a small effector) binds to the lac repressor, causing a conformational change that prevents the repressor from binding the operator 3.RNA polymerase transcribes the lacZ, lacY, and lacA genes at a high rate 4.Translation produces associated proteins

What happens when E.coli is exposed to lactose? (BACTERIA)

-(catabolite activator protein) is an activator of the lac operon -CAP is controlled by a small effector, cyclic AMP (cAMP), which is produced from ATP -The cAMP-CAP complex binds to the CAP site and enhances the ability of RNA polymerase to bind the promoter The level of cAMP, and associated CAP activity, is influenced by glucose Glucose present---> low cAMP Glucose absent --->high cAMP

What is CAP? What is CAP controlled by? What does the cAMP-CAP complex do? What influences the level of cAMP and assoctated CAP activity? (BACTERIA)

When CAP and cAMP bind to the CAP site, this enhances binding of RNA polymerase to the promoter site.

How do CAP and cAMP increase the transcription of the lac operon?