Biology I- unit 3: ch 11

Methylation can inhibit transcription in __ ways.

2

In mammals __% of DNA is methylated

5

TATA box

5'-TATAAAA-3' , 25 base pairs up stream from transcriptional start site, and determines precise starting point for transcription

Short-interfering RNAs

A class of double stranded RNA molecules, 20-25 base pairs in length that operate within the RNA interference pathway. Also called silencing RNA

The term combinatorial control refers to the observation that

A combination of different factors may regulate the expression of a given gene

The core promoter for eukaryotic structural genes usually contains

A transcriptional start site, and a TATA box

Chromatin

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

Activators

Activator proteins stimulate RNA polymerase to initiate transcription

Transcription factors that bind to DNA and stimulate transcription are

Activators

_______ increase the rate of transcription(positive control)

Activators

For active eukaryotic genes, the core promoter is found at a nucleosome-free region (NFR). This NFR region is needed so that

Activators can promote the formation of a preinitiation complex

Unmethylated CpG islands are correlated with ______ genes

Active

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.

An operon, a polycistronic

______ gene regulation responds to changes in the environment. Example: escherichia coli & lactose

Bacterial

1. Lactose becomes available in the environment of the the bacterium 2. Due to gene regulation, the bacterium increases production of the lactose permease and B-Galactosidase proteins 3. The bacterium readily uses the lactose until it is gone 4. Most proteins involved with the use of lactose are degraded These are the steps of what?

Bacterial gene regulation

B-galactosidase

Breaks down lactose

Alternative splicing

Causes mRNAs to contain different patterns of exons

A chromatin-remodeling complex may

Change the locations of nucleosomes, exchange standard histones for histones variants, evict histones

Proteins are recruited to loosen DNA compaction - the _______ ______ _______

Chromatin remodeling complex

________ _______ ________ includes change in nucleosome position, histone eviction, and replacement with variant histones

Chromatin remodeling complex

Transcription is difficult or impossible in the _______ conformation of tightly packed chromatin

Closed

Activators Repressors Modulation Chromatin DNA methylation These are all ______ _______ of transcription

Combinatorial control (many factors)

DNA is associated with proteins to form ______ _______

Compact chromatin

Genes that are expressed at all times at relatively constant levels are known as _____ genes.

Constitutive

_________ genes are unregulated and have essentially constant levels of expression.

Constitutive

____ _______ are near promoters in vertebrates and plants.

CpG islands

Some activators ______ DNA compaction near a gene

Diminish

There are two kind of _______ in regulatory transcription factors. 1 site where protein binds to DNA, 1 site specifically for small effector molecules

Domains

Activators bind to DNA regions called ________

Enhancers

______ gene regulation involves, cell differentiation, the necessary production of different cell types in an organism. And all of the organisms cells contain the same genome but express different proteomes due to gene regulation which has different proteins as well as different amounts of the same protein.

Eukaryotic

In regulation of RNA processing and translation in eukaryotes the added benefits include; produce more than one mRNA transcript from a single gene (gene encodes 2 or more polypeptides) & _____ regulation is achieved by controlling steps after RNA transcript made.

Faster

When iron is abundant in the cytosol the iron binds directly to IRP and prevents it from binding to the IRE, and ferritin mRNA is translated to make more ferritin protein. This is ______ than transcriptional regulation which would require gene activation and transcription prior to the synthesis of more ferritin protein

Faster

To prevent toxicity, mammalian cells synthesize a protein called _______, which forms a hollow, spherical complex that can store excess iron.

Ferritin

In transcriptional regulation most do not bind directly to RNA polymerase II, instead they influence the function of _______

General transcription factors (GTFs)

When tryptophan levels are _____, tryptophan turns off the trp operon.

High

Activators

Increase the rate of transcription.. proteins stimulate RNA polymerase to initiate transcription

In the lac repressor operons for catabolism are often _______(allolactose induces transcription) and the genes are turned off unless the appropriate substance is available.

Inducible

1. The methylation of CpG islands may prevent an activator from binding to an enhancer element 2. Converting chromatin from an open to a closed conformation These are the two ways methylation can ______ transcription.

Inhibit

DNA methylation usually _______ transcription.

Inhibits

The binding is IRP to the IRE ______ translation of the ferritin mRNA

Inhibits

The binding of repressor to trp operator site ______ tranacription

Inhibits

Roles of transcription factors in eukaryotes have some of the same principles as in prokaryotes, activator and repressor proteins influence ability of RNA polymerase to initiate transcription and is regulated by small effector proteins. However there are many differences such as genes being almost always organized indictable and regulation being more ________.

Intricate

____ is a vital cofactors for many cellular enzymes. However, it is toxic at high levels

Iron

When iron in cytosol is low and ferritin is not needed IRP binds to a response element within the ferritin mRNA known as the ______ _______ _______

Iron regulatory element (IRE)

mRNA that encodes ferritin is controlled by a RNA binding protein known as ______ _______ _______

Iron regulatory protein (IRP)

An miRNA usually

Is not a perfect match to an mRNA and inhibits translation of an mRNA

Let's suppose that a mutation in the lacl gene prevented the lac repress or from being made. How would this mutation affect the expression of the lac operon?

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

___ repressor binds to its operator in the absence of its small effector molecule.

Lac

When lactose is available, 2 proteins are made, what are they?

Lactose permease and B-Galactoseidase

Gene regulation is an important process that allows organisms to proceed through developmental stages. This phase refers to which biology principle?

Living organisms grow and develop

When tryptophan levels are _____, trp repressor cannot bind to operator site and operon genes are transcribed.

Low

The iron regulatory protein (IPR) binds to the IRE when iron levels are ______ and ______ translation of ferritin mRNA.

Low, inhibits

________-____-_________ proteins bind to methylated sequences and recruit proteins that condense the chromatin

Methyl-CpG-binding

In DNA methylation DNA ____________ attaches to methyl groups. This is common in some eukaryotes but not all.

Methyltransferase

Transcriptional regulation regulates rate of transcription of a ______ gene

Nearby

When lactose levels drop, the proteins are either (made or not made)

Not made

Access to the DNA is allowed in the loosely packed _____ conformation.

Open

Chromatin _______ affects gene expression

Packing

Cytosine and guanine are connected by ________ bonds

Phosphodiester

In _________ _______ RNA Pol II transcribed genes that encode proteins. It requires 5 different general transcription factors (GTFs) to initiate transcription and they come together at the core promoter.

Preinitiation complex

Regulation of transcription in bacteria involves regulatory transcription factors which bind to DNA in the vicinity of a _______ & affects the rate of transcription of 1 or more nearby genes. It also has repressors and activators.

Promoter

Most genes are regulated to ensure _______ are produced at the correct time and amount; it saves energy by producing only when needed.

Proteins

Alternative splicing increases the ______ size without increasing the total number of genes. The general trend is that less complex organisms tend to have fewer genes and that the frequency of alternative splicing increases with more biological complexity.

Proteome

____________ is not considered a common level of gene regulation in bacteria?

RNA processing

In eukaryotes, gene expression is commonly regulated at the level of ____ ________ and ________

RNA processing and translation.

Regulatory or response elements

Recognized by regulatory proteins that control initiation of transcription, and has enhancers and silencers

Gene regulation

Refers to the ability of cells to control their level of gene expression.

_______ genes contain methylated CpG islands

Repressed

In the trp repressor, operons for anabolism are often _______(tryptophan represses transcription) and when enough of the product is present, genes are turned off to prevent over production.

Repressible

Trp operon is regulated by a _______ protein encoded by trpR gene.

Repressor

Repressors

Repressor proteins inhibit RNA polymerase from initiating transcription

________ inhibit transcription(negative control)

Repressors

Alternative splicing

Results in two or more mRNAs from a single type or pre-mRNA, in erases the size of the proteome without increasing the size of a genome, is more prevalent in complex eukaryotes

Alternative splicing of pre-mRNAs allow ______ genes to make different proteins... at different stages of development, in different cell types, and in response to a change in the environmental conditions

Same

Repressors bind to DNA regions called _______

Silencers

Transcriptional regulation also involves _____ effector molecules

Small

______ ________ ________bind to regulatory transcription factor and causes conformational change. Change weather or not regulatory transcription factor can bind to DNA

Small effector molecules

Modulation

Small effector molecules, protein-protein interactions, and covalent modifications can modulate activators and repressors

In eukaryotes, a pre-mRNA transcript is processed before it becomes a mature mRNA, when a pre-mRNA has multiple introns and exons ________ may occur in more than one way.

Splicing

Three features of most promoters

TATA box Transcriptional Start Site Regulatory or Response Elements

A key difference between the trp repression and the lac depressor is that

The binding of a small effector molecule to the trp repressor causes it to bind to its operator, but the binding of a small effector molecule to the lac repressor prevents it from binding to its operator.

Proteomes

The entire complement of proteins that is or can be expressed by a cell, tissue or organism

cell differentiation

The necessary production of different cell types in an organism

For the lac operon, what would be the expected effects of a mutation in the operator that prevented the binding of the repressor protein?

The operon would always be turned on, except when glucose is present

Gene expression

The process by which possession of a gene leads to the appearance in the phenotype of the corresponding character

A reason for gene regulation is

To respond to environment changes, to make proteins in specific cell types, to make proteins at specific stages of development

Gene regulation occurs at different points, bacterial gene regulation most commonly occurs at the level of _________(governs how much mRNA is made), it can also control the rate of translation (governs protein production), and can be regulated at post-translation level (governs amount or function of proteins)

Transcription

The most common point of gene regulation in bacteria is

Transcription

In eukaryotic gene regulation __________ regulation is very common, RNA processing, translation, and post translation occur.

Transcriptional

1. An activator binds to an enhancer, a coactivator then binds to the activator 2. The activator/coactivator complex enhances the ability of a GTF called TFHD to bind to the TATA box 3. TFHD promotes the assembly of the preinitiation complex These are the steps of what?

Transcriptional regulation

Another way to regulate translation involves RNA-binding proteins that directly affect ________ _________

Translational initiation

Lactose permease

Transports lactose into the cell

___ repressor binds to its operator only in the presence of its small effector molecule.

Trp

___ _______ in E. coli, encodes enzymes required to make the amino acid tryptophan

Trp operon

________ acts as a small repressor molecule or corepressor

Tryptophan

Respressible operons

Tryptophan represses transcription.

DNA methylation

Usually inhibits transcription, either by blocking an activator protein or by recruiting proteins that make DNA more compact

DNA methylation

Usually inhibits transcription, either by blocking an activator proteins or by recruiting proteins that make DNA more compact

Gene regulation provides a way for cells to avoid ______ ______ & to make proteins only when they are needed.

Wasting energy

Transcriptional start site

Where transcription begins, With TATA box forms a core promoter, If it's by itself it results in low level basal transcription

Lac operon

a gene system whose operator gene and three structural genes control lactose metabolism in E. coli