Chapter 13

how are nucleosomes altered during gene transcription

???? depending on the locations/arrangements of nucleosomes, a region containing a gene may be in a closed conformation and transcription may be difficult or impossible. transcription requires a change in chromatin structure that allows transcription factors to gain access to bind to the DNA in the promoter region.

how does RNA polymerase and general transcription factors initiate transcription at the core promoter

????RNA polymerase 2 and GTFs must come together at the TATA box of the core of the promoter, so transcription can be initiated series of interactions occurs between these proteins so RNA polymerase 2 can bind to the DNA.

general transcription factors (GTFs)

______ are needed for RNA polymerase 2 to bind to the core promoter forming a pre initiation complex

operons

allow for control of genes with a common function

various ways that organisms benefit from gene regulation

conserves energy (proteins that are encoded by genes are produced only when needed). ensures that genes are expressed in the appropriate cell types and at the correct stage of development eukaryotic gene regulation enables multicellular organisms to proceed through developmental stages gene regulation plays a vital role in ensuring that an embryo and fetus get the proper amount of oxygen

small effector molecules

control the ability of regulatory transcription factors to bind to DNA

eukaryote gene regulation

enables gene products to reproduced at different developmental stages

combinatorial control

eukaryotic genes experience _______ meaning that many factors control the expression of a single gene

lac operon

example of an inducible operon

encode proteins

for genes that ______ the regulation of gene expression can occur at any of the steps that are needed to produce a functional protein

where does gene regulation occur in the pathway of gene expression for eukaryotes

in ______ gene regulation occurs at many levels including transcription, RNA modification, translation, and after translation is completed

eukaryotes

in _______ gene regulation leads to the production of different cell types, such as neurons, muscle cells, and skin cells, within an organism

combinational control

most eukaryotic genes, particularly those found in multi-cellular species are regulated by many factors this phenomenon is called ______ because the combo of many factors determines the expression of any given gene

vary

most genes are regulated so the level of gene expression can _____ under different conditions

______ regulate genes to respond to changes in the environment

prokaryotes

transcriptional regulation

prominent form of gene regulation for both bacteria and eukaryotes

activators and repressors

regulate RNA polymerase 2 by affecting the function of TF2D (a GTF) or mediator, a protein complex that wraps around RNA polymerase 2

lac repressor

the ______ exerts negative control by binding to the operator site and preventing RNA polymerase from transcribing the operon. when allolactose binds to the repressor, a conformational change occurs that prevents the repressor from binding to the operator site so transcription can proceed

repressible

trp operon is considered to be a _______ operon because its small effector molecule, namely tryptophan represses transcription

genes that are not produced at certain times

unregulated

gene regulation

_____ has a dramatic influence on the ability of organisms to respond to environmental changes, produce different types of cells, and progress through developmental stages

compare and contrast how activators, coactivators, repressors, TF2D, and mediator play a role in gene regulation

activators and repressors bind to enhancers or silencer and regulate the rate of transcription of genes activators and repressors affect the function of GTFs which controls gene regulation An activator may improve the ability of a GTF, transcription factor 2 D (TF2D) to initiate transcription Repressors may bind to a silencer and inhibit the function of TF2D.. some repressors exert their effects by preventing the binding of TF2D to the TATA box or inhibiting the ability of TF2D to assemble other GTFs and RNA polymerase 2 at the core promoter

eukaryotic promoters

consist of a core promoter (containing a TATA box and transcriptional start site) and regulatory elements, such as enhancers or silencers that regulate the rate of transcription

eukaryotic genes

for _______ a pre initiation complex forms at a nucleosome free region. during elongation, nucleosomes are displaced ahead of RNA polymerase and re-form after RNA polymerase has passed. DNA methylation, which occurs at CpG islands near promoters, usually inhibits transcription by (1) preventing the binding of activator proteins or (2) promoting the binding of proteins that inhibit transcription

gene products

gene regulation ensures that _____ are made only when they are needed for example synthesis of the ____ needed for the lactose utilization in bacteria

alternative splicing

in _____ a single type of pre-mRNA can be spliced in more than one way, producing polypeptides with somewhat different sequences. this is a common way for complex eukaryotes to increase the size of their proteomes

where does gene regulation occur in the pathway of gene expression for bacteria

in _____ gene regulation most commonly occurs at the level of transcription, which means that _____ regulate how much mRNA is made from genes

bacteria

in ______ gene regulation commonly occurs at the level of transcription which means that_____ regulate how much mRNA is made from genes second way for ____ to regulate gene expression is to control the ability of an mRNA to be translated into protein

eukaryotes

in _________ gene regulation occurs at many different levels, including transcription, RNA modification, translation, and after is translation is completed

glucose

inhibits cAMP production, which in turn inhibits the expression of the lac operon, because CAP cannot bind to the CAP site. This form of regulation provides bacteria with a more efficient utilization of their resources because they use one sugar at a time

transcriptional regulation in bacteria

involves regulatory transcription factors proteins

inducible

lac operon is categorized as an ________ operon because allolactose, its small effector molecule induces transcription

how is the trp operon under negative control

under negative control by a repressor protein the binding of the repressor to the trp operator site inhibits transcription extra info: when the tryptophan level within the cell is high, tryptophan acts as a small effector molecule, or corepressor, by binding to the trp repressor protein This causes a conformational change in the repressor that allows it to bind to the trp operator site, inhibit the ability of RNA polymerase to transcribe the operon (negative control)

all organisms

______ can regulate gene expression at a variety of levels, including transcription, translation, and post-translation. Eukaryotes also regulate RNA modification

positive control

_______ of the lac operon occurs when the catabolite activator protein (CAP) binds to the CAP site in the presence of cAMP. this causes a bend in the DNA, which promotes the binding of RNA polymerase to the promoter

lac repressor, trp repressor

________ binds to its operator in the absence of its small effector molecule whereas the trp repressor binds to its operator only in the presence of its small effector molecule.

Explain how DNA methylation affects transcription

inhibits the transcription of eukaryotic genes particularly when it occurs in the vicinity of the promoter it can inhibit transcription in 2 ways may prevent an activator from binding to an enhancer element, thus inhibiting the initiation of transcription it can inhibit transcription is by altering chromatin structure

some genes are _____ (only produced at certain times)

regulated

process of alternative splicing and how it increases protein diversity

a form of gene regulation that allows an organism to use the same gene to make different proteins at different stages of development, in different cell types and or in response to a change in environmental conditions an advantage of this process is that 2 or more different polypeptides can be derived from a single gene which increases the size of a proteome while minimizing the size of the genome

how are regulatory transcription factors involved in the regulation of transcription

regulatory transcription factors either increase or decrease the rate of transcription

repressors and activators

regulatory transcription factors that bind to the DNA and affect the transcription of genes

constitutive genes

relatively constant levels of expression in all conditions over time encode proteins that are constantly required for the survival of an organism

how are small effector molecules involved in the regulation of transcription

small effector molecule exerts its affects by binding to a regulatory transcription factor and causing a conformational change in the protein- effect of conformational change determines whether or not the protein can bind to the DNA when small effector molecule is not present in the cytoplasm, the repressor binds to the DNA and inhibits transcription when small effector molecule is found in the cytoplasm it will bind to the repressor and cause a conformational change that inhibits the ability of the protein to bind to the DNA. (Transcription can occur because the repressor is not able to bind to the DNA).

organization of the lac operon and how is it under negative and positive control

operon organization allows a bacterium to coordinately regulate a group of genes that encode proteins whose functions are used in a common pathway contains the genes for the proteins that allow it to metabolize lactose lac operon is under negative control by a repressor protein (because once bound the lac repressor prevents RNA polymerase from transcribing the lacZ, lacY, and lacA genes. lac repressor binds to the operator site and inhibits transcription lac operon is under positive control by an activator protein, the catabolite activator protein (CAP). gene regulation involving CAP and cAMP is an example of positive control when cAMP binds to CAP, the cAMP-CAP complex binds to the CAP site near the lac promoter, which causes a bend in the DNA that enhances the ability of RNA polymerase to bind to the promoter, in this way rate of transcription is increased