Regulation of Transcription

Transcription Transcription Transcription of genetic information is the first step in gene expression. Transcription is the process by which DNA is used as a template to make mRNA. This process is divided into 3 stages: initiation, elongation, and termination. Stages of Transcription is the process by which DNA DNA The molecule DNA is the repository of heritable genetic information. In humans, DNA is contained in 23 chromosome pairs within the nucleus. The molecule provides the basic template for replication of genetic information, RNA transcription, and protein biosynthesis to promote cellular function and survival. DNA Types and Structure is used as a template to make mRNA via an enzyme called RNA RNA Ribonucleic acid (RNA), like deoxyribonucleic acid (DNA), is a polymer of nucleotides that is essential to cellular protein synthesis. Unlike DNA, RNA is a single-stranded structure containing the sugar moiety ribose (instead of deoxyribose) and the base uracil (instead of thymine). RNA generally carries out the instructions encoded in the DNA but also executes diverse non-coding functions. RNA Types and Structure polymerase. Transcription Transcription Transcription of genetic information is the first step in gene expression. Transcription is the process by which DNA is used as a template to make mRNA. This process is divided into 3 stages: initiation, elongation, and termination. Stages of Transcription is an important step in gene expression, and as such, it is highly regulated. In prokaryotes, genes are grouped together into DNA DNA The molecule DNA is the repository of heritable genetic information. In humans, DNA is contained in 23 chromosome pairs within the nucleus. The molecule provides the basic template for replication of genetic information, RNA transcription, and protein biosynthesis to promote cellular function and survival. DNA Types and Structure sequences, known as operons, that can be induced or repressed to regulate expression of these genes together. Regulation in eukaryotes is much more complicated and involves a number of transcription factors and regulatory sequences of DNA DNA The molecule DNA is the repository of heritable genetic information. In humans, DNA is contained in 23 chromosome pairs within the nucleus. The molecule provides the basic template for replication of genetic information, RNA transcription, and protein biosynthesis to promote cellular function and survival. DNA Types and Structure. Epigenetic mechanisms, including how the DNA DNA The molecule DNA is the repository of heritable genetic information. In humans, DNA is contained in 23 chromosome pairs within the nucleus. The molecule provides the basic template for replication of genetic information, RNA transcription, and protein biosynthesis to promote cellular function and survival. DNA Types and Structure is packaged, also play a role in transcription regulation by controlling what segments of DNA DNA The molecule DNA is the repository of heritable genetic information. In humans, DNA is contained in 23 chromosome pairs within the nucleus. The molecule provides the basic template for replication of genetic information, RNA transcription, and protein biosynthesis to promote cellular function and survival. DNA Types and Structure are available to the RNA RNA Ribonucleic acid (RNA), like deoxyribonucleic acid (DNA), is a polymer of nucleotides that is essential to cellular protein synthesis. Unlike DNA, RNA is a single-stranded structure containing the sugar moiety ribose (instead of deoxyribose) and the base uracil (instead of thymine). RNA generally carries out the instructions encoded in the DNA but also executes diverse non-coding functions. RNA Types and Structure polymerase.

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Editorial responsibility: Stanley Oiseth, Lindsay Jones, Evelin Maza

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Overview

Review of transcription

Definition:

  • Central dogma: To express a gene, DNA DNA The molecule DNA is the repository of heritable genetic information. In humans, DNA is contained in 23 chromosome pairs within the nucleus. The molecule provides the basic template for replication of genetic information, RNA transcription, and protein biosynthesis to promote cellular function and survival. DNA Types and Structure is transcribed into RNA RNA Ribonucleic acid (RNA), like deoxyribonucleic acid (DNA), is a polymer of nucleotides that is essential to cellular protein synthesis. Unlike DNA, RNA is a single-stranded structure containing the sugar moiety ribose (instead of deoxyribose) and the base uracil (instead of thymine). RNA generally carries out the instructions encoded in the DNA but also executes diverse non-coding functions. RNA Types and Structure, which is then translated into a protein (or a protein fragment known as a polypeptide).
  • Transcription Transcription Transcription of genetic information is the first step in gene expression. Transcription is the process by which DNA is used as a template to make mRNA. This process is divided into 3 stages: initiation, elongation, and termination. Stages of Transcription is the process by which DNA DNA The molecule DNA is the repository of heritable genetic information. In humans, DNA is contained in 23 chromosome pairs within the nucleus. The molecule provides the basic template for replication of genetic information, RNA transcription, and protein biosynthesis to promote cellular function and survival. DNA Types and Structure is used as a template to make mRNA.
  • RNA RNA Ribonucleic acid (RNA), like deoxyribonucleic acid (DNA), is a polymer of nucleotides that is essential to cellular protein synthesis. Unlike DNA, RNA is a single-stranded structure containing the sugar moiety ribose (instead of deoxyribose) and the base uracil (instead of thymine). RNA generally carries out the instructions encoded in the DNA but also executes diverse non-coding functions. RNA Types and Structure polymerase: enzyme that “reads” the DNA DNA The molecule DNA is the repository of heritable genetic information. In humans, DNA is contained in 23 chromosome pairs within the nucleus. The molecule provides the basic template for replication of genetic information, RNA transcription, and protein biosynthesis to promote cellular function and survival. DNA Types and Structure template strand and creates the mRNA
  • Promoter sequence: sequences of DNA DNA The molecule DNA is the repository of heritable genetic information. In humans, DNA is contained in 23 chromosome pairs within the nucleus. The molecule provides the basic template for replication of genetic information, RNA transcription, and protein biosynthesis to promote cellular function and survival. DNA Types and Structure just upstream from the target gene that indicate the start site and direction of the gene

DNA DNA The molecule DNA is the repository of heritable genetic information. In humans, DNA is contained in 23 chromosome pairs within the nucleus. The molecule provides the basic template for replication of genetic information, RNA transcription, and protein biosynthesis to promote cellular function and survival. DNA Types and Structure:

DNA DNA The molecule DNA is the repository of heritable genetic information. In humans, DNA is contained in 23 chromosome pairs within the nucleus. The molecule provides the basic template for replication of genetic information, RNA transcription, and protein biosynthesis to promote cellular function and survival. DNA Types and Structure is a double-helix molecule made up of 2 antiparallel strands. DNA DNA The molecule DNA is the repository of heritable genetic information. In humans, DNA is contained in 23 chromosome pairs within the nucleus. The molecule provides the basic template for replication of genetic information, RNA transcription, and protein biosynthesis to promote cellular function and survival. DNA Types and Structure has a structure that looks like a twisted ladder.

  • The “sides” of each ladder are made up of alternating deoxyribose (a 5-carbon sugar) and phosphate molecules.
  • The “rungs” of the ladder are made up of matched nitrogen-containing molecules called nucleotides, frequently referred to as “bases.”
  • DNA DNA The molecule DNA is the repository of heritable genetic information. In humans, DNA is contained in 23 chromosome pairs within the nucleus. The molecule provides the basic template for replication of genetic information, RNA transcription, and protein biosynthesis to promote cellular function and survival. DNA Types and Structure base pairs:
    • Guanine (G), cytosine (C), adenine (A), and thymine (T)
    • G pairs with C (and vice versa) via 3 hydrogen bonds.
    • A pairs with T (and vice versa) via 2 hydrogen bonds.
    • These base pairs can be “read” as a string of letters(e.g., GTATCGA).
    • This string of letters is the “code,” or instruction manual, that is ultimately used to create proteins.
  • Grooves:
    • The DNA DNA The molecule DNA is the repository of heritable genetic information. In humans, DNA is contained in 23 chromosome pairs within the nucleus. The molecule provides the basic template for replication of genetic information, RNA transcription, and protein biosynthesis to promote cellular function and survival. DNA Types and Structure helix is asymmetrical as it rotates.
    • This rotation creates major and minor grooves between coils. 
    • The major groove is wide enough that many regulatory proteins can bind directly to the DNA DNA The molecule DNA is the repository of heritable genetic information. In humans, DNA is contained in 23 chromosome pairs within the nucleus. The molecule provides the basic template for replication of genetic information, RNA transcription, and protein biosynthesis to promote cellular function and survival. DNA Types and Structure through this space.

RNA RNA Ribonucleic acid (RNA), like deoxyribonucleic acid (DNA), is a polymer of nucleotides that is essential to cellular protein synthesis. Unlike DNA, RNA is a single-stranded structure containing the sugar moiety ribose (instead of deoxyribose) and the base uracil (instead of thymine). RNA generally carries out the instructions encoded in the DNA but also executes diverse non-coding functions. RNA Types and Structure:

  • A single-stranded molecule made up of alternating ribose (a 5-carbon sugar) and phosphate molecules
  • Each ribose is bound to an RNA RNA Ribonucleic acid (RNA), like deoxyribonucleic acid (DNA), is a polymer of nucleotides that is essential to cellular protein synthesis. Unlike DNA, RNA is a single-stranded structure containing the sugar moiety ribose (instead of deoxyribose) and the base uracil (instead of thymine). RNA generally carries out the instructions encoded in the DNA but also executes diverse non-coding functions. RNA Types and Structure nucleotide:
    • Guanine (G), cytosine (C), adenine (A), and uracil (U)
    • Note that instead of thymine, A binds with U (and vice versa) via 2 hydrogen bonds.
Transcription nucleic-acids

Structure of RNA RNA Ribonucleic acid (RNA), like deoxyribonucleic acid (DNA), is a polymer of nucleotides that is essential to cellular protein synthesis. Unlike DNA, RNA is a single-stranded structure containing the sugar moiety ribose (instead of deoxyribose) and the base uracil (instead of thymine). RNA generally carries out the instructions encoded in the DNA but also executes diverse non-coding functions. RNA Types and Structure and DNA DNA The molecule DNA is the repository of heritable genetic information. In humans, DNA is contained in 23 chromosome pairs within the nucleus. The molecule provides the basic template for replication of genetic information, RNA transcription, and protein biosynthesis to promote cellular function and survival. DNA Types and Structure

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Overview of transcription regulation

  • Many different types of signals can influence whether or not a particular gene is transcribed. Examples of these signals include:
    • Hormones Hormones Hormones are messenger molecules that are synthesized in one part of the body and move through the bloodstream to exert specific regulatory effects on another part of the body. Hormones play critical roles in coordinating cellular activities throughout the body in response to the constant changes in both the internal and external environments. Hormones: Overview
    • Enzymes Enzymes Enzymes are complex protein biocatalysts that accelerate chemical reactions without being consumed by them. Due to the body's constant metabolic needs, the absence of enzymes would make life unsustainable, as reactions would occur too slowly without these molecules. Basics of Enzymes
    • Pharmaceutical agents
    • The presence or absence of certain nutrients or other molecules (e.g., lactose or tryptophan)
  • Mechanisms of transcription regulation:
    • Controlling access of polymerase to the target DNA DNA The molecule DNA is the repository of heritable genetic information. In humans, DNA is contained in 23 chromosome pairs within the nucleus. The molecule provides the basic template for replication of genetic information, RNA transcription, and protein biosynthesis to promote cellular function and survival. DNA Types and Structure sequence via:
      • Transcriptions factors
      • Enhancers and repressors
      • DNA DNA The molecule DNA is the repository of heritable genetic information. In humans, DNA is contained in 23 chromosome pairs within the nucleus. The molecule provides the basic template for replication of genetic information, RNA transcription, and protein biosynthesis to promote cellular function and survival. DNA Types and Structure packaging
    • Controlling elongation of the RNA RNA Ribonucleic acid (RNA), like deoxyribonucleic acid (DNA), is a polymer of nucleotides that is essential to cellular protein synthesis. Unlike DNA, RNA is a single-stranded structure containing the sugar moiety ribose (instead of deoxyribose) and the base uracil (instead of thymine). RNA generally carries out the instructions encoded in the DNA but also executes diverse non-coding functions. RNA Types and Structure via elongation factors/activators
    • Controlling termination of the polymerase
  • Positive regulation: 
    • Gene expression is increased.
    • Uses positive regulators, activators, or enhancers
  • Negative regulation:
    • Gene expression is decreased.
    • Uses negative regulators, repressors, or insulators.

Regulatory Proteins

Transcription Transcription Transcription of genetic information is the first step in gene expression. Transcription is the process by which DNA is used as a template to make mRNA. This process is divided into 3 stages: initiation, elongation, and termination. Stages of Transcription regulation is mediated in part by regulatory proteins that can bind to the DNA DNA The molecule DNA is the repository of heritable genetic information. In humans, DNA is contained in 23 chromosome pairs within the nucleus. The molecule provides the basic template for replication of genetic information, RNA transcription, and protein biosynthesis to promote cellular function and survival. DNA Types and Structure in its helical form (unwinding is not necessary) and regulate the transcriptional activity of RNA RNA Ribonucleic acid (RNA), like deoxyribonucleic acid (DNA), is a polymer of nucleotides that is essential to cellular protein synthesis. Unlike DNA, RNA is a single-stranded structure containing the sugar moiety ribose (instead of deoxyribose) and the base uracil (instead of thymine). RNA generally carries out the instructions encoded in the DNA but also executes diverse non-coding functions. RNA Types and Structure polymerase.

Overview of regulatory proteins

  • Regulate transcription by binding to regulatory sequences of the DNA DNA The molecule DNA is the repository of heritable genetic information. In humans, DNA is contained in 23 chromosome pairs within the nucleus. The molecule provides the basic template for replication of genetic information, RNA transcription, and protein biosynthesis to promote cellular function and survival. DNA Types and Structure:
    • Promoters
    • Enhancer sequences
    • Insulator sequences 
  • Regulatory proteins have different domains:
    • DNA DNA The molecule DNA is the repository of heritable genetic information. In humans, DNA is contained in 23 chromosome pairs within the nucleus. The molecule provides the basic template for replication of genetic information, RNA transcription, and protein biosynthesis to promote cellular function and survival. DNA Types and Structure binding domain: portion of the protein that binds to the DNA DNA The molecule DNA is the repository of heritable genetic information. In humans, DNA is contained in 23 chromosome pairs within the nucleus. The molecule provides the basic template for replication of genetic information, RNA transcription, and protein biosynthesis to promote cellular function and survival. DNA Types and Structure
    • Functional domain: portion of the protein that interacts with the DNA DNA The molecule DNA is the repository of heritable genetic information. In humans, DNA is contained in 23 chromosome pairs within the nucleus. The molecule provides the basic template for replication of genetic information, RNA transcription, and protein biosynthesis to promote cellular function and survival. DNA Types and Structure and/or other proteins to carry out its function
  • Regulatory proteins typically contain 1 of 3 primary DNA DNA The molecule DNA is the repository of heritable genetic information. In humans, DNA is contained in 23 chromosome pairs within the nucleus. The molecule provides the basic template for replication of genetic information, RNA transcription, and protein biosynthesis to promote cellular function and survival. DNA Types and Structure binding motifs:
    • Helix–turn–helix
    • Zinc fingers
    • Leucine zippers

Helix–turn–helix

Regulatory proteins with the helix–turn–helix DNA DNA The molecule DNA is the repository of heritable genetic information. In humans, DNA is contained in 23 chromosome pairs within the nucleus. The molecule provides the basic template for replication of genetic information, RNA transcription, and protein biosynthesis to promote cellular function and survival. DNA Types and Structure binding motif have the following characteristics:

  • Structure: 2 helical segments oriented perpendicular to one another and connected to each other via a looping segment of protein
  • Looping segment contains the functional domain
  • Proteins bind the DNA DNA The molecule DNA is the repository of heritable genetic information. In humans, DNA is contained in 23 chromosome pairs within the nucleus. The molecule provides the basic template for replication of genetic information, RNA transcription, and protein biosynthesis to promote cellular function and survival. DNA Types and Structure through the major groove
  • Often work in pairs
  • A subset of helix–turn–helix proteins are known as homeodomain proteins, which are regulatory proteins often involved in development.
2 helix–turn–helix regulatory proteins bound to dna in the major groove

2 helix–turn–helix regulatory proteins bound to DNA DNA The molecule DNA is the repository of heritable genetic information. In humans, DNA is contained in 23 chromosome pairs within the nucleus. The molecule provides the basic template for replication of genetic information, RNA transcription, and protein biosynthesis to promote cellular function and survival. DNA Types and Structure in the major groove

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Zinc finger

  • 3 finger-like structures interact with DNA DNA The molecule DNA is the repository of heritable genetic information. In humans, DNA is contained in 23 chromosome pairs within the nucleus. The molecule provides the basic template for replication of genetic information, RNA transcription, and protein biosynthesis to promote cellular function and survival. DNA Types and Structure through the major groove.
  • Uses zinc to closely associate with the DNA DNA The molecule DNA is the repository of heritable genetic information. In humans, DNA is contained in 23 chromosome pairs within the nucleus. The molecule provides the basic template for replication of genetic information, RNA transcription, and protein biosynthesis to promote cellular function and survival. DNA Types and Structure
  • This same motif is seen in steroid receptors, which contain a zinc-finger domain → allows the activated receptors to bind directly to the DNA DNA The molecule DNA is the repository of heritable genetic information. In humans, DNA is contained in 23 chromosome pairs within the nucleus. The molecule provides the basic template for replication of genetic information, RNA transcription, and protein biosynthesis to promote cellular function and survival. DNA Types and Structure and directly affect transcription
The zinc-finger binding motif

The zinc-finger binding motif:
Often used in steroid receptor binding mechanisms

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Leucine zipper

Leucine zippers consist of 2 proteins, each containing a helical subunit and a hydrophobic subunit.

  • The helical subunits:
    • Enter the DNA DNA The molecule DNA is the repository of heritable genetic information. In humans, DNA is contained in 23 chromosome pairs within the nucleus. The molecule provides the basic template for replication of genetic information, RNA transcription, and protein biosynthesis to promote cellular function and survival. DNA Types and Structure through the major groove
    • Associate with opposite ends of the DNA DNA The molecule DNA is the repository of heritable genetic information. In humans, DNA is contained in 23 chromosome pairs within the nucleus. The molecule provides the basic template for replication of genetic information, RNA transcription, and protein biosynthesis to promote cellular function and survival. DNA Types and Structure within the groove
  • The hydrophobic subunits:
    • Remain outside the DNA DNA The molecule DNA is the repository of heritable genetic information. In humans, DNA is contained in 23 chromosome pairs within the nucleus. The molecule provides the basic template for replication of genetic information, RNA transcription, and protein biosynthesis to promote cellular function and survival. DNA Types and Structure (because DNA DNA The molecule DNA is the repository of heritable genetic information. In humans, DNA is contained in 23 chromosome pairs within the nucleus. The molecule provides the basic template for replication of genetic information, RNA transcription, and protein biosynthesis to promote cellular function and survival. DNA Types and Structure is hydrophilic)
    • Contain leucine molecules that “zip” the two proteins together
  • Additional portions of the proteins contain functional domains that can then interact with the DNA DNA The molecule DNA is the repository of heritable genetic information. In humans, DNA is contained in 23 chromosome pairs within the nucleus. The molecule provides the basic template for replication of genetic information, RNA transcription, and protein biosynthesis to promote cellular function and survival. DNA Types and Structure or surrounding proteins.
The leucine-zipper binding mot

The leucine-zipper binding motif:
Has 2 subunits that zip together

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Related videos

Prokaryotic Transcription Regulation

Overview

  • Prokaryotic Prokaryotic Prokaryotes are unicellular organisms that include 2 of the 3 domains of life: bacteria and archaea. Prokaryotic cells consist of a single cytoplasm-filled compartment enclosed by a cell membrane and cell wall. Cell Types: Eukaryotic versus Prokaryotic gene expression is regulated primarily at the level of transcription.
  • Prokaryotic Prokaryotic Prokaryotes are unicellular organisms that include 2 of the 3 domains of life: bacteria and archaea. Prokaryotic cells consist of a single cytoplasm-filled compartment enclosed by a cell membrane and cell wall. Cell Types: Eukaryotic versus Prokaryotic genes are organized into groups called operons.
  • Transcription Transcription Transcription of genetic information is the first step in gene expression. Transcription is the process by which DNA is used as a template to make mRNA. This process is divided into 3 stages: initiation, elongation, and termination. Stages of Transcription regulation is primarily through inducing or repressing the operons.
  • Genes are always on in the absence of other factors (e.g., repressors) 

Operons

Operons are clusters of coregulated genes plus all the components that come together to regulate those genes. Operons contain 2 primary regions of DNA DNA The molecule DNA is the repository of heritable genetic information. In humans, DNA is contained in 23 chromosome pairs within the nucleus. The molecule provides the basic template for replication of genetic information, RNA transcription, and protein biosynthesis to promote cellular function and survival. DNA Types and Structure sequences:

  • Regulatory region contains:
    • Promoter: binds sigma factor and RNA RNA Ribonucleic acid (RNA), like deoxyribonucleic acid (DNA), is a polymer of nucleotides that is essential to cellular protein synthesis. Unlike DNA, RNA is a single-stranded structure containing the sugar moiety ribose (instead of deoxyribose) and the base uracil (instead of thymine). RNA generally carries out the instructions encoded in the DNA but also executes diverse non-coding functions. RNA Types and Structure polymerase to initiate transcription
    • Operator: a DNA DNA The molecule DNA is the repository of heritable genetic information. In humans, DNA is contained in 23 chromosome pairs within the nucleus. The molecule provides the basic template for replication of genetic information, RNA transcription, and protein biosynthesis to promote cellular function and survival. DNA Types and Structure sequence that can bind a repressor 
      • Repressor: proteins that prevent RNA RNA Ribonucleic acid (RNA), like deoxyribonucleic acid (DNA), is a polymer of nucleotides that is essential to cellular protein synthesis. Unlike DNA, RNA is a single-stranded structure containing the sugar moiety ribose (instead of deoxyribose) and the base uracil (instead of thymine). RNA generally carries out the instructions encoded in the DNA but also executes diverse non-coding functions. RNA Types and Structure polymerase from moving down the gene 
      • Transcription Transcription Transcription of genetic information is the first step in gene expression. Transcription is the process by which DNA is used as a template to make mRNA. This process is divided into 3 stages: initiation, elongation, and termination. Stages of Transcription is inhibited when repressors bind to their operators.
    • Regulatory gene: genes for an activator or repressor protein
    • Promoter for the regulatory gene
  • Coding region: 
    • Often contains multiple genes for several different proteins
    • These genes are either all turned on or all turned off.
Example of a prokaryotic operon

Example of a prokaryotic operon:
Prokaryotic Prokaryotic Prokaryotes are unicellular organisms that include 2 of the 3 domains of life: bacteria and archaea. Prokaryotic cells consist of a single cytoplasm-filled compartment enclosed by a cell membrane and cell wall. Cell Types: Eukaryotic versus Prokaryotic gene expression is regulated primarily at the level of transcription.
Operons are clusters of coregulated genes in prokaryotes.

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Inducible operons

Inducible operons are operons that are off in the “normal” state and turn on under certain conditions. A common example is the lac operon in Escherichia coli Escherichia coli The gram-negative bacterium Escherichia coli is a key component of the human gut microbiota. Most strains of E. coli are avirulent, but occasionally they escape the GI tract, infecting the urinary tract and other sites. Less common strains of E. coli are able to cause disease within the GI tract, most commonly presenting as abdominal pain and diarrhea. Escherichia coli. Under normal circumstances, E. coli uses glucose for energy. When glucose is unavailable and/or lactose is present, the presence of lactose induces the lac operon:

  • Coding region: contains genes involved in lactose metabolism
  • Regulatory region codes for:
    • A repressor
    • An activator: catabolite activator protein (CAP)
Lac operon

Lac operon:
In the presence of lactose, expression is activated.

Image by Lecturio.

Gene regulation via the lac repressor:

  • Lactose prevents the binding of the repressor to the operator sequence
  • In the presence of lactose: repressor is unable to bind → transcription of the genes can occur
  • When lactose is absent: repressor binds to the operator sequence → transcription is inhibited because the RNA RNA Ribonucleic acid (RNA), like deoxyribonucleic acid (DNA), is a polymer of nucleotides that is essential to cellular protein synthesis. Unlike DNA, RNA is a single-stranded structure containing the sugar moiety ribose (instead of deoxyribose) and the base uracil (instead of thymine). RNA generally carries out the instructions encoded in the DNA but also executes diverse non-coding functions. RNA Types and Structure polymerase is blocked
  • Therefore, the presence of lactose induces the transcription of genes for lactose metabolism.

Gene regulation via the CAP activator:

  • When glucose is low: CAP is produced → binds to the enhancer region (see “Enhancer sequences” below) → activates/accelerates transcription
  • When glucose is abundant: CAP is not produced → transcription is not enhanced

Repressible operons

Repressible operons are operons that are on in the “normal” state and turn off under certain conditions. The trp operon is a common example:

  • Coding region contains several genes that code for enzymes necessary for tryptophan synthesis.
  • :Regulatory region codes for a repressor
    • The repressor requires tryptophan in order to be activated.
    • Without tryptophan, the repressor is inactive.

The default state is for the operon to be on and producing tryptophan.

  • When tryptophan is present:
    • Tryptophan binds to its repressor → repressor is activated
    • The repressor binds to its operator → prevents transcription
    • Result: The presence of tryptophan turns off the genes that would make more tryptophan.
  • When tryptophan is not present:
    • There is no tryptophan to bind to the repressor → the repressor is inactive
    • Repressor cannot bind to the operator → transcription occurs
    • Result: When no tryptophan is present, the genes that code for enzymes to synthesize tryptophan are transcribed.
Trp operon

Trp operon:
Tryptophan activates the repressor.

Image by Lecturio.

Eukaryotic Transcriptional Regulation

Overview

  • Regulation of transcription in eukaryotes is more complex than in prokaryotes because the development of eukaryotes is vastly more complicated. 
  • Eukaryotic Eukaryotic Eukaryotes can be single-celled or multicellular organisms and include plants, animals, fungi, and protozoa. Eukaryotic cells contain a well-organized nucleus contained by a membrane, along with other membrane-bound organelles. Cell Types: Eukaryotic versus Prokaryotic genes are always off in the absence of a multitude of transcription factors that must be recruited. 
  • Eukaryotic Eukaryotic Eukaryotes can be single-celled or multicellular organisms and include plants, animals, fungi, and protozoa. Eukaryotic cells contain a well-organized nucleus contained by a membrane, along with other membrane-bound organelles. Cell Types: Eukaryotic versus Prokaryotic gene expression is regulated at every step of the pathway:
    • DNA DNA The molecule DNA is the repository of heritable genetic information. In humans, DNA is contained in 23 chromosome pairs within the nucleus. The molecule provides the basic template for replication of genetic information, RNA transcription, and protein biosynthesis to promote cellular function and survival. DNA Types and Structure packaging in chromatin
    • Transcription Transcription Transcription of genetic information is the first step in gene expression. Transcription is the process by which DNA is used as a template to make mRNA. This process is divided into 3 stages: initiation, elongation, and termination. Stages of Transcription
    • Posttranscriptional modification
    • Translation Translation Translation is the process of synthesizing a protein from a messenger RNA (mRNA) transcript. This process is divided into three primary stages: initiation, elongation, and termination. Translation is catalyzed by structures known as ribosomes, which are large complexes of proteins and ribosomal RNA (rRNA). Stages and Regulation of Translation
    • Protein modification and degradation
  • Transcription Transcription Transcription of genetic information is the first step in gene expression. Transcription is the process by which DNA is used as a template to make mRNA. This process is divided into 3 stages: initiation, elongation, and termination. Stages of Transcription is regulated primarily by:
    • Transcription Transcription Transcription of genetic information is the first step in gene expression. Transcription is the process by which DNA is used as a template to make mRNA. This process is divided into 3 stages: initiation, elongation, and termination. Stages of Transcription factors
    • Regulatory sequences of DNA DNA The molecule DNA is the repository of heritable genetic information. In humans, DNA is contained in 23 chromosome pairs within the nucleus. The molecule provides the basic template for replication of genetic information, RNA transcription, and protein biosynthesis to promote cellular function and survival. DNA Types and Structure

Transcription Transcription Transcription of genetic information is the first step in gene expression. Transcription is the process by which DNA is used as a template to make mRNA. This process is divided into 3 stages: initiation, elongation, and termination. Stages of Transcription factors

Transcription Transcription Transcription of genetic information is the first step in gene expression. Transcription is the process by which DNA is used as a template to make mRNA. This process is divided into 3 stages: initiation, elongation, and termination. Stages of Transcription factor (TF) is a generic term for proteins necessary for transcription. Each of these factors helps to regulate gene expression.

  • General transcription factors:
    • Bind to the promoter sequence
    • Are required for the binding of RNA RNA Ribonucleic acid (RNA), like deoxyribonucleic acid (DNA), is a polymer of nucleotides that is essential to cellular protein synthesis. Unlike DNA, RNA is a single-stranded structure containing the sugar moiety ribose (instead of deoxyribose) and the base uracil (instead of thymine). RNA generally carries out the instructions encoded in the DNA but also executes diverse non-coding functions. RNA Types and Structure polymerase II to the DNA DNA The molecule DNA is the repository of heritable genetic information. In humans, DNA is contained in 23 chromosome pairs within the nucleus. The molecule provides the basic template for replication of genetic information, RNA transcription, and protein biosynthesis to promote cellular function and survival. DNA Types and Structure to initiate transcription
  • Initiation complex: 
    • The complex of transcription factors and RNA RNA Ribonucleic acid (RNA), like deoxyribonucleic acid (DNA), is a polymer of nucleotides that is essential to cellular protein synthesis. Unlike DNA, RNA is a single-stranded structure containing the sugar moiety ribose (instead of deoxyribose) and the base uracil (instead of thymine). RNA generally carries out the instructions encoded in the DNA but also executes diverse non-coding functions. RNA Types and Structure polymerase II at the promoter sequence
    • Once the initiation complex is assembled on the promoter, transcription can begin.
  • Transcription Transcription Transcription of genetic information is the first step in gene expression. Transcription is the process by which DNA is used as a template to make mRNA. This process is divided into 3 stages: initiation, elongation, and termination. Stages of Transcription-associated factors: specific proteins that act in a time- or tissue-dependent manner to initiate transcription 

Enhancer sequences

Enhancer sequences of DNA DNA The molecule DNA is the repository of heritable genetic information. In humans, DNA is contained in 23 chromosome pairs within the nucleus. The molecule provides the basic template for replication of genetic information, RNA transcription, and protein biosynthesis to promote cellular function and survival. DNA Types and Structure help to initiate or augment transcription, which further promotes gene expression.

  • These sequences can bind to:
    • Activator proteins: 
      • Specific types of TFs that help to assemble and/or interact with TFs on the promoter 
      • Function to activate or augment transcription
    • Repressor proteins: repress transcription
  • Usually located several thousand base pairs upstream of the target gene
    • Create a loop in the DNA DNA The molecule DNA is the repository of heritable genetic information. In humans, DNA is contained in 23 chromosome pairs within the nucleus. The molecule provides the basic template for replication of genetic information, RNA transcription, and protein biosynthesis to promote cellular function and survival. DNA Types and Structure when they interact with the promoter
    • Allow for further fine-tuning of regulation:
      • A single enhancer sequence may interact with multiple promoters/genes.
      • A single gene may interact with multiple enhancer sequences.
  • Insulator sequences: other sequences of DNA DNA The molecule DNA is the repository of heritable genetic information. In humans, DNA is contained in 23 chromosome pairs within the nucleus. The molecule provides the basic template for replication of genetic information, RNA transcription, and protein biosynthesis to promote cellular function and survival. DNA Types and Structure that can prevent the enhancers from looping to interact with the promoter region

Epigenetics

Epigenetic regulation Epigenetic regulation Epigenetic regulation is regulation of gene expression that does not involve alterations to the DNA sequence or any of its transcribed products. The most common forms of epigenetic regulation are DNA methylation, which suppresses gene expression, and modifications to the histone proteins, which affect the structure of DNA packaging. Epigenetic Regulation is the regulation of gene expression that does not involve alterations to the DNA DNA The molecule DNA is the repository of heritable genetic information. In humans, DNA is contained in 23 chromosome pairs within the nucleus. The molecule provides the basic template for replication of genetic information, RNA transcription, and protein biosynthesis to promote cellular function and survival. DNA Types and Structure sequence or any of its transcribed products. Epigenetics include:

  • How accessible the DNA DNA The molecule DNA is the repository of heritable genetic information. In humans, DNA is contained in 23 chromosome pairs within the nucleus. The molecule provides the basic template for replication of genetic information, RNA transcription, and protein biosynthesis to promote cellular function and survival. DNA Types and Structure is to RNA RNA Ribonucleic acid (RNA), like deoxyribonucleic acid (DNA), is a polymer of nucleotides that is essential to cellular protein synthesis. Unlike DNA, RNA is a single-stranded structure containing the sugar moiety ribose (instead of deoxyribose) and the base uracil (instead of thymine). RNA generally carries out the instructions encoded in the DNA but also executes diverse non-coding functions. RNA Types and Structure polymerase based on how it is packaged: DNA DNA The molecule DNA is the repository of heritable genetic information. In humans, DNA is contained in 23 chromosome pairs within the nucleus. The molecule provides the basic template for replication of genetic information, RNA transcription, and protein biosynthesis to promote cellular function and survival. DNA Types and Structure is wrapped around a nucleosome with a histone tail.
  • Histone modification via:
    • Acetylation → “unpacks” DNA DNA The molecule DNA is the repository of heritable genetic information. In humans, DNA is contained in 23 chromosome pairs within the nucleus. The molecule provides the basic template for replication of genetic information, RNA transcription, and protein biosynthesis to promote cellular function and survival. DNA Types and Structure and allows transcription
    • Methylation → protects inactive regions and prevents accidental transcription
  • Nucleosome modification:
    • Can slide up and down the DNA DNA The molecule DNA is the repository of heritable genetic information. In humans, DNA is contained in 23 chromosome pairs within the nucleus. The molecule provides the basic template for replication of genetic information, RNA transcription, and protein biosynthesis to promote cellular function and survival. DNA Types and Structure, changing which DNA DNA The molecule DNA is the repository of heritable genetic information. In humans, DNA is contained in 23 chromosome pairs within the nucleus. The molecule provides the basic template for replication of genetic information, RNA transcription, and protein biosynthesis to promote cellular function and survival. DNA Types and Structure is accessible for transcription
    • Can be remodeled
    • Can be temporarily removed

References

  1. Cooper GM (Ed.). (2000). The cell: a molecular approach. In Regulation of Transcription in Eukaryotes, 2nd ed. https://www.ncbi.nlm.nih.gov/books/NBK9904/
  2. Lodish H, Berk A, Zipursky SL, et al. (Ed.) (2000). Molecular cell biology. In The Three Roles of RNA in Protein Synthesis, 4th ed. https://www.ncbi.nlm.nih.gov/books/NBK21603/
  3. Christensen K, Hulick PJ. (2020). Basic genetics concepts: DNA regulation and gene expression. UpToDate. Retrieved April 15, 2021, from https://www.uptodate.com/contents/basic-genetics-concepts-dna-regulation-and-gene-expression 

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