Genes

Genetic Regulation

• It refers to the control of gene activity.

  • Genes can be turned on or off or adjusted regarding how much product they produce.

• Genes are sections of DNA that are transcribed into messenger RNA (mRNA) and then translated into proteins.

• Scope of Lesson

• Gene regulation was explored in both:

  • Prokaryotic organisms, such as E. coli.

  • Eukaryotic organisms, including human cells.

• The topic was introduced as a high-level overview of a much larger and complex field.

  • Genetic regulation is a major area of research and study.

• Purpose of the Lesson

  • To understand how genes can exist in a cell without being expressed.

  • To explore mechanisms that activate or suppress gene expression.

  • To relate these mechanisms to real-life genetic conditions.

    • Example

      • Cancer results from the uncontrolled growth of cells, often due to faulty gene regulation.

• Cell cycle checkpoints, controlled by proteins produced from DNA, are crucial in regulating growth.
  

Cell-Specific Gene Expression

Comparison of White Blood Cells and Nerve Cells

• Both types of cells contain the same 23 pairs of chromosomes.

  • Despite identical DNA, they perform very different functions due to differential gene expression.

• White Blood Cells (Leukocytes)

  • Function in immune defense by fighting infections.

  • Genes related to immunity are expressed.

• Nerve Cells (Neurons)

  • Function in signal transmission and communication with the brain.

  • Genes related to electrical signaling and synaptic communication are expressed.

Functional Differences

• Each cell type activates only the genes necessary for its specific function.

  • In white blood cells, immune-related genes are active.

  • In nerve cells, signaling-related genes are active.

• Different sections of the same chromosome may be active in each cell type.

  • Some gene regions are transcribed in one cell but silenced in another.

  • These diverse cell types and functions can arise from the same genetic material.

Chromatin Structure and Gene Expression

• Chromosome Basics:

  • Consists of DNA wound around histone proteins.

  • Genes are located at specific points along the chromosome.

  • Gene sizes can vary; some are large while others are relatively small.

• Expression at the Chromosomal Level

  • Chromosomes include both active and inactive regions.

  • Euchromatin

    • Actively expressed regions of the chromosome.

    • Associated with gene transcription and protein production.

    • Easily remembered by associating “E” with “expressed.”

• Heterochromatin

  • Regions that are not expressed.

  • Often found near the centromere.

  • Associated with gene silencing and tightly packed DNA.

Gene Expression at the DNA Level

Euchromatin Regions

Euchromatin contains both coding and non-coding sequences.

• Exons

  • Segments of DNA that are transcribed and translated into proteins.

  • Represent the functional, expressed portions of a gene.

• Introns

  • Segments of DNA that are transcribed but not translated into proteins.

  • Removed during RNA processing and do not contribute to the final protein product.

Clarifying Chromatin vs. Gene Structure

Chromatin Level

• Euchromatin

  • Expressed regions of the chromosome.

• Heterochromatin

  • Unexpressed regions of the chromosome.

    DNA Sequence Level within Chromatin

• Exons

  • Expressed coding sequences.

• Introns

  • Non-coding sequences that are not translated into protein.

Gene Expression and Regulation in Prokaryotic and Eukaryotic Cells

Gene Expression in Bacterial Chromosomes

• The entire bacterial chromosome is expressed, with no inactive regions.

  • Every gene, such as gene 1, gene 2, and gene 3, is transcribed into RNA.

  • These RNA molecules are translated into proteins that carry out cellular functions.

• Gene expression involves the building of bonds between biological monomers.

  • Nucleotides are bonded to form mRNA.

  • Amino acids are bonded to form proteins.

  • Both processes require energy input in the form of ATP.

• Because energy is limited in bacterial cells, they must use it efficiently.

  • Over-expression of unnecessary genes would lead to energy waste.

  • Bacteria selectively express only the genes necessary for their survival at a given time.

  Gene Elimination in Bacteria through Natural Selection

• Bacteria eliminate genes they no longer use to conserve resources.

  • Example:

    • If gene 2 is responsible for carbon fixation and the bacterium stops performing that function, the gene is removed over time.

    • Carbon fixation involves converting smaller carbon compounds like CO₂ into larger carbon compounds.

    • If this process is replaced by an alternative pathway, the original gene becomes obsolete.

• Once a gene is eliminated:

  • No mRNA is produced from it.

  • No protein is translated from it.

  • The cell saves nucleotides, amino acids, and especially ATP.

• This gene loss contributes to greater energy efficiency and cellular function in bacteria.

  Energy Efficiency: Prokaryotes vs. Eukaryotes

• Bacteria are extremely energy-efficient because they only retain and express functional genes.

• Eukaryotes, including humans, are comparatively inefficient.

  • Human chromosomes contain both expressed and unexpressed regions.

  • Euchromatin: Expressed DNA.

  • Heterochromatin: Unexpressed DNA that remains in the chromosome.

  Persistence of Non-Functional DNA in Eukaryotes

• Eukaryotic cells retain large DNA regions that are never expressed.

  • These DNA sequences are replicated every time a cell divides, even if they serve no apparent purpose.

• In contrast to bacteria, eukaryotes do not eliminate unused DNA from their chromosomes.

  • These regions have been present since the beginning and are simply inherited across generations.

• The inefficiency is compared to wasting energy by leaving lights on in an unused room.

  • Humans "leave the lights on" by continuing to replicate and carry unused DNA.

  Revising the Concept of "Junk DNA"

• Previously, unexpressed DNA was labeled as "junk DNA."

  • This term refers to heterochromatin that does not produce RNA or proteins.

• Modern research shows that heterochromatin plays a regulatory role.

  • It may influence whether euchromatin is expressed.

  • If heterochromatin is removed, the expression of nearby euchromatin may also be disrupted.

  • Therefore, the term "junk DNA" is no longer considered accurate.

  Proportion of Expressed DNA in Bacteria and Humans

• In bacteria, nearly 100% of the chromosome is expressed.

• In humans (eukaryotes), only about 2% of the genome is actively expressed.

  • This 2% accounts for all proteins required for human function and survival.

  • The remaining 98% is non-coding and not translated into proteins.

• Popular culture has explored the idea of unlocking the remaining 98%.

  • In the movie Lucy, the concept of accessing unused genetic potential is portrayed as unlocking superhuman abilities.

  • In reality, expressing this DNA would not result in extraordinary powers.

  Limitations of Unlocking Non-Expressed DNA

• The sequence of nucleotides determines the resulting proteins.

  • Specific sequences are required to create functional proteins.

• Expressing unknown or random DNA would not lead to enhancements like color-changing skin or super strength.

  • It could instead lead to non-functional or harmful proteins.

• Despite this, the idea continues to fascinate scientists and storytellers alike.

  Gene Regulation 

• Understanding chromosome structure is key to understanding gene regulation.

  • Gene expression is influenced by environmental conditions.

  • Regulation allows cells to respond to changing needs and conserve energy.

• The presence of a gene does not guarantee it will be expressed.

• Genes may remain inactive unless triggered by specific signals.

• Example: BRCA Gene and Cancer

  • BRCA gene (Breast Cancer gene) is associated with increased cancer risk.

    • People with this gene are predisposed to developing breast cancer.

• However, not all individuals with breast cancer have the BRCA gene.

  • Breast cancer can arise through multiple pathways and mutations.

• This complexity makes curing cancer particularly difficult.

  • The diversity of causes means no single treatment or cure fits all cases.

Gene Regulation and Cancer Expression

Gene Expression vs. Gene Possession

• Possessing a gene does not guarantee it will be expressed.

  • A gene may produce RNA and proteins or remain inactive.

• The BRCA gene, known to predispose individuals to cancer, may remain unexpressed throughout a person’s life.

  • Some individuals with the gene develop cancer, while others do not.

  • Some individuals without the gene may still develop cancer due to other causes.

  Oncogenes and Their Role

• Genes that can lead to cancer are called oncogenes.

• The term “onco” relates to cancer.

• An oncologist is a physician who specializes in cancer diagnosis and treatment.

  Variability in Cancer Development

• People with the BRCA gene may or may not develop cancer.

• People without the BRCA gene may still develop cancer.

• The relationship between gene expression and disease development is complex.

  BRCA Gene and Risk Factors

• The BRCA gene is a predisposing factor for cancer, not a direct cause.

• Other environmental factors can activate the gene, leading to RNA transcription and protein production associated with cancer.

• Factors that activate such genes are called predisposing risks or risk factors.

  Common Risk Factors

• Smoking is a major risk factor for several types of cancer, including lung, breast, and thyroid.

• Cigarettes contain carcinogens, substances that promote the development of cancer.

• Carcinogens do not directly cause cancer but increase the likelihood of its development.

  Evaluating Cancer Risk

• Risk factor evaluation includes:

  • Smoking habits

  • Dietary patterns (e.g., specific meat consumption)

  • Family medical history

  • Physical activity levels

• Clinicians assess these to determine an individual's cancer risk level, which can be low or high.

  Controllable vs. Uncontrollable Risks

• Controllable factors include smoking, exposure to hazardous chemicals, and lifestyle choices.

• Uncontrollable factors include inherited genetics.

• Some genes can be passed down that influence the likelihood of developing diseases like cancer.

  Genetic Signals and Expression

• Risk factors communicate with cells to turn genes on or off.

• When signals activate the BRCA gene, it can lead to cancer development.

• Signals in this context refer to communication at the cellular level, prompting gene activation.

  Gene Regulation

• It includes understanding how genes are turned on or off and how that affects protein production.

• Gene regulation includes both the structure of the chromosome and the proteins involved in switching genes on or off.

  Prokaryotic Gene Regulation

• The focus is on bacteria, where gene regulation is simpler than in eukaryotes.

• Bacterial genes are usually arranged next to each other.

  • Gene one is adjacent to gene two, followed by gene three.

  • These genes often function together and are expressed together.

  Gene Location and Terminology

• The DNA before a gene is called upstream.

• The DNA after a gene is called downstream.

• Upstream regions are where proteins responsible for transcription bind.

  • Transcription is the process of producing mRNA from DNA.

• Proteins bind upstream, not directly on the gene.

  Promoter and Operator Regions

• The promoter region is located upstream of a gene and facilitates the gene’s expression.

• Within the promoter is the operator, an on/off switch that regulates gene activity.

  • It can initiate or stop transcription based on the cell’s needs.

  Operon System

• The operon includes the promoter, operator, and the genes (e.g., gene one, two, and three).

  • It controls the simultaneous expression of genes with related functions.

• Genes in an operon usually contribute to the same function, such as energy production.

  Operon Function in Metabolism

• In cellular respiration, bacterial genes needed for this function are located close together.

  • Activating one gene activates all related genes in the operon.

• Examples of Prokaryotic Operons:

  • Trp operon

  • It is involved in the production of tryptophan, an essential amino acid.

• Lac operon

  • It controls the metabolism of lactose in bacteria.

Gene Regulation

• RNA Polymerase

  • The major protein responsible for transcribing DNA into RNA is called RNA polymerase.

  • RNA polymerase cannot function alone and requires additional helper proteins to initiate transcription.

• Role of Repressors and Activators

  • Repressors are products of regulatory genes located either upstream or downstream of the operon.

    • A repressor binds to the operator to prevent transcription and turns off the operon.

    • The repressor effectively acts as an off switch for gene expression.

• Activators are proteins that bind to the operator and help turn on transcription.

  • The activator facilitates the attachment of RNA polymerase to the operator region, initiating transcription.

• Tryptophan Synthesis Regulation in Bacteria

  • Tryptophan is an essential amino acid required for protein synthesis.

  • Genes responsible for producing tryptophan are regulated in bacteria to ensure sufficient but not excessive levels.

• The synthesis of tryptophan involves multiple enzymes:

  • Trypt-E, Trypt-B, Trypt-C, and Trypt-A are involved in tryptophan biosynthesis.

  • The biosynthesis of tryptophan follows a chemical pathway where intermediates are produced by enzymes.

• Feedback inhibition is used to regulate the amount of tryptophan:

  • When tryptophan levels are high, the feedback inhibition mechanism reduces the production of tryptophan.

  • Excess tryptophan binds to the repressor, activating it to bind to the operator and shutting off the gene expression that produces tryptophan.

• Feedback Inhibition

• Feedback inhibition occurs when the final product of a reaction, like tryptophan, inhibits the enzymes responsible for its production.

  • High levels of tryptophan lead to the repression of the operon responsible for its synthesis.

  • The binding of tryptophan to the repressor protein causes the repressor to attach to the operator, halting the transcription process.

  Repressible and Inducible Operons

  Repressible Operon

  • A repressible operon is typically on and can be turned off when a product, like tryptophan, is abundant.

  • The trp operon (responsible for tryptophan production) is repressible. When tryptophan accumulates, it binds to the repressor, which then binds to the operator and turns off gene expression.

  Inducible Operon

  • An inducer is usually off and can be turned on when an inducer is present.

  • The lac operon is an example of an inducible operon. It regulates the breakdown of lactose.

  • In the presence of lactose, it binds to the repressor, inactivating it, which allows RNA polymerase to initiate transcription.

  Lac Operon and Lactose Metabolism

• The lac operon is responsible for producing enzymes that break down lactose into smaller sugars for ATP production.

  • When lactose is absent, the lac operon is off, and a repressor binds to the operator to prevent transcription.

  • When lactose is present, it acts as an inducer by binding to the repressor and causing it to release from the operator.

  • This enables RNA polymerase to transcribe the genes involved in lactose breakdown.

Gene Regulation in Eukaryotes

• Gene regulation in eukaryotes is more complex than in bacteria, involving multiple levels of control.

  • Eukaryotic gene regulation occurs at several stages, including chromatin modification, transcription factors, and other regulatory mechanisms.

• Eukaryotic cells can regulate genes by modifying chromatin structure (e.g., euchromatin vs. heterochromatin).

  • Euchromatin is loosely packed and expressed, while heterochromatin is tightly packed and generally not expressed.

Prokaryotes vs. Eukaryotes

• In prokaryotes (bacteria), gene regulation mainly occurs through a single system—the operon system.

• In eukaryotes, multiple levels and mechanisms regulate gene expression, providing a more sophisticated method of control.

Gene Expression Regulation in Eukaryotes

• Euchromatin and Promoter Regions

  • Euchromatin is loosely packed, allowing for genetic expression.

  • DNA contains promoter regions, which are crucial for initiating transcription and are regulated by additional elements.

  • DNA has upstream and downstream regions, with proximal control elements that bind to proteins to help regulate genetic expression.

• Enhancer Regions and RNA Polymerase Binding

  • Enhancer regions increase the likelihood of gene expression by binding to proteins, promoting stronger activation of genes.

  • RNA polymerase binds to the promoter region to start transcription, but additional proteins are required for this process.

• RNA Modifications

  • After transcription, RNA undergoes modifications including the addition of a 5' cap and a poly A tail to increase stability and protect the RNA.

  • The poly A tail is a series of adenines added to the 3' end of the RNA molecule.

• RNA Splicing and Exon-Intron Removal

  • The primary RNA transcript contains both exons (coding sequences) and introns (non-coding sequences).

  • RNA splicing removes introns and joins exons together to create mature mRNA, which is ready for translation.

• Translation of mRNA

  • Mature mRNA, with the 5' cap and poly A tail, is translated in the ribosome.

  • Translation can occur in the cytoplasm or on the rough endoplasmic reticulum (RER).

  • Once translated, proteins are either retained in the cell or secreted.

• Degradation of mRNA

  • mRNA has a lifespan and is eventually degraded to regulate protein production.

  • The degradation of mRNA is an important mechanism for regulating gene expression and preventing excess protein production.

• mRNA in Vaccines

  • mRNA in vaccines like Pfizer and Moderna does not alter DNA.

  • mRNA is used to instruct cells to produce proteins, after which it is degraded and does not integrate into the DNA.

• Protein Modification and Degradation

  • After translation, proteins may undergo modifications, which are crucial for their functionality.

  • Proteins that are improperly modified are degraded to ensure only functional proteins persist.

• Histone Modifications and Gene Expression

  • Histone acetylation involves adding acetyl groups to histones, which relaxes the chromatin structure and allows for gene transcription.

  • Histone methylation tightens the chromatin, preventing transcription and turning off gene expression.

• DNA Methylation and Gene Silencing

  • DNA methylation involves adding methyl groups to the DNA, which inhibits gene expression by blocking transcription.

  • Removing methyl groups from histones or DNA can reactivate gene expression.