Molecular Biology of Cell Cycle and Signaling

The proportion of phage particles that carry two or more genes simultaneously during transduction.

The measure (in minutes) of the physical separation between two genes based on cotransduction frequency.

The transfer of genetic material between different organisms or species. It's not the transmission from parent to offspring.

Mechanism of horizontal gene transfer where bacteria take up free DNA fragments from the environment.

Horizontal gene transfer process where bacteriophages (viruses that infect bacteria) carry bacterial DNA from a donor to a recipient bacterium.

ATAC-seq identifies regions of open chromatin, which are accessible to proteins like transcription factors. This helps locate promoters and enhancers, regions involved in gene regulation.

ATAC-seq utilizes a hyperactive transposase, Tn5, which inserts sequencing primers into open chromatin regions. These fragments are then sequenced and aligned to the genome, revealing areas of accessibility.

Chromatin remodeling involves repositioning or removing nucleosomes by specialized enzymes. This influences gene expression by changing the accessibility of DNA to transcription factors.

This refers to the dynamic addition or removal of chemical groups like acetyl, methyl, phosphate, or small proteins like ubiquitin to histone tails. This process alters chromatin structure and gene activity.

Chemical modifications to histone proteins, like acetylation or methylation, impact chromatin structure and gene expression. They can either activate or repress gene transcription.

The process of controlling which genes are turned on (expressed) and off in a cell, determining the proteins produced and the cell's function.

Genes that are only expressed when a specific factor is present, like a signal or molecule.

Genes that are normally expressed but are turned off when a specific factor is present, like a signal or molecule.

Proteins that bind to specific DNA sequences and regulate the transcription of genes, controlling gene expression.

A transcription factor that increases the rate of transcription of a gene.

A transcription factor that decreases the rate of transcription of a gene.

Part of a transcription factor that binds to specific DNA sequences.

Part of a transcription factor that controls its activity, often by interacting with regulatory molecules.

Parts of a transcription factor that influence the rate of transcription, either increasing it (AD) or decreasing it (RD).

Genes that are always expressed, regardless of environmental conditions.

Breaks in both strands of DNA that can lead to mutations or be used for gene replacement. They are more efficient in creating gene knockouts and replacements than homologous recombination.

A DNA repair pathway that joins broken DNA ends without using a template. Often results in small insertions or deletions (indels) at the repair site.

A DNA repair pathway that uses a homologous template to accurately repair broken DNA ends. Can be used for precise gene editing.

An adaptive immune system found in bacteria that protects against bacteriophages. Uses CRISPR loci and Cas9 protein to recognize and cleave invading phage DNA.

A double-stranded nuclease enzyme in the CRISPR/Cas system. It cleaves DNA at specific sites guided by the crRNA.

A small CRISPR RNA containing a spacer sequence complementary to the target DNA and a repeat sequence. Guides Cas9 to the target site.

A short DNA sequence recognized by Cas9. Must be present immediately downstream of the target sequence for successful cleavage.

p53 is a tumor suppressor protein that acts as a gatekeeper, preventing cells with damaged DNA from entering the cell cycle. It does this by inducing cell cycle arrest at the G1-to-S checkpoint, allowing time for DNA repair.

Upon sensing DNA damage, p53 activates the transcription of genes, including the CDK inhibitor p21. This p21 protein then binds to and inhibits the activity of CDK4-cyclinD complexes, preventing phosphorylation of Rb. This keeps Rb active, which in turn prevents E2F from activating genes needed for S phase entry.

Mutations in both copies of TP53 gene, which encodes p53, lead to a loss of function. This disables the cell's ability to arrest the cell cycle in response to DNA damage, allowing damaged cells to proliferate. This increases the risk of cancer.

Signaling pathways are chains of molecular events that relay information from outside the cell, like hormones or growth factors, to the nucleus, ultimately affecting gene expression and cell behavior.

Steroid hormones like estrogen and testosterone can directly enter the cell and bind to specific receptors. This complex then translocates to the nucleus, where it regulates gene expression, potentially promoting cell division.

Cancer arises from both internal and external factors. Intrinsic factors include cell division rates and age, while extrinsic factors encompass environmental influences and genetic inheritance.

Evidence suggesting cancer originates within the body includes: higher cancer rates in organs with frequent stem cell division, increased risk with age, and replication-related mutations.

Evidence suggesting cancer arises from outside factors includes: clear environmental causes like smoking and sun exposure, rising cancer rates, and non-age-related mutations.

Inheriting specific mutations in tumor suppressor genes can increase the risk of developing cancer.

The G1 phase in the cell cycle is where a cell grows in size and prepares for replication. It's like a factory stocking up before production.

If a cell doesn't receive proper signals or nutrients, it enters the G0 phase, a resting state outside the active cell cycle.

This checkpoint acts as the 'point of no return', deciding if a cell commits to replication. It can also pause the cycle for repairs.

Signals from outside the cell, like growth factors, can activate or deactivate genes involved in cell growth and progression into the cell cycle.

A group of genes in bacteria responsible for lactose metabolism. It includes the genes for lactose permease (lacY) and beta-galactosidase (lacZ), which are needed to transport and break down lactose, respectively.

A type of gene regulation where a repressor protein binds to a specific DNA sequence, preventing the transcription of the gene. The lac operon is negatively regulated by the LacI repressor, which binds to the lac operator.

Mutants that have genes expressed continuously, regardless of the presence of a specific inducer. In the case of the lac operon, constitutive mutants of lacI or lacO result in the continuous production of LacZ and LacY, even in the absence of lactose.

To determine whether a gene encodes a protein or functions as a binding site, researchers can use techniques like complementation analysis. If a mutated gene can be complemented by a wild-type copy of the same gene, it indicates the gene encodes a protein. Conversely, if a mutated gene can be complemented by a DNA segment containing a binding site, it suggests that the mutated gene acts as a binding site.

A protein that binds to the lac operator region of the lac operon, blocking the transcription of the lac genes. This prevents the expression of lactose-utilizing enzymes when lactose is absent.

Naturally occurring small double-stranded RNAs that regulate gene expression by binding to the 3' UTR of mRNAs, either preventing translation or causing degradation.

MicroRNAs bind to the 3'UTR of mRNAs, often with incomplete complementarity, preventing translation. This blocks protein production without degrading the mRNA.

A technique that uses double-stranded RNAs (dsRNAs) to silence gene expression. It mimics natural microRNA pathways to knock down specific genes.

Both RNAi and microRNAs utilize dsRNAs to target and silence specific genes. RNAi uses artificially introduced dsRNAs, while microRNAs are naturally occurring.

RNAi allows researchers to study gene function by specifically knocking down genes in various organisms. This helps understand gene function and impacts on phenotypes.

RNAi can have variable effects, sometimes not completely mirroring a gene knockout, and off-target effects where other genes with similar sequences are silenced.

The control of which genes are turned on or off in a cell, determining the proteins produced and the cell's functions.

Gene expression regulation ensures cells produce the right proteins at the right time and in the right amounts, allowing for cell specialization and proper functioning.

An error in a gene that helps control cell growth, causing it to lose its ability to stop uncontrolled cell division.

A mutation that only affects a cell when both copies of the gene are faulty. A single good copy is usually enough for normal function.

A genetic change that occurs in a regular body cell, not in the cells that produce eggs or sperm. These mutations can cause cancer, but can't be passed on to offspring.

A mutation in a gene that promotes uncontrolled cell growth, leading to cancer. Often only one copy of the gene needs to be mutated to cause problems.

A mutation in the cells that produce eggs or sperm. These mutations are passed on to offspring. They can increase risk for cancer.

A technique used to determine which genes are being transcribed in a specific tissue or cell type. It provides information about the expression levels of different genes and their potential role in the cell.

RT-PCR uses reverse transcriptase (RT) to convert RNA into cDNA, which is then amplified using PCR. This allows measuring gene expression levels, detecting splicing variants, and comparing expression between different samples.

ISH allows visualization of specific RNA transcripts within a fixed tissue or embryo. It helps determine the location and distribution of a particular gene's expression within a cell or tissue.

A labeled probe complementary to the target RNA is synthesized and hybridized to the fixed tissue. The probe is detected using antibodies against the label, producing a color change at the site of hybridization.

RNA-seq is a high-throughput sequencing technique that analyzes all the RNA transcripts present in a sample. It provides a comprehensive profile of gene expression, including identification of novel transcripts and splicing variants.

RNA is extracted from tissue, converted to cDNA, and sequenced using NGS technology. The sequenced reads are then aligned to the genome, allowing quantification of transcript abundance and identification of transcript isoforms.

RNA expression analysis tools like RT-PCR, ISH, and RNA-seq are used to study gene expression in various contexts, including developmental biology, disease diagnosis, and drug discovery.

By analyzing the expression of specific genes, researchers can identify potential disease biomarkers, understand disease mechanisms, and develop targeted therapies.

The G1-to-S checkpoint is a control point in the cell cycle that decides if a cell should commit to DNA replication and enter the S phase. It ensures that the cell has grown adequately and that its DNA is undamaged before proceeding.

p53 is a tumor suppressor protein that acts as a guardian of the genome. It detects DNA damage and, if necessary, arrests the cell cycle at the G1-to-S checkpoint, allowing time for DNA repair. If the damage is too severe, p53 can trigger apoptosis, programmed cell death.

p53 induces the production of p21, a protein that inhibits the activity of CDK4-cyclinD complexes. This prevents the phosphorylation of Rb, a key protein for cell cycle progression. Unphosphorylated Rb blocks E2F, a transcription factor needed for S phase entry.

Mutations in both copies of TP53, the gene that encodes p53, can lead to a loss of its tumor suppressor function. This allows cells with damaged DNA to bypass the G1-to-S checkpoint and continue dividing, increasing the risk of cancer development.

Signaling pathways are chains of events that relay information from outside the cell (e.g., hormones, growth factors) to the nucleus. This information can activate or deactivate genes that influence cell growth and the decision to enter the cell cycle.

A gene that acts as a master control for eye development in organisms. Its expression can lead to the formation of eyes in unexpected locations.

Organisms that have been genetically modified to carry new genes, typically for desirable traits such as disease resistance or increased yield.

Human proteins can be produced in bacteria like E.coli but require specific elements like a promoter and ribosome binding site for expression.

Some human proteins need post-translational modifications that bacteria can't provide. This is often done by introducing the gene into a farm animal for milk production.

Transgenic crops can be engineered to contain a bacterial gene that provides resistance to the herbicide glyphosate.

Genetically modified organisms can offer several benefits such as enhanced disease resistance, increased yield, longer shelf-life, and reduced reliance on pesticides.

While GMOs offer potential benefits, concerns exist regarding their safety, environmental impact, and potential for unintended consequences.