Eukaryotic gene regulation

What is a promoter in eukaryotic gene regulation?

Region right before the transcriptional unit that contains initiator sequences important for starting transcription. (where RNA binds)

What is the function of the TATA box in eukaryotic gene regulation?

It is an initiator sequence in the promoter where transcription factors bind.

What is the promoter proximal region?

It is the region upstream of the promoter that contains regulatory sequences for regulatory protein binding.

How do regulatory proteins interact with the promoter proximal region?

They can inhibit or enhance transcription by binding to regulatory sequences.

What is an enhancer in eukaryotic gene regulation?

A regulatory sequence far from the transcriptional unit (promoter) that enhances or inhibits transcription by binding regulatory proteins.

What effect does an enhancer have on transcription?

It increases transcription by binding to specific regulatory proteins.

What are transcription factors?

Proteins that bind to promoter proximal elements and work with RNA polymerase II to initiate transcription.

What is the role of activators in transcription?

Regulatory proteins that enhance transcription by binding to promoter proximal elements along with transcription factors.

What is a coactivator?

A protein that forms a bridge between activators and enhancer sequences, facilitating transcription by creating a loop.

What do repressors do?

Regulatory proteins that inhibit transcription by binding to promoter proximal elements.

What is a corepressor?

A large protein complex that forms a bridge between enhancer and promoter proximal regions to repress transcription.

What is chromatin remodeling?

The process by which DNA is released from histones, allowing transcription to occur.

What is the structure of chromatin?

DNA wrapped around histones, forming a structure known as a nucleosome.

What is the charge of DNA and histones?

DNA carries a negative charge, while histones carry a positive charge.

What is acetylation in the context of chromatin remodeling?

The addition of acetyl groups, which neutralizes the positive charge of histones and loosens their interaction with DNA, leading to transcriptional activation.

What is methylation and its role in gene expression?

The addition of methyl groups (-CH3) to DNA, which can either activate or repress gene expression, depending on the context.

What are histone acetyltransferases?

Enzymes that add acetyl groups to lysine residues on histone tails, promoting transcription.

What is the function of histone de-acetyltransferases?

Enzymes that remove acetyl groups from histones, leading to tighter binding of DNA and reduced transcription.

How does acetylation affect histone tails and DNA interaction?

Acetylation changes the charge of histone tails, loosening their interaction with DNA and facilitating transcription.

What occurs during deacetylation of histones?

Deacetylation leads to inactive chromatin, where DNA is tightly bound and transcription is inhibited.

What are DNA methyltransferases?

Enzymes that add methyl groups to cytosine residues in DNA, affecting gene expression.

What is the role of methylation in promoter regions?

Methylation in promoter regions silences DNA transcription and promotes chromatin condensation.

What is epigenetics?

The study of changes in gene expression that occur without altering the DNA sequence itself.

What is genomic imprinting?

A process where methylation silences the transcription of an inherited maternal or paternal allele of a gene, such as X-chromosome inactivation in females.

What are the types of gene regulation in eukaryotes?

Short-term regulation turns genes off/on in response to environmental or physiological needs; long-term regulation is for organism development and differentiation.

How is eukaryotic DNA organized?

Eukaryotic DNA is organized with histones into chromatin, which is compacted within the nucleus.

What role does the nuclear envelope play in eukaryotic cells?

The nuclear envelope separates transcription (in the nucleus) and translation (in the cytoplasm).

What are the four levels of gene regulation?

1. Transcriptional regulation: determines which genes are transcribed.
   2. Post-transcriptional regulation: affects the type and availability of mRNA.
   3. Translational regulation: influences the rate at which proteins are made.
   4. Post-translational regulation: determines the availability of finished proteins.

What is combinatorial gene regulation?

A method where combinations of a small number of transcription factors regulate a large array of genes.

What is meant by cell-specific gene regulation?

The presence of multiple activators for gene transcription that only occurs in cells containing the specific activators.

What is coordinated gene regulation?

A process where one signal controls the transcription of multiple genes sharing the same regulatory sequence.

How do steroid hormones illustrate coordinated gene regulation?

Steroid hormones affect only the cells with steroid receptors, allowing a single hormone to regulate all genes that share the same receptor.

What are long noncoding RNAs (lncRNAs)?

Transcribed RNAs that are not translated into proteins but regulate gene expression.

What is the function of the lncRNA Xist?

Silences the transcription of genes on the inactivated X chromosome in females.

What is pre-mRNA processing?

The modification process mRNA undergoes before it can be translated into protein.

What is alternative splicing?

A process where introns (noncoding regions) are removed and exons (coding regions) are retained, allowing for multiple protein variants from a single gene.

What is RNA interference (RNAi)?

A mechanism in which non-coding single-stranded RNA binds to mRNA to regulate translation.

What are microRNAs (miRNAs)?

Small RNA molecules derived from miRNA genes that regulate gene expression by pairing with mRNAs.

What is the miRNA-induced silencing complex (miRISC)?

A complex that binds to the 3’ UTRs of mRNAs to mediate miRNA effects on translation.

What happens when miRNA forms an imperfect bond with mRNA?

The mRNA is not destroyed but its expression is silenced.

What occurs when miRNA and mRNA form a perfect pair?

The enzyme cleaves the mRNA, leading to silencing of its expression.

What are short interfering RNAs (siRNAs)?

RNA molecules derived from double-stranded RNA that target and degrade complementary mRNA sequences.

What is the siRNA-induced silencing complex (siRISC)?

A complex that cuts double-stranded RNA into short pieces to promote degradation and silence gene expression.

How do siRNAs provide cellular protection against viruses?

siRNAs target and cleave complementary RNA from viruses, thus preventing viral replication.

What is translational regulation?

The control of the rate at which mRNAs are used for the synthesis of new proteins.

How does the Poly A tail length affect translation?

An increased length of the Poly A tail leads to increased translation, while a decreased length results in decreased translation.

What are chemical modifications in post-translational control?

The addition or removal of chemical groups (e.g., phosphate groups) that can activate or deactivate a protein's activity.

What is the role of processing in post-translational control?

Proteins are synthesized in an inactive form and must undergo processing for activation, such as pepsinogen being converted into pepsin.

What is the significance of ubiquitin tags in protein degradation?

Proteins marked with ubiquitin tags are targeted for degradation and broken down by proteasomes.

What is cancer genomics?

The study of genomes to identify the genetic causes and effects of cancer.

How is cell division regulated?

Through cell signaling involving growth factors that stimulate division and growth-inhibiting factors that inhibit it.

What is a tumor?

An abnormal growth and division of cells, often characterized by dedifferentiation.

What differentiates benign tumors from malignant tumors?

Benign tumors remain localized with cells staying together, whereas malignant tumors invade and disrupt surrounding tissues, indicating cancer.

What is metastasis?

The process by which malignant tumors spread through the blood or lymphatic system to other parts of the body.

What are hereditary cancers?

Cancers that run in families due to inherited genetic mutations.

What are sporadic cancers?

Cancers that are not linked to family inheritance, caused by somatic mutations.

What are driver mutations?

Mutations that drive tumor formation by providing a growth advantage to cancer cells.

What are the core processes affected by cancer genetics?

1. Cell survival genes: promote cell division (proto-oncogenes).
   2. Cell fate genes: determine cell differentiation.
   3. Genome maintenance genes: maintain the integrity of the genome.

What are proto-oncogenes?

Unmutated genes in normal cells that are responsible for regulating cell division.

What are oncogenes?

Mutated proto-oncogenes that cause overactive cell division, often due to mutations in the promoter, coding regions, or gene translocations.

What are tumor suppressor genes?

Genes that code for proteins inhibiting cell division; both alleles must be mutated or inactivated for cancer to develop.

What role does the P53 gene play in cancer?

P53 is a tumor suppressor gene that acts as a regulatory transcription factor, crucial for preventing cancer progression.

What are microRNAs (miRNAs)?

Small RNA molecules derived from miRNA genes that regulate gene expression by degrading mRNAs.

How do miRNAs contribute to cancer?

Altered miRNA genes can degrade tumor suppressor transcripts (removing inhibition on cell division) or transcripts for proto-oncogenes, leading to increased cell proliferation.

What is the role of short-term regulation in transcription?

Short-term regulation involves quickly turning gene sets on or off in response to environmental or physiological changes.

What does long-term gene regulation involve in multicellular eukaryotes?

Long-term regulation involves regulatory events necessary for development and differentiation of an organism.

How is eukaryotic DNA organized?

Eukaryotic DNA is organized with histones into chromatin, facilitating complex regulation of gene expression.

What separates transcription and translation in eukaryotic cells?

The nuclear envelope separates transcription (in the nucleus) from translation (in the cytoplasm).

Name the four levels at which gene expression is regulated in eukaryotes.

1. Transcriptional regulation
2. Post-transcriptional regulation
3. Translational regulation
4. Posttranslational regulation

What is a nucleosome?

A nucleosome is formed by DNA wrapped around a core of histones H2A, H2B, H3, and H4.

What are the two states of a eukaryotic promoter?

1. Inactive state: Nucleosomes prevent binding of transcription factors and RNA polymerase II.
   2. Active state: Transcription factors and RNA polymerase II bind, allowing transcription.

What happens to histone tails in inactive chromatin?

In inactive chromatin, histone tails are not acetylated, leading to tight association with DNA.

What is the histone code?

A regulatory mechanism that alters chromatin structure and gene activity based on chemical modification patterns in histone tails.

What occurs during DNA methylation?

DNA methylation involves adding a methyl group to cytosine bases, silencing transcription in promoter regions
- Is involved in genomic imprinting
- Turn off genes

What is the role of transcription factors in gene expression?

Transcription factors recognize and bind to specific DNA sequences (like the TATA box) to initiate transcription by recruiting RNA polymerase II.

What are enhancers in gene regulation?

Enhancers are regulatory sequences that, when bound by proteins, stimulate or inhibit transcription initiation rates from a distance.

How do activators enhance transcription?

Activators bind to promoter proximal elements and interact with general transcription factors to stimulate transcription initiation.

What role do repressors play in transcription?

Repressors can block or reduce transcription by preventing activators from binding or recruiting corepressors that inhibit initiation.

What is combinatorial gene regulation?

Combinatorial gene regulation involves the specific combination of transcription factors to control the expression of multiple genes.

What defines cell-specific gene expression?

Only cells containing the required combination of activators will transcribe specific genes, leading to varied gene expression.

How do long non-coding RNAs (lncRNAs) function in gene regulation?

lncRNAs can negatively or positively regulate the expression of protein-coding genes without being translated into proteins.

What is alternative splicing?

A process that produces different RNA variants by removing different combinations of exons from pre-mRNA.

How do small non-coding RNAs affect mRNA in RNA interference (RNAi)?

Small non-coding RNAs bind to mRNAs to regulate their translation, with microRNAs (miRNAs) and short interfering RNAs (siRNAs) being key players.

What is the function of miRNAs in gene regulation?

miRNAs bind to target mRNAs to either silence gene expression by degrading the mRNA or blocking translation.

What are the mechanisms of posttranslational regulation?

Mechanisms include chemical modification, processing of inactive precursors, and degradation via ubiquitin tagging and proteasomes.

What triggers cell division in target cells?

Growth factors binding to surface receptors trigger signal transduction pathways that result in changes in gene expression promoting cell division.

What type of tumors are benign tumors?

Benign tumors are composed of abnormal cells that stay together without invading surrounding tissues.

What are driver mutations in cancer?

Driver mutations are genetic changes that confer a selective growth advantage, leading to tumor formation.