Controlling Gene Expression

what prevents a transcription regulator from looping in the wrong direction and inappropriately influencing the transcription of a neighboring gene

chromosomal DNA of plants and animals is arranged in loops that hold individual genes and their regulatory regions. This restricts the action of enhancers preventing unintended interactions.

combinatorial control

of gene expression involves multiple transcription factors working together, which helps maintain specificity in gene regulation. This system ensures precise activation or repression of genes in response to various signals.

how do bacteria coordinate the expression of genes

having them clustered together in an operon under the control of a single promoter

what is a good example of how a single transcription regulator can coordinate the expression of many different genes

cortisol

combinations of a few transcription regulators can

generate many cell types during development

what does differentiation of a particular cell type involve

changes in the expression of thousands of genes

because each gene is typically controlled by many different transcription regulators

a relatively small number of regulators acting in different combinations can form the enormously complex regulatory networks that generate specialized cell types

Ey is a master transcription regulator

triggers differentiation of all of the specialized cell types that come together to form the eye

a master transcription regulator

can direct the formation of an entire organ

Three special genes that acts as a master switch flipped on in a fibroblast nucleus turns it into an

iPS cell, behaves almost exactly like an embryonic stem cell

what kind of cells are terminally differentiated (never divide again)

skeletal cells and neurons

what causes cell memory

1. positive feedback loop

2. DNA methylationand histone modification

what is cell memory a form of

epigenetic inheritance

positive feedback loop

can generate cell memory a master transcription regulator activates its own gene and other genes, resulting in sustained expression. The regulator gets produced in subsequent generations

Ex. Ey protein and iPS cells take part in positive feedback loops

DNA methylation

is a process by which methyl groups are added to the DNA molecule on certain cytosine bases turns off affected genes by attracting proteins that inhibit transcription, this is passed onto daughter cells using enzyme that copies methylation pattern

what is the enzyme that carries on DNA methylation throughout generations

maintenance methyltransferase

modification of histones in inheriting gene expression

when a cell replicates its DNA each daughter double helix receives half of its parent’s histone proteins and their associated modifications as heterochromatin, which can influence gene expression in the offspring cells.

post transcriptional controls

are mechanisms that regulate gene expression after RNA has been transcribed, influencing mRNA stability, translation efficiency, and ultimately protein synthesis.

by blocking or exposing the ribosome binding sequence the bacterium can inhibit or promote

the translation of mRNA

a bacterial gene’s expression can be controlled

by regulating translation of its mRNA

In eukaryotes, specialized repressor proteins can similarly inhibit translation initiation by binding to

Specific nucleotide sequences in the 5′ untranslated region of the mRNA, thereby preventing the ribosome from finding the first AUG. When conditions change, the cell can inactivate the repressor to initiate translation of the mRNA.

noncoding RNA is also referred to as

regulatory RNA

What are the regulatory RNAs

1. MicroRNA

2. small interfering RNAs

3. CRISPR RNAs

4. long non coding RNAs

MicroRNA

Small noncoding RNA molecules that regulate gene expression by binding to complementary sequences on target mRNA, leading to mRNA degradation or inhibition of translation. After mRNA is bound by microRNA, it may be marked for degradation or translation may be blocked from occurring. Once the mRNA is destroyed, RISC miRNAs can seek out other mRNAs

small interfering RNA

Protect cells from infections by degrading the viral long double-stranded RNA molecules and thus preventing the expression of viral genes through the RNAi process

RNAi steps

1. Double-stranded foreign RNA is cut into short fragments in the cytosol by the Dicer enzyme, these pieces are called siRNAs,

2. Then incorporated into the RISC complex to guide the degradation of complementary mRNA.

3. RISC throws away one strand of the RNA and keeps the other, and uses it as a search tool to destroy any matching RNA in the cell

RNAi silencing genes using RNA induced transcriptional silencing (RITS)

RITS parks itself at RNA polymerase making the target mRNA it calls in other proteins to guide the methylation of histones and promote chromatin condensation, leading to gene silencing.

RNAi defense response is a

mechanism that protects cells from foreign RNA, such as viruses, by degrading their RNA and preventing gene expression.

bacteria use small noncoding RNAs to protect themselves from

viruses, this process is known as CRISPR

CRISPR

makes use of small noncoding RNAs (similar to siRNAs as guides that direct the identification and destruction of viral genomes

CRISPR what does it stand for

Clustered Regularly Interspaced Short Palindromic Repeats

What is the CRISPR locus

a genomic region containing repetitive sequences that are interspaced with unique fragments derived from past viral infections, aiding in adaptive immunity in bacteria.

what do bacterial cells use the CRISPR locus for

The cell uses the CRISPR locus to produce a collection of short guide crRNAs which are individually loaded onto a CRISPER associated enzyme called Cas. This allows for targeted cleavage of matching viral DNA during subsequent infections.

Long noncoding RNAs

are RNA molecules greater than 200 nucleotides in length that do not code for proteins, playing crucial roles in the regulation of gene expression and chromatin structure.

Example of long noncoding RNAs

include XIST which are involved in X-chromosome inactivation, attracts repressive complexes that silence one of the X chromosomes in female mammals.

Long noncoding RNAs can serve as

scaffolds that bring together proteins that function in the same cell process