Regulation of Gene Expression

Complex organisms typically possess larger genomes compared to simpler ones.
Example of genomic size comparisons:
- Homo sapiens (human): 6270 megabases.
- Drosophila 34(fruit fly): 180 megabases.
The human genome contains approximately 35 times more DNA than that of a fruit fly.
Grapes (Vitis vinifera) have an even greater number of genes but overall, humans possess approximately 1.5 times more genes than fruit fly.

A significant portion of the DNA in complex organisms is made up of non-coding DNA.
Generally, the more complex the organism, the higher the percentage of non-coding DNA.
In humans, roughly 75% of our DNA is not transcribed into proteins; of the transcribed DNA, a substantial part is made up of introns.
Hence, only about 15% of human DNA is responsible for encoding proteins.

Most regulatory systems occur within the non-coding regions.
Non-coding DNA includes regulatory sequences that are crucial for gene expression regulation.

Major regulatory mechanisms include:
- Chromatin Remodeling: Adjusting the availability of DNA for transcription.
- Transcriptional Control: Regulating RNA polymerase activity.
- Post-Transcriptional Control: Regulating mRNA processing and stability.
- Translational Control: Regulating ribosome access to mRNA in the cytoplasm.

In bacteria, transcription is the primary level of gene expression control.
DNA packaging is relatively limited; thus, chromatin remodeling is not critical.
Positive and negative control occurs through:
- Regulatory proteins acting close to the promoter site.
- Sigma factors interacting with promoters.

Eukaryotic regulation involves extensive chromatin packaging, necessitating chromatin remodeling for transcription initiation.
A basal transcription complex interacts with the promoter, and a mediator complex is essential.
Extensive RNA processing includes:
- Alternative splicing of introns.
- Addition of a 5' cap and a 3' poly-A tail.
- RNA interference regulating mRNA lifespan and translation rate.

An operon is a cluster of functionally related genes controlled by a single on-off switch, allowing coordination of gene expression.
Example: The Lac Operon in E. coli governs lactose metabolism.
Operons typically entail a promoter, operator, and structural genes.
Polycistronic mRNA allows expression of multiple genes contained within a single operon.
E. coli regulates lactose metabolism using specific proteins:
- Lac Permease: Transports lactose and is a misnomer (not an enzyme).
- b-Galactosidase: Necessary for lactose utilization.

Operator: A region where the Lac Repressor can bind, blocking RNA Polymerase movement.
Lactose Presence:
- A small amount of lactose is taken up, which is converted to allolactose.
- Allolactose binds to and inactivates the Lac Repressor, allowing transcription to occur.
- Transcription is termed de-repression or induction of the operon.
- This leads to increased production of b-Galactosidase only in the presence of lactose.

Catabolite Repression is a regulatory mechanism whereby the presence of glucose inhibits the lac operon, even when lactose is present.
When glucose levels are high, cAMP levels are low.
CAP (Catabolite Activator Protein) binds upstream of RNA Polymerase and requires cAMP to activate the lac operon.
High glucose levels prevent CAP from binding, thus preventing transcription despite available lactose.

Chromatin in nuclei exists in two forms during interphase:
- Euchromatin: Loosely packed, transcriptionally active.
- Heterochromatin: Tightly packed, transcriptionally inactive.
Control of chromatin states involves several mechanisms.

Histone Acetylation neutralizes the positive charge of lysine residues, allowing chromatin to become less tightly packed.
Enzymes involved:
- Histone Acetyltransferase (HAT): Adds acetyl groups.
- Histone Deacetylase (HDAC): Removes acetyl groups.

DNA methylation, often occurring on cytosines within CpG islands, results in tighter chromatin packing, inhibiting transcription.
DNA methylation is generally more stable than histone modifications.

Histone Acetylation:
- Generally reversible and associated with activation.
- Enables more dynamic changes in gene expression.
DNA Methylation:
- More permanent and typically associated with gene silencing, especially in developmental processes.

Changes in gene activity without altering the DNA sequence are referred to as epigenetic modifications.
Examples include acetylation and methylation on histones and DNA.

Transcription factors (TFs) are proteins that assist in RNA Polymerase binding to promoters.
Proximal TFs: Bind to Proximal Control Elements near the promoter.
Distal TFs: Bind to Distal Regulatory Sites, which can be many bases upstream or downstream.

Activators and Repressors:
- Activators bind to enhancer sites and promote transcription.
- Repressors bind to silencer sites and block transcription.
- The interaction determines whether transcription occurs in different cell types.

Alternative splicing allows for different proteins to be produced from a single primary RNA transcript (e.g., Doublesex protein in Drosophila).
Regulatory proteins influence how RNA is spliced.

Regulation of proteins like Transferrin and Ferritin is based on available iron levels.
Ferritin is produced only in iron-rich cells, while IRE-BP binds to iron response elements (IRE) and affects mRNA stability and translation.

Review Concept 20.1 in your textbook with a focus on analytical tools in gene expression regulation.
Learn about plasmids and restriction endonucleases, including their action and sites of effect on DNA.
Understand the basic mechanism of DNA synthesis primarily concerning DNA polymerase III's requirements.
Familiarize yourself with the Polymerase Chain Reaction (PCR) methodology.