Chapter 11 – Gene Expression 11.1 – 11.3 Skip 11.4 AP Biology Radjewski 2014

Some rats are genetically programmed to prefer alcohol to water Understanding Gene expression Can help alcoholics get effective Treatment or Prevent it altogether.

Review Level of protein produced varies DNA  RNA  Protein Level of protein produced varies Influenced by environmental conditions and the developmental stage of cell

Gene expression is precisely regulated. Examples When an extracellular signal binds to its receptor, it sets in motion a signal transduction pathway that may end in some genes being activated and some being repressed. During cell cycle, cyclins are synthesized only at specific points. What does this mean? Gene expression is precisely regulated.

So basically, there are 2 types of genes In some cases: Gene expression is modified to counteract changes in environment to help maintain homeostasis In other cases, gene expression changes so that the cell can perform a specific function. For example, all of our cells carry the genes to encode keratin (protein in hair) and hemoglobin. But keratin is only made in specialized epithelial cells and hemoglobin is only made by developing RBC’s In contrast, all cells express the genes that encode for enzymes for metabolism So basically, there are 2 types of genes

Two types of genes Our focus Constitutive genes Inducible genes Actively expressed all the time Inducible genes Expressed only when their proteins are needed by the cell Our focus

Genes are subject to positive and negative regulation Positive regulation – there is a binding of an activator that stimulates transcription Negative regulation – there is a binding of a repressor, that prevents transcription Activators and repressors Are Transcription factors! Let’s look at mechanisms of: Viruses, bacteria and eukaryotes

What are viruses? Non living particle that can only reproduce within a host cell Not cellular Can have ds DNA, ssDNA, dsRNA or ssRNA Takes over the host cells protein synthesis machinery within minutes of entering the host 2 types of reproductive cycles Lytic Lysogenic

Lytic Cycle Lytic – “break”, meaning host cell is destroyed afterwards 6 steps Bacteriophage (virus infecting a bacteria cell) infects a host cell – viral DNA enters It uses the bacterium’s RNA polymerase to transcribe early genes One early protein shuts down host (bacterial) gene transcription Another protein stimulates viral genome replication Another protein stimulates late gene transcription New viral capsid proteins and a protein lyses the host cell

Now let’s look at eukaryote

HIV Review Human immunodeficiency virus Typically infects only cells of the immune system that express a surface receptor called CD4. Proteins on the membrane are involved in the infection of new cells, which HIV enters by direct fusion of the viral envelope with the host plasma membrane It is a retrovirus

Retrovirus Genome is single stranded RNA Carries an enzyme, reverse transcriptase that makes a DNA strand that is complementary to the RNA, while at the same time degrading the RNA and making a second DNA strand that is complementary to the first The resulting dsDNA becomes integrated into the host’s chromosome, where it resides and the virus can become dormant. Eventually cellular triggers result and stimulates transcription of the viral DNA, resulting in mRNAs that are translated into viral proteins, and in new copies of the viral genome

Negative regulation of HIV Normally a host cell has a negative regulatory system that can repress the expression of invading viral genes. However HIV can counteract this with a virus-encoded protein called Tat (Transactivator of transcription) Tat binds to the viral mRNA along with proteins that allow RNA polymerase to transcribe the viral genome.

Without Tat (normal Human)

With Tat (HIV infected humans)

Operon Cluster of genes with a single promotor that code for proteins in the DNA of bacteria Codes for 3 lactose-metabolizing enzymes in E. Coli Called the lac operon Example of negative regulation 4 major components

Component #1 Promotor region Region of DNA to which the RNA polymerase attaches to begin transcription

Component #2 Structural genes Contain DNA sequences that code for several enzymes

Component #3 Operator Located between the promotor and the structural genes Region of DNA that is able to control RNA polymerase’s access to structural genes It’s like a switch that can turn the operon on or off

Component #4 Repressor protein A substance that can prevent gene expression by binding to the operator and prevents RNA polymerase from transcribing the structural genes Transcription would resume when the repressor is removed by a molecule called an inducer

Background Information When you consume milk, the disaccharide lactose is soon present in your intestinal tract and available to the E. Coli living there. Before E. Coli can absorb lactose, it must first make beta-galactosidase, the enzyme that breaks down lactose into glucose and galactose.

Lactose 3 enzymes are needed to metabolize lactose: B-galactoside permease – moves sugar into cell B-galactosidase – hydrolyzes lactose to glucose and galactose B-galactoside transacetylase – transfers acetyl groups from acetyl CoA to certain B-galactosides. Role is unclear.

Therefore E. Coli should only make the enzyme when lactose is present. It is in E. Coli’s best interest to focus its energy on using available nutrients Therefore E. Coli should only make the enzyme when lactose is present. How does E. Coli do this? By an operon!

So if lactose is absent: RNA polymerase structural genes that aren't transcribed Repressor binds to operator and it prevents RNA polymerase from binding to promotor, so transcription is blocked. No mRNA is produced, so no enzyme is produced.

And if lactose is present: Lactose binds to repressor. The repressor becomes inactive! Binds to promotor Operator is free so transcription takes place and the enzymes are made!!

Now let’s look at A repressible Operon, trp operon Inducible System Lac operon is called an inducible system Allolactose (alternative form of lactose) is the inducer and it leads to the synthesis of enzymes in the lactose-metabolizing pathway by binding to the repressor protein and preventing its binding to the operator. Now let’s look at A repressible Operon, trp operon

Trp Operon Trp – tryptophan, an amino acid A co-repressor is involved. It is a molecule that binds to the repressor, causing it to change shape and bind to the operator, thereby inhibiting transcription. When tryptophan is adequately present in the cell, it is energy efficient to stop making the enzymes for tryptophan synthesis Therefore tryptophan functions as a co-repressor and binds to the repressor of the trp operon! This causes the repressor to bind to the trp operator to prevent transcription.

Tryptophan is inadequate/absent

Tryptophan is present/too much!

Repressible System Trp operon The product of a metabolic pathway (the co-repressor) binds to the repressor protein, which is then able to bind to the operator and block transcription.

Eukaryotic Cells Can also regulate the transcription of large stretches of DNA (containing many genes) by reversible, non-sequence-specific alterations to either the DNA or the chromosomal proteins These alterations can be passed on to daughter cells after mitosis or meiosis Are called Epigenetic changes (not mutations)

DNA Methylation 1-5% of cytosines in the DNA are chemically modified by the addition of a methyl group to form 5-methyl-cytosine. Catalyzed by the enzyme DNA methyltransferase Usually occurs when C’s that are adjacent to G’s Areas rich in the methylation are called CpG islands, and are abundant in promotors

DNA Methylation continued… This change in DNA is heritable When DNA is replicated, an enzyme called maintenance methylase catalyzes the formation of 5-methylcytosine in the new DNA strand But it is reversible by demethylase, which catalyzes the removal of the methyl group from cytosine. Methylated DNA binds specific proteins that are involved in the repression of transcription; thus heavily methylated genes tend to be inactive