Cell Biology Chapter 8 (Exam 2)

Control of Gene Expression

What is differential gene expression?

The process in which cells activate or silence specific genes to create different cell types in response to the changing environment or under different conditions

What are the 2 cell types that are an example of differential gene expression?

The neuron and the liver cell

What is unique about the neuron and the liver cell?

They both contain the exact same genetic code (sequence)

What are neurons?

Controls electrical signal that interact with conciousness

What are liver cell?

Metabolizes drugs, metabolism, and detoxification

Why do liver cells and neurons behave differently regardless of them having the same genetic code?

They are differentiated - developed into distinct cell types

Cell differentiation is determined by…

Selective gene expression of the same genetic code

What does selective gene expression allow the cell to do?

Produce unique sets of proteins that define the cells function. All using the exact same DNA

What did the frog and cow cloning experiments prove?

Every single cell in an organism (no matter the type) keeps a copy of the entire genome within it. They then use chemical tags to turn specific genes on or off, depending on what proteins they need to build to do their job.

Give a quick overview of the frog cloning experiment?

Inserted a nucleus from a gut cell and placed into an empty egg cell. All chemical tags were reset and the egg began to grow and divide into a fully formed tadpole.

What are the genes that every cell expresses called?

Basal/constitutive genes

What do Basal/constitutive genes make…

Housekeeping proteins

What are Basal/constitutive gene expression?

Means a gene is turned on at all times in every cell. This gene’s DNA is always kept in an open and loose structure so it can be read continuously

What are housekeeping proteins?

The proteins made by the basal/constitutive genes. They do the basic chores that keep the cell from dying (Energy production, DNA repair)

How are housekeeping genes (basal/constitutive genes) expressed?

Constitutively - At a continuous constant/steady rate

What signals do you need to make housekeeping proteins?

None - Happens on its own, all the time

What does differential gene expression do?

Allows one cell to divide and transform into every single type of cell in your body.

How do cells know when to do what?

Through cell signaling

Signaling cascades quick overview

Extracellular signaling molecule (ligand)

Bind to receptor on cell surface

Activate signaling cascades

Some happen fast (PTM)

Some happen slow (signaling cascade goes into the nucleus and changes the gene expression)

What are transcription controls?

The mechanisms that determine whether or not a gene gets transcribed from DNA to RNA (ex: PTM on histone tails, Chromatin remodeling complex, activators and repressors)

Changes the shape and chemical switches of DNA

Which enzyme does acetylation on the histone tails?

Acetylase

Which enzyme does methylation on the histone tails?

Methylase

Explain how everything in the cell is reversible using the example with acetyl.

Can do a deacetylase to take off the acetyl group. This closes DNA and leads to no gene expression.

What is the promoter region?

Only in transcription. A specific sequence of DNA right before the actual gene. Has a TATA box to tell RNA polymerase where it needs to start

What is the terminator region?

A sequence of DNA located at the end of the gene. RNA polymerase snaps off of the DNA here and stops transcription.

What are regulatory regions?

Specific segments of non-coding DNA (dark) that control when, where and how much a gene is expressed.

What is an example of a regulatory region?

The promoter region. It is on the dark DNA but before the transcription start site. It recruits RNA polymerase to start transcription. Without dark DNA, we would not have a start spot for transcription

What are regulatory sequences?

Regulatory Sequences: Spreads of DNA inside dark DNA that control how, when, and how much a gene is expressed. (promoters, enhancers, silencers)

Location: Can be located anywhere—thousands of base pairs away, before the gene, after the gene, or even on a different chromosome.

How do Transcription Factors (TFs) find and bind to regulatory regions?

TFs are proteins that recognize the chemical code of the DNA bases.

They bind to the genetic sequence tightly and they do not make mistakes.

Binding to these dark DNA regulatory regions is required to turn gene expression up or down.

What are the two types of regulatory TFs (in dark DNA) and how do they alter mRNA expression?

Activators: Bind to regulatory regions (enhancers) to increase expression from its baseline level, forcing the cell to make more mRNA.

Repressors: Bind to regulatory regions (silencers) to decrease expression, forcing the cell to make less or no mRNA.

These are only in dark DNA

How can a regulatory sequence (in dark DNA) thousands of base pairs away affect a gene's promoter?

DNA Bending: The DNA molecule physically loops and bends to touch the promoter region of coding DNA

This allows the activators/repressors to physically touch the promoter region, telling the cell exactly how much to express the gene.

What is the difference between TFIIA/TFIIB and Activators/Repressors?

TFIIA & TFIIB: General transcription factors. They only bind straight to the promoter of normal genes to act as the direct landing gear for RNA Polymerase.

Activators & Repressors: Specific regulatory transcription factors. They bind to the far away dark DNA regions to dictate the speed/volume of transcription via DNA looping.

How do cells control gene expression?

By controlling transcription factors

Why do we need to turn off gene expression?

Necessary to keep the dosage of proteins at a safe level. Uncontrolled division or expression causes cancer/cell death

Transcription factors can act as both…

Activators and repressors

For example, you can turn genes off through both of these ways:

Methylation: an epigenetic modification

Repressor TF’s

What is tryptophan and why must its genes be regulated?

An amino acid that costs the cell massive amounts of energy to make. The cell must turn off the genes that express tryptophan if its levels are high, in order to avoid wasting resources.

What happens when tryptophan levels are high?

Tryptophan binds directly to the inactive repressor TF. This changes the shape of it and activates the repressor. This binds directly to the promoter region which block RNA polymerase from expressing that gene.

What must occur for a gene to stop being expressed?

The repressor transcription factor must physically bind to the DNA at the promoter region

How many promoters per gene does a eukaryote have?

One promoter per individual gene

How many promoters per gene does a prokaryote have?

One single promoter controls a cluster of multiple genes. Multiple genes shares 1 promoter to start it

What is the impact of a prokaryote having one promoter controlling multiple genes?

Makes gene expression very efficient. Can turn on one promoter to build many proteins

What is the impact of a eukaryote having one promoter controlling one genes?

Makes gene expression very precise. Every single gene that codes for a protein has its own on/off switch. Allows humans to control how much of a specific protein is made. Controls the “dose”

Eukaryotes can have only 1 promoter per gene but they can have multiple genes that share…

The same transcription factors (Basal/specific)

What does combinatorial gene expression mean and what is its effect?

Means that a genes expression is controlled by a unique combination of different transcription factors binding to its regulatory regions. Different combinations can either increase (activate) or decrease (repress) the level of gene expression.

Where are regulatory regions?

On dark DNA

What are regulatory regions?

Act as switches to turn genes on or off and control how much of a protein a cell makes. Have elements like activators and repressors.

In combinatorial expression, how does a cell signal turn up the expression of multiple separate genes (like Genes 1, 2, and 3) that are running at a low level?

Each separate gene already has some TF’s bound and running at a low expression. A cell triggers a signal cascade that activates the final transcription factor needed to turn up each expression. This new TF binds to a shared regulatory region on the dark DNA of all 3 separate genes. This completes the TF combination and increases their expression

How the do interaction of transcription factors alter gene expression?

The ways in which they touch or combine at specific areas decides the fate of the gene.

What type of signaling cascade does the cell use to do combinatorial gene expression with different transcription factors?

Slow - enters the nucleus and changes genetic information

What happens if you add a new or extra signaling molecule into the signaling cascade in combinatorial gene expression?

It creates a brand new signaling cascade which activates an entirely new TF that enters the nucleus and joins the existing group of TF’s in the dark DNA. This will change the level of expression

What are the 2 types of TF’s a signaling cascade can activate?

Activator TF or repressor TF

Different groups of TF proteins on regulatory regions change…

What cell type you have

What is the EY (ey) gene and what role does it play in development?

It is a regulator gene that codes for a transcription factor that has the ability to build other transcription factors. All of these TF’s turn on many genes, which sets off the cascade to build an entire eye.

How did scientists create an eye on a fruit fly's leg, and what happened to the cells?

Scientists forced the ey gene to be expressed inside stem cells of a baby fly larva. The ey transcription factor activated more TFs, setting off a domino effect that forced those cells to build a complete eye on the adult fly's leg.

What two major concepts did the ey gene experiment prove?

A single TF can control the fate of an entire organ's development.

Injecting an eye gene into a fly still makes a fly eye, proving that the master switches of life are universally shared across species.

How does a cell know which gene to turn on and when? How does it know which cell type to be?

Does positive feedback loops - Increases the expression of a gene

Explain how a positive feedback differentiates a cell and keeps it differentiated.

A stem cell receives the signal to activate a signaling cascade within itself. This will activate the initial Transcription factor that enters the nucleus, binds to a master gene, and turns it on. The cell will now read the gene and make a protein, which is a TF. This new TF will bind to the regulatory region of its own gene it was just created from. This acts as a continuous on switch because the gene is always making the TF protein, and that TF protein is continuously keeping it on. This loop is self-sustaining and keeps a cell differentiated.

What is another way besides positive feedback loops that can differentiate and keep a cell differentiated?

Histone Tail modifications. (Epigenetics - changes to gene expression that do not alter the DNA sequence). Example, in a heart cell, all of the liver, brain, and skin genes get locked away and the heart genes are acetylated, opening them.

Are DNA methylation and histone-tail methylation 2 different things?

Yes - They are both example of epigenetic modifications.

What is the difference between DNA methylation and histone-tail methylation?

DNA methylation modifies the actual DNA strand itself by adding a methyl group while histone-tail methylation adds the methyl groups on the tails of the histones in the nucleosomes. Add it to the spools that DNA wraps around.

Where does DNA methylation add the methyl group?

On DNA, specifically, Cytosine base.

What does DNA methylation do?

Block transcription factors from binding to DNA and compresses chromatin

What does DNA histone-tail methylation do?

Acts as a molecular tag that recruits proteins to pack chromatin tight.

Can DNA methylation be passed down from generation to generation?

Yes, the methylation patterns can be passed down. After DNA replication, the new strand is methylated based off of the template strand.

What is the difference between post-transcriptional and post-translational modifications?

post-transcriptional: Occur on mRNA after transcription

post-translational: Occur on proteins after translation

When do post-transcriptional modifications occur?

After the cell has already made the decision to turn a gene off or not. Transcription only occurs on genes that want to be turned on. Then the PTM will occur on the new mRNA.

What are the post-transcriptional modifications?

5’ capping, Splicing, 3’ Tailing

Turns pre-mRNA to mature mRNA

What are untranslated regions?

Regions part of dark DNA. They lie just outside of the 5’ and 3’ end of the new mRNA and the DNA that codes for it. Lie just outside of the protein coding regions. It is the region right before AUG and the region right after the stop codon (UAA, UGA, UAG)

Why is the 5’ UTR important?

Contains the ribosome binding site for translation to occur.

What does the ribosome look for in order to know which proteins can be made during translation?

Shape of the mRNA and shape of the 5’ UTR. If either is tight, then this means very little to none proteins get made on the tight region. Shape of mRNA needs to be open to make proteins.

How can temperature change shape of mRNA?

RNA is highly sensitive to heat. At wrong temperatures, the 5' UTR of mRNAs naturally folds into tight hairpins, physically hiding the ribosome binding site.

Changing the shape of UTR’s changes…

How we express our genes

Explain the ribosomes open and closed states

Open: easily able to scan mRNA to find the start codon. Only open before it find start codon

Closed: As soon as a ribosome finds AUG, immediately clamps/closes to mRNA so translation can begin

How can protein binding to the ribosome binding site change its shape in translation?

If a regulatory protein binds onto the RBS, it acts as a roadblock. This forces it to form a tight structure. This stops the ribosome from finding the RBS to start translation

How can a small molecule binding to the ribosome binding site change its shape in translation?

The presence of that molecule changes the shape of RBS This change either completely hides the RBS (turning translation off) or opens it up (turning translation on).

What are the 2 types of RNA that can bind to mRNA? What do they do?

MicroRNA (miRNA) and Short interfering RNA (siRNA). They bind to mRNA to control gene expression - They both cause gene silencing

Explain miRNA and what they do

miRNA comes off of the Dark DNA. Then, it is processed by RISC and DICER proteins. Now, the processed miRNA binds to the regulatory regions in 3’ UTR to decrease the expression of the mRNA - Slowly degrades the strand

Untranslated regions are the same as…

Regulatory regions

What is the ribosome binding site?

A smaller sequence within the 5’ UTR that recruits the ribosome to start translation

How much of the human genes have either miRNA or siRNA bind to regulatory regions to control the expression of genes?

1/3 of human genes.

Explain siRNA and what they do

Comes from outside of the cell (exogenous), like a virus with double stranded RNA or injected. It is processed by RISC and DICER proteins. Then, it binds to the middle of mRNA abd completely destroys mRNA immediately.

What shape does mRNA become if miRNA were to bind to its regulatory region in the 3’ UTR?

Double strands where they both wrap around.

How can your body use miRNA/siRNA as a defense from viruses?

When a virus infects a cell, it injects its own RNA into the cell and uses our resources to make its proteins in the cell. The cell will recognize the foreign RNA and signal siRNA and miRNA (processed by RISC and DICER) to bind to the viral mRNA to stop it from being translated and its proteins being made. This stops the virus’s ability to multiple

How can a gene not be fully expressed even if you end with a protein after translation?

Because if the protein is never turned on, the gene is not truly expressed. You can still control gene expression at the protein level!

How can gene expression be controlled at the protein level: explain Protelysis

After translation, the protein is made. When the cell decides it does not need this protein anymore, ubiquitin is added on to the protein (poof). This tag will activate proteasome which will destroy the protein into it amino acids. The ubiquitin will be recycled.

What is ubiquitin?

A small protein. It attaches to proteins to mark them for destruction

What is protease?

An enzyme that reacts to the ubiquitin tag and breaks down the protein into its amino acids

What is proteolysis?

The breakdown of proteins into its smaller amino acids via proteases from ubiquitin tags.

Every step of the central dogma is…

Controlled