BIO EXAM #2 - Chapter 16 : Gene Expression & Regulation

What is a somatic cell?

non reproductive cells

What does it mean to be diploid? Draw it haploid vs. diploid.

diploid means you contain all the same DNA (genes)

you have two complete sets of chromosomes, one from mom and one from dad

haploid means you just have one chromosome, versus diploid means you have two sister chromatids (classic x) and one of those chromatids is from mom and the other is from dad. They can only be combined into this iconic x because they are the same gene.

What is a gene?

made in DNA and stored in chromosomes

the basic physical and functional unit of heredity

What is gene expression and the process associated with it?

the process of producing a product from a gene

transcription and translation (central dogma)

Do all cells have the same DNA and if so, why is that important?

Yes, all somatic cells in multicellular organisms have the same DNA

this is important because we have to express and regulate them

allows for cell differentiation (specialized cells)

Why is gene expression regulation important?

to stay energy efficient, space, and time

What are three ways gene expression can be regulated?

1. how much we want to express

2. where we want to express

3. when we want expression to occur

What is cell differentiation?

the biological process by which a young, unspecialized cell changes into a mature, specialized cell with a distinct shape, size, and function

What level does most of gene expression regulation occur for prokaryotic cells?

Transcriptional Level

What is an operon?

an operon is a section of a prokaryote’s DNA that contains a set of genes that produce products involved in the same biochemical pathway or have a similar function

Three ways that operons are regulated?

1. repressors

2. activators

3. inducers

What is the difference between activators, repressors, and inducers?

Repressors are suppressing/stropping gene expression (transcription)

activators are increasing/starting gene expression (transcription)

• produced in the cell

Inducers can suppress or activate transcription depending on the needs of the cell and its environment

• produced in the cell or in the environment

Draw the basic structure of an operon

What is the purpose of the operator region of an operon?

acts as a molecular switch that controls the transcription of genes

where repressors or activators bind!

What is the purpose of the promoter region of an operon?

this is where the RNA poly. binds to allow for transcription

What condition will allow the tryptophan operon to be transcribed?

low levels of tryptophan (cells internal enviroment)

What type of operon is the tryp operon?

repressible operon because it is regulated by a repressor

it is always running and we need a repressor to stop it

Draw a picture showing low tryptophan and high tryptophan levels.

What is the tryp repressor doing when there is low levels of tryptophan?

inactive, just floating nearby for when its needed

What happens when tryptophan levels are high?

a spot before the promoter (and operator) region called trpR creates a trp repressor. Then, tryptophan (which is our product after translation) comes back and binds to the trp repressor, telling it to bind to the operator region and halt the RNA poly. from expressing the gene. This is a form of feedback inhibition lol

How is the trp operon turned off?

when tryptophan levels are high enough that tryptophan comes back and binds to the trp repressor, which then binds to the operator region

What does low tryptophan mean?

What does high tryptophan mean?

high expression

low expression

What does it mean to be an inducible opron?

means you are either activated or repressed by an inducer

What is the purpose of the lac operon?

to break down and transport lactose for fuel

What does lactose get broken down into by the lac operon?

glucose and galolactose

If there is no lactose present what does the repressor do?

the repressor binds to the operator region to stop transcription because why would we make the proteins that break down lactose if we don’t have any lactose?

Draw the usual structure of the lac operon.

Describe the lac operon briefly and what its two inducers are.

Lac operon is a sequence that when it goes through transcription and translation, makes end products that break down lactose. So this means that it is usually off. We only turn it on when we have lactose to break down. When there is no lactose, there is no reason to waste energy. So we use two inducers : allolactose and CAP. Both are activating the lac operon because remember it is usually defaulted off. They sense the lactose and the allolactose will bind to the repressor, making it fall off. This removes the roadblock from RNA poly. and it can now transcript. CAP on the other hand, will bind to the

Draw the Lac Operon when there is no lactose present. Then draw it with lactose present!

Talk about the affect of glucose on the lac operon.

Okay so basically, glucose is the most easiest sugar for our bodies to break down. as such, our lazy bodies will utilize the glucose over the lactose. This is bad. So what this means is we want low glucose levels, and high lactose levels, for the MOST transcription. High glucose causes low transcription because our body will break that one down first.

ALR where the FREAK did allolactose come from??

when we have lactose, we convert a small amount of it into allolactose so that it will bibd with the repressor, unlock it, and allow transcription to occur.

Draw what the lac operon looks like with high glucose and low glucose levels.

What is an important characteristic of our most optimal condition (and also what is it)?

high lactose ——— low glucose

the CAP is able to bind to the cAMP, thus forming a complex that binds to the CAP site. This just serves to speed transcription up.

What would be the effect on the lac operon and what would be happening with the proteins involved in the regulation of the lac operon when glucose levels were low and lactose levels are high?

this is our most optimal scenario!

this means that the effect on the lac operon would be allolactose removing the repressor, the CAP/cAMP complex forming and binding to enhance transcription. And in all this means there is high levels of transcription occurring. This means we are producing a bunch of the proteins that break down lactose.

What stages of gene expression are affected by regulation?

1. Epigenetic stage

2. Transcriptional stage

3. Post-transcriptional stage

Epigenetic Regulation - lets hear all about it!

• all about accessibility

• is inheritable but does not change the DNA sequence

• affects chromatin structure (think histones)

  • acetyls will loosen the histones so that the DNA is more accesible to be expressed

  • methyls will tighten the histones so that the DNA is hard to access and therefore cannot be expressed

• can be temporary or permanent

Transcriptional Regulation - lets hear all about it!

• key way to regulate gene expression is through the initiation of transcription (starting it or stoping it)

• promoters, enhancers, and repressors

• literally just are we allowing RNA poly. to do its job or not

• RNA poly. requires transcription factors to initiate transcription

  • transcription factors are proteins that control the binding and initiation of transcription

  • bind to the promoter sequence

  • use promoters (like the TATA box) to bind

What does RNA polymerase bind to in order to start transcription in eukaryotes?

the promotor sequence, often the TATA box, with the help of Transcription Factors

What are enhancers and silencers and what do they bind?

• Enhancers: DNA sequences that increase or boost gene transcription.

• Silencers: DNA sequences that decrease, repress, or turn off gene transcription

  • are specialized non-coding DNA sequences that act as remote control switches to regulate how much and when a gene is transcribed into mRNA

Post-transcriptional Regulation - lets hear all about it!

RNA must be processed in the nucleus before it can leave to the cytoplasm

• 5 Cap

• 3 Poly A Tail

• RNA Altrenative Splicing

Why is alternative splicing considered part of gene expression regulation?

because it acts like an editor that decides what kind of protein a gene makes and how much of it gets built

What is the difference between Regular Splicing and Alternative Splicing?

Regular splicing always builds the exact same message from a gene, while alternative splicing chooses which parts to keep or skip to build different messages

What is translational regulation?

basically the same as transcriptional regulation where we regulate it through the initiation (stopping or starting)

• results in the formation of a initiation complex

Why is eIF-2 important for translational regulation?

this is the first protein to bind to the small subunit of the ribosome

basically think of this as an on/off switch

when elF-2 is phosphorylated (a phosphate is added to it) the switch is turned off and translation cannot occur

when there is no phosphorylation, then the switch is kept on and translation occurs

Post-translational regulation - lets hear all about it!

this involves the chemical modification of proteins

these chemical changes affect protein activity or how long they remain in the cell

best example : ubiquitin

• proteins marked with ubiquitin tags are marked for degradation

What does adding Ubiquitin do to a protein?

alter the proteins fate, activity, location, etc

usually results in it being degraded

How is the cell cycle regulated?

regulated through internal checkpoints

• end of G1 phase

• end of G2 phase

• Metaphase

regulated by internal and external triggers!

• external - initiate or inhibit the cell cycle

  • examples : death or nearby cells, release of growth hormone, cell crowding

• internal - regulate progress

  • examples : G1, G2, M checkpoints

Explain the G1 checkpoint.

determines whether all conditions are favorable before allowing into the S phase

• external influences

• adequate cell reserves

• cell size

• DNA damage

if a cell fails this checkpoint

• mistakes are corrected

• sent into G0 until conditions are favorable

Explain the G2 checkpoint.

prevents entry into the mitotic phase if certain conditions arent met regarding…

• cell size

• protein reserves

MOST IMPORTANT ROLE

• DNA is not damaged

• All chromosomes have been replicated

if not met…

• halts the cycle

• tries to repair the DNA

• makes any missing chromosomes

Explain the M checkpoint.

determines whether all sister chromatids are correctly attached to the spindle microtubules

Intracellular Regulators

positive regulators

• promotes movement to the next stage of the cell cycle

• proto-oncogenes, cyclins, cdks, CAP

• are proteins or enzymes or allosteric helpers

negative regulators

• stop the advancement to the next step of the cell cycle

• Tumor-Supressor Genes

• examples; Rb, p53, p21

What causes cancer?

a mutation that leads to unregulated and uncontrolled cell growth (cell cycle on overload)

what happens in a normal cell when it has a DNA mutation that cannot be fixed, but this does not happen in a cancer cell?

apoptosis

What is the difference between a proto-oncogene and an oncogene?

proto-oncogenes are normal and positive cell cycle regulators

oncogenes are abnormal cancer causing versions of the proto-oncogene. Drives uncontrolled cell division and tumor growth.

What is the product of a tumor-suppressor gene and what does it do in the cell cycle?

a tumor-suppressor protein

brakes of the cell cycle that ensures cells do not grow or divide uncontrollably

What is a mutagen?

any physical or chemical agent that permanently changes genetic material—usually DNA—in an organism and increases the frequency of mutations above natural background levels

What does it mean to be predisposed to cancer?

having an elevated chance or vulnerability to developing cancer compared to the average person

• caused by…

  • inherited genetics

  • environmental exposures

  • exposure to mutagens

What is a circadian clock?

the body's internal, roughly 24-hour timing system that coordinates physical, mental, and behavioral changes