gene expression and regulation

what is gene expression?

Gene expression is the process by which the information in a gene is used to make a functional product, usually a protein.

what is a gene?

A gene is a segment of DNA that contains the instructions to make a specific protein

what is gene regulation?

Gene regulation is the process of controlling when, where, and how much a gene is expressed (turned on or off).

Examples

• Only certain genes are active in skin cells vs brain cells

• Bacteria turn genes on/off depending on available nutrients

Name 3 things gene regulation allows us to do

• Cell specialization
  → Different cells express different genes (e.g., muscle vs nerve cells)

• Respond to environmental changes
  → Turn genes on/off depending on conditions (e.g., nutrients, stress)

• Control growth and development
  → Regulate when cells grow, divide, and differentiate

Your skin cell and nerve cells have the same DNA but the structure and function of these cells are different. Explain why these cells differ?

Even though skin cells and nerve cells have the same DNA, they are different because they express different genes.

Which cell type below expresses the gene that codes for the protein myosin? (myosin is a protein responsible for muscle contraction)

muscle cells

muscle cells, nerve cells, skin cells

differences between prokaryotic and eukaryotic gene regulation?

prokaryote

location : in cytoplasm no nuclues

transcription and translation : occur simultanously in cytoplasm

regulation focus : mostly transcriptional level

DNA packaging : Less complex; some epigenetic modifications occur

Eukaryote

location : in nucleus

Transcription and translation : Transcription in nucleus, translation in cytoplasm

Regulation Focus : Multiple levels: transcription, post-transcription, translation, post-translation

DNA packaging : DNA wrapped around histones; epigenetic marks like methylation affect expression

what are transcription factors?

Transcription factors are proteins that bind to specific DNA sequences and control the rate of transcription (gene expression).

• Help turn genes ON or OFF

• Control how much mRNA is produced

• Bind to DNA regions like:

  • Promoters (start site)

  • Enhancers (increase expression)

• Then they:

  • Recruit RNA polymerase → start transcription

  • Or block it → stop transcription

Types of transcription factors?

Activators

• Increase transcription

• Help RNA polymerase bind

Repressors

• Decrease transcription

• Block RNA polymerase

what is a promoter?

A promoter is a specific DNA sequence located before a gene where RNA polymerase binds to start transcription.

what is an enhancer?

An enhancer is a DNA sequence that increases transcription by allowing activator proteins to enhance the binding of RNA polymerase to a gene.

👉 Promoter = start site
👉 Enhancer = increases how much transcription happens

what is an operator?

An operator is a DNA sequence in an operon that acts as an on/off switch by controlling whether transcription can occur.

🧠 Key idea

👉 The operator controls access to the gene

⚙ How it works 🔴 OFF (gene not expressed)

• Repressor protein binds to operator

• Blocks RNA polymerase
  👉 Transcription stops

🟢 ON (gene expressed)

• Repressor is removed/inactivated

• RNA polymerase can pass
  👉 Transcription occurs

operons are mainly used in?

prokaryotes

(rare in eukaryotes)

ex.)Lac operon

Structure of lac operon?

Parts of the lac operon

• Regulatory gene (lacI) → makes the repressor protein

• Promoter (P) → where RNA polymerase binds

• Operator (O) → the on/off switch (repressor binding site)

• Structural genes:

  • lacZ → β-galactosidase (breaks lactose)

  • lacY → permease (brings lactose into the cell)

  • lacA → transacetylase (minor role)

• CAP site → binding site for CAP (activator)

what is a lac operon and how does it function?

The lac operon is a prokaryotic gene-regulation system in E. coli that turns lactose-metabolism genes ON or OFF depending on lactose and glucose levels.

PROG

promoter repessor operator genes

Lactose present binds to represser allowing RNA polymerase to transcribe and make mRNA which will be used to synthesis enzyme for breaking down lactose(Sugar)

Lactose not present represser binds to operator RNA polymerase cannot synthesis enzyme

what is a TRP operon and its function

The trp operon is a repressible operon in bacteria that controls the production of enzymes needed to make the amino acid tryptophan.

Main function

👉 Prevents the cell from wasting energy making tryptophan when enough is already present.

Low tryptophan → operon ON

• Repressor is inactive

• Cannot bind operator

• RNA polymerase transcribes genes

👉 Cell makes enzymes to produce tryptophan

High tryptophan → operon OFF

• Tryptophan acts as a corepressor

• Binds to repressor → activates it

• Repressor binds operator

👉 Transcription stops

opposite to lac operon as trp operon is normally on and stops transcription when tryptophan is high while lac operon is off and stops when lactose is low

inducible operon = usually OFF, turned ON when needed
Repressible operon = usually ON, turned OFF when enough product exists

what is a regulatory sequence?

A regulatory sequence is a segment of DNA that controls gene expression by providing binding sites for proteins that turn transcription on or off.

PROG

TATA box in eukaryotes

what is a regulatory gene?

regulatory gene is a gene that codes for a regulatory protein (such as a repressor or activator) that controls the expression of other genes.

In the lac operon:

The lacI regulatory gene produces the repressor protein that binds to the operator and blocks transcription.

what is methylation?

Methylation is the addition of methyl groups to DNA that typically silences genes by reducing transcription

How it works

• Enzymes add methyl groups to DNA

• This makes DNA more tightly packed or blocks transcription factor binding

• RNA polymerase cannot easily access the gene

👉 Gene is usually turned OFF

when does DNA methylation happen?

During development

• As embryonic cells specialize into different cell types

• Helps turn off genes a cell no longer needs

Example: skin cells silence neuron-specific genes

In response to environment

Can be influenced by:

• Diet

• Stress

• toxins

• aging

These can change gene expression without changing DNA sequence

Eukaryotic trancription

DNA opens → transcription factors bind → RNA polymerase makes mRNA → mRNA is processed → leaves nucleus

1.)Initiation

• Transcription factors bind to the promoter (ex: TATA box in eukaryotes)

• RNA polymerase binds to the promoter

• DNA unwinds/unzips

👉 Transcription begins

2.) Elongation

• RNA polymerase reads the template DNA strand

• Adds complementary RNA nucleotides

👉 mRNA strand grows

3.)Termination

• RNA polymerase reaches a termination sequence

• Stops transcription

• mRNA is released

• DNA rewinds

In eukaryotes only (after transcription)

mRNA processing

• Introns removed

• Exons joined

• 5’ cap added

• Poly-A tail added

In eukaryotic cells the default position of most genes is ‘off’, (they’re not expressed). Explain why.

Most eukaryotic genes are off by default because their DNA is tightly packed into chromatin, making it inaccessible to RNA polymerase and transcription factors.

Explain the process of initiation in DNA transcription

transcription factors bind promoter region(TATA box) - forms initiation complex

(may bind to enhancer if needed )

attracts RNA polymerase and unzips DNA - forms transcription bubble

transcription bubble has 2 different strands

sense strand - coding strand (original strand)

antisense strand - template strand

mRNA resembles coding strand

activators/reppresers(transcription factors) initiate or stop transcription factors from binding or rna polymerase directly therefor stopping transcription

explain the process of elongation in DNA transcription?

Transcription bubble opens up in DNA

RNA polymerase adds nucleotides to antisense strand

reads 3’-5’ template writes down 5’-3’ on pre mRNA

explain the process of termination in DNA Transcription?

RNA Polymerase reaches termination sequence which releases RNA Polymerase from template strand

(Rho proteins may facilitate this process)

Explain the processing in DNA transcription?

1.)splicing - removes introns from exons ,exons are joined

alternative splicing - exons are joined in different seqeunces to code for a variety of different protiens

2.) 5 cap added - prevents against degradation

3.) Poly A tail added - prevents against degradation

what are splicesomes?

Splicesomes splice exons from introns

made of snRNA -snRNP(snurps)

introns enable alternative splicing

DNA translation - initiation

The ribosome has two pieces:

Small subunit

• Binds to the mRNA

• “Reads” the codons (like AUG)

Large subunit

• Joins after the start codon is found

• Forms peptide bonds between amino acids

these subunits combine to form ribosome and tRNA joins forming initation complex

ribosome size differ in prokaryotes and eukaryotes

what is a svedberg unit and explain sedimation?

A Svedberg unit is a measure of a particle’s sedimentation coefficient, which describes how fast it settles during centrifugation.

DNA translation elongation phase

The ribosome has three critical sites that facilitate elongation:

• A site (Aminoacyl site): Arrival site for the incoming tRNA carrying the next amino acid.

• P site (Peptidyl site): Holds the tRNA attached to the growing polypeptide chain.

• E site (Exit site): Where the now empty tRNA exits the ribosome.

follows A-P-E and repeats cycle

The transfer and movement of tRNAs are powered by the hydrolysis of GTP, a guanine-based triphosphate similar to ATP.