Module 1: Gene Expression and Nucleus

Genes

• hereditary information transmitted in the form of units

• consist of DNA that codes for proteins

• during cell division, the DNA undergoes replication to produce two identical copies to each daughter cell

Cells

• possess instructions that specify their structures, functions and regulate their activities

Transcription

• Where instruction stored in DNA are transmitted

• Copying genetic information from DNA into RNA

Translation

• Where instruction stored in DNA are transmitted

• Synthesizing a protein based on the mRNA sequence

Regulation

• critical aspect of selective gene expression

• enables different cell types to carry out specialized function without wasting energy or resouces on unnecessary synthesis

Multi-cellular Eukaryotes

• composed of specialized cell types

• distinguished from each other based on difference in appearance and protein products

• these differences create differentiated cells

Differentiated Cells

• Produced from non specialized cells

• These starting cells change into specific types for distinct functions

5 Levels of Gene Regulation

1. genomic control

2. transcription control

3. post transcriptional control

4. translation control

5. post-translational control

Genomic Control

• All cells in a multicellular organism have the same DNA, but different cell types use only specific genes

• This selective gene expression allows cells to become specialized and perform different functions, despite sharing the same genetic material

• considered the regulatory change in the make-up or organization of the genom

Exceptions in Genomic Control

1. Gene amplification

2. Gene deletion

3. DNA rearrangement

4. Chromatin decondensation

5. DNA methylation

Gene Amplification

• used to make multiple copies of the same gene

Gene Deletion

• occurs when the cells delete genes whose product is not required

DNA Rearrangement

• based on the movement of DNA segments from one location to another within the genome → generates diversity

Chromatin Decondensation

• regulated by histone modifications and chromatin remodelling factors

DNA Methylation

• methyl groups associated with inactive regions of the genome

• these regions are transcriptionally repressed

Transcriptional Control

• Different cells turn on different genes depending on what they need

• This is controlled by transcription factors, which bind to DNA

• This allows for cellular specialization and proper functioning

Post-Transcriptional Control

• fine-tunes gene expression after mRNA is made

• involves RNA splicing and alternative splicing

RNA Splicing

• control site where introns (non-coding regions) are removed and exons (coding regions) are joined to form mature mRNA

Alternative Splicing

• allows cells to produce various mRNAs from a single pre-mRNA transcript by mixing and matching exons

Translational Control

• Regulates how much protein is made from mRNA in the cytoplasm

  1. Affects ribosome/protein synthesis:

     • involves mechanism to alter activity or availability of ribosomes, changing overall rate of protein synthesis

  2. Affects mRNA stability:

     • Proteins or small RNAs (like microRNAs) can inhibit translation or break down mRNA, helping the cell quickly adjust protein levels without making new mRNA

Post-Transcriptional Control

Includes mechanisms such as:

1. Changes to proteins structure

2. Proper protein folding

3. Directed to specific locations

4. Interaction with regulatory molecules to turn on their activity

Process of Protein Degradation & Proteins Involved

• Ubiquitin: Ubiquitin is a small protein that tags other proteins for degradation. Once tagged, those proteins are sent to proteasomes, which break them down.

• Proteasomes: large, cylindrical protein complexes in the cytosol that are primarily responsible for degrading proteins

Process:

• the ubiquitin labelled proteins are tagged and sent to the proteasomes

• the proteasomes recognizes ubiquitin tagged proteins, removes it and processes the tagged protein

• within the proteasomes, it uses ATP to break it down into smaller peptides

• this helps maintain protein quality and gets rid of defective proteins

Ubiquitin

• Ubiquitin is a small protein that tags other proteins for degradation

• Once tagged, those proteins are sent to proteasomes, which break them down

Proteasome

• large, cylindrical protein complexes in the cytosol that are primarily responsible for degrading proteins

• maintains protein quality control by eliminating defective or misfolded proteins

Post-transcriptional control in eukaryotes includes:

a. Chromatin decondensation, RNA processing, mRNA degradation, and protein import into target organelles 

b. RNA processing, mRNA degradation, protein modifications, and protein import into target organelles

c. mRNA degradation, protein import into target organelles, and protein-DNA promoter complexing

d. A and B

e. All of the answers are correct 

b. RNA processing, mRNA degradation, protein modifications, and protein import into target organelles

Nucleus

• houses chromosomes that carry DNA

• site where DNA replication occurs

• also where DNA is transcribed into RNA, then exits the nucleus to be translated into proteins in the cytoplasm

Nuclear Envelope

• double membrane structure that surrounds the nucleus

• separated by the perinuclear space (space between inner membrane and outer membrane)

• consist of tubular invagination: forms tubes extending into nucleus, increasing surface area and enhancing nuclear processes

Tubular Invaginations

• parts of the nuclear envelope that forms tubes extending into the nucleus

• increases surface area and enhances nuclear processes

Outer membrane is continuous with

ER

• contains proteins that bind actin and intermediate filaments of the cytoskeleton

• this provides structural support and facilitates intracellular connections

Nuclear Pores

• specialized channels inside the nuclear envelope that fuses the inner and outer membranes

• provides direct contact between cytosol and nucleoplasm (inner nuclear space)

Nuclear Pore Complex

• large protein structure lined with nuclear pores

• regulates selective transport of molecules between nucleus and cytoplasm

• built from 30 nucleoporins, which are proteins

• consists of central granule (transporter): helps move molecules across nuclear envelope

Central Granule

• found inside the nuclear pore complex

• helps move molecules across the nuclear envelope

• facilitates selective transport of large molecules while allowing passive diffusion (high to low concentration w/o energy) of smaller molecules

what molecules are moving inside the nucleus?

• enzymes and proteins

• synthesized in the cytoplasm and required for nuclear functions

• molecules enter and exit through nuclear pores

what molecules are moving out of the nucleus?

• RNA’s (mRNA, tRNA, rRNA)

• need to be exported for translation in the cytoplasm

• molecules enter and exit through nuclear pores

Simple Diffusion

movement of small molecules from area of high to low concentration, without using energy

• this movement occurs through nuclear pores

How do molecules move through nuclear pores?

Small Molecules (less than 10nm in diameter):

• move through simple diffusion

• NPC has tiny diffusion channels that allow for passive movement of small molecules

Large Molecules:

• move through active transport

• nuclear localization signals (NLS) is a specific amino acid sequence within the protein that acts as an address label

• the NLS consist of importins that guide the protein through NPC

• ensures that only proteins with NLS are transported into nucleus

Nuclear Localization Signals (NLS)

• involved in movement of large molecules through nuclear pores via active transport

• has a specific amino acid sequence within a protein that acts as an address label

• consists of importins that guide the protein through NPC

• ensures that only proteins with NLS are transported into the nucleus

Active Transport

• movement of large molecules from area of low to high concentration, using energy

How do molecules get transported into and out of the nucleus?

1. Nuclear import via ran/importin pathway

2. nuclear export via ran-independent and ran-dependent pathways

Nuclear Import via Ran/Importin Pathway

• Proteins with a nuclear localization signal (NLS) are recognized by importins, which guide them to the nuclear pore complex (NPC)

• The importin-protein complex is actively transported into the nucleus

• Inside the nucleus, Ran-GTP binds importin, causing it to release the protein

• The Ran-GTP-importin complex then returns to the cytoplasm, where Ran hydrolyzes GTP to GDP, releasing importin to start the cycle again

• This process ensures only the right proteins enter the nucleus

Nuclear Export via Ran-Independent and Ran-Dependent Pathways

• Nuclear export mainly moves RNA (like mRNA, tRNA, rRNA) from the nucleus to the cytoplasm

• Some RNA, like mRNA, is exported without needing Ran

• Adaptor proteins bind to the RNA and carry Nuclear Export Signals (NES)

• These signals are recognized by exportins

• Exportins guide the RNA-protein complexes through the nuclear pore complex (NPC) into the cytoplasm

Function of the Ran-GTP Gradient

The Ran-GTP gradient (high in the nucleus, low in the cytoplasm) is key for nuclear transport:

• In the nucleus, Ran-GTP:

  • Releases NLS-cargo from importin

  • Helps NES-cargo bind to exportin

• In the cytoplasm, Ran-GTP is hydrolyzed to Ran-GDP, ending the transport process.

• NTF2 carries Ran-GDP back into the nucleus

• Ran-GEF converts Ran-GDP back to Ran-GTP, to keep the cycle going

Nuclear Matrix (nucleoskeleton)

• insoluble fiber network that helps maintain the shape of the nucleus

Nuclear Lamina

• thin, dense network of protein fibers

• lines the inside of the inner nuclear membrane

• made of lamins, which are structural proteins (type of IF)

Chromatin Organization in the Nucleus

• Chromatin is not randomly arranged in the nucleus; it follows a specific organization

• During interphase, chromatin is spread out to allow access for transcription and other processes

• Each chromosome stays in its own distinct area, called a chromosome territory

Chromosome Territory

• each chromosome staying in its own distinct area

• prevents mixing of chromatin from different chromosomes

Nucleolus

• involved in ribosomal RNA synthesis and assembly of ribosomal subunits

Fibrils

• found in the nucleolus

• contains DNA that is actively transcribed into ribosomal RNA

Granules

• found in the nucleolus

• where ribosomal RNA molecules are combined with ribosomal proteins to form subunits

If you are studying a protein that is taken up into the nucleus, which part of the nucleus is most relevant for your study?

1. Nuclear pore

2. Nucleosome

3. Nucleolus

4. Histone

5. mRNA

1. Nuclear pore