A collection of blog posts connected to my teaching on biomedical sciences and biochemistry degrees. All views and opinions expressed are my own, and not connected to my past, present or future employers.
In the video, I examine the history and functions of mitochondria. I start with Rudolf Albert von Kölliker's initial description in 1852 and subsequent naming by Carl Benda in 1898. I explain how these organelles are more than just static power plants of the cell. I highlight the dynamic nature of mitochondria, their ability to form networks, and their crucial roles in energy production and cellular metabolism.
In this video, I explore the organisation within the nucleus, emphasising that it is structured rather than chaotic. I explain how Spectral Karyotyping reveals that chromosomes occupy specific territories and highlights the structured nature of chromatin, which can be either open or closed and influences transcription and replication. I also examine the nucleolus, describing its crucial role in producing ribosomes and signal recognition particles (SRP) and outlining the complex processes of ribosomal RNA (rRNA) synthesis and assembly.
In the video, I explore the structure and function of the nuclear envelope and its critical role in maintaining the environment of the nucleus. I explain how the nuclear pore facilitates gated transport, allowing materials to move between the nucleus and the cytosol. Highlighting its complexity, I described how the nuclear pore is composed of numerous nucleoporins, forming a cylindrical channel that selectively regulates the passage of molecules based on their size, with larger molecules requiring active transport mechanisms.
The video explains that the nuclear envelope, consisting of inner and outer membranes, protects DNA from mechanical stress and regulates the nucleus's internal environment, essential for proper mRNA processing. I highlight the role of the nuclear lamina in safeguarding DNA. I describe the challenges posed by the nuclear envelope, such as the need to disassemble during cell division and manage material exchange via nuclear pores. Overall, the nuclear envelope is crucial for maintaining nuclear integrity and function despite its associated complexities.
The video explains the cell nucleus, highlighting its roughly spherical shape and double membrane structure, which includes an inner and outer membrane with a perinuclear space. It describes the nucleus's contents, such as chromatin for gene transcription and mRNA splicing, and features like nuclear pores for transport and the nuclear lamina for structural support and various cellular functions. Additionally, I note that the outer nuclear membrane and perinuclear space are continuous with the endoplasmic reticulum.
Endosomes are cellular compartments that sort and traffic proteins from the Golgi apparatus and the plasma membrane. They are formed by vesicle fusion and are divided into three types
Early endosomes - receive proteins and decide their next destination
Recycling endosomes - return proteins to the plasma membrane either immediately (constitutive pathway) or based on signals (regulated pathway).
Late endosomes - forward proteins to lysosomes or back to the Golgi.
The endosomal system relies on specific signals on proteins to direct their correct routing, ensuring efficient cellular function.
Blog Bonus: Free step-by-step guide explaining the calculation - download.
The video is a response to two questions I was asked:
How do I calculate the size of a protein on an SDS-PAGE gel?
Can the DNA method be used for proteins?
In the video and the free step-by-step guide explaining the calculation, I go over the necessary steps for working out the size of a protein band on a gel, explain the Retention Factor (Rf value) and how to use it, and outline the method's limitations.
Feel free to leave any questions or comments below. If you need further clarification on any step or have suggestions for future topics, let me know!
The Golgi apparatus (possibly my favourite organelle) was discovered by Camillo Golgi in 1898 and confirmed in the 1950s.
Structurally, the Golgi resembles a stack of plates, and it has three distinct regions: the cis face (closest to the ER), the medial Golgi, and the trans face (furthest from the ER). The primary function of the Golgi is to process and sort proteins received from the ER, directing them to lysosomes, endosomes, or the plasma membrane.
There are two main theories for how the Golgi operates:
Vesicle Transport Model - proteins move to the machinery.
Cisternal Maturation Model - machinery moves to the proteins.
Evidence, such as vesicular tubular clusters and vesicles' size constraints, supports the Cisternal Maturation Model. In this model, the Golgi's cisternae mature over time, recycling enzymes via COPI vesicles.
Upon leaving the Golgi, proteins can enter one of two pathways:
Constitutive secretory pathway - direct to the cell surface)
Regulated secretory pathway - via secretory vesicles and requires a signal for the vesicles to traffic further.
The ER is a vital cellular structure with two types: rough ER (RER) and smooth ER (SER). The RER is covered in ribosomes and is essential for protein production. Proteins are synthesised and threaded into the ER lumen via a process involving signal recognition particles (SRP) and the Sec61 complex.
Membrane-spanning proteins are produced at the RER by using various signal sequences that direct their insertion into or through the membrane. The ER also plays a role in N-linked glycosylation, adding N-linked oligosaccharides to proteins and in quality control, ensuring proteins are correctly folded and functional.
In contrast, the SER lacks ribosomes, synthesises lipids, and forms vesicles for transporting proteins and lipids to the Golgi apparatus.
When I was a student, one of my go-to books was a glossary of terms for bioscientists. I used the glossary when I was learning new material to look up things I didn’t understand and remind myself of what I had previously learned. I found it an invaluable learning and revision tool.
Sadly, the book is no longer in print, so I decided to write my own and I have just published The Biosciences Glossary on the Google Play Book Store.
The Biosciences Glossary
The book defines over 2,000 words, phrases, terms, and abbreviations used in the biosciences. It also includes 80+ chemical structures with links to additional information and to my videos on YouTube.
If you go to The Biosciences Glossary on the Google Play Book Store, you can review 20% of the book for free and decide if it would help you in your studies.
Peroxisomes are involved in fatty acid oxidation and detoxification. The import of proteins into the peroxisomes relies on a short SKL motif at the C-terminal of the protein, which acts as an address.
The SKL motif binds to the PTS1R receptor in the cytosol, which then interacts with the Pex14P receptor on the peroxisome membrane. The protein can either be imported with or without the receptor entering the peroxisome.
Proteins destined for the mitochondria begin their journey in the cell's cytosol, guided by a signal peptide that acts like a "postcode." This signal, located at the N-terminal of the precursor protein, directs the protein to the mitochondria.
The video looks at the role of the Translocase of the Outer Membrane (TOM) and the Translocase of the Inner Membrane (TIM), along with the OXA complex, during the import process and discusses how proteins are targeted to the outer and inner membranes, the intermembrane space and the matrix of the mitochondria.
Vesicle trafficking is a crucial cellular process where vesicles transport materials to specific organelles or membranes. This process involves the SNARE hypothesis, where vesicles have vesicle SNAREs (vSNAREs) and target membranes have target SNAREs (tSNAREs). The vSNAREs and tSNAREs recognise each other, ensuring that vesicles dock at the correct membranes.
However, the SNARE proteins are promiscuous and can bind with multiple partners, posing challenges for precise docking. To address this, cells use Tether proteins, which operate over greater distances and add an additional layer of specificity. Tether proteins help vesicles recognise their target membranes, while SNAREs facilitate the fusion process.
This combined mechanism ensures accurate vesicle targeting and fusion, which is regulated by a GTP timer that coordinates the events.
Protein sorting involves directing proteins, which originate on ribosomes in the cytosol, to their appropriate cellular locations using specific amino acid sequences known as sorting signals. These sorting signals function like postcodes, guiding proteins to various organelles or membranes within the cell, such as the nucleus, peroxisomes, or the endoplasmic reticulum. The cell employs different types of transport mechanisms—gated, transmembrane, and vesicular—to move proteins to their correct destinations, ensuring proper cellular function.
Vesicles are crucial for transporting molecules, and they are formed in one of three ways:
Clathrin-coated vesicles - Traffic from the Golgi to the endosomes and from the plasma membrane to the endosomes.
COPI-coated vesicles - Move from the Golgi to the endoplasmic reticulum, within the Golgi stack, and from the Golgi to the plasma membrane.
COPII-coated vesicles - Travel from the endoplasmic reticulum to the Golgi.
In this video, I look at how vesicles are formed and targeted within a cell.
In the video, I explore some common themes and look at the formation of the coat (clathrin, COPI, or COPII) and the pinching off of the vesicle from the membrane.
This is an interesting question: "How much membrane is in a cell?".
In this video, I use a football and some sheets of material to explore how much membrane we have in a cell and which organelles have the most membrane.
This was a fun video to make, and I got some very odd looks from passing dog walkers.
Cells have organelles, and they need to transport the correct molecules to those organelles — if they don't, the cell will not function correctly and will die.
The cell has three ways of moving molecules around:
Vesicular transport
Gated transport
Transmembrane transport
This video also looks at vesicular transport, which uses small membrane-bound sacs to move proteins, lipids, and other molecules throughout the cell.
The video introduces the concepts of Endocytosis and Exocytosis - including Phagocytosis, Pinocytosis and Receptor-Mediated Endocytosis, along with Constitutive and Regulated Pathways.
In this video, I look at why cells have organelles - my answer might surprise you.
I also examine the different organelles, discuss how proteins are targeted to these organelles, and describe the mechanisms used to get proteins across membranes.