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Summary - Cell Biology (AB_1047) Vrije Universiteit Amsterdam

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Cell Biology (AB_1047)

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Vrije Universiteit Amsterdam (VU)

This summary covers the complete study material including the lectures and workgroups for the first exam of the course Experimental Cell Biology at VU Amsterdam.

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Uploaded on October 25, 2023
Number of pages 48
Written in 2022/2023
Type Summary

cell biology
processes
cell structure
apoptosis

Institution
Vrije Universiteit Amsterdam (VU)
Education
Biomedical Sciences
Course
Cell Biology (AB_1047)

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Cell biology – the basics

The cell (from latin cella, meaning ‘small room) is the basic structural, functional and biological unit of all organisms. A cell is
the smallest unit of life. Cells are often called the ‘building blocks of life’. The study of cells is called biology, cellular biology
or cytology. Cells come in different shapes and sized but they all share common properties.

Cells consist of a cytoplasm enclosed within a membrane, which contains many biomolecules such as proteins and nucleic
acids. Cells have their own metabolism and can regulate their growth and division. They also respond to environmental
signals through internal and external communication. most plant and animal cells are only visible under a microscope, with
dimensions between 1 and 1100 micrometers. Organisms can be classified as unicellular (= consisting of a single cell such as
bacteria) or multicellular (= including plants and animals). Most unicellular organisms are classed as microorganisms.

Cell biology is a branch of biology studying the structure and function of the cell, also known as the basic unit of life. Cell
biology encompasses both prokaryotic and eukaryotic cells and can be divided in many sub-topics. The study of cells is
performed using several techniques such as cell culture, various types of microscopy, and cell fractionation. These have
allowed for and are currently being used for discoveries and research pertaining to how cell functions, giving insight into
understanding larger organisms. Knowing these cell components is fundamental to all biological sciences while also being
essential for research in biomedical fields such as cancer, and other diseases. Cell biology is interdisciplinary; research in cell
biology is interconnected to other fields such as genetics, molecular genetics, biochemistry, molecular biology, medical
microbiology, immunology, and cytochemistry.

The basic features of all cells:

- Membrane-enclosed unit of life
- Metabolism → chemical reactions involved in maintaining the living state of the cells and the organism.
- Growth and division
- Response to environmental signals, internal and external communication.

All cells, whether prokaryotic or eukaryotic, have a membrane that envelops the cell, regulates what moves in and out
(selectively permeable), and maintains the electric potential of the cell. inside the membrane, the cytoplasm takes up most
of the cell’s volume. All cells (Except red blood cells which lack a nucleus and most organelles to accommodate maximum
space for hemoglobin) possess DNA, the hereditary material of genes, and RNA, containing information necessary to build
various proteins e.g. enzymes. Building proteins from DAN is seen as the cell’s primary machinery. There are also other
kinds of biomolecules in cells, called metabolites (=molecules produced or altered by cells).

The central dogma of molecular biology is an explanation of the flow of genetic information within a biological system.
DNA → RNA → protein. The central dogma of molecular biology deals with the detailed residue-by-residue transfer of
sequential information. It states that such information cannot be transferred back from protein to either protein or nucleic
acid. a second version of the central dogma is popular but incorrect. Nowadays, it is stated that interplay between these
factors (DNA, proteins and metabolites) are very important.

- DNA: genetic material
- Proteins: workhorses
- Metabolites: molecules that are produced/altered by the cell.

Prokaryotic cell (= type of cell that does not have a nucleus or membrane-
bound organelles) → bacteria and archaea. The outer layer is the capsule.
Underneath the capsule, we have the cell wall. Under the cell wall, the plasma
membrane is located. After the plasma membrane, we have the cytoplasm which
contains the nucleoid (circular DNA), bacterial flagellum, ribosomes and plasmids.
The capsule contains pili as well.

Prokaryotes include bacteria and archaea, two of the 3 domains of life.
Prokaryotic cells were the first form of life on earth, characterized by having vital
biological processes including cell signalling. They are simpler and smaller than
eurkaryotic cells, and lack a nucleus and other membrane-enclosed organelles.
The DNA of prokaryotic cells consist of single circular chromosomes that is in
direct contact with the cytoplasm. the nuclear region of the cytoplasm is called

,the nucleoid. Most prokaryotes are the smallest of all organisms ranging from 1-5 µm in diameter. Prokaryotic cells are
biochemically flexible. A prokaryotic cell has 3 regions:

1. cell envelope → enclosing the cell is the cell envelope (the cell capsule, cell wall and plasma membrane together).
Though most prokaryotes have both a cell membrane and a cell wall, there are exceptions such as the Mycoplasma bacteria
and Thermoplasma archaea which only have the cell membrane layer; all prokaryotic cells have a cell membrane, but do
not necessarily need to have the cell wall and cell capsule. The cell envelope gives rigidity to the cell and separates the
interior of the cell from its environment, serving as a protective filter. The cell wall contains peptidoglycan in bacteria, and
acts as an additional barrier against exterior forces. It also prevents the cell from expanding and bursting (cytolysis; the
dissolution/disruption of cells, especially by an external agent) from osmotic pressure due to the hypotonic environment.
some eukaryotic cells (plant cells and fungal cells) also have a cell wall.

2. cytoplasm → inside the cell we have the cytoplasmic region that contains the genome (DNA), ribosomes and various
sorts of inclusions. The genetic material is freely found in the cytoplasm. prokaryotes can carry extrachromosomal DNA
elements called plasmids, which are usually circular. Although there is no nucleus in prokaryotes, the DNA is in fact
condensed in a nucleoid. Plasmids encode additional genes, such as antibiotic resistance genes. Nucleoid= space within a
prokaryotic cell where the genetic material is found.

3. On the outside of prokaryotic cells, we have flagella and pili project from its surface. These are structures (not present in
all prokaryotes) made of proteins that facilitate movement and communication between cells.

Thus a typical prokaryote is small (1-5µm), single-cell, no membrane-enclosed compartments and biochemically flexible.

Eukaryotic cells → plants, animals, fungi, slime moulds, protozoa, and algae are all eukaryotes. These cells are larger
than a typical prokaryote (20-50µm) and can be as much as thousand times greater in volume. The main distinguishing
feature of eukaryotes as compared to prokaryotes is compartmentalization = the presence of membrane-bound organelles
(Compartments) in which specific activities take place. Most important among these is a the cell nucleus (= an organelle
that houses the cell’s DNA). this nucleus gives the eukaryotes its name, which means ‘’trye kernel (=nucleus). Other
differences include:

1. the plasma membrane resembles thar of prokaryotes in function, with minor differences in setup. Cell walls may or may
not be present.

2. the eukaryotic DNA is organized in one/more linear molecules (= chromosomes), which are associated with histone
proteins. all chromosomal DNA is stored in the cell nucleus, separated from the cytoplasm by a membrane. Some
eukaryotic organelles e.g. mitochondria also contain some DNA.

3. Many eukaryotic cells are ciliated with primary cilia. Primary cilia play roles in chemosensation, mechanosensation, and
thermosensation. Each cilium may thus be viewed as a sensory cellular antennae that coordinate a large number of cellular
signalling pathways, sometimes coupling the signalling to ciliary motility or alternatively to cell division and differentiation.

4. most eukaryotes can move using motile cilia or flagella. Motile cells are absent in flowering plants and conifers.
Eukaryotic flagella is more complex than the prokaryotic flagella.

Thus, a eukaryotic cell is typically larger (20-50µm), is multi-cellular and has membrane-enclosed compartments. Its
compartments:

- Nucleus (DNA synthesis, transcription, RNA synthesis (nucleolus) → = the cell’s information center. It houses the
cell’s chromosomes, and is the place where almost all DNA replication and RNA synthesis (transcription) occur.
the nucleus is spheric and separated from the cytoplasm by a double membrane called the nuclear envelope. The
nuclear envelope isolates and protects the cell’s DNA from various molecules that could accidently damage its
structure or interfere with its processing. During processing, DNA is transcribed, or copied in mRNA. this mRNA is
then transported our of the nucleus, where it is translated into a specific protein.
The nucleolus is a specialized region within the nucleus where ribosomes are assembled; ribosome/RNA synthesis
takes place. The nucleolus is involved in protein quality control. Not in every region of the nucleolus there is
equal distribution of proteins; some regions are more dense than others; this has to do with the folding/unfolding
of proteins. In prokaryotes, DNA processing takes place in the cytoplasm!!!!!!!!!!!! In eukaryotes, DNA processing
happens in the nucleus.

The nuclear pores in the nuclear envelope make exchange/transport possible. the nucleus is surrounded by a
phospholipid membrane.

- Endoplasmatic reticulum (protein modification + transport/sorting): is a transport network for molecules
targeted for certain modifications and specific destinations (first station for secreted proteins), as compared to
molecules that float freely in the cytoplasm. we have the rough ER (which has ribosomes on its surface that
secrete proteins into the ER) and the smooth ER (which lacks ribosomes). The SMOOTH ER plays a role in calcium

, sequestration and release! The ER is closely related to protein synthesis. Membrane proteins are inserted in the
ER and mitochondrial division is initiated in the ER.

- Golgi apparatus (packaging) → the primary function of the Golgi is to process and package the macromolecules
e.g. proteins and lipids that are synthesized by the cell. modification, in particular glycosylation occurs in the Golgi
to sort the newly synthesized proteins. there are various mechanisms for glycosylation, although most share
several features

glycosylation is an enzymatic process. it is the most complex post-translational
modification, because of the large number of enzymatic steps involved. the donor
molecule is often an activated nucleotide sugar. The process is non-templated;
glycosylation is a site-specific modification because the cell relies on the segregating
enzymes into different cellular compartments.

An eukaryotic cell typically contains 40-100 stacks of cisternae. This collection of cisternae
can be broken down into a cis, medial and trans compartments, making up 2
compartments: the cis Golgi network (CGN) and the trans Golgi network (TGN). The CGN is
the first cisternal structure, and the TGN is the final, from which proteins are packaged into
vesicles. The TGN may acts as an early endosome in yeast and plants. In some yeasts, Golgi
stacking is not observed so there might be structural and organizational differences in the Golgi among
eukaryotes.

- Mitochondria + chloroplast → generate energy for the cell. mitochondria are self-replicating organelles that
occur in various numbers, shapes and sizes in the cytoplasm of all eukaryotic cells. respiration (= metabolic
process by which oxygen is combined with a carbon to form CO2 and generate energy) occurs in the cell
mitochondria, which generate the cell’s energy by oxidative phosphorylation, using oxygen to release energy
stored in cellular nutrients (typically pertaining to glucose) to generate ATP. Mitochondria multiply by binary
fission, like prokaryotes. Experiments show that the ER might be responsible for the division of the mitochondria.
Chloroplasts can only be found in plants and algae, and they capture the sun’s energy to make carbohydrates
through photosynthesis. In the mitochondria, energy metabolism and fatty acid oxidation takes place. You can
find here the citric acid cycle (which is a key cycle of metabolism that produces energy) of which ATP is produced.
Mitochondria have an inner membrane and an outer membrane. Inside you can find the matrix (=liquid).

- Lysosomes (hydrolytic enzymes, degradation processes) → lysosomes contain
digestive enzymes (hydrolytic enzymes). They digest excess/worn-out organelles,
food particles, and engulfed viruses or bacteria. The primary function of a
lysosome is to degrade particles, but it is found that lysosomes are involved in
signalling and secretion as well! lysosomes play a key role in autophagy (=
destruction of damaged/redundant cellular components occurring in vacuoles
within a cell). lysosomes are surrounded by a lipid bilayer; the most outer later
contains glycosylated membrane transport proteins.

Signalling and secretion → when a lysosome degrades an autophagosome or a
late endosome, a signal is sent to the nucleus; the nucleus will take up this signal and send a feedback to the
lysosome to control its function. As a respond to this feedback of the nucleus, the lysosome can secrete
specialized molecules e.g. plasma membrane repair molecules.

- Transport vesicles → a vesicle is a structure within/outside a cell, consisting of liquid or cytoplasm enclosed by a
lipid bilayer. Vesicles form naturally during the processes of secretion (exocytosis), uptake (endocytosis) and
transport of materials within the plasma membrane. Transport vesicles can move molecules between locations
inside the cell e.g. proteins from the RER to the Golgi apparatus. Membrane-bound and secreted proteins are
made on ribosomes found in the RER. Most of these proteins mature in the Golgi before going to their final
destination. These proteins travel within the cell inside of transport vesicles.

They are crucial for distribution of material and information from cell to cell. the transport vesicles are closely
related to the ER and the Golgi apparatus.

- The cytosol (water-based gel) and cytoplasm: is the liquid matrix inside the cells. it occurs in both eukaryotic and
prokaryotic cells. in eukaryotic cells, the cytosol includes liquid enclosed within the cell membrane but NOT in in
the nucleus, organelles (e.g. chloroplasts, mitochondria, vacuoles) or fluid contained within organelles. In
contrast, all of the liquid within a prokaryotic cell is cytoplasm, since prokaryotes lack organelles or a nucleus. The
cytosol is a component of the cytoplasm; the cytoplasm includes the cytosol, all organelles, and the liquid

, contents inside these organelles. The cytoplasm does not include the nucleus. Most metabolic reactions take
place in the cytosol. The cytosol is a complex mixture of substances dissolved in water. the concentrations of ions
is different in the cytosol than in the extracellular
fluid; these differences in ion levels are important in
processes e.g. osmoregulation, cell signalling, and
the generation action potentials in excitable cells
such as endocrine, nerve and muscle cells. the
cytosol also contains large amounts of
macromolecules, which can alter how molecules
behave, through macromolecular crowding.

In the cytosol, you can find a broad range of
molecules (micro and macro molecules) and many
chemical reactions take place here. It is very
crowded which makes the effective concentrations
(and reaction rates) higher. When the cytosol is
highly concentrated/crowded, then that means that
the effective concentration of the metabolites is
higher. This is because the rate of chemical
reactions depend on the concentrations of the
metabolites that are present in the cytosol. So
crowding can affect the rates of the chemical reactions.

- The cytoskeleton: the cytoskeleton acts to organize and maintain the cell’s shape. It anchors organelles in place
and helps during endocytosis, the uptake of external materials, cytokinesis, the separation of daughter cells after
cell division and moves parts of the cell in processes of growth and mobility. The eukaryotic cytoskeleton is
composed of microfilaments, intermediate filaments and microtubules. There are a great number of proteins
associated with them, each controlling a cell’s structure by directing, bundling and aligning filaments. The subunit
of microtubules in a monomeric protein is actin, the subunit of microtubules in a dimeric molecule is tubulin.
Intermediate filaments are heteropolymers whose subunits vary among cell types in different tissues. But some of
the subunit protein of intermediate filaments include keratin.
- Ribosomes → the ribosome is a large complex of RNA and protein molecules. They each consist of 2 subunits and
act as an assembly line where RNA from the nucleus is used for the synthesis of proteins from amino acids.
Ribosomes can be found either floating freely or bound to a membrane (the RER in eukaryotes of the cell
membrane in prokaryotes).

Energy metabolism

Metabolism the set of life-sustaining reactions in organisms. The 3 main purposes of metabolism are:

- The conversion of food to energy in order to run cellular processes
- The conversion of food/fuel to building blocks for proteins, lipids, nucleic acids and some carbohydrates
- The elimination of metabolic wastes.

Cells need energy for metabolism e.g. biosynthesis, transport and movement. Energy for these energy consuming processes
to be provided by breakdown of molecules in diet: carbohydrates, lipids and proteins. energy derived from diet molecules
and stored according to universal principle (‘energy currencies’) are Adenosine triphosphate (ATP) and the ion motive
forces across the membranes.

The word metabolism can also refer to the sum of all chemical reactions that occur in living cells, including digestion and
the transport of substances into and between different cells → intermediate metabolism.

- ATP is an organic compound and hydrotrope that provides energy to drive many processes in living cells e.g.
muscle contraction, nerve impulse propagation, condensate dissolution, and chemical synthesis. Found in all
known forms of life, ATP is often referred as the ‘molecular unit of currency’ of intracellular energy transfer.
When consumed in metabolic processes, it converts either to ADP or AMP. Other processes regenerate ATP so
that the human body recycles its own body weight equivalent in ATP each day.
when ATP is used, a phosphate group is released from the ATP, making it ADP and this phosphate group us used
for energonic reactions.
- Proton-motive force (bacteria, mitochondria, chloroplasts): the movement of ions across the membrane
depends on a combination of factors:
a. diffusion force caused by a concentration gradient – all particles tend to diffuse from a high concentration to a
low concentration.

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