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CORE NOTES CHAPTER A2.2: CELL STRUCTURE
Cells as the basic structural unit of all living organisms Based on cell theory, a newly discovered organism can be predicted to consist of one or more cells.
Microscopy skills
Microscopes with a high magnification and resolution are needed to observe cells and their subunits. Magnification is the increase in an object’s image size compared to its actual size. 𝑀𝑎𝑔𝑛𝑖𝑓𝑖𝑐𝑎𝑡𝑖𝑜𝑛 =×
Resolution is the minimal distance between two points or objects at which they can still be distinguished as two. As the resolution of a microscope increases, the greater the detail that microscope will reveal. Types of microscope Light microscope uses light to pass through living or dead specimens, forming an image. Stains can be used to improve the visibility of the structures. Electron microscopes provide the greatest magnification and resolution. These use electrons passing through a specimen to form an information. Light microscope Electron microscope Inexpensive to purchase and operate Expensive to purchase and operate Simple and easy specimen preparation Complex and lengthy specimen preparation Magnifies up to 2000 times Magnifies over 500000 times Specimens may be living or dead Specimens are dead and are fixed in a plastic material Comparison of size to cells largest smallest cells organelles bacteria viruses membrane molecules atoms Comparison of size of organelles largest smallest nucleus rER mitochondria Golgi body sER lysosome ribosome Units and its conversions Unit Equivalent measurement 1 metre (𝑚) 1 centimetre (𝑐𝑚) 0. 01 𝑚 ( 10 !"^ 𝑚) 1 millimetre (𝑚𝑚) 0.^001 𝑚^ (^10 !#^ 𝑚) 1 micrometre (𝜇𝑚) 0. 0000001 𝑚 ( 10 !$^ 𝑚) 1 nanometre (𝑛𝑚) 0.^0000000001 𝑚^ (^10 !%^ 𝑚)
Microscopy
Electron microscope A significant development in microscopy would be the development of the electron microscope (EM). The EM utilises a beam of electrons rather than a beam of light, which has a much shorter wavelength. The shorter wavelength of electrons would mean that it is 1000 times greater resolving power than the light microscope (LM), and the ability to magnify objects over 500000 times compared to the maximum magnification of 2000 times for a LM. Freeze-fracture electron microscopy Freeze fracture is a process of preparing a sample for observation with an EM. It involves rapidly freezing a biological specimen (plunged into a cold liquid e.g. liquefied propane at −190℃), followed by fracturing the frozen sample. This technique reveals a plane through the sample which then, can be examined. With this technique, our understanding of the cell membrane has been greatly enhanced. Cryogenic electron microscopy Cryogenic electron microscopy (CEM) also furthered our knowledge of structural biology. With CEM, using computer enhancement, an image that shows the 3D framework of proteins is formed. This technique advanced our understanding of virus composition and structure, cell membrane components and their arrangement, cellular protein synthesis and even hereditary expression and regulation.
Structures common to all cells
Deoxyribonucleic acid (DNA) Four different nucleotides (the building block of DNA), ATCG, make up DNA. Following the cell theory, for new cells to be formed form pre-existing cells, DNA must be present in order to store and transfer information. It is also needed for producing mRNA by transcription, so proteins can be synthesised. Cytoplasm The cytoplasm, which is mainly composed of water, is found within the boundary of a cell. It is the location of a cell where most chemical reactions take place. The region of a cell which consists of a matrix composed mainly of water is called cytosol. The cytosol contains all the ingredients (e.g. carbon compounds, ions and other inorganic compounds) necessary for a cell to conduct its day-to-day activities. Note! Cytoplasm and cytosol are different! Cytosol is a part of the cytoplasm.
Plasma membrane (more in B2.1: Membranes and Membrane Transport) The plasma membrane, composed of lipids, encloses the cell and protects its contents from the surrounding environment. It controls interaction between a cell’s content and the exterior. Its major component is two layers of lipids, combined as a bilayer, but proteins and 𝑃 element are also associated with this bilayer. Membrane proteins provide identity properties to the cell which is important for multicellular organisms. It also engages in communication and transport between cells.
Prokaryotes
Prokaryotes are organisms (bacteria and archaea) whose cells lack a nucleus and some organelles. Most prokaryotes are small, single-celled organisms that have a relatively simple structure. In prokaryotes, although there is no nucleus, there is still DNA but it is found in the cytoplasm itself. It is usually a single chromosome which is circular and naked (which means not associate with histones). There are also many ribosomes in the cytoplasm and they are “70S” which indicates the size of the ribosome (eukaryotes have 80S ribosomes). When numerous, they give a granular appearance to the prokaryotic cell under a EM. They function as sites of protein synthesis. Plasmids Bacteria may also contain plasmids, which are small and circular DNA molecules which are not connected to the main bacterial chromosome. They replicate independently of the chromosomal DNA. It helps the cell adapt to unusual circumstances. Gram-positive and Gram-negative bacteria Bacteria can be classified further by their ability to retain a dye called crystal violet. Bacteria that are “Gram-positive” (e.g. Bacillus and Staphylococcus) have cell walls that take on a violet or blue appearance when exposed to crystal violet. “Gram-negative)” bacteria do not retain this dye and appear neither violet or blue with a microscope. pili 70S ribosomes naked DNA in a loop Composed of carbohydrate-protein complex called peptidoglycan. Protects and maintains the shape of the cell, keeping the bacterial cell from rupturing especially when water pressure is greater inside of the cell than outside. Similar in composition to the membranes of eukaryotic cells. Plasma membrane controls the movement of materials into and out of the cell and plays a role in binary fission (not mitosis and meiosis). They join bacteria cells in preparation for the transfer of DNA from one cell to another (sexual reproduction). Flagella (plural) are always longer than the pili. Flagella is anchored to the cell wall and plasma membrane; it allows the cell to move. cytoplasm Involved with cell control and reproduction.
Cytoplasm The cytoplasm, is found within the boundary of a cell. It is the location of a cell where most chemical reactions take place. The region of a cell which consists of a matrix composed mainly of water is called cytosol. Eukaryotic cytoplasm has a cytoskeleton (network of fibres), which creates a complex internal structure. Prokaryotic cytoplasm does not have a cytoskeleton. These fibres are composed of protein and performs the following functions:
- maintaining the cell shape
- anchoring some organelles
- aiding cellular movements
- providing means for some organelles to move within the cell The cytoskeleton contains the following:
- Actin filaments Actin filaments (also known as microfilaments) function in cell division and cell movement, especially involving contractions (e.g. in muscle cells).
- Intermediate filaments Intermediate filaments are found in most animal cells and reinforce cell shape and anchoring some organelles.
- Microtubules Microtubules also shape and support the cell and also function as movement paths of tracks through the cell for some organelles. Nucleus The nucleus in eukaryotic cells is an isolated region where DNA resides. It is bordered by a double membrane , known as the nuclear envelope. The nuclear envelope does have pores which allow communication with the cell’s cytoplasm. It allows for compartmentalisation of the eukaryotic DNA, providing an area where DNA can conduct its functions without being affected by other processes occurring in the cell. DNA of a eukaryotic cell often occurs in the form of chromosomes which carry all the information that is necessary for the cell to exist, thus, allowing an organism to survive (for both unicellular and multicellular). Note! DNA is the genetic material of the cell and certain traits are passed on to the next generation. Chromosomes are not visible in interphase and they are in the form of chromatin. Chromatin is formed on strands of DNA and proteins called histones. The combination of a strand of DNA wrapped around eight spherical histone and secured with a linker histone results in structures called nucleosome. made of spindle bundle e.g. the movement of vesicles from the rER to the Golgi body
Most eukaryotic cells possess a single nucleus, but some do not have a nucleus at all, while some have multiple nuclei. Without a nucleus, cells cannot reproduce. However, the loss of reproductive ability is often paired with increased specialisation to carry out certain functions. An example would be human’s RBC which does not have a nucleus so that they are able to carry more haemoglobin, hence, more oxygen as their function is to transport respiratory gases. Most nuclei also contain nucleolus (plural: nucleoli). The nucleolus’ function is to transcribe ribosomal RNA (rRNA). Smooth endoplasmic reticulum (sER) sER does not have ribosomes on its exterior surface. Its function includes:
- production of phospholipid membrane and cellular lipids
- production of sex hormones (e.g. testosterone – there would be more sER in the testes)
- detoxification (e.g. of drugs, in the liver)
- storage of calcium ions in muscle cells (needed for contraction)
- transportation of lipid-based compounds
- helping the liver release glucose into the bloodstream when needed (homeostasis) Rough endoplasmic reticulum (rER) rER has ribosomes on the exterior of its channels and is usually closer to the nuclear membrane. It participates in protein synthesis, so it engages in protein development and transport. Usually these proteins by the rER would be secreted out of the cell (via exocytosis). Ribosomes Ribosomes are composed of rRNA and protein. They do not have an exterior membrane and they can be found free in the cytoplasm or attached to the surface of ER. They conduct protein synthesis within the cell. Free ribosomes in the cytoplasm synthesise proteins for the cell. Note! The ribosomes of eukaryotic cells are larger and denser (80S) than those of prokaryotic cells (70S). Golgi apparatus The Golgi apparatus, or Golgi body, consists of flattened sacs which are stacked one on top of another, called cisternae. The Golgi apparatus functions in the collection, packaging, modification and distribution of materials synthesised in the cell. The cis side, usually the side nearer to the rER, receives products for the ER. The products move into the cisternae of the Golgi body and move to the trans face, the discharging side. Vesicles will be secreted out.
Chloroplast (adaptations found in greater detail in Chapter B2.2: Organelles and Compartmentalisation) Chloroplasts also has a double membrane and can only be found in algae and plant cells. Chloroplast DNA takes the form of a ring. Like mitochondria, chloroplasts also contain their own DNA (so they can reproduce independently of the cell) have their own 70S ribosomes. Centrosome (animal cells only) Centrosome (an area that is composed of centrioles) is present in all eukaryotic cells. In animal cells, the centrosome contains a pair of centrioles that are at right angle to one another. The centrioles are important for the assembly of microtubules (which provide structure, allow movement and is important for cell division). Plant and fungal cells do not have centrioles but they are able to produce microtubules from centrosome-like regions, suggesting that centrioles are not necessary for production of microtubules. Basal bodies are structures related to the centrosome of eukaryotic cells which are located near the base of cilia and flagella. Basal bodies direct the assembly of microtubules within the associated cilia or flagella. Not all eukaryotic cells have cilia and flagella, so not all eukaryotic cells have basal bodies. Vacuoles Vacuoles are storage organelles which are membrane-bound, formed from the Golgi apparatus. In plant cells, they occupy a large space (called a central vacuole) while in animal cells, they are small and may be numerous. Vacuoles may store several different substances including, food (provide nutrition in plant cells), metabolic waste, toxins (to be expelled from the cell) and water. In plants, vacuoles also allow an uptake of water to provide rigidity to the organism. inner membrane outer membrane granum (plural: grana) stroma thylakoid intermembrane space Thylakoids are flattened membrane sacs that contains chlorophyll which is necessary for absorption of light. A stack of thylakoid is called granum, a few stacks of thylakoid is called grana. Thylakoids are arranged into stacks to increase SA:V ratio of the thylakoid membrane. The stroma is like the cytoplasm, it is within the double membrane. It is a colourless fluid around the thylakoids which contain many enzymes and provide a suitable pH for Calvin cycle to occur.
Differences of eukaryotic cell structure between animal, fungi and plants
Feature Animals Fungi Plants Cell wall No cell wall Outer cell wall composed of chitin Outer cell wall composed of cellulose Shape Cell wall absent – flexible and (usually) a rounded shape Cell wall allows a degree of flexibility and support of the cell, shape varies Rigid cell wall present – so it has a fixed and (usually) angular shape Chloroplasts No chloroplasts No chloroplasts Chloroplasts are present, allowing for the production of carbohydrates Vacuole Generally small and numerous with many unique functions Generally small and numerous with many unique functions Large central vacuole for the storage of carbohydrates Carbohydrate form Carbohydrate stored as glycogen Carbohydrate stored as glycogen Carbohydrate stored as starch Cilia, flagella, basal bodies May have cilia or flagella, and its associated basal bodies May have cilia or flagella, but does not have associated basal bodies Does not contain cilia, flagella or basal bodies Centrosomes and centrioles Possess both centrosomes and centrioles Possess centrosomes but no centrioles Possess centrosomes but not centrioles When an organelle is present in each of the eukaryotic cell types, it usually has the same structure and function. No centrioles – no basal bodies!
Atypical cell structures in eukaryotes
Fungal hyphae Some multicellular fungi produces filaments called hyphae. They consists of chains separated by cross-walls with pores, allowing various organelles and cytoplasm to flow from cell to cell. However, some fungi produce hyphae that lack cross- walls (aseptate / coenocytic). This causes one cell to have more than one nucleus in a single mass of cytoplasm. Phloem sieve tube elements Phloem sieve tube elements have end walls with pores and no cellular components such as nuclei , ribosomes , cytoskeleton and cytoplasm. They are connected end to end, forming tube structures. However, these cells can only remain alive with the help of companion cells. Red blood cells Red blood cells carries oxygen which throughout the body. Oxygen is carried by combining with haemoglobin present in the RBC. Red blood cells do not have a nucleus , which allows them to carry even more oxygen. Human skeletal muscle The human skeletal muscle specialises in allowing body movement. It carries out this function with the presence of specialised proteins arranged in bands that contract and relax. The presence of cell membrane is limited, resulting in large, tubular cells with multiple nuclei which helps in the coordination of protein molecules.
Endosymbiosis
Evidence suggests that all eukaryotes evolved from a common unicellular ancestor that had a nucleus and reproduced sexually. This common ancestor respired anaerobically but it ingested an aerobically respiring bacterium (developed into the mitochondria) which remained alive inside a vacuole in the cytoplasm, giving the common ancestor a supply of ATP produced efficiently by aerobic respiration. The bacterium was provided with food, allowing it to grow and divide and be passed on to daughter cells when the host cell divided. This type of relationship is endosymbiosis because the organisms live together (symbiosis) with one inside the other (endo) – it is a mutualistic relationship because they both benefit. Some eukaryotes also ingested photosynthetic bacteria, which developed into the chloroplasts of plants and eukaryotic algae.
Evidence supporting endosymbiotic theory of mitochondria and chloroplasts Both mitochondria and chloroplasts have:
- a loop of naked DNA
- 70S ribosomes (so they make their own proteins which suggests they were once independent cells; the size of ribosome is the same of that in bacteria)
- reproduce by splitting in two
- double membrane (bacterium with its own plasma membrane was ingested in a vacuole formed by endocytosis will result in double membrane)
Cell specialisation
Apart from endosymbiosis, another very important process that helped the development of the cell was compartmentalisation. Membranes play a major role in the formation of compartments, enabling efficient reactions and processes to proceed. This resulted in specialisation within the cell. For example, the nucleus has a nuclear envelope which allows DNA molecules to function without the interference from other reactions that are taking place in the cytoplasm. The mitochondria also has a membrane which allows energy to be produced for the cell.
Multicellularity
Even with specialisation, a single-celled organism has its limits. Multiple cells present in eukaryotic organism led to cell differentiation in the organism which allowed for highly specialised tissues and organs. Multicellularity is advantageous because:
- its lifespan would be longer (the death of one cell does not prevent the continued survival of the organism)
- larger body size is possible (useful in predatory animals or plants that compete for light)
- cell differentiation (each cell carries out its function more effectively and more complex body forms can develop) All cells in a multicellular organism have the same genetic information but for specialisation and differentiation to occur, mechanisms have developed to control and coordinate gene expression.
© IB Biology 2023 Edition Oxford Study Guide
