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1. UNIT 1 - Molecules to Organisms: Structures and Processes
CHAPTER 1.1-PROKARYOTIC AND EUKARYOTIC CELLS
Scope: Prokaryotic cells differ from eukaryotic cells in their structure and functions. Prokaryotic cells lack organelles and have less developed sub-cellular structures while eukaryotic cells have well- developed organelles with specific functions. Structures such as cell membrane, cytoplasm, DNA, and ribosomes are present in both prokaryotic cells. Prokaryotes are unicellular organisms that are small and have a simpler structural organization, and compose the Kingdom Monera. Eukaryotes are both unicellular and multicellular organisms having complex structures and constitute the Protista, fungi, plant, and animal kingdoms. Eukaryotes are presumed to have evolved from prokaryotes. Objective(s):
- Explain with scientific reasons that eukaryotic cells are more complex than prokaryotic cells.
- Construct arguments using scientific reasons that eukaryotes are more evolved than prokaryotes.
- Design a model (illustration or simulation) to demonstrate the changes during the evolution of eukaryotes from prokaryotes. Comparing Prokaryotic and Eukaryotic Cells Cells fall into one of two broad categories: prokaryotic and eukaryotic cells. The predominantly single- celled organisms of the domains Bacteria and Archaea are classified as prokaryotes. Animal cells, plant cells, fungi, and protists are eukaryotes. All cells share four common components: a plasma membrane , an outer covering that separates the cell’s interior from its surrounding environment; cytoplasm , consisting of a jelly-like region within the cell in which other cellular components are found; DNA, the genetic material of the cell; and ribosomes, particles that synthesize proteins. However, prokaryotes differ from eukaryotic cells in several ways. The most fundamental differences between prokaryotes and eukaryotes relate to how their cells are set up. Specifically: Eukaryotic cells have a nucleus, a membrane-bound chamber where DNA is stored, while
prokaryotic cells don't. This is the feature that formally separates the two groups. Eukaryotes usually have other membrane-bound organelles in addition to the nucleus, while prokaryotes don't. Cells in general are small, but prokaryotic cells are really small. Typical prokaryotic cells range from 0.2-2μm in diameter, while typical eukaryotic cells range from 10- 100 μm in diameter. Components of Prokaryotic Cells
- CAPSULE Many prokaryotes have a sticky outermost layer called the capsule, which is usually made of polysaccharides (sugar polymers). The capsule helps prokaryotes cling to each other and to various surfaces in their environment, and also helps prevent the cell from drying out. In the case of disease-causing prokaryotes that have colonized the body of a host organism, the capsule or slime layer may also protect against the host’s immune system.
- CELL WALL All prokaryotic cells have a stiff cell wall, located underneath the capsule (if there is one). This structure maintains the cell’s shape, protects the cell interior, and prevents the cell from bursting when it takes up water. The cell wall of most bacteria contains peptidoglycan, a polymer of linked sugars and polypeptides. Some of the antibiotics used to treat bacterial infections in humans and other animals act by targeting the bacterial cell wall. Although most bacterial cell walls contain peptidoglycan, they can differ in other ways. In fact, these differences are used to classify bacteria using a technique called the Gram stain. This technique categorizes strains of bacteria into one of two groups: gram-positive or gram-negative. Gram-positive bacteria have a thick cell wall of peptidoglycan, which traps the bulky violet dye-iodine molecules while staining. Gram-negative bacteria, on the other hand, have a thin layer of peptidoglycan and an additional outer membrane. The thin peptidoglycan layer only retains the red dye, giving gram-negative bacteria a pinkish hue.
- PLASMA MEMBRANE The basic building block of the plasma membrane is the phospholipid, a lipid composed of a glycerol molecule attached a hydrophilic (water-attracting) phosphate head and to two hydrophobic (water-repelling) fatty acid tails. The phospholipids of a eukaryotic or bacterial membrane are organized into two layers, forming a structure called a phospholipid bilayer. The bacterial plasma membrane usually gets modified to form various structures namely mesosomes and desmosomes. Mesosomes are associated with various functions viz., cell division, electron transport mechanism of respiration, as sites of DNA-replication enzymes. They also help in the distribution of daughter chromosomes, i.e., DNA to daughter bacterial cells.
- APPENDAGES Prokaryotic cells often have appendages (protrusions from the cell surface) that allow the cell to stick to surfaces, move around, or transfer DNA to other cells. Thin filaments called fimbriae (singular: fimbria), are used for adhesion—that is, they
Each bacterial ribosome is made of two subunits, 3 0S and 50S, and contain slightly more RNA (65 per cent) than protein (35 per cent) as compared to eukaryotic ribosomes. During protein synthesis 30S and 50S ribosomal subunits associate to form 70S ribosomes. In addition, 70S ribosomes are seen to form groups so called polysomes or polyribosomes.
- INTERNAL COMPARTMENTS Prokaryotes aren't "supposed" to have internal compartments like the organelles of eukaryotes, and for the most part, they don't. However, prokaryotic cells sometimes need to increase membrane surface area for reactions or concentrate a substrate around its enzyme, just like eukaryotic cells. Because of this, some prokaryotes have membrane folds or compartments functionally similar to those of eukaryotes. Reproduction in prokaryotic cells is by binary fission; a process of growth, enlargement and division. Eukaryotic Cells Eukaryotic Cell Structure Like a prokaryotic cell, a eukaryotic cell has a plasma membrane, cytoplasm, and ribosomes. However, unlike prokaryotic cells, eukaryotic cells have: a membrane-bound nucleus numerous membrane-bound organelles (including the endoplasmic reticulum, Golgi apparatus, chloroplasts, and mitochondria) several rod-shaped chromosomes Because a eukaryotic cell’s nucleus is surrounded by a membrane, it is often said to have a “true nucleus”. Organelles have specialized cellular roles, just as the organs of your body have specialized roles. They allow different functions to be compartmentalized in different areas of the cell.
- The Nucleus & Its Structures Eukaryotic cells have a true nucleus, which means the cell’s DNA is surrounded by a membrane. Therefore, the nucleus houses the cell’s DNA and directs the synthesis of proteins and ribosomes, the cellular organelles responsible for protein synthesis. The nuclear envelope is a double-membrane structure that constitutes the outermost portion of the nucleus. Both the inner and outer membranes of the nuclear envelope are phospholipid bilayers. The nuclear envelope is punctuated with pores that control the passage of ions, molecules, and RNA between the nucleoplasm and cytoplasm. The nucleoplasm is the semi-solid fluid inside the nucleus where we find the chromatin
and the nucleolus. In prokaryotes, DNA is organized into a single circular chromosome. In eukaryotes, chromosomes are linear structures.
2. CELL MEMBRANE
Like prokaryotes, eukaryotic cells have a plasma membrane made up of a phospholipid bilayer with embedded proteins that separates the internal contents of the cell from its surrounding environment. A phospholipid is a lipid molecule composed of two fatty acid chains, a glycerol backbone, and a phosphate group. The plasma membrane regulates the passage of some substances, such as organic molecules, ions, and water, preventing the passage of some to maintain internal conditions, while actively bringing in or removing others. Other compounds move passively across the membrane.
3. Cell Wall
A cell wall is a rigid structure present outside the plant cell. It is, however, absent in animal cells. It provides shape to the cell and helps in cell-to-cell interaction. It is a protective layer that protects the cell from any injury or pathogen attacks.
Vesicles-these are small, spherical sacs that branch off from the ER and carry chemicals to other organelles or to the cell’s surface. These are round and oval and are usually related to protein synthesis. These help in transporting various cellular materials, including proteins and lipids, Tubules- are long, cylindrical structures that make up part of the ER network and provide flexibility to the ER structure. These tubules are involved in the extension and connection of the ER throughout the cell and facilitate the movement of materials within the organelle. Types of Endoplasmic Reticulum There two types of Endoplasmic reticulum according to the presence of ribosomes are: Rough Endoplasmic Reticulum The RER is made up of phospholipid bilayers, which is similar to the structure of the plasma membrane.
- RER have ribosomes attached to its cytoplasmic surface. These ribosomes are involved in protein synthesis.
- The membranes of the RER have number of flattened sacs called cisternae, which are interconnected and allow the exchange of material and information.
- Inside the cisternae is a central space or lumen which serves as a site where protein synthesis, folding, and modification occur.
- After synthesis and modification, proteins are packaged into transport vesicles. These vesicles bud off from the RER and carry the proteins to their respective destinations within or outside the cell. Smooth Endoplasmic Reticulum The SER shares a similar membranous structure with the RER, consisting of a network of tubules and cisternae. However, it lacks ribosomes on its surface, giving it a smooth appearance.
- A major function of the SER is lipid synthesis and produces phospholipids and steroids, which are essential components of cell membranes.
- The SER contains enzymes involved in detoxifying drugs and toxins.
- The SER is responsible for storing and releasing calcium ions (Ca2+). These ions play pivotal roles in various cellular processes, including muscle contraction, cell signalling, and enzyme activation.
- The SER is involved in various metabolic processes and can serve as a storage site for certain molecules, such as glucose. ii. The Golgi Apparatus The Golgi apparatus is a central organelle found in eukaryotic cells. It is characterized by stacked membrane sacs known as cisternae. These cisternae are stacked on top of each other to form the Golgi complex. It is mostly found near the nucleus. It consists of cis and trans faces. The cis face receives material from the endoplasmic reticulum, and the trans face releases vesicles carrying processed substances to various cellular organs. The plant cells contain many freely distributed subunits of the Golgi Apparatus, called dictyosomes. The Golgi body is not present in bacteria, blue-green algae, mature sperms,
and red blood cells of mammals and other animals. It processes, modifies and packages the proteins and lipids that are synthesized in the ER for transport within or outside the cell. iii. Lysosomes In animal cells, the lysosomes are the cell’s “garbage disposal.” Digestive enzymes within the lysosomes aid the breakdown of proteins, polysaccharides, lipids, nucleic acids, and even worn-out organelles. In single-celled eukaryotes, lysosomes are important for digestion of the food they ingest and the recycling of organelles. These enzymes are active at a much lower pH (more acidic) than those located in the cytoplasm. Function: Devour foreign substances Removes worn out organelles (Autophagy) Dissolves specialized parts of cells Helps in programmed cell death (Apoptosis) Helps in formation Sperm acrosome iv. Vesicles and Vacuoles Vesicles and vacuoles are membrane-bound sacs that function in storage and transport. Vacuoles are somewhat larger than vesicles, and the membrane of a vacuole does not fuse with the membranes of other cellular components. The vacuole is bound by a single membrane called tonoplast. In plant cells the vacuoles can occupy up to 90% of the volume of the cell. In plants, the tonoplast facilitates the transport of a number of ions and other materials against concentration gradients into the vacuole, hence their concentration is significantly higher in the vacuole than in the cytoplasm. Types of vacuoles- Contractile vacuoles-present in amoeba and regulates water content. Food vacuoles- engulfing food particles. Gas vacuoles– vacuoles containing metabolic gases, that helps in buoyancy Unlike vacuoles, vesicles can fuse with other membranes within the cell system.
2. Mitochondria Mitochondria are often called the “powerhouses” or “energy factories” of a cell because they are responsible for making adenosine triphosphate (ATP), the cell’s main energy-carrying molecule. The formation of ATP from the breakdown of glucose is known as cellular respiration. Mitochondria are oval-shaped, double-membrane organelles that have their own ribosomes and DNA. Each membrane is a phospholipid bilayer embedded with proteins. The inner layer has folds called cristae, which increase the surface area of the inner membrane. The area surrounded by the folds is called the mitochondrial matrix. The cristae and the matrix have different roles in cellular respiration. In keeping with our theme of form following function , it is important to point out that muscle cells have a very high concentration of mitochondria because muscle cells need a lot of energy to contract. 3. Plastids Plastids are found in all plant cells and in Euglenoides. These are easily observed under the microscope as they are large. They bear some specific pigments, thus imparting specific colours to the plants. Based on the type of pigments plastids can be classified into Chloroplasts, chromoplasts and leucoplasts. Chloroplasts Like mitochondria, chloroplasts also have their own DNA and ribosomes. Chloroplasts function in photosynthesis and can be found in eukaryotic cells such as plants and algae. Majority of the chloroplasts of the green plants are found in the mesophyll cells of the leaves. These are lens-shaped, oval, spherical, discoid or even ribbon-like organelles having variable
a cytoplasm. The nucleoid lacks a membrane. The eukaryotic cell consists of nucleus that is membrane bound structure and stores the genetic material of the eukaryotic cell. The double membrane makes the nucleus more complex over the nucleoid. The mitochondria, ribosome, and Golgi bodies are cell organelles that are present in the eukaryotic cells that have their own genetic material but prokaryotic cells lack them reducing the complexity of prokaryotic cells. Evolution in Action-Evolution of Eukaryotes Endosymbiosis: We have mentioned that both mitochondria and chloroplasts contain DNA and ribosomes. Have you wondered why? Strong evidence points to endosymbiosis as the explanation. Symbiosis is a relationship in which organisms from two separate species live in close association and typically exhibit specific adaptations to each other. Endosymbiosis (endo-= within) is a relationship in which one organism lives inside the other. Endosymbiotic relationships abound in nature. Microbes that produce vitamin K live inside the human gut. This relationship is beneficial for us because we are unable to synthesize vitamin K. It is also beneficial for the microbes because they are protected from other organisms and are provided a stable habitat and abundant food by living within the large intestine. ENDOSYMBIOTIC THEORY It is thought that life arose on earth around four billion years ago. The endosymbiotic theory states that some of the organelles in today's eukaryotic cells were once prokaryotic microbes. In this theory, the first eukaryotic cell was probably an amoeba-like cell that got nutrients by phagocytosis and contained a nucleus that formed when a piece of the cytoplasmic membrane pinched off around the chromosomes. Some of these amoeba-like organisms ingested prokaryotic cells that then survived within the organism and developed a symbiotic relationship. Mitochondria formed when bacteria capable of aerobic respiration were ingested; chloroplasts formed when photosynthetic bacteria were ingested. They eventually lost their cell wall and much of their DNA because they were not of benefit within the host cell. Mitochondria and chloroplasts cannot grow outside their host cell. Evidence for endosymbiosis Why should we think that a mitochondrion/chloroplast used to be a free-living organism in its own right? It turns out that many lines of evidence support this idea. Most important are the many striking similarities between prokaryotes (like bacteria) and mitochondria/chloroplast:
- Membranes — Mitochondria/chloroplast have their own cell membranes, just like a prokaryotic cell does.
- DNA — Each mitochondrion/chloroplast has its own circular DNA genome, like a bacteria's genome, but much smaller. This DNA is passed from a mitochondrion to its offspring and is separate from the "host" cell's genome in the nucleus. - bacteria/mitochondria structural comparison
- Reproduction — Both mitochondria and chloroplast multiply by pinching in half — the same process used by Bacteria [binary fission]. Every new mitochondrion must be produced from a parent mitochondrion in this way; if a cell's mitochondria are removed, it can't build new ones from scratch. Bacteria/mitochondria reproduction
- Mitochondria and chloroplasts have their own ribosomes that have 30S and 50S subunits (70S) similar to prokaryotes.
- Mitochondria and chloroplast are said to be semi-autonomous organelles because they can function on their own and require less amount of command from the nucleus Despite their many similarities, mitochondria (and chloroplasts) aren't free-living bacteria anymore. The first eukaryotic cell evolved more than a billion years ago. Since then, these organelles have become completely dependent on their host cells. For example, many of the key proteins needed by the mitochondrion are imported from the rest of the cell. Sometime during their long-standing relationship, the genes that code for these proteins were transferred from the mitochondrion to its host's genome. Scientists consider this mixing of genomes to be the irreversible step at which the two independent organisms become a single individual. How important is endosymbiosis? Endosymbiosis explains the origin of mitochondria and chloroplasts, but could it also explain other features of the eukaryotic cell? Endosymbiotic origins have been suggested for many structures, including flagella (structures like the tail of a sperm), cilia (hair-like structures that help in locomotion), and even the nucleus. Why have endosymbiosis and symbiosis been so important to evolution? The answer to these questions points us to one of the basic processes of evolution: natural selection. As Darwin observed, organisms that are fit enough to succeed in the game of survival have a good chance of passing on their genes to the next generation. Any survival or reproductive advantage can help a species out-compete another species or simply avoid becoming extinct itself. It seems likely that the first eukaryotic cells gained a slight edge over their neighbors when the mitochondria, a rich source of energy, moved in with them.
