Chapter 3

Cell Biology

Introduction

Cells are the basic biological unit of living organisms. They are the smallest unit of life that can replicate independently, though they are not the smallest structure within an organism. Cells first emerged on Earth approximately 3.5 billion years ago. Organisms can be either unicellular or multicellular. Humans are multicellular organisms, containing about 100 trillion cells. Most cells of multicellular organisms, particularly plants and animals, are only visible under a microscope. Due to this, the first cell was discovered in 1665 by Robert Hooke, a non-magical person. In 1839, Matthias Jakob Schleiden and Theodor Schwann developed the first cell theory. The theory states that all organisms are made of one or more cells, all cells come from preexisting cells, all cells contain the information to regulate cell functions and transmit the information to the next generation of cells, and that the vital functions of organisms occur within cells.

Prokaryotes

Prokaryotic cells were the first cells to form on Earth, and, consequently, were the first form of life. Prokaryotic cells are simpler than eukaryotic cells and have no membrane-bound organelles. Instead of a nucleus, prokaryotic cells have DNA composed of a single strand which is in direct contact with the cytoplasm. The nuclear area of the cytoplasm is the nucleoid. Prokaryotes are either bacteria or archaea, most of which are the smallest of all organisms.

There are three architectural regions of prokaryotic cells. Flagella and pili are found projecting from the cell’s surface. Flagella and pili are composed of proteins and facilitate moment, as well as communication, between cells. Next is the cell envelope, usually consisting of a cell wall that covers the plasma membrane, which encloses the cell. The envelope protects and separates the cell from its external environment. It also provides structure and rigidity for the cell. Some bacteria also have a covering layer known as a capsule, in addition to the cell envelope. Most prokaryotes have a cell wall, though there are a few exceptions. In bacteria, the cell wall is composed of peptidoglycan. Cell walls acts as barriers against external forces and prevents the cell from expanding to the point of cytolysis due to osmotic pressure caused by the hypotonic environment. Some eukaryotes also have a cell wall.

The inside of prokaryotic cells is a cytoplasmic region which contains DNA, ribosomes, and other assorted structures. In prokaryotes, the chromosome is regularly a circular molecule. Though there is no nucleus, the DNA condenses upon itself in a nucleoid. Prokaryotes may also carry plasmids, extrachromosomal DNA elements. Plasmids are normally circular and encode for additional genes, such as those that cause antibiotic resistance.

Eukaryotes

Eukaryotes include all fungi, slime molds, protozoa, algae, plants, and animals. Eukaryotic cells are larger than the typical prokaryote, about fifteen times wider and up to a thousand times greater in volume. The main feature which separates prokaryotes from eukaryotes is compartmentalization. Unlike prokaryotes, which have free-floating material in the cytoplasm, Eukaryotes have membrane-bound organelles which carry out specific functions for metabolic activity. The most important of these structures is the nucleus, the compartment which houses the eukaryotic cell’s DNA. Eukaryotes received their name due to this nucleus, since “eukaryote” can be translated to “true nucleus”.

Eukaryotic cells have a plasma membrane that resembles that have prokaryotes, with only minor differences in its construction. Some eukaryotes have cell walls. Unlike prokaryotic DNA, which is found on a single strand, eukaryotic DNA is organized into one or more chromosomes and stored in the cell nucleus. Chromosomes are associated with histone proteins. Some DNA can also be found in other eukaryotic organelles, most notably the mitochondria.

Many eukaryotes also have primary cilia. Primary cilia function for thermosensation, chemosensation, and mechanosensation. Therefore, cilia are the sensory cellular antennae of a cell. Eukaryotes can move using flagella or motile cilia. The flagella of eukaryotic cells is less complex than that of prokaryotic cells. However, not all eukaryotic cells have cilia or flagella.

Though there are six forms of eukaryotic cells, fungi, plants, and animals are the three largest kingdoms.

Fungi

The kingdom of fungi is separate from plants, animals, bacteria, and protists. It includes a large group of organisms, from yeasts and molds to mushrooms. One characteristic that makes fungal cells distinct from the other eukaryotes is the fungal cell wall. Unlike cell walls in other eukaryotic cells, which contain cellulose, or the cell walls of bacteria, fungal cell walls contain chitin. Along with other differences, this characteristic shows fungi to be a distinct, single group or related organisms. This group is the Eumycota or true fungi. This monophyletic group has a common ancestor and is distinct from myxomycetes (slime molds) and oomycetes (water molds).

The study of fungi is mycology. Mycology is usually regarded as a branch of botany despite the fact that fungi reside in a separate kingdom from plants taxonomically. Genetic studies have even shown that fungi are more closely related to animals than to plants.

Most fungi are small and inconspicuous, though they are abundant worldwide. Fungi live on dead matter, in soil, and as symbionts on other fungi, animals, and plants. They are sometimes visible when fruiting, whether as molds or mushrooms. Fungi are essential to the decomposition of organic matter, as well as nutrient cycling and exchange. Fungi have been used as a direct source of food, leavening agent in bread, and fermenter of various food and beverage products. Non-magical humans have also used fungi in the production of antibiotics since the 1940s.

There are an estimated 1.5 million to 5 million extant species in the Kingdom Fungi. Only about 5% of these species has been formally classified, making the true biodiversity of fungi largely unknown. Based on the species that have been identified, the fungus kingdom has an enormous diversity of taxa with extremely varied morphologies, life cycle strategies, and ecologies. All the fungi found in a specific area or geographic region is known as a mycobiota.

Since the 18th and 19th centuries, non-magical humans have classified fungi by their morphology or physiology. Since advances in molecular genetics have occurred, DNA analysis has been conducted which, in many cases, has challenged the historical cataloguing of these organisms. In the last decade, phylogenetic studies have reshaped the traditional classification structure of the Kingdom Fungi. The kingdom is currently divided into one subkingdom, seven phyla, and ten subphyla.

Before molecular methods of phylogenetic analysis were introduced, taxonomists classified fungi as members of the Plant Kingdom. This is due to similarities in the lifestyles of plants and fungi. Plants and fungi are both immobile and have similar growth habitats and general morphology. The also both can grow in soil and, in some cases, form fruit bodies. Of course, fungi are now separated into their own kingdom which is distinct from both animals and plants. Fungi appear to have separated into their own kingdom approximately one billion years ago.

Fungi have some features in common with other organisms. Like other eukaryotes, fungal cells have a nucleus which contains the DNA in the form of chromosomes. Fungal cells also have membrane-bound organelles like mitochondria. Fungi and animal cells both lack chloroplasts and require organic compounds as energy sources. Fungal cells and plant cells both have cell walls and vacuoles. Both reproduce by asexual and sexual reproduction and can produce spores. Fungi also usually have haploid nuclei, like mosses and algae. Some fungi, euglenoids, and some bacteria produce L-lysine in the α-aminoadipate pathway. Fungi and oomycetes both grow as filamentous hyphal cells; tubular, elongated, and thread-like cells. Finally, over 60 species of fungi bioluminesce, a trait they share with some plants and animals.

Unlike the phloem and xylem of many plants, most fungi do not have an efficient system for the transport of nutrients and water over long-distances. To combat this limitation, some fungi have formed rhizomorphs. Rhizomorphs perform functions similar to plant roots. Fungi and plants also both utilize a biosynthetic pathway to produce terpenes. However, fungi do not have chloroplasts, which allow plants another terpene pathway. Fungi also produce secondary metabolites similar in structure the the metabolites of plants. However, many of the enzymes that make these compounds differ in sequence and characteristics between fungi and plants. This indicates a separate evolutionary track and origin of these enzymes in plants and fungi.

Despite this, many features of fungi are unique, clearly classifying them into their own kingdom. Some fungal species grow as unicellular yeasts. These yeasts reproduce by binary fission or budding. Dimorphic fungi have the ability to switch between a hyphal phase and yeast phase, dependent on environmental conditions. In addition, fungal cells walls are composed of chitin and glucans. Glutens can also be found in plants and chitin is found in the exoskeleton of arthropods. However, fungi are the only organisms which combine glutens and chitin in their cell walls. These cell walls do not contain cellulose, unlike the cell walls of oomycetes and plants.

Plant

Plant cells have several distinctive features which separates them from the other eukaryotes and the prokaryotes. Perhaps the most distinctive feature of plant cells is the large central vacuole. This water-filled volume is enclosed by a tonoplast membrane. The vacuole controls the movement of molecules between sap and the cytosol, maintains the cell’s turgor, digests waste proteins and organelles, and stores useful material. As mentioned previously, plant cell walls are composed of cellulose, hemicellulose, pectin, and sometimes lignin, in contrast to the cell walls of fungi and bacteria.

Plant cells also have plasmodesmata, pores in the primary cell wall which allow cell-to-cell communication. Through the plasmodesmata, the endoplasmic reticulum and plasmalemma of adjacent cells becomes continuous. Plastids are another distinct feature of plant cells. Plastids, most notably the chloroplast, contain their own genomes, just like mitochondria. It is believed that plastids arose from living organisms which survived within a host cell.

Though some species of plants have sperm with flagella, similar to animals, higher plants lack the centrioles and flagella found in animal cells. Land plants and a few algae groups divide cellularly by constructing a phragmoplast. This serves as a template for building the new cell plate in late cytokinesis.

Finally, there are three types of cells exclusive to plants. Parenchyma cells function to store, support, phloem load, and photosynthesize. Apart from phloem and xylem in vascular bundles, parenchyma cells are the main component of leaves. Some of these cells are specialized for light penetration and gas exchange, but others are the least specialized components of plant tissue. Parenchyma cells containing numerous chloroplasts are focused on photosynthesis and are known as chlorenchyma cells. Parenchyma cells are classified by their thin, permeable primary walls. This allows for the transport of small molecules between cells. The cytoplasm of these cells is also responsible for a wide range of biochemical functions, including secretion and protection.

Collenchyma cells only have a primary wall. These cells do not develop plastids, but the ER and Golgi secrete additional primary wall. The wall becomes thickest at the corners, where three cells make contact, and thinnest on the sides, where two cells make contact.

Lastly, Sclerenchyma cells are tough cells which function for mechanical support. Broadly, there are two types; sclereids and fibres. These cells develop an extensive secondary cell wall, directly on the inside of the primary wall. This secondary wall has lignin, making it impermeable to water and hard. These cells do not survive for long due to their inability to exchange enough material for metabolism. Sclereid cells function to discourage herbivory, damage digestive passages, and physically protect the cell. Fibre cells function to provide load-bearing support and tensile strength in the stems and leaves of herbaceous plants.

Animal

Animal cells have a smaller central vacuole than plant cells and completely lack cell walls. Since they lack a cell wall, animal cells are able to become highly specialized and take on a wide variety of shapes. There are approximately 210 distinct varieties of cells in the human body. A typical animal cell contains many organelles, including the nucleus, golgi apparatus, ribosomes, smooth and rough endoplasmic reticulum, actin filaments, peroxisomes, microtubule, lysosomes, free ribosomes, mitochondria, intermediate filaments, cytoplasm, secretory vesicles, centrosomes, a plasma membrane, and, in some cases, flagellum. Most known animal phyla appeared as marine animals in the Cambrian explosion, approximately 542 million years ago.

The nucleus is the central structure of the cell which contains every gene that codes for the traits of the living being. These genes are encoded on strands of deoxyribonucleic acid, otherwise known as DNA. It is known that there is a magical gene which is encoded in DNA, so the nucleus is extremely important to the study of magical beings.

Mitochondria are the powerhouse of cells, but have also been implicated in several genetic disorders. Mitochondrial DNA is instrumental in molecular genetics for identifying ancestry, as mitochondrial DNA is only inherited from the mother. There is also the theory of magical mitochondria. This theory states that there are organelles in magical beings that function similarly to mitochondria, but unlike mitochondria which produce ATP, the energy food of cells, these magical mitochondria produce magic on the cellular level. This theory, though widely accepted in the magical scientific community, has yet to be confirmed because, as the theory states, these organelles are identical to mitochondria.

The Golgi Apparatus, also known as the Golgi body, Golgi complex, or Golgi, is found in most eukaryotic cells. This organelle packages proteins inside the cell prior to them heading to their destination. Ribosomes are dense structures in cells which catalyse the assembly of protein chains. Ribosomes read messenger RNA and bind amino acids to transfer RNA to build protein structures in the process of translation. Free ribosomes are suspended in the cell’s cytoplasm. Many ribosomes, instead of being free, are attached to the rough endoplasmic reticulum.

The rough endoplasmic reticulum, or rough ER is involved in protein folding, some protein production, quality control, and despatch. It is identified as the rough ER due to the presence of ribosomes along its surface. The smooth ER helps with the production and metabolism of steroid hormones and fats. The smooth ER does not have ribosomes on its surface and is associated with fats.

Actin filaments are either microfilaments, a major component of the cytoskeleton, or thin filaments, part of the contractile apparatus of muscle cells. As their name suggests, these filaments are formed from actin. Microtubules are another component of the cytoskeleton and are found throughout the cytoplasm. They can grow as long as 50 micrometers in length. Intermediate filaments are another cytoskeletal component found in many animal species.

Peroxisomes are small organelles which contain enzymes for metabolic reactions. Lysosomes are another membrane-bound organelle found in animals cells. They are capable of breaking down biomolecules, including carbohydrates, lipids, proteins, nucleic acids, and cellular debris. Centrosomes are organelles which serve as the main site for microtubule organization. Centrosomes also regulate the cell division cycle. These organelles are only found in animal cells.

Secretory vesicles mediate the vesicular transport of hormones or neurotransmitters from an organelle to a specific region of the cell membrane. The vesicle transports its cargo to this area where it fuses with the membrane and releases its contents.