Introduction To Biology Lecture Notes PDF

INTRODUCTION TO BIOLOGY BIO-106 Lecture-1  Cell Structure and Function Mitosis and Meiosis DNA & RNA Replication Transcription & Translation Course Content Genetic Code & Gene Expressi...

INTRODUCTION TO BIOLOGY BIO-106 Lecture-1  Cell Structure and Function Mitosis and Meiosis DNA & RNA Replication Transcription & Translation Course Content Genetic Code & Gene Expression Mendelian Laws Multiple Alleles and X-linkage GMOs Genomics 1  Bioenergetics Carbohydrates Glycolysis TCA Gluconeogenesis Course Content Glycogen & Oxidative Phosphorylation Blood & Homeostasis Human Biological Systems (Nervous System, Digestive System, Endocrine Glands, Excretory System) Antibiotics – types, mode of action/mechanism and its applications 2  Full course; 20 lectures Mid-term; 10 lectures; 30 marks Final Term; next 10 lectures; 50 marks Course Assignment; 10 marks Presentation; same group; 5 marks Structure Quiz; 5 marks; every two lectures Assignment due; October 15th, 2024 Presentations; November, 2024 3  Introduction to Cells All living things (or organisms) are built from cells: small, membrane-enclosed units filled with a concentrated aqueous solution of chemicals and endowed with the extraordinary ability to create copies of themselves. by growing and then dividing in two. The simplest forms of life are solitary cells. Higher organisms, including ourselves, are communities of cells derived by growth and division from a single founder cell. Every animal or plant is a vast colony of individual cells, each of which performs a specialized function that is regulated by intricate systems of cell-to-cell communication. 4  Unity and Diversity of Cells Cell biologists often speak of “the cell” without specifying any particular cell. But cells are not all alike; in fact, they can be wildly different. Biologists estimate that there may be up to 100 million distinct species of living things on our planet. 5  Cells vary enormously in Appearance and Function A bacterial cell—say a Lactobacillus in a piece of cheese—is a few micrometers, or μm, in length. That’s about 25 times smaller than the width of a human hair. A frog egg—which is also a single cell—has a diameter of about 1 millimeter. If we scaled them up to make the Lactobacillus the size of a person, the frog egg would be half a mile high. Cells vary just as widely in their shape (Figure 1–1). A typical nerve cell in your brain, for example, is enormously extended; it sends out its electrical signals along a fine protrusion that is 10,000 times longer than it is thick, and it receives signals from other nerve cells through a mass of shorter processes that sprout from its body like the branches of a tree (Figure 1–1A). A Paramecium in a drop of pond water is shaped like a submarine and is covered with thousands of cilia—hairlike extensions whose sinuous beating sweeps the cell forward, rotating as it goes (Figure 1–1B). 6 Figure 1–1: Cells come in a variety of shapes and sizes. Note the very different scales of these micrographs. (A) Drawing of a single nerve cell from a mammalian brain. This cell has a huge branching tree of processes, through which it receives signals from as many as 100,000 other nerve cells. (B) Paramecium. This protozoan—a single giant cell—swims by means of the beating cilia that cover its surface. (C) Chlamydomonas. This type of single-celled green algae is found all over the world—in soil, fresh water, oceans, and even in the snow at the top of mountains. The cell makes its food like plants do—via photosynthesis—and it pulls itself through the water using its paired flagella to do the breaststroke. (D) Saccharomyces cerevisiae. This yeast cell, used in baking bread, reproduces itself by a process called budding. (E) Helicobacter pylori. This bacterium—a causative agent of stomach ulcers—uses a handful of whiplike flagella to propel itself through the stomach lining. 7  Living Cells all have a Similar Basic Chemistry Cells resemble one another to an astonishing degree in the details of their chemistry. They are composed of the same sorts of molecules, which participate in the same types of chemical reactions. In all organisms, genetic information—in the form of genes—is carried in DNA molecules. This information is written in the same chemical code, constructed out of the same chemical building blocks, interpreted by essentially the same chemical machinery, and replicated in the same way when an organism reproduces. Thus, in every cell, the long DNA polymer chains are made from the same set of four monomers, called nucleotides, strung together in different sequences like the letters of an alphabet to convey information. 8  Living Cells all have a Similar Basic Chemistry In every cell, the information encoded in the DNA is read out, or transcribed, into a chemically related set of polymers called RNA. A subset of these RNA molecules is in turn translated into yet another type of polymer called a protein. This flow of information— from DNA to RNA to protein—is so fundamental to life that it is referred to as the central dogma (Figure 1–2). The appearance and behavior of a cell are dictated largely by its protein molecules, which serve as structural supports, chemical catalysts, molecular motors, and so on. Proteins are built from amino acids, and all organisms use the same set of 20 amino acids to make their proteins. But the amino acids are linked in different sequences, giving each type of protein molecule a different three-dimensional shape, or conformation, just as different sequences of letters spell different words. 9 Figure 1-2: In all living cells, genetic information flows from DNA to RNA (transcription) and from RNA to protein (translation)—a sequence known as the central dogma. The sequence of nucleotides in a particular segment of DNA (a gene) is transcribed into an RNA molecule, which can then be translated into the linear sequence of amino acids of a protein. Only a small part of the gene, RNA, and protein are shown. 10  Living Cells all have a Similar Basic Chemistry In this way, the same basic biochemical machinery has served to generate the whole gamut of life on Earth (Figure 1–3). If cells are the fundamental unit of living matter, then nothing less than a cell can truly be called living. Viruses, for example, are compact packages of genetic information—in the form of DNA or RNA—encased in protein but they have no ability to reproduce themselves by their own efforts. Instead, they get themselves copied by parasitizing the reproductive machinery of the cells that they invade. Thus, viruses are chemical zombies: they are inert and inactive outside their host cells, but they can exert a malign control over a cell once they gain entry. 11 Figure 1–3: All living organisms are constructed from cells. A colony of bacteria, a butterfly, a rose, and a dolphin are all made of cells that have a fundamentally similar chemistry and operate according to the same basic principles. 12  All Present-Day Cells have apparently evolved from the same ancestor A cell reproduces by replicating its DNA and then dividing in two, passing a copy of the genetic instructions encoded in its DNA to each of its daughter cells. That is why daughter cells resemble the parent cell. However, the copying is not always perfect, and the instructions are occasionally corrupted by mutations that change the DNA. For this reason, daughter cells do not always match the parent cell exactly. Mutations can create offspring that are changed for the worse (in that they are less able to survive and reproduce), changed for the better (in that they are better able to survive and reproduce), or changed in a neutral way (in that they are genetically different but equally viable). The struggle for survival eliminates the first, favors the second, and tolerates the third. The genes of the next generation will be the genes of the survivors. On occasion, the pattern of descent may be complicated by sexual reproduction, in which two cells of the same species fuse, pooling their DNA. 13  All Present-Day Cells have apparently evolved from the same ancestor The genetic cards are then shuffled, re-dealt, and distributed in new combinations to the next generation, to be tested again for their ability to promote survival and reproduction. These simple principles of genetic change and selection, applied repeatedly over billions of cell generations, are the basis of evolution—the process by which living species become gradually modified and adapted to their environment in more and more sophisticated ways. Evolution offers a startling, but compelling explanation of why present-day cells are so similar in their fundamentals: they have all inherited their genetic instructions from the same common ancestor. It is estimated that this ancestral cell existed between 3.5 and 3.8 billion years ago, and we must suppose that it contained a prototype of the universal machinery of all life on Earth today. Through a very long process of mutation and natural selection, the descendants of this ancestral cell have gradually diverged to fill every habitat on Earth with organisms that exploit the potential of the machinery in an endless variety of ways. 14  Genes provide the instructions for Cellular Form, Function, and Complex Behavior A cell’s genome—that is, the entire sequence of nucleotides in an organism’s DNA— provides a genetic program that instructs the cell how to behave. For the cells of plant and animal embryos, the genome directs the growth and development of an adult organism with hundreds of different cell types. Within an individual plant or animal, these cells can be extraordinarily varied. Fat cells, skin cells, bone cells, and nerve cells seem as dissimilar as any cells could be. Yet all these differentiated cell types are generated during embryonic development from a single fertilized egg cell, and all contain identical copies of the DNA of the species. Their varied characters stem from the way that individual cells use their genetic instructions. Different cells express different genes: that is, they use their genes to produce some proteins and not others, depending on their internal state and on cues that they and their ancestor cells have received from their surroundings—mainly signals from other cells in the organism. 15  Genes provide the instructions for Cellular Form, Function, and Complex Behavior The DNA, therefore, is not just a shopping list specifying the molecules that every cell must make, and a cell is not just an assembly of all the items on the list. Each cell is capable of carrying out a variety of biological tasks, depending on its environment and its history, and it selectively uses the information encoded in its DNA to guide its activities. 16  The Procaryotic Cell Of all the types of cells revealed by the microscope, bacteria have the simplest structure and come closest to showing us life stripped down to its essentials. Indeed, a bacterium contains essentially no organelles—not even a nucleus to hold its DNA. This property—the presence or absence of a nucleus—is used as the basis for a simple but fundamental classification of all living things. Organisms whose cells have a nucleus are called eukaryotes (from the Greek words eu, meaning “well” or “truly,” and karyon, a “kernel” or “nucleus”). Organisms whose cells do not have a nucleus are called prokaryotes (from pro, meaning “before”). The terms “bacterium” and “prokaryote” are often used interchangeably, although the category of prokaryotes also includes another class of cells, the archaea (singular archaeon), which are so remotely related to bacteria that they are given a separate name. 17  The Procaryotic Cell Prokaryotes are typically spherical, rodlike, or corkscrew-shaped (Figure 1–4). They are also small—generally just a few micrometers long, although there are some giant species as much as 100 times longer than this. Prokaryotes often have a tough protective coat, or cell wall, surrounding the plasma membrane, which encloses a single compartment containing the cytoplasm and the DNA. In the electron microscope, the cell interior typically appears as a matrix of varying texture, without any obvious organized internal structure (Figure 1–5). The cells reproduce quickly by dividing in two. Under optimum conditions, when food is plentiful, many prokaryotic cells can duplicate themselves in as little as 20 minutes. In 11 hours, by repeated divisions, a single prokaryote can give rise to more than 8 billion progeny (which exceeds the total number of humans presently on Earth). Thanks to their large numbers, rapid growth rates, and ability to exchange bits of genetic material by a process akin to sex, populations of prokaryotic cells can evolve fast, rapidly acquiring the ability to use a new food source or to resist being killed by a new antibiotic. 18 Figure 1-4: Bacteria come in different shapes and sizes. Typical spherical, rodlike, and spiral-shaped bacteria are drawn to scale. The spiral cells shown are the organisms that cause syphilis. 19 Figure 1–5: The bacterium Escherichia coli (E. coli ) has served as an important model organism. An electron micrograph of a longitudinal section is shown here; the cell’s DNA is concentrated in the lightly stained region. 20  Prokaryotes are the most Diverse and Numerous Cells on Earth Most prokaryotes live as single-celled organisms, although some join together to form chains, clusters, or other organized multicellular structures. In shape and structure, prokaryotes may seem simple and limited, but in terms of chemistry, they are the most diverse and inventive class of cells. Members of this class exploit an enormous range of habitats, from hot puddles of volcanic mud to the interiors of other living cells, and they vastly outnumber all eukaryotic organisms on Earth. Some are aerobic, using oxygen to oxidize food molecules; some are strictly anaerobic and are killed by the slightest exposure to oxygen. Mitochondria—the organelles that generate energy in eukaryotic cells—are thought to have evolved from aerobic bacteria that took to living inside the anaerobic ancestors of today’s eukaryotic cells. Thus, our own oxygen-based metabolism can be regarded as a product of the activities of bacterial cells. Virtually any organic, carbon-containing material—from wood to petroleum—can be used21 as food by one sort of bacterium or another.  Prokaryotes are the most Diverse and Numerous Cells on Earth Even more remarkably, some prokaryotes can live entirely on inorganic substances: they can get their carbon from CO2 in the atmosphere, their nitrogen from atmospheric N2, and their oxygen, hydrogen, sulfur, and phosphorus from air, water, and inorganic minerals. Some of these prokaryotic cells, like plant cells, perform photosynthesis, using energy from sunlight to produce organic molecules from CO2 (Figure 1–6); others derive energy from the chemical reactivity of inorganic substances in the environment (Figure 1–7). In either case, such prokaryotes play a unique and fundamental part in the economy of life on Earth: other living. things depend on the organic compounds that these cells generate from inorganic materials. Plants, too, can capture energy from sunlight and carbon from atmospheric CO2. But plants unaided by bacteria cannot capture N2 from the atmosphere, and in a sense even plants depend on bacteria for photosynthesis. It is almost certain that the organelles in the plant cell that perform photosynthesis—the chloroplasts—have evolved from photosynthetic bacteria that long ago found a home inside 22 the cytoplasm of a plant cell ancestor. Figure 1–6: Some bacteria are photosynthetic. (A) Anabaena cylindrica forms long, multicellular filaments. This light micrograph shows specialized cells that either fix nitrogen (that is, capture N2 from the atmosphere and incorporate it into organic compounds; labeled H), fix CO2 through photosynthesis (labeled V), or become resistant spores (labeled S). (B) An electron micrograph of a related species, Phormidium laminosum, shows the intracellular membranes where photosynthesis occurs. These micrographs illustrate that even some prokaryotes can form simple multicellular organisms. 23 Figure 1–7: A sulfur bacterium gets its energy from H2S. Beggiatoa, a prokaryote that lives in sulfurous environments, oxidizes H2S to produce sulfur and can fix carbon even in the dark. In this light micrograph, yellow deposits of sulfur can be seen inside both of the cells. 24  The world of Procaryotes is divided into two Domains: Bacteria and Archaea Traditionally, all prokaryotes have been classified together in one large group. But molecular studies reveal that there is a gulf within the class of prokaryotes, dividing it into two distinct domains called the bacteria and the archaea. Remarkably, at a molecular level, the members of these two domains differ as much from one another as either does from the eukaryotes. Most of the prokaryotes familiar from everyday life—the species that live in the soil or make us ill—are bacteria. Archaea are found not only in these habitats, but also in environments that are too hostile for most other cells: concentrated brine, the hot acid of volcanic springs, the airless depths of marine sediments, the sludge of sewage treatment plants, pools beneath the frozen surface of Antarctica, and in the acidic, oxygen-free environment of a cow’s stomach where they break down cellulose and generate methane gas. Many of these extreme environments resemble the harsh conditions that must have existed on the primitive Earth, where living things first evolved before the atmosphere became rich in oxygen. 25  The Eucaryotic Cell Eukaryotic cells, in general, are bigger and more elaborate than bacteria and archaea. Some live independent lives as single-celled organisms, such as amoebae and yeasts (Figure 1–8); others live in multicellular assemblies. All of the more complex multicellular organisms—including plants, animals, and fungi— are formed from eukaryotic cells. By definition, all eukaryotic cells have a nucleus. But possession of a nucleus goes hand- in-hand with possession of a variety of other organelles, most of which are membrane- enclosed and common to all eukaryotic organisms. 26 Figure 1–8: Yeasts are simple free-living eukaryotes. The cells shown in this micrograph belong to the species of yeast, Saccharomyces cerevisiae, used to make dough rise and turn malted barley juice into beer. As can be seen in this image, the cells reproduce by growing a bud and then dividing asymmetrically into a large mother cell and a small daughter cell; for this reason, they are called budding yeast. 27  The Nucleus is the Information Store of the Cell The nucleus is usually the most prominent organelle in a eukaryotic cell (Figure 1–9). It is enclosed within two concentric membranes that form the nuclear envelope, and it contains molecules of DNA—extremely long polymers that encode the genetic information of the organism. In the light microscope, these giant DNA molecules become visible as individual chromosomes when they become more compact before a cell divides into two daughter cells (Figure 1–10). DNA also carries the genetic information in prokaryotic cells; these cells lack a distinct nucleus not because they lack DNA, but because they do not keep their DNA inside a nuclear envelope, segregated from the rest of the cell contents. 28 Figure 1–9: The nucleus contains most of the DNA in a eukaryotic cell. (A) This drawing of a typical animal cell shows its extensive system of membrane-enclosed organelles. The nucleus is colored brown, the nuclear envelope is green, and the cytoplasm (the interior of the cell outside the nucleus) is white. (B) An electron micrograph of the nucleus in a mammalian cell. Individual chromosomes are not visible because at this stage of the cell’s growth its DNA molecules are dispersed as fine threads throughout the nucleus. 29 Figure 1–10: Chromosomes become visible when a cell is about to divide. As a eukaryotic cell prepares to divide, its DNA molecules become progressively more compacted (condensed), forming wormlike chromosomes that can be distinguished in the light microscope. The photographs show three successive steps in this process in a cultured cell from a newt’s lung; note that in the last micrograph on the right, the nuclear envelope has broken down. 30  Essential Cell Biology Fourth Edition 2014 Bruce Alberts, Dennis Bray, Karen Hopkin, Reading Alexander Johnson, Julian Lewis, Martin Raff, Keith Roberts and Peter Walter Taylor and Francis NY USA 31 Topics for Assignment 32  Topics for Assignment 6. 33 Thank you 34