Introduction to Biology PDF

LESSON 1 INTRODUCTION TO BIOLOGY TOPICS 1. The scientific study of organisms 2. Properties of Life 3. Assumptions, methods, and limitations of science 4. Underlying themes of Biology 5. Evolution as...

LESSON 1 INTRODUCTION TO BIOLOGY TOPICS 1. The scientific study of organisms 2. Properties of Life 3. Assumptions, methods, and limitations of science 4. Underlying themes of Biology 5. Evolution as a unifying concept LEARNING OUTCOMES At the end of the lesson, you should be able to: 1. Discuss scientific processes and how they are used in studying biology. 2. Distinguish between living organisms and nonliving matter. 3. Identify some limitations of science. 4. Discuss some underlying themes of biology (e.g. hierarchy, homeostasis, emergent properties) 5. Explain evolution and natural selection TOPIC 1: The Scientific Study of Organisms Biology is a natural science concerned with the study of life and living organisms. Modern biology is a vast and eclectic field composed of many specialized disciplines that study the structure, function, growth, distribution, evolution, or other features of living organisms. However, despite the broad scope of biology, there are certain general and unifying concepts that govern all study and research:  the cell is the basic unit of life  genes (consisting of DNA or RNA) are the basic unit of heredity  evolution accounts for the unity and diversity seen among living organisms  all organisms survive by consuming and transforming energy  all organisms maintain a stable internal environment Biological research indicates the first forms of life on Earth were microorganisms that existed for billions of years before the evolution of larger organisms. The mammals, birds, and flowers so familiar to us are all relatively recent, originating within the last 200 million years. Modern-appearing humans, Homo sapiens, are a relatively new species, having inhabited this planet for only the last 200,000 years (approximately). HISTORY OF BIOLOGICAL SCIENCE Although modern biology is a relatively recent development, sciences related to and included within it have been studied since ancient times. Natural philosophy was studied as early as the ancient civilizations of Mesopotamia, Egypt, the Indian subcontinent, and China. However, the origins of modern biology and its approach to the study of nature are most often traced back to ancient Greece. (Biology is derived from the Greek word “bio” meaning “life” and the suffix “ology” meaning “study of.”) Advances in microscopy also had a profound impact on biological thinking. In the early 19th century, a number of biologists pointed to the central importance of the cell and in 1838, Schleiden and Schwann began promoting the now universal ideas of the cell theory. Jean-Baptiste Lamarck was the first to present a coherent theory of evolution, although it was the British naturalist Charles Darwin who spread the 1 theory of natural selection throughout the scientific community. In 1953, the discovery of the double helical structure of DNA marked the transition to the era of molecular genetics. SCIENCE AND PSEUDOSCIENCE Science is a process for learning about the natural world. Most scientific investigations involve the testing of potential answers to important research questions. For example, oncologists (cancer doctors) are interested in finding out why some cancers respond well to chemotherapy while others are unaffected. Based on their growing knowledge of molecular biology, some doctors suspect a connection between a patient’s genetics and their response to chemotherapy. Many years of research have produced numerous scientific papers documenting the evidence for a connection between cancer, genetics, and treatment response. Once published, scientific information is available for anyone to read, learn from, or even question/dispute. This makes science an iterative, or cumulative, process, where previous research is used as the foundation for new research. Our current understanding of any issue in the sciences is the culmination of all previous work. Pseudoscience is a belief presented as scientific although it is not a product of scientific investigation. Pseudoscience is often known as fringe or alternative science. It usually lacks the carefully-controlled and thoughtfully-interpreted experiments which provide the foundation of the natural sciences and which contribute to their advancement. THE PROCESS OF SCIENCE Science (from the Latin scientia, meaning “knowledge”) can be defined as knowledge that covers general truths or the operation of general laws, especially when acquired and tested by the scientific method. The steps of the scientific method will be examined in detail later, but one of the most important aspects of this method is the testing of hypotheses (testable statements) by means of repeatable experiments. Although using the scientific method is inherent to science, it is inadequate in determining what science is. This is because it is relatively easy to apply the scientific method to disciplines such as physics and chemistry, but when it comes to disciplines like archaeology, paleoanthropology, psychology, and geology, the scientific method becomes less applicable as it becomes more difficult to repeat experiments. These areas of study are still sciences, however. Consider archaeology: even though one cannot perform repeatable experiments, hypotheses may still be supported. For instance, an archaeologist can hypothesize that an ancient culture existed based on finding a piece of pottery. Further hypotheses could be made about various characteristics of this culture. These hypotheses may be found to be plausible (supported by data) and tentatively accepted, or may be falsified and rejected altogether (due to contradictions from data and other findings). A group of related hypotheses, that have not been disproven, may eventually lead to the development of a verified theory. A theory is a tested and confirmed explanation for observations or phenomena that is supported by a large body of evidence. Science may be better defined as fields of study that attempt to comprehend the nature of the universe. SCIENTIFIC REASONING One thing is common to all forms of science: an ultimate goal “to know.” Curiosity and inquiry are the driving forces for the development of science. Scientists seek to understand the world and the way it operates. To do this, they use two methods of logical thinking: inductive reasoning and deductive reasoning. Figure 1. Comparison of the two types of reasoning Source: Biolibretexts 2 Inductive reasoning is a form of logical thinking that uses related observations to arrive at a general conclusion. This type of reasoning is common in descriptive science. A life scientist such as a biologist makes observations and records them. These data can be qualitative or quantitative and the raw data can be supplemented with drawings, pictures, photos, or videos. From many observations, the scientist can infer conclusions (inductions) based on evidence. Inductive reasoning involves formulating generalizations inferred from careful observation and the analysis of a large amount of data. Brain studies provide an example. In this type of research, many live brains are observed while people are doing a specific activity, such as viewing images of food. The part of the brain that “lights up” during this activity is then predicted to be the part controlling the response to the selected stimulus; in this case, images of food. The “lighting up” of the various areas of the brain is caused by excess absorption of radioactive sugar derivatives by active areas of the brain. The resultant increase in radioactivity is observed by a scanner. Then researchers can stimulate that part of the brain to see if similar responses result. Deductive reasoning or deduction is the type of logic used in hypothesis-based science. In deductive reason, the pattern of thinking moves in the opposite direction as compared to inductive reasoning. Deductive reasoning is a form of logical thinking that uses a general principle or law to forecast specific results. From those general principles, a scientist can extrapolate and predict the specific results that would be valid as long as the general principles are valid. Studies in climate change can illustrate this type of reasoning. For example, scientists may predict that if the climate becomes warmer in a particular region, then the distribution of plants and animals should change. These predictions have been written and tested, and many such predicted changes have been observed, such as the modification of arable areas for agriculture correlated with changes in the average temperatures. Both types of logical thinking are related to the two main pathways of scientific study: descriptive science and hypothesis-based science. Descriptive (or discovery) science, which is usually inductive, aims to observe, explore, and discover, while hypothesis-based science, which is usually deductive, begins with a specific question or problem and a potential answer or solution that can be tested. The boundary between these two forms of study is often blurred and most scientific endeavors combine both approaches. The fuzzy boundary becomes apparent when thinking about how easily observation can lead to specific questions. For example, a gentleman in the 1940s observed that the burr seeds that stuck to his clothes and his dog’s fur had a tiny hook structure. Upon closer inspection, he discovered that the burrs’ gripping device was more reliable than a zipper. He eventually developed a company and produced the hook-and- loop fastener popularly known today as Velcro. Descriptive science and hypothesis-based science are in continuous dialogue. TWO TYPES OF SCIENCE The scientific community has been debating for the last few decades about the value of different types of science. Is it valuable to pursue science for the sake of simply gaining knowledge, or does scientific knowledge only have worth if we can apply it to solving a specific problem or to bettering our lives? This question focuses on the differences between two types of science: basic science and applied science. Basic science or “pure” science seeks to expand knowledge regardless of the short-term application of that knowledge. It is not focused on developing a product or a service of immediate public or commercial value. The goal of basic science is knowledge for knowledge’s sake; though this does not mean that, in the end, it may not result in a practical application. In contrast, applied science or “technology” aims to use science to solve real-world problems such as improving crop yields, finding a cure for a particular disease, or saving animals threatened by a natural disaster. In applied science, the problem is usually defined for the researcher. REPORTING SCIENTIFIC WORK Scientists must share their findings in order for other researchers to expand and build upon their discoveries. Collaboration with other scientists—when planning, conducting, and analyzing results—are all important for scientific research. For this reason, a major aspect of a scientist’s work is communicating with peers and disseminating results to peers. Scientists can share results by presenting them at a scientific meeting or conference, but this approach can reach only the select few who are present. Instead, 3 most scientists present their results in peer-reviewed manuscripts that are published in scientific journals. Peer-reviewed manuscripts are scientific papers that are reviewed by a scientist’s colleagues or peers. These colleagues are qualified individuals, often experts in the same research area, who judge whether or not the scientist’s work is suitable for publication. The process of peer review helps to ensure that the research described in a scientific paper or grant proposal is original, significant, logical, and thorough. Grant proposals, which are requests for research funding, are also subject to peer review. Scientists publish their work so other scientists can reproduce their experiments under similar or different conditions to expand on the findings. The experimental results must be consistent with the findings of other scientists. TOPIC 2: Properties of Life Figure 2. Properties of Life Source: (Jane B. Reece, 2014) TOPIC 3: Assumptions, Methods, and Limitations of Science BASIC ASSUMPTIONS AND METHODS OF SCIENCE The process of science builds reliable knowledge about the natural world. To see evidence of this reliability, one can look around at the everyday products of scientific knowledge: from airplanes to antibiotics, from batteries to bridges. These technologies only work because science does. The process of building scientific knowledge relies on a few basic assumptions that are worth acknowledging. Science operates on the assumptions that: 4   There are natural causes for things that happen in the world around us. For example, if a ball falls to the ground, science assumes that there must be a natural explanation for why the ball moves downward once released. Right now, scientists can describe gravity in great detail, but exactly what gravity is remains elusive. Still, science assumes that there is an explanation for gravity that relies on natural causes, just as there is for everything in nature.  Evidence from the natural world can be used to learn about those causes. Science assumes that we can learn about gravity and why a ball falls by studying evidence from the natural world. Scientists can perform experiments with other falling objects, observe how gravity affects the orbits of the planets, etc. Evidence from a wide range of experiments and observations helps scientists understand more about the natural causes of gravity.  There is consistency in the causes that operate in the natural world. In other words, the same causes come into play in related situations and these causes are predictable. For example, science assumes that the gravitational forces at work on a falling ball are related to those at work on other falling objects. It is further assumed that the workings of gravity don't change from moment to moment and object to object in unpredictable ways. Hence, what we learn about gravity today by studying falling balls can also be used to understand, for example, modern satellite orbits, the formation of the moon in the distant past, and the movements Figure 3. Flowchart of the Scientific Method of the planets and stars in the future, because the same natural cause is at work regardless of when and where things happen. These assumptions are important and are not controversial in science today. In fact, they form much of the basis for how we interact with the world and each other everyday. Science operates on the assumptions that natural causes explain natural phenomena, that evidence from the natural world can inform us about those causes, and that these causes are consistent. SCIENTIFIC INQUIRY Fundamentally, the various scientific disciplines are alike in their reliance on evidence, the use of hypothesis and theories, the kinds of logic used, and much more. Nevertheless, scientists differ greatly from one another in what phenomena they investigate and in how they go about their work; in the reliance they place on historical data or on experimental findings and on qualitative or quantitative methods; in their recourse to fundamental principles; and in how much they draw on the findings of other sciences. Still, the exchange of techniques, information, and concepts goes on all the time among scientists, and there are common understandings among them about what constitutes an investigation that is scientifically valid. Scientific inquiry is not easily described apart from the context of particular investigations. There simply is no fixed set of steps that scientists always follow, no one path that leads them unerringly to scientific knowledge. There are, however, certain features of science that give it a distinctive character as a mode 5 of inquiry. Although those features are especially characteristic of the work of professional scientists, everyone can exercise them in thinking scientifically about many matters of interest in everyday life. Science Demands Evidence Sooner or later, the validity of scientific claims is settled by referring to observations of phenomena. Hence, scientists concentrate on getting accurate data. Such evidence is obtained by observations and measurements taken in situations that range from natural settings (such as a forest) to completely contrived ones (such as the laboratory). To make their observations, scientists use their own senses, instruments (such as microscopes) that enhance those senses, and instruments that tap characteristics quite different from what humans can sense (such as magnetic fields). Scientists observe passively (earthquakes, bird migrations), make collections (rocks, shells), and actively probe the world (as by boring into the earth's crust or administering experimental medicines). In some circumstances, scientists can control conditions deliberately and precisely to obtain their evidence. They may, for example, control the temperature, change the concentration of chemicals, or choose which organisms mate with which others. By varying just one condition at a time, they can hope to identify its exclusive effects on what happens, uncomplicated by changes in other conditions. Often, however, control of conditions may be impractical (as in studying stars), or unethical (as in studying people), or likely to distort the natural phenomena (as in studying wild animals in captivity). In such cases, observations have to be made over a sufficiently wide range of naturally occurring conditions to infer what the influence of various factors might be. Because of this reliance on evidence, great value is placed on the development of better instruments and techniques of observation, and the findings of any one investigator or group are usually checked by others. Science Is a Blend of Logic and Imagination Although all sorts of imagination and thought may be used in coming up with hypotheses and theories, sooner or later scientific arguments must conform to the principles of logical reasoning—that is, to testing the validity of arguments by applying certain criteria of inference, demonstration, and common sense. Scientists may often disagree about the value of a particular piece of evidence, or about the appropriateness of particular assumptions that are made—and therefore disagree about what conclusions are justified. But they tend to agree about the principles of logical reasoning that connect evidence and assumptions with conclusions. Scientists do not work only with data and well-developed theories. Often, they have only tentative hypotheses about the way things may be. Such hypotheses are widely used in science for choosing what data to pay attention to and what additional data to seek, and for guiding the interpretation of data. In fact, the process of formulating and testing hypotheses is one of the core activities of scientists. To be useful, a hypothesis should suggest what evidence would support it and what evidence would refute it. A hypothesis that cannot in principle be put to the test of evidence may be interesting, but it is not likely to be scientifically useful. The use of logic and the close examination of evidence are necessary but not usually sufficient for the advancement of science. Scientific concepts do not emerge automatically from data or from any amount of analysis alone. Inventing hypotheses or theories to imagine how the world works and then figuring out how they can be put to the test of reality is as creative as writing poetry, composing music, or designing skyscrapers. Sometimes discoveries in science are made unexpectedly, even by accident. But knowledge and creative insight are usually required to recognize the meaning of the unexpected. Aspects of data that have been ignored by one scientist may lead to new discoveries by another. Science Explains and Predicts Scientists strive to make sense of observations of phenomena by constructing explanations for them that use, or are consistent with, currently accepted scientific principles. Such explanations—theories—may be either sweeping or restricted, but they must be logically sound and incorporate a significant body of scientifically valid observations. The credibility of scientific theories often comes from their ability to show 6 relationships among phenomena that previously seemed unrelated. The theory of moving continents, for example, has grown in credibility as it has shown relationships among such diverse phenomena as earthquakes, volcanoes, the match between types of fossils on different continents, the shapes of continents, and the contours of the ocean floors. The essence of science is validation by observation. But it is not enough for scientific theories to fit only the observations that are already known. Theories should also fit additional observations that were not used in formulating the theories in the first place; that is, theories should have predictive power. Demonstrating the predictive power of a theory does not necessarily require the prediction of events in the future. The predictions may be about evidence from the past that has not yet been found or studied. A theory about the origins of human beings, for example, can be tested by new discoveries of human-like fossil remains. This approach is clearly necessary for reconstructing the events in the history of the earth or of the life forms on it. It is also necessary for the study of processes that usually occur very slowly, such as the building of mountains or the aging of stars. Stars, for example, evolve more slowly than we can usually observe. Theories of the evolution of stars, however, may predict unsuspected relationships between features of starlight that can then be sought in existing collections of data about stars. Scientists Try to Identify and Avoid Bias When faced with a claim that something is true, scientists respond by asking what evidence supports it. But scientific evidence can be biased in how the data are interpreted, in the recording or reporting of the data, or even in the choice of what data to consider in the first place. Scientists' nationality, sex, ethnic origin, age, political convictions, and so on may incline them to look for or emphasize one or another kind of evidence or interpretation. For example, for many years the study of primates—by male scientists— focused on the competitive social behavior of males. Not until female scientists entered the field was the importance of female primates' community-building behavior recognized. Bias attributable to the investigator, the sample, the method, or the instrument may not be completely avoidable in every instance, but scientists want to know the possible sources of bias and how bias is likely to influence evidence. Scientists want, and are expected, to be as alert to possible bias in their own work as in that of other scientists, although such objectivity is not always achieved. One safeguard against undetected bias in an area of study is to have many different investigators or groups of investigators working in it. Science Is Not Authoritarian It is appropriate in science, as elsewhere, to turn to knowledgeable sources of information and opinion, usually people who specialize in relevant disciplines. But esteemed authorities have been wrong many times in the history of science. In the long run, no scientist, however famous or highly placed, is empowered to decide for other scientists what is true, for none are believed by other scientists to have special access to the truth. There are no preestablished conclusions that scientists must reach on the basis of their investigations. In the short run, new ideas that do not mesh well with mainstream ideas may encounter vigorous criticism, and scientists investigating such ideas may have difficulty obtaining support for their research. Indeed, challenges to new ideas are the legitimate business of science in building valid knowledge. Even the most prestigious scientists have occasionally refused to accept new theories despite there being enough accumulated evidence to convince others. In the long run, however, theories are judged by their results: When someone comes up with a new or improved version that explains more phenomena or answers more important questions than the previous version, the new one eventually takes its place. LIMITATIONS OF THE SCIENTIFIC METHOD Due to the need to have completely controlled experiments to test a hypothesis, science can not prove everything. For example, ideas about God and other supernatural beings can never be confirmed or denied, as no experiment exists that could test their presence. Supporters of Intelligent Design attempt to convey their beliefs as scientific, but nonetheless the scientific method can never prove this. Science is 7 meant to give us a better understanding of the mysteries of the the natural world, by refuting previous hypotheses, and the existence of supernatural beings lies outside of science all together. Another limitation of the scientific method is when it comes making judgements about whether certain scientific phenomenons are "good" or "bad". For example, the scientific method cannot alone say that global warming is bad or harmful to the world, as it can only study the objective causes and consequences. Furthermore, science cannot answer questions about morality, as scientific results lay out of the scope of cultural, religious and social influences. TOPIC 4: Underlying Themes of Biology From amoebas to baboons, all living things have a few things in common. Five central themes of biology set the living apart from the inanimate. Take viruses: They seem to be alive, but many biologists don't consider them so since they lack one or more of these unifying characteristics. Here are the factors that help distinguish the living from the not-so-living. Structure and Function of Cells All life-forms consist of at least one cell. In the 17th century, scientists Robert Hooke and Anton von Leeuwenhoek observed cells and noted their characteristics under microscopes. These and subsequent observations led to the formation of the cell theory, stating that cells make up all life, carry out all biological processes and can only come from other cells. All cells contain genetic material and other structures floating in a jelly-like matrix, acquire energy from their surroundings, and are enveloped in protection from the external environment. Interactions Between Organisms Organisms don't exist in vacuums. Each living thing has uniquely adapted to a particular habitat and developed specific relationships with other organisms in the same area. In ecosystems, plants use light energy from the sun to make their own food, which becomes a source of energy for other organisms that consume the plants. Other creatures eat these plant-eating organisms and receive the energy. When plants and animals die, their energy flow doesn't stop; instead, the energy transfers to the soil and back into the environment, thanks to scavengers and decomposers that break down dead organisms. There are various connections between life-forms. Predators eat prey, parasites find nutrients and shelter at the expense of others, and some organisms form mutually beneficial relationships with one another. As a result, changes affecting one species influence the survival of others within the ecosystem. Reproduction and Genetics All organisms reproduce and pass on characteristics to their offspring. In asexual reproduction, offspring are exact replicas of their parents. More complex life-forms lean toward sexual reproduction, which involves two individuals producing offspring together. In this case, the offspring show characteristics of each parent. In the mid 1800s, an Austrian monk named Gregor Mendel conducted a series of famous experiments exploring the relationship between sexual reproduction and heredity. Mendel realized that units called genes determined heredity and could be passed from parent to offspring. Evolution and Natural Selection In the early 1800s, French biologist Jean Baptiste de Lamarck hypothesized that the use of certain features would strengthen their existence, and nonuse would cause them to eventually disappear in subsequent generations. This would explain how snakes evolved from lizards when their legs weren't being used, and how giraffe necks grew longer with stretching, according to Lamarck. Charles Darwin constructed his own theory of evolution called natural selection. Following his stint as a naturalist on the ship HMS Beagle, Darwin formulated a theory that claimed all individuals possess differences that allow them to survive in a particular environment, reproduce, and pass on their genes to 8 their descendants. Individuals that adapt poorly to their environments would have fewer opportunities to mate and pass on their genes. Eventually, the genes of the stronger individuals would become more prominent in subsequent populations. Darwin’s theory has become the most accepted theory for evolution. TOPIC 5: Evolution as a Unifying Concept Evolution is the change in living things over time. More specifically, evolution is a change in the genetic makeup of a subgroup, or population, of a species. The concept of evolution links observations from all levels of biology, from cells to the biosphere. A wide range of scientific evidence, including the fossil record and genetic comparisons of species, show that evolution is continuing today. Adaptation One way evolution occurs is through natural selection of adaptations. In natural selection, a genetic, or inherited, trait helps some individuals of a species survive and reproduce more successfully than other individuals in a particular environment. An inherited trait that gives an advantage to individual organisms and is passed on to future generations is an adaptation. Over time, the makeup of a population changes because more individuals have the adaptation. Two different populations of the same species might have different adaptations in different environments. The two populations may continue to evolve to the point at which they are different species Consider the orchid and the thorn bug in the figure below. Both organisms have adapted in ways that make them resemble other organisms. The orchid that looks like an insect lures other insects to it. The insects that are attracted to the orchid can pollinate the flower, helping the orchid to reproduce. The thorn bug’s appearance is an adaptation that makes predators less likely to see and eat it Figure 4. Different appearance of Thorn bugs This adaptation allows the thorn bug to survive and reproduce. In different environments, however, you would find other orchid and insect species that have different adaptations. Adaptation in evolution is different from the common meaning of adaptation. For example, if you say that you are adapting to a new classroom or to a new town, you are not talking about evolution. Instead, you are talking about consciously getting used to something new. Evolutionary adaptations are changes in a species that occur over many generations due to environmental pressures, not through choices made by organisms. Evolution is simply a longterm response to the environment. The process does not necessarily lead to more complex organisms, and it does not have any special end point. Evolution continues today, and it will continue as long as life exists on Earth. Unity and Diversity Evolution is a unifying theme of biology because it accounts for both the diversity and the similarities, or the unity, of life. As you study biology, you will see time after time that organisms are related to one another. When you read about cells and genetics in the next lessons, you will see that all organisms have similar cell structures and chemical processes. These shared characteristics result from a common evolutionary descent. 9 Humans and bacteria have much more in common than you may think. Both human and bacterial genetics are based on the same molecules—DNA and RNA. Both human and bacterial cells rely upon the same sources of energy, and they have similar cell structures. Both human and bacterial cells have membranes made mostly of fats that protect the inside of the cell from the environment outside the cell. Now think about the vast number of different types of organisms. All of the species now alive are the result of billions of years of evolution and adaptation to the environment. How? Natural selection of genetic traits can lead to the evolution of a new species. In the end, this genetic diversity is responsible for the diversity of life on Earth. 10  LESSON 2 INTRODUCTION TO CELL STRUCTURE AND FUNCTION TOPICS 1. Cell Theory 2. Structures and functions of prokaryotic and eukaryotic cells 3. Cell cycle 4. Membrane Transport LEARNING OUTCOMES At the end of the lesson, you should be able to: 1. Describe the cell theory 2. Describe the typical prokaryotic and eukaryotic cells 3. Discuss diversity among the eukaryotic cell types 4. Describe binary fission in prokaryotic cells 5. Discuss eukaryotic cell cycles 6. Describe mitosis 7. Distinguish between cytokinesis of plant and animal cells 8. Describe meiosis I and II 9. Compare and contrast mitosis and meiosis 10. Describe the fluid mosaic model of membrane structure and explain the structure ad functions of component molecules 11. Compare and contrast diffusion, osmosis, and dialysis 12. Explain cell transport of large and small molecules across biological membranes TOPIC 1: Cell Theory In 1665, Robert Hooke published Micrographia, a book filled with drawings and descriptions of the organisms he viewed under the recently invented microscope. The invention of the microscope led to the discovery of the cell by Hooke. While looking at cork, Hooke observed box-shaped structures, which he called “cells” as they reminded him of the cells, or rooms, in monasteries. This discovery led to the development of the classical cell theory. By the late 1830s, botanist Matthias Schleiden and zoologist Theodor Schwann were studying tissues and proposed the unified cell theory. The unified cell theory states that: all living things are composed of one or more cells; the cell is the basic unit of life; and new cells arise from existing cells. Rudolf Virchow later made important contributions to this theory. Schleiden and Schwann proposed spontaneous generation as the method for cell origination, but spontaneous generation (also called abiogenesis) was later disproven. Rudolf Virchow famously stated “Omnis cellula e cellula”… “All cells only arise from pre-existing cells. “The parts of the theory that did not have to do with the origin of cells, however, held up to scientific scrutiny and are widely agreed upon by the scientific community today. The generally accepted portions of the modern Cell Theory are as follows: 1. The cell is the fundamental unit of structure and function in living things. 2. All organisms are made up of one or more cells. 11 3. Cells arise from other cells through cellular division. Since the formation of classical cell theory, technology has improved, allowing for more detailed observations that have led to new discoveries about cells. These findings led to the formation of the modern cell theory, which has three main additions: first, that DNA is passed between cells during cell division; second, that the cells of all organisms within a similar species are mostly the same, both structurally and chemically; and finally, that energy flow occurs within cells. Figure 5. Proponents of the cell theory The expanded version of the cell theory can also include: 1. Cells carry genetic material passed to daughter cells during cellular division 2. All cells are essentially the same in chemical composition 3. Energy flow (metabolism and biochemistry) occurs within cell TOPIC 2: STRUCTURES AND FUNCTIONS OF PROKARYOTIC AND EUKARYOTIC CELLS Prokaryotic Cell Structure Prokaryotic cells are not as complex as eukaryotic cells. They have no true nucleus as the DNA is not contained within a membrane or separated from the rest of the cell, but is coiled up in a region of the cytoplasm called the nucleoid. Prokaryotic organisms have varying cell shapes. The most common bacteria shapes are spherical, rod- shaped, and spiral. Using bacteria as our sample prokaryote, the following structures and organelles can be found in bacterial cells:  Capsule: Found in some bacterial cells, this additional outer covering protects the cell when it is engulfed by other organisms, assists in retaining moisture, and helps the cell adhere to surfaces and nutrients.  Cell Wall: The cell wall is an outer covering that protects the bacterial cell and gives it shape.  Cytoplasm: Cytoplasm is a gel-like substance composed mainly of water that also contains enzymes, salts, cell components, and various organic molecules.  Cell Membrane or Plasma Membrane: The Figure 6. Anatomy of a prokaryotic cell cell membrane surrounds the cell's cytoplasm and regulates the flow of substances in and out of the cell.  Pili (Pilus singular): Hair-like structures on the surface of the cell that attach to other bacterial cells. Shorter pili called fimbriae help bacteria attach to surfaces.  Flagella: Flagella are long, whip-like protrusions that aid in cellular locomotion. 12   Ribosomes: Ribosomes are cell structures responsible for protein production.  Plasmids: Plasmids are gene-carrying, circular DNA structures that are not involved in reproduction.  Nucleoid Region: Area of the cytoplasm that contains the single bacterial DNA molecule. Prokaryotic cells lack organelles found in eukaryoitic cells such as mitochondria, endoplasmic reticuli, and Golgi complexes. According to the Endosymbiotic Theory, eukaryotic organelles are thought to have evolved from prokaryotic cells living in endosymbiotic relationships with one another. Like plant cells, bacteria have a cell wall. Some bacteria also have a polysaccharide capsule layer surrounding the cell wall. This is the layer where bacteria produce biofilm, a slimy substance that helps bacterial colonies adhere to surfaces and to each other for protection against antibiotics, chemicals, and other hazardous substances. Similar to plants and algae, some prokaryotes also have photosynthetic pigments. These light- absorbing pigments enable photosynthetic bacteria to obtain nutrition from light. Binary Fission Most prokaryotes reproduce asexually through a process called binary fission. During binary fission, the single DNA molecule replicates and the original cell is divided into two identical cells. Steps of Binary Fission 1. Binary fission begins with DNA replication of the single DNA molecule. Both copies of DNA attach to the cell membrane. 2. Next, the cell membrane begins to grow between the two DNA molecules. Once the bacterium just about doubles its original size, the cell membrane begins to pinch inward. 3. A cell wall then forms between the two DNA molecules dividing the original cell into two identical daughter cells. Eukaryotic cells are defined as cells containing organized nucleus and organelles which are enveloped by membrane-bound organelles. Examples of eukaryotic cells are plants, animals, protists, fungi. Parts of Eukaryotic cells Cytoplasmic Membrane It is also called plasma membrane or cell membrane. The plasma membrane is a semi- permeable membrane that separates the inside of a cell from the outside. Structure and Composition: In eukaryotic cells, the plasma membrane consists of proteins, carbohydrates and two layers of phospholipids (i.e. lipid with a phosphate group). These phospholipids are arranged as follows:  The polar, hydrophilic (water-loving) heads face the outside and inside of the cell. These heads interact with the aqueous environment outside and within a cell.  The non-polar, hydrophobic (water-repelling) tails are sandwiched between the heads and are protected from the aqueous environments. Figure 7 (top). Anatomy of a eukaryotic cell Scientists Singer and Nicolson described the structure Figure 8 (bottom). Cell Membrane of the phospholipid bilayer as the ‘Fluid Mosaic Model’. Components 13 The reason is that the bi-layer looks like a mosaic and has a semi-fluid nature that allows lateral movement of proteins within the bilayer. Functions  The plasma membrane is selectively permeable i.e. it allows only selected substances to pass through.  It protects the cells from shock and injuries.  The fluid nature of the membrane allows the interaction of molecules within the membrane. It is also important for secretion, cell growth, and division etc.  It allows transport of molecules across the membrane. This transport can be of two types: o Active transport – This transport occurs against the concentration gradient and therefore, requires energy. It also needs carrier proteins and is a highly selective process. o Passive transport – This transport occurs along the concentration gradient and therefore, does not require energy. Thus, it does not need carrier proteins and is not selective. Cell Wall The cell wall is a non-living, rigid structure outside the plasma membrane in plant cells and fungi. It is absent in Eukaryotic cells of animals Structure and composition: It is made of different components in different Eukaryotes:  Cellulose, hemicellulose, proteins, and pectin – in plants.  Cellulose, galactans, mannans and calcium carbonate – in fungi. The cell wall is divided into the following three layers:  Middle lamella – It is the outermost layer and is made of calcium pectates. It holds adjoining cells together.  Primary wall – It is the middle layer and is made of cellulose and hemicellulose. It is present in young, growing cells and is capable of growth.  Secondary wall – It is the innermost layer and similar in composition to the primary wall. Functions  Provides shape to the cell.  Helps in cell-cell interaction.  Protects the cell from injury, undesirable molecules and pathogens. Endoplasmic reticulum (ER) Description: It is a network of small, tubular structures. It divides the space inside of Eukaryotic cells into two parts – luminal (inside ER) and extra-luminal (cytoplasm). Structure: ER can be of two types: Smooth Endoplasmic Reticulum (SER) Rough Endoplasmic Reticulum (RER) Smooth due to lack of ribosomes Rough due to the presence of ribosomes Main site of lipid synthesis Site of protein synthesis Functions  SER is involved in lipid synthesis and RER is involved in protein synthesis.  RER helps in folding proteins and transports it to the Golgi apparatus in vesicles. Golgi Apparatus It is named after the scientist who discovered it, Camillo Golgi. Golgi is made of many flat, disc- shaped structures called cisternae. It is present in all eukaryotic cells except human red blood cells and sieve cells of plants. Structure: The cisternae are arranged in parallel and concentrically near the nucleus as follows: 14   Cis face (forming face) – It faces the plasma membrane and receives secreted material in vesicles.  Trans face (maturing face) – It faces the nucleus and releases the received material into the cell. Functions  An important site for packaging material within the cell.  Proteins are modified in the Golgi.  An important site for the formation of glycolipids (i.e. lipids with carbohydrate) and glycoproteins (i.e. proteins with carbohydrates). Ribosomes These structures are not bound by a membrane. Ribosomes are also called ‘Protein factories’ since they are the main site of protein synthesis. They are made of ribonucleic acids and proteins. Eukaryotic ribosomes are of the 80S type, with 60S (large subunit) and 40S (small subunit). Mitochondria They are membrane-bound organelles, also known as ‘powerhouses of the cell’. Structure: It has two membranes – outer and inner. The outer membrane forms a continuous boundary around the mitochondria. The inner membrane is semi-permeable and divided into folds called ‘cristae’. The membranes divide the lumen of the mitochondria into an inner and outer compartment. The inner compartment is called matrix and outer compartment forms the intermembrane space. Functions  They produce energy (ATP) and therefore Figure 9. Anatomy of the Mitochondria are called the ‘powerhouse of the cell’.  Helps in regulating cell metabolism.  Mitochondria possess their own DNA, RNA and components required for protein synthesis. Lysosomes They are membrane-bound vesicles formed in the Golgi apparatus. Lysosomes are also called ‘suicidal bags’ since they are rich in hydrolytic enzymes such as lipases, proteases, carbohydrates etc. These enzymes are optimally active at acidic pH (less than 7). Function: The main function of lysosomes is to digest lipids, proteins, carbohydrates and nucleic acids. Nucleus Nucleus is the main organelle of a cell. It is a double membrane structure with all the genetic information. Therefore, it is also called the ‘brain’ of a cell. The nucleus is found in all eukaryotic cells except human RBCs and sieve cells of plants. Structure: A nucleus has the following parts: 15  Figure 10. Anatomy of the Nucleus  Nuclear envelope – It is a double membrane structure that surrounds the nucleus. The outer membrane is continuous with the endoplasmic reticulum. The inner membrane has small pores called ‘nuclear pores’.  Nucleoplasm – It is the fluid material in the nucleus that contains the nucleolus and chromatin.  Nucleolus – Nucleoli are not membrane-bound and are active sites for ribosomal RNA synthesis.  Chromatin – It consists of DNA and proteins called ‘histones’. The DNA is organised into chromosomes. Chromosomes have certain constriction sites called ‘centromeres’. Based on the position of the centromere, they can be divided as follows: o Metacentric – With centromere in the centre and having equal chromosome arms. o Sub-metacentric – Centromere is slightly off-centre creating one short and one long arm. o Acrocentric – Centromere is extremely off-centre with one very long and one very short chromosome arm. o Telocentric – Centromere is placed at one end of the chromosome. Humans do not possess telocentric chromosomes. Functions  It stores genetic information (in the form of DNA) necessary for development and reproduction.  It contains all information necessary for protein synthesis and cellular functions. Cytoskeleton  It is the filamentous network present in the cytoplasm of a cell.  Function: It provides mechanical support, maintains the shape of the cell and helps in motility. Cilia and Flagella o They are both responsible for the movement of a cell. 16 Plastids They are double membrane organelles found in plant cells. They contain pigments and are of three types:  Chloroplasts – They contain chlorophyll and are involved in photosynthesis, where light energy is converted to chemical energy. Chloroplasts contain compartments called stroma and grana. Grana contains structures called thylakoids that contain chlorophyll. Stroma contains enzymes needed for carbohydrate and protein synthesis.  Chromoplasts – These give plants yellow, red or orange colours because they contain pigments like carotene.  Leucoplasts – These are colourless plastids that store either carbohydrates (Amyloplasts), oils and fats (Elaioplasts) or proteins (Aleuroplasts). TOPIC 3: Cell Cycle Cell Division— involves the distribution of identical genetic material or DNA to two daughter cells. What is most remarkable is the fidelity with which the DNA is passed along, without dilution or error, from one generation to the next. Cell Division functions in reproduction, growth, and repair. The Cell Cycle control system is driven by a built-in clock that can be adjusted by external stimuli (i.e.,chemical messages). Checkpoint—a critical control point in the Cell Cycle where ‘stop’ and ‘go-ahead’ signals can regulate the cell cycle. Animal cells have built-in ‘stop’ signals that halt the cell cycles and checkpoints until overridden by ‘go-ahead’ signals. Figure 11. Cell Cycle 17  Three major checkpoints are found in the G1, G2, and M phases of the Cell Cycle. The G1 Checkpoint—the Restriction Point The G1 checkpoint ensures that the cell is large enough to divide and that enough nutrients are available to support the resulting daughter cells. If a cell receives a ‘go-ahead’ signal at the G1 checkpoint, it will usually continue with the Cell Cycle. If the cell does not receive the ‘go-ahead’ signal, it will exit the Cell Cycle and switch to a non-dividing state called G0. Most cells in the human body are in the G0 phase. The G2 Checkpoint—ensures that DNA replication in S phase has been successfully completed. The Metaphase Checkpoint—ensures that all of the chromosomes are attached to the mitotic spindle by a kinetochore. Kinase—a protein which activates or deactivates another protein by phosphorylating them. Kinases give the ‘go-ahead’ signals at the G1 and G2 checkpoints. The kinases that drive these checkpoints must themselves be activated. The activating molecule is a cyclin, a protein that derives its name from its cyclically fluctuating concentration in the cell. Because of this requirement, these kinases are called cyclin-dependent kinases or CDKs. Cyclins accumulate during the G1, S, and G2 phases of the Cell Cycle. By the G2 checkpoint, enough cyclin is available to form MPF complexes (aggregations of CDK and cyclin) which initiate mitosis. MPF functions by phosphorylating key proteins in the mitotic sequence. Later in mitosis, MPF switches itself off by initiating a process which leads to the destruction of cyclin. CDK, the non-cyclin part of MPF, persists in the cell as an inactive form until it associates with new cyclin molecules synthesized during the interphase of the next round of the Cell Cycle. Mitosis (apparent division)—is nuclear division; the process by which the nucleus divides to produce two new nuclei. Mitosis results in two daughter cells that are genetically identical to each other and to the parental cell from which they came. Cytokinesis—is the division of the cytoplasm. Both mitosis and cytokinesis last for around one to two hours. Prophase—is the preparatory stage, During prophase, centrioles move toward opposite sides of the nucleus. The initially indistinct chromosomes begin to condense into visible threads. Chromosomes first become visible during early prophase as long, thin, and intertwined filaments but by late prophase, chromosomes are more compacted and can be clearly discerned as much shorter and rod-like structures. As the chromosomes become more distinct, the nucleoli also become more distinct. By the end of prophase, the nucleoli become less distinct, often disappearing altogether. 18 Metaphase—is when chromosomes become arranged so that their centromeres become aligned in one place, halfway between the two spindle poles. The long axes of the chromosomes are 90 degrees to the spindle axis. The plane of alignment is called the metaphase plate. Anaphase—is initiated by the separation of sister chromatids at their junction point at the centromere. The daughter chromosomes then move toward the poles. Telophase—is when daughter chromosomes complete their migration to the poles. The two sets of progeny chromosomes are assembled into two-groups at opposite ends of the cell. The chromosomes uncoil and assume their extended form during interphase. A nuclear membrane then forms around each chromosome group and the spindle microtubules disappear. Soon, the nucleolus reforms. Meiosis—reduces the amount of genetic information. While mitosis in diploid cells produces daughter cells with a full diploid complement, meiosis produces haploid gametes or spores with only one set of chromosomes. During sexual reproduction, gametes combine in fertilization to reconstitute the diploid complement found in parental cells. The process involves two successive divisions of a diploid nucleus. First Meiotic Division The first meiotic division results in reducing the number of chromosomes (reduction division). In most cases, the division is accompanied by cytokinesis Prophase I—has been subdivided into five substages: leptonema, zygonema, pachynema, diplonema, and diakinesis. Leptonema—Replicated chromosomes have coiled and are already visible. The number of chromosomes present is the same as the number in the diploid cell. Fig 12. Stages of Mitosis and Meiosis Fig 17. Endocytosis and Exocytosis Zygonema—Homologue chromosomes begin to pair and twist around each other in a highly specific manner. The pairing iscalled synapsis. And because the pair consists of four chromatids it is referred to as bivalent tetrad. Pachynema—Chromosomes become much shorter and thicker. A form of physical exchange between homologues takes place at specific regions. The process of physical exchange of a chromosome region is called crossing-over. Through the mechanism of crossing-over, the parts of the homologous chromosomes are recombined (genetic recombination). Diplonema—The two pairs of sister chromatids begin to separate from each other. It is at this point where crossing-over is shown to have taken place. The area of contact between two non-sister chromatids, called chiasma, become evident. Diakinesis—The four chromatids of each tetrad are even more condensed and the chiasma often terminalize or move down the chromatids to the ends. This delays the separation of homologous chromosomes. 19 In addition, the nucleoli disappear, and the nuclear membrane begins to break down. Metaphase I—The spindle apparatus is completely formed and the microtubules are attached to the centromere regions of the homologues. The synapsed tetrads are found aligned at the metaphase plate (the equatorial plane of the cell) instead of only replicated chromosomes. Anaphase I—Chromosomes in each tetrad separate and migrate toward the opposite poles. The sister chromatids (dyads) remain attached at their respective centromere regions. Telophase I—The dyads complete their migration to the poles. New nuclear membranes may form. In most species, cytokinesis follows, producing two daughter cells. Each has a nucleus containing only one set of chromosomes (haploid level) in a replicated form. Second Meiotic Division The events in the second meiotic division are quite similar to mitotic division. The difference lies, however, in the number of chromosomes that each daughter cell receives. While the original chromosome number is maintained in mitosis, the number is reduced to half in meiosis. Prophase II—The dyads contract. Metaphase II—The centromeres are directed to the equatorial plate and then divide. Anaphase II—The sister chromatids (monads) move away from each other and migrate to the opposite poles of the spindle fiber. Telophase II—The monads are at the poles, forming two groups of chromosomes. A nuclear membrane forms around each set of chromosomes and cytokinesis follows. The chromosomes uncoil and extend. TOPIC 4: Membrane Transport Cell membranes act as barriers to most, but not all, molecules. Development of a cell membrane that could allow some materials to pass while constraining the movement of other molecules was a major step in the evolution of the cell. Cell membranes are differentially (or semi-) permeable barriers separating the inner cellular environment from the outer cellular (or external) environment. Water potential is the tendency of water to move from an area of higher concentration to one of lower concentration. Energy exists in two forms: potential and kinetic. Water molecules move according to differences in potential energy between where they are and where they are going. Gravity and pressure are two enabling forces for this movement. Fig 13. Passive transport 20 PASSIVE TRANSPORT Passive transport requires no energy from the cell. Examples include the diffusion of oxygen and carbon dioxide, osmosis of water, and facilitated diffusion. Simple Diffusion In simple diffusion, small noncharged molecules or lipid soluble molecules pass between the phospholipids to enter or leave the cell, moving from areas of high concentration to areas of low concentration (they move down their concentration gradient). Oxygen and carbon dioxide and most lipids enter and leave cells by simple diffusion. Fig 14. Diffusion Osmosis Osmosis is a type of simple diffusion in which water molecules diffuse through a selectively permeable membrane from areas of high water concentration to areas of lower water concentration. (Note that the more particles dissolved in a solution, the less water there is in it, so osmosis is sometimes described as the diffusion of water from areas of low solute concentration to areas of high solute concentration). Fig. 15. Comparison of Hypotonic, Isotonic and Facilitated diffusion Hypertonic solution In facilitated diffusion, substances move into or out of cells down their concentration gradient through protein channels in the cell membrane. Simple diffusion and facilitated diffusion are similar in that both involve movement down the concentration gradient. The difference is how the substance gets through the cell membrane. In simple diffusion, the substance passes between the phospholipids; in facilitated diffusion there are a specialized membrane channels. Charged or polar molecules that cannot fit between the phospholipids generally enter and leave cells through facilitated diffusion. Fig 16. Facilitated Diffusion ACTIVE TRANSPORT The types of membrane transport discussed so far always involve substances moving down their concentration gradient. It is also possible to move substances across membranes against their concentration gradient (from areas of low concentration to areas of high concentration). Since this is an energetically unfavorable reaction, energy is needed for this movement. The source of energy is the breakdown of ATP. If the energy of ATP is directly used Fig 17. Active Transport 21 to pump molecules against their concentration gradient, the transport is called primary active transport. Endocytosis and Exocytosis: movement of large particles It is possible for large molecules to enter a cell by a process called endocytosis, where a small piece of the cell membrane wraps around the particle and is brought into the cell. If the particle is solid, endocytosis is also called phagocytosis. If fluid droplets are taken in, the processes is called pinocytosis. The opposite of endocytosis is exocytosis. Cells use exocytosis to secrete molecules too large to pass through the cell membrane by any other mechanism. Fig 18. Endocytosis and Exocytosis 22  LESSON 3 BIOMOLECULES TOPICS 1. Carbohydrates 2. Proteins 3. Lipids 4. Nucleic Acids LEARNING OUTCOMES At the end of the lesson, you should be able to: 1. Describe the ways in which carbon is critical to life 2. Explain the impact of slight changes in amino acids on organisms 3. Describe the four major types of biological molecules 4. Understand the functions of the four major types of molecules The large molecules necessary for life that are built from smaller organic molecules are called biological macromolecules. There are four major classes of biological macromolecules (carbohydrates, lipids, proteins, and nucleic acids), and each is an important component of the cell and performs a wide array of functions. Combined, these molecules make up the majority of a cell’s mass. Biological macromolecules are organic, meaning that they contain carbon. In addition, they may contain hydrogen, oxygen, nitrogen, phosphorus, sulfur, and additional minor elements. Carbon It is often said that life is “carbon-based.” This means that carbon atoms, bonded to other carbon atoms or other elements, form the fundamental components of many, if not most, of the molecules found uniquely in living things. Other elements play important roles in biological molecules, but carbon certainly qualifies as the “foundation” element for molecules in living things. It is the bonding properties of carbon atoms that are responsible for its important role. Carbon Bonding Carbon contains four electrons in its outer shell. Therefore, it can form four covalent bonds with other atoms or molecules. The simplest organic carbon molecule is methane (CH4), in which four hydrogen atoms bind to a carbon atom. 23 However, structures that are more complex are made using carbon. Any of the hydrogen atoms can be replaced with another carbon atom covalently bonded to the first carbon atom. In this way, long and branching chains of carbon compounds can be made (Figure a). The carbon atoms may bond with atoms of other elements, such as nitrogen, oxygen, and phosphorus (b). The molecules may also form rings, which themselves can link with other rings (c). This diversity of molecular forms accounts for the diversity of functions of the biological macromolecules and is based to a large degree on the ability of carbon to form multiple bonds with itself and other atoms. TOPIC 1: Carbohydrates Carbohydrates are macromolecules with which most consumers are somewhat familiar. To lose weight, some individuals adhere to “low-carb” diets. Athletes, in contrast, often “carb-load” before important competitions to ensure that they have sufficient energy to compete at a high level. Carbohydrates are, in fact, an essential part of our diet; grains, fruits, and vegetables are all natural sources of carbohydrates. Carbohydrates provide energy to the body, particularly through glucose, a simple sugar. Carbohydrates also have other important functions in humans, animals, and plants. Carbohydrates can be represented by the formula (CH2O)n, where n is the number of carbon atoms in the molecule. In other words, the ratio of carbon to hydrogen to oxygen is 1:2:1 in carbohydrate molecules. Carbohydrates are classified into three subtypes: monosaccharides, disaccharides, and polysaccharides. Monosaccharides (mono- = “one”; sacchar- = “sweet”) are simple sugars, the most common of which is glucose. In monosaccharides, the number of carbon atoms usually ranges from three to six. Most monosaccharide names end with the suffix -ose. Depending on the number of carbon atoms in the sugar, they may be known as trioses (three carbon atoms), pentoses (five carbon atoms), and hexoses (six carbon atoms). Monosaccharides may exist as a linear chain or as ring-shaped molecules; in aqueous solutions, they are usually found in the ring form. The chemical formula for glucose is C6H12O6. In most living species, glucose is an important source of energy. During cellular respiration, energy is released from glucose, and that energy is used to help make adenosine triphosphate (ATP). Plants synthesize glucose using carbon dioxide and water by the process of photosynthesis, and the glucose, in turn, is used for the energy requirements of the plant. The excess synthesized glucose is often stored as starch that is broken down by other organisms that feed on plants. Galactose (part of lactose, or milk sugar) and fructose (found in fruit) are other common monosaccharides. Although glucose, galactose, and fructose all have the same chemical formula 24 (C6H12O6), they differ structurally and chemically (and are known as isomers) because of differing arrangements of atoms in the carbon chain. Disaccharides (di- = “two”) form when two monosaccharides undergo a dehydration reaction (a reaction in which the removal of a water molecule occurs). During this process, the hydroxyl group (–OH) of one monosaccharide combines with a hydrogen atom of another monosaccharide, releasing a molecule of water (H2O) and forming a covalent bond between atoms in the two sugar molecules. Common disaccharides include lactose, maltose, and sucrose. Lactose is a disaccharide consisting of the monomers glucose and galactose. It is found naturally in milk. Maltose, or malt sugar, is a disaccharide formed from a dehydration reaction between two glucose molecules. The most common disaccharide is sucrose, or table sugar, which is composed of the monomers glucose and fructose. A long chain of monosaccharides linked by covalent bonds is known as a polysaccharide (poly- = “many”). The chain may be branched or unbranched, and it may contain different types of monosaccharides. Polysaccharides may be very large molecules. Starch, glycogen, cellulose, and chitin are examples of polysaccharides. Starch is the stored form of sugars in plants and is made up of amylose and amylopectin (both polymers of glucose). Plants are able to synthesize glucose, and the excess glucose is stored as starch in different plant parts, including roots and seeds. The starch that is consumed by animals is broken down into smaller molecules, such as glucose. The cells can then absorb the glucose. Glycogen is the storage form of glucose in humans and other vertebrates, and is made up of monomers of glucose. Glycogen is the animal equivalent of starch and is a highly branched molecule usually stored in liver and muscle cells. Whenever glucose levels decrease, glycogen is broken down to release glucose. Cellulose is one of the most abundant natural biopolymers. The cell walls of plants are mostly made of cellulose, which provides structural support to the cell. Wood and paper are mostly cellulosic in nature. Cellulose is made up of glucose monomers that are linked by bonds between particular carbon atoms in the glucose molecule. 25 Every other glucose monomer in cellulose is flipped over and packed tightly as extended long chains. This gives cellulose its rigidity and high tensile strength—which is so important to plant cells. Cellulose passing through our digestive system is called dietary fiber. While the glucose- glucose bonds in cellulose cannot be broken down by human digestive enzymes, herbivores such as cows, buffalos, and horses are able to digest grass that is rich in cellulose and use it as a food source. In these animals, certain species of bacteria reside in the rumen (part of the digestive system of herbivores) and secrete the enzyme cellulase. The appendix also contains bacteria that break down cellulose, giving it an important role in the digestive systems of ruminants. Cellulases can break down cellulose into glucose monomers that can be used as an energy source by the animal. Carbohydrates serve other functions in different animals. Arthropods, such as insects, spiders, and crabs, have an outer skeleton, called the exoskeleton, which protects their internal body parts. This exoskeleton is made of the biological macromolecule chitin, which is a nitrogenous carbohydrate. It is made of repeating units of a modified sugar containing nitrogen. Thus, through differences in molecular structure, carbohydrates are able to serve the very different functions of energy storage (starch and glycogen) and structural support and protection (cellulose and chitin). TOPIC 2: Lipids Lipids include a diverse group of compounds that are united by a common feature. Lipids are hydrophobic (“water-fearing”), or insoluble in water, because they are nonpolar molecules. This is because they are hydrocarbons that include only nonpolar carbon-carbon or carbon-hydrogen bonds. Lipids perform many different functions in a cell. Cells store energy for long-term use in the form of lipids called fats. Lipids also provide insulation from the environment for plants and animals. For example, they help keep aquatic birds and mammals dry because of their water- repelling nature. Lipids are also the building blocks of many hormones and are an important constituent of the plasma membrane. Lipids include fats, oils, waxes, phospholipids, and steroids. 26 A fat molecule, such as a triglyceride, consists of two main components—glycerol and fatty acids. Glycerol is an organic compound with three carbon atoms, five hydrogen atoms, and three hydroxyl (–OH) groups. Fatty acids have a long chain of hydrocarbons to which an acidic carboxyl group is attached, hence the name “fatty acid.” The number of carbons in the fatty acid may range from 4 to 36; most common are those containing 12–18 carbons. In a fat molecule, a fatty acid is attached to each of the three oxygen atoms in the –OH groups of the glycerol molecule with a covalent bond. During this covalent bond formation, three water molecules are released. The three fatty acids in the fat may be similar or dissimilar. These fats are also called triglycerides because they have three fatty acids. Some fatty acids have common names that specify their origin. For example, palmitic acid, a saturated fatty acid, is derived from the palm tree. Arachidic acid is derived from Arachis hypogaea, the scientific name for peanuts. Fatty acids may be saturated or unsaturated. In a fatty acid chain, if there are only single bonds between neighboring carbons in the hydrocarbon chain, the fatty acid is saturated. Saturated fatty acids are saturated with hydrogen; in other words, the number of hydrogen atoms attached to the carbon skeleton is maximized. When the hydrocarbon chain contains a double bond, the fatty acid is an unsaturated fatty acid. Most unsaturated fats are liquid at room temperature and are called oils. If there is one double bond in the molecule, then it is known as a monounsaturated fat (e.g., olive oil), and if there is more than one double bond, then it is known as a polyunsaturated fat (e.g., canola oil). Saturated fats tend to get packed tightly and are solid at room temperature. Animal fats with stearic acid and palmitic acid contained in meat, and the fat with butyric acid contained in butter, are examples of saturated fats. Mammals store fats in specialized cells called adipocytes, where 27 globules of fat occupy most of the cell. In plants, fat or oil is stored in seeds and is used as a source of energy during embryonic development. Unsaturated fats or oils are usually of plant origin and contain unsaturated fatty acids. The double bond causes a bend or a “kink” that prevents the fatty acids from packing tightly, keeping them liquid at room temperature. Olive oil, corn oil, canola oil, and cod liver oil are examples of unsaturated fats. Unsaturated fats help to improve blood cholesterol levels, whereas saturated fats contribute to plaque formation in the arteries, which increases the risk of a heart attack. In the food industry, oils are artificially hydrogenated to make them semi-solid, leading to less spoilage and increased shelf life. Simply speaking, hydrogen gas is bubbled through oils to solidify them. During this hydrogenation process, double bonds of the cis-conformation in the hydrocarbon chain may be converted to double bonds in the trans-conformation. This forms a trans-fat from a cis-fat. The orientation of the double bonds affects the chemical properties of the fat. Margarine, some types of peanut butter, and shortening are examples of artificially hydrogenated trans-fats. Recent studies have shown that an increase in trans-fats in the human diet may lead to an increase in levels of low-density lipoprotein (LDL), or “bad” cholesterol, which, in turn, may lead to plaque deposition in the arteries, resulting in heart disease. Many fast food restaurants have recently eliminated the use of trans-fats, and U.S. food labels are now required to list their trans-fat content. Essential fatty acids are fatty acids that are required but not synthesized by the human body. Consequently, they must be supplemented through the diet. Omega-3 fatty acids fall into this category and are one of only two known essential fatty acids for humans (the other being omega- 6 fatty acids). They are a type of polyunsaturated fat and are called omega-3 fatty acids because the third carbon from the end of the fatty acid participates in a double bond. Salmon, trout, and tuna are good sources of omega-3 fatty acids. Omega-3 fatty acids are important in brain function and normal growth and development. They may also prevent heart disease and reduce the risk of cancer. Like carbohydrates, fats have received a lot of bad publicity. It is true that eating an excess of fried foods and other “fatty” foods leads to weight gain. However, fats do have important functions. Fats serve as long-term energy storage. They also provide insulation for the body. Therefore, “healthy” unsaturated fats in moderate amounts should be consumed on a regular basis. 28 Phospholipids are the major constituent of the plasma membrane. Like fats, they are composed of fatty acid chains attached to a glycerol or similar backbone. Instead of three fatty acids attached, however, there are two fatty acids and the third carbon of the glycerol backbone is bound to a phosphate group. The phosphate group is modified by the addition of an alcohol. A phospholipid has both hydrophobic and hydrophilic regions. The fatty acid chains are hydrophobic and exclude themselves from water, whereas the phosphate is hydrophilic and interacts with water. Cells are surrounded by a membrane, which has a bilayer of phospholipids. The fatty acids of phospholipids face inside, away from water, whereas the phosphate group can face either the outside environment or the inside of the cell, which are both aqueous. Steroids and Waxes Unlike the phospholipids and fats discussed earlier, steroids have a ring structure. Although they do not resemble other lipids, they are grouped with them because they are also hydrophobic. All steroids have four, linked carbon rings and several of them, like cholesterol, have a short tail. Cholesterol is a steroid. Cholesterol is mainly synthesized in the liver and is the precursor of many steroid hormones, such as testosterone and estradiol. It is also the precursor of vitamins E and K. Cholesterol is the precursor of bile salts, which help in the breakdown of fats and their subsequent absorption by cells. Although cholesterol is often spoken of in negative terms, it is necessary for the proper functioning of the body. It is a key component of the plasma membranes of animal cells. Waxes are made up of a hydrocarbon chain with an alcohol (–OH) group and a fatty acid. Examples of animal waxes include beeswax and lanolin. Plants also have waxes, such as the coating on their leaves, that helps prevent them from drying out. TOPIC 3: Proteins Proteins are one of the most abundant organic molecules in living systems and have the most diverse range of functions of all macromolecules. Proteins may be structural, regulatory, contractile, or protective; they may serve in transport, storage, or membranes; or they may be toxins or enzymes. Each cell in a living system may contain thousands of different proteins, each with a unique function. Their structures, like their functions, vary greatly. They are all, however, polymers of amino acids, arranged in a linear sequence. The functions of proteins are very diverse because there are 20 different chemically distinct amino acids that form long chains, and the amino acids can be in any order. For example, proteins can function as enzymes or hormones. Enzymes, which are produced by living cells, are catalysts in biochemical reactions (like digestion) and are usually proteins. Each enzyme is specific for the substrate (a reactant that binds to an enzyme) upon which it acts. Enzymes can function to break molecular bonds, to rearrange bonds, or to form new bonds. An example of an enzyme is salivary amylase, which breaks down amylose, a component of starch. Hormones are chemical signaling molecules, usually proteins or steroids, secreted by an endocrine gland or group of endocrine cells that act to control or regulate specific physiological processes, including growth, development, metabolism, and reproduction. For example, insulin is a protein hormone that maintains blood glucose levels. 29 Proteins have different shapes and molecular weights; some proteins are globular in shape whereas others are fibrous in nature. For example, hemoglobin is a globular protein, but collagen, found in our skin, is a fibrous protein. Protein shape is critical to its function. Changes in temperature, pH, and exposure to chemicals may lead to permanent changes in the shape of the protein, leading to a loss of function or denaturation (to be discussed in more detail later). All proteins are made up of different arrangements of the same 20 kinds of amino acids. Amino acids are the monomers that make up proteins. Each amino acid has the same fundamental structure, which consists of a central carbon atom bonded to an amino group (– NH2), a carboxyl group (–COOH), and a hydrogen atom. Every amino acid also has another variable atom or group of atoms bonded to the central carbon atom known as the R group. The R group is the only difference in structure between the 20 amino acids; otherwise, the amino acids are identical. Protein Structure As discussed earlier, the shape of a protein is critical to its function. To understand how the protein gets its final shape or conformation, we need to understand the four levels of protein structure: primary, secondary, tertiary, and quaternary. The unique sequence and number of amino acids in a polypeptide chain is its primary structure. The unique sequence for every protein is ultimately determined by the gene that encodes the protein. Any change in the gene sequence may lead to a different amino acid being added to the polypeptide chain, causing a change in protein structure and function. In sickle cell anemia, the hemoglobin β chain has a single amino acid substitution, causing a change in both the structure and function of the protein. What is most remarkable to consider is that a hemoglobin molecule is made up of two alpha chains and two beta chains that each consist of about 150 amino acids. 30 The molecule, therefore, has about 600 amino acids. The structural difference between a normal hemoglobin molecule and a sickle cell molecule—that dramatically decreases life expectancy in the affected individuals—is a single amino acid of the 600. Because of this change of one amino acid in the chain, the normally biconcave, or disc-shaped, red blood cells assume a crescent or “sickle” shape, which clogs arteries. This can lead to a myriad of serious health problems, such as breathlessness, dizziness, headaches, and abdominal pain for those who have this disease. Folding patterns resulting from interactions between the non-R group portions of amino acids give rise to the secondary structure of the protein. The most common are the alpha (α)-helix and beta (β)-pleated sheet structures. Both structures are held in shape by hydrogen bonds. In the alpha helix, the bonds form between every fourth amino acid and cause a twist in the amino acid chain. In the β-pleated sheet, the “pleats” are formed by hydrogen bonding between atoms on the backbone of the polypeptide chain. The R groups are attached to the carbons, and extend above and below the folds of the pleat. The pleated segments align parallel to each other, and hydrogen bonds form between the same pairs of atoms on each of the aligned amino acids. The α-helix and β-pleated sheet structures are found in many globular and fibrous proteins. The unique three-dimensional structure of a polypeptide is known as its tertiary structure. This structure is caused by chemical interactions between various amino acids and regions of the polypeptide. Primarily, the interactions among R groups create the complex three-dimensional tertiary structure of a protein. There may be ionic bonds formed between R groups on different amino acids, or hydrogen bonding beyond that involved in the secondary structure. When protein folding takes place, the hydrophobic R groups of nonpolar amino acids lay in the interior of the protein, whereas the hydrophilic R groups lay on the outside. The former types of interactions are also known as hydrophobic interactions. In nature, some proteins are formed from several polypeptides, also known as subunits, and the interaction of these subunits forms the quaternary structure. Weak interactions between the subunits help to stabilize the overall structure. For example, hemoglobin is a combination of four polypeptide subunits. 31 Each protein has its own unique sequence and shape held together by chemical interactions. If the protein is subject to changes in temperature, pH, or exposure to chemicals, the protein structure may change, losing its shape in what is known as denaturation as discussed earlier. Denaturation is often reversible because the primary structure is preserved if the denaturing agent is removed, allowing the protein to resume its function. Sometimes denaturation is irreversible, leading to a loss of function. One example of protein denaturation can be seen when an egg is fried or boiled. The albumin protein in the liquid egg white is denatured when placed in a hot pan, changing from a clear substance to an opaque white substance. Not all proteins are denatured at high temperatures; for instance, bacteria that survive in hot springs have proteins that are adapted to function at those temperatures. TOPIC 4: Nucleic Acids Nucleic acids are key macromolecules in the continuity of life. They carry the genetic blueprint of a cell and carry instructions for the functioning of the cell. The two main types of nucleic acids are deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). DNA is the genetic material found in all living organisms, ranging from single-celled bacteria to multicellular mammals. The other type of nucleic acid, RNA, is mostly involved in protein synthesis. The DNA molecules never leave the nucleus, but instead use an RNA intermediary to communicate with the rest of the cell. Other types of RNA are also involved in protein synthesis and its regulation. DNA and RNA are made up of monomers known as nucleotides. The nucleotides combine with each other to form a polynucleotide, DNA or RNA. Each nucleotide is made up of three components: a nitrogenous base, a pentose (five-carbon) sugar, and a phosphate group. Each nitrogenous base in a nucleotide is attached to a sugar molecule, which is attached to a phosphate group. 32 DNA Double-Helical Structure DNA has a double-helical structure. It is composed of two strands, or polymers, of nucleotides. The strands are formed with bonds between phosphate and sugar groups of adjacent nucleotides. The strands are bonded to each other at their bases with hydrogen bonds, and the strands coil about each other along their length, hence the “double helix” description, which means a double spiral The alternating sugar and phosphate groups lie on the outside of each strand, forming the backbone of the DNA. The nitrogenous bases are stacked in the interior, like the steps of a staircase, and these bases pair; the pairs are bound to each other by hydrogen bonds. The bases pair in such a way that the distance between the backbones of the two strands is the same all along the molecule. The rule is that nucleotide A pairs with nucleotide T, and G with C. 33  LESSON 4 PRINCIPLES OF CELL METABOLISM TOPICS 1. Chemical reactions and Energy 2. Role of ATP in coupled chemical reactions 3. Function of catalysts 4. Enzymes LEARNING OUTCOMES At the end of the lesson, you should be able to: 1. Distinguish between potential and Kinetic energy 2. Describe the roles of ATP and ADP in the coupling of chemical reactions. 3. Describe enzyme structure, how enzymes work, regulation of enzyme activity (e.g. cofactors and inhibitors) and factors that affect enzyme activity. TOPIC 1: Chemical Reactions and Energy Figure 19. Energy transfer in the environment Energy cycling between the environment and living organisms is one of the fundamental concepts of biology. All cells use energy from their environment to grow, make new parts, and reproduce. Plants trap radiant energy from the sun and store it as chemical bond energy through the process of photosynthesis (Fig. 4.1). They extract carbon and oxygen from carbon dioxide, nitrogen from the soil, and hydrogen and oxygen from water to make biomolecules such as glucose and amino acids. Animals, on the other hand, cannot trap energy from the sun or use carbon and nitrogen from the air and soil to synthesize biomolecules. They must import chemical-bond energy by ingesting 34 the biomolecules of plants or other animals. Ultimately, however, energy trapped by photosynthesis is the energy source for all animals, including humans. Animals extract energy from biomolecules through the process of respiration, which consumes oxygen and produces carbon dioxide and water. If animals ingest more energy than they need for immediate use, the excess energy is stored in chemical bonds, just as it is in plants. Glycogen (a glucose polymer) and lipid molecules are the main energy stores in animals. These storage molecules are available for use at times when an animal’s energy needs exceed its food intake. ENERGY IS USED TO PERFORM WORK All living organisms obtain, store, and use energy to fuel their activities. Energy can be defined as the capacity to do work, but what is work? We use this word in everyday life to mean various things, from hammering a nail to sitting at a desk writing a paper. In biological systems, however, the word means one of three specific things: chemical work, transport work, or mechanical work. Chemical work is the making and breaking of chemical bonds. It enables cells and organisms to grow, maintain a suitable internal environment, and store information needed for reproduction and other activities. Forming the chemical bonds of a protein is an example of chemical work. Transport work enables cells to move ions, molecules, and larger particles through the cell membrane and through the membranes of organelles in the cell. Transport work is particularly useful for creating concentration gradients, distributions of molecules in which the concentration is higher on one side of a membrane than on the other. For example, certain types of endoplasmic reticulum use energy to import calcium ions from the cytosol. This ion transport creates a high calcium concentration inside the organelle and a low concentration in the cytosol. If calcium is then released back into the cytosol, it creates a “calcium signal” that causes the cell to perform some action, such as muscle contraction. Mechanical work in animals is used for movement. At the cellular level, movement includes organelles moving around in a cell, cells changing shape, and cilia and flagella beating. At the macroscopic level in animals, movement usually involves muscle contraction. Most mechanical work is mediated by motor proteins that make up certain intracellular fibers and filaments of the cytoskeleton Figure 20. Forms of energy 35  THERMODYNAMICS Two basic rules govern the transfer of energy in biological systems and in the universe as a whole. The first law of thermodynamics, also known as the law of conservation of energy, states that the total amount of energy in the universe is constant. The universe is considered to be a closed system—nothing enters and nothing leaves. Energy can be converted from one type to another, but the total amount of energy in a closed system never changes. The human body is not a closed system, however. As an open system, it exchanges materials and energy with its surroundings. Because our bodies cannot create energy, they import it from outside in the form of food. By the same token, our bodies lose energy, especially in the form of heat, to the environment. Energy that stays within the body can be changed from one type to another or can be used to do work. The second law of thermodynamics states that natural spontaneous processes move from a state of order (nonrandomness) to a condition of randomness or disorder, also known as entropy. Creating and maintaining order in an open system such as the body requires the input of energy. Disorder occurs when open systems lose energy to their surroundings without regaining it. When this happens, we say that the entropy of the open system has increased. TOPIC 2: ROLE OF ATP IN COUPLED CHEMICAL REACTIONS ATP: Adenosine Triphosphate Adenosine triphosphate (ATP) is the energy currency for cellular processes. ATP provides the energy for both energy-consuming endergonic reactions and energy-releasing exergonic reactions, which require a small input of activation energy. When the chemical bonds within ATP are broken, energy is released and can be harnessed for cellular work. The more bonds in a molecule, the more potential energy it contains. Because the bond in ATP is so easily broken and reformed, ATP is like a rechargeable battery that powers cellular process ranging from DNA replication to protein synthesis. Molecular Structure Adenosine triphosphate (ATP) is comprised of the molecule adenosine bound to three phosphate groups. Adenosine is a nucleoside consisting of the nitrogenous base adenine and the five-carbon sugar ribose. The three phosphate groups, in order of closest to furthest from the ribose sugar, are labeled alpha, beta, and gamma. Together, these chemical groups constitute an energy powerhouse. The two bonds between the phosphates are equal high-energy bonds (phosphoanhydride bonds) that, when broken, release sufficient energy to power a variety of cellular reactions and processes. The bond between the beta and gamma phosphate is considered “high-energy” because when the bond breaks, the products [adenosine diphosphate (ADP) and one inorganic phosphate group (Pi)] have a lower free energy than the reactants (ATP and a water molecule). ATP breakdown into ADP and P i is called hydrolysis because it consumes a water molecule (hydro-, meaning “water”, and lysis, meaning “separation”). 36  Figure 21. Components of ATP Adenosine Triphosphate (ATP): ATP is the primary energy currency of the cell. It has an adenosine backbone with three phosphate groups attached. ATP Hydrolysis and Synthesis ATP is hydrolyzed into ADP in the following reaction: ATP+H2O→ADP+Pi+free energy Like most chemical reactions, the hydrolysis of ATP to ADP is reversible. The reverse reaction combines ADP + Pi to regenerate ATP from ADP. Since ATP hydrolysis releases energy, ATP synthesis must require an input of free energy. ADP is combined with a phosphate to form ATP in the following reaction: ADP+Pi+free energy→ATP+H2O ATP and Energy Coupling Exactly how much free energy (∆G) is released with the hydrolysis of ATP, and how is that free energy used to do cellular work? The calculated ∆G for the hydrolysis of one mole of ATP into ADP and Pi is −7.3 kcal/mole (−30.5 kJ/mol). However, this is only true under standard conditions, and the ∆G for the hydrolysis of one mole of ATP in a living cell is almost double the value at standard conditions: 14 kcal/mol (−57 kJ/mol). ATP is a highly unstable molecule. Unless quickly used to perform work, ATP spontaneously dissociates into ADP + Pi, and the free energy released during this process is lost as heat. To harness the energy within the bonds of ATP, cells use a strategy called energy coupling. Energy Coupling in Sodium-Potassium Pumps 37  Figure 22. Sodium-Potassium Pumps Energy Coupling: Sodium-potassium pumps use the energy derived from exergonic ATP hydrolysis to pump sodium and potassium ions across the cell membrane. Cells couple the exergonic reaction of ATP hydrolysis with the endergonic reactions of cellular processes. For example, transmembrane ion pumps in nerve cells use the energy from ATP to pump ions across the cell membrane and generate an action potential. The sodium-potassium pump (Na+/K+ pump) drives sodium out of the cell and potassium into the cell. When ATP is hydrolyzed, it transfers its gamma phosphate to the pump protein in a process called phosphorylation. The Na+/K+ pump gains the free energy and undergoes a conformational change, allowing it to release three Na + to the outside of the cell. Two extracellular K+ ions bind to the protein, causing the protein to change shape again and discharge the phosphate. By donating free energy to the Na+/K+ pump, phosphorylation drives the endergonic reaction. Energy Coupling in Metabolism During cellular metabolic reactions, or the synthesis and breakdown of nutrients, certain molecules must be altered slightly in their conformation to become substrates for the next step in the reaction series. In the very first steps of cellular respiration, glucose is broken down through the process of glycolysis. ATP is required for the phosphorylation of glucose, creating a high-energy but unstable intermediate. This phosphorylation reaction causes a conformational change that allows enzymes to convert the phosphorylated glucose molecule to the phosphorylated sugar fructose. Fructose is a necessary intermediate for glycolysis to move forward. In this example, the exergonic reaction of ATP hydrolysis is coupled