BIO101 Study Guide PDF

BIO101 Study Guide Site: Saylor Academy Printed by: Guest user Course: BIO101: Introduction to Molecular and Cellular Biology Date: Wednesday, December 4, 2024, 6:28 PM Book: BIO101 Study Guide https://learn.sa...

BIO101 Study Guide Site: Saylor Academy Printed by: Guest user Course: BIO101: Introduction to Molecular and Cellular Biology Date: Wednesday, December 4, 2024, 6:28 PM Book: BIO101 Study Guide https://learn.saylor.org/mod/book/tool/print/index.php?id=51885 12/4/24, 8 30 PM Page 1 of 44 :  Table Table of of contents contents Navigating Navigating this this Study Study Guide Guide Unit Unit 1: 1: Introduction Introduction to to Biology Biology Unit Unit 2: 2: Basic Basic Chemistry Chemistry Unit Unit 3: 3: Biological Biological Molecules Molecules Unit Unit 4: 4: Cells Cells and and Cell Cell Membranes Membranes Unit Unit 5: 5: Enzymes, Enzymes, Metabolism, Metabolism, and and Cellular Cellular Respiration Respiration Unit Unit 6: 6: Photosynthesis Photosynthesis Unit Unit 7: 7: Cellular Cellular Reproduction: Reproduction: Mitosis Mitosis Unit Unit 8: 8: Cellular Cellular Reproduction: Reproduction: Meiosis Meiosis Unit Unit 9: 9: Mendelian Mendelian Genetics Genetics and and Chromosomes Chromosomes Unit Unit 10: 10: Gene Gene Expression Expression https://learn.saylor.org/mod/book/tool/print/index.php?id=51885 12/4/24, 8 30 PM Page 2 of 44 :  Navigating Navigating this this Study Study Guide Guide Study Study Guide Guide Structure Structure In this study guide, the sections in each unit (1a., 1b., etc.) are the learning outcomes of that unit. Beneath each learning outcome are: questions for you to answer independently; a brief summary of the learning outcome topic; and and resources related to the learning outcome. At the end of each unit, there is also a list of suggested vocabulary words. How How to to Use this this Study Study Guide Guide  Review the entire course by reading reading the learning outcome summaries and suggested resources.  Test your understanding of the course information by answering answering questions related to each unit learning outcome and defining defining and memorizing memorizing the vocabulary words at the end of each unit. By clicking on the gear button on the top right of the screen, you can print the study guide. Then you can make notes, highlight, and underline as you work. Through reviewing and completing the study guide, you should gain a deeper understanding of each learning outcome in the course and be better prepared for the final exam! https://learn.saylor.org/mod/book/tool/print/index.php?id=51885 12/4/24, 8 30 PM Page 3 of 44 :  Unit Unit 1: 1: Introduction Introduction to to Biology Biology 1a. 1a. List the the basic basic characteristics characteristics of of life that that are common to to all living living things things How is a nonliving thing (such as a rock) different from a living organism (such as a mouse)? Can you point to examples of nonliving things that have some characteristics of life? How is a dead organism different from a living organism? Biology Biology is the study of living things, which are also known as organisms. To determine what makes something alive, we must consider characteristics that are common to organisms. Chemistry Chemistry is the study of non-living matter. Though there are many different kinds of organisms, all organisms share these characteristics: Response Response to the environment Growth Growth and developmental change Reproduction Reproduction Energy Energy processing and chemical metabolism metabolism Regulation Regulation and maintenance of homeostasis homeostasis Orderly Orderly structure structure with cellular basis Evolutionary Evolutionary adaptation adaptation based on the transmission of heritable traits Some nonliving things have some of these characteristics, but to be alive, something must have all of the characteristics. For example, a crystal has a high degree of order and can grow, but it does not maintain homeostasis. Review this material in Advanced Characteristics of Life and Introduction to Biological Systems. 1b. 1b. List List the the levels of of organization organization of of life life and characteristics characteristics of of each level What makes each level different from the one below it (or the level above it)? The levels of organization in biology are characterized by increasing complexity and order. They are structured in a hierarchical (or nested) arrangement. For example, atoms of different types form more complex structures called molecules. Molecules can form more complex structures called organelles, and so on. You should be able to list the levels of organization – from atoms all the way up to the biosphere. Atom Atom - basic building block of matter Molecule Molecule - multiple atoms bonded together Organelle Organelle - subcellular structure with specific functions Cell Cell - basic unit of life Tissue Tissue - collection of cells Organ Organ - multiple tissues packaged for a particular function Organ Organ System System - group of functionally related organs Organism Organism - a living individual Population Population - group of individuals of the same species Community Community - different populations living together https://learn.saylor.org/mod/book/tool/print/index.php?id=51885 12/4/24, 8 30 PM Page 4 of 44 :  Ecosystem Ecosystem - a community along with the nonliving surroundings Biosphere Biosphere - includes all living things and their surroundings Review the levels of biological organization in Introduction to Biological Systems. It addresses the biological hierarchy starting at 15:10. 1c. 1c. Describe the the steps steps of of the the scientific scientific method method and and the the importance of using using the the scientific method method in in research What is science? How does science work? Science Science is a logical system of inquiry. Consequently, science allows us to learn about ourselves and the universe we live in. A critically important aspect of science is that it is based on evidence and is observational. Beyond mere observation, science involves the systematic testing of hypotheses. A hypothesis is an explanation for an observation observation, the process of gaining information. A hypothesis hypothesis (which might be correct or incorrect) is a prediction prediction and attempts to explain why something is the way it is. The active part of science is devising experiments to test hypotheses. A hypothesis is supported (although not proven) if an appropriate experiment yields the results the hypothesis predicted. Otherwise, you must modify or reject the hypothesis. This basic process has allowed us to learn about the universe. Biology is the corner of science that deals with living things in the universe, but biology is otherwise no different from science in general. As you review the nature and process of science, pay particular attention to the steps in the following flowchart, which demonstrates how science is a process. You should also understand the distinction between basic and applied science. https://learn.saylor.org/mod/book/tool/print/index.php?id=51885 12/4/24, 8 30 PM Page 5 of 44 :  To review this material, see The Process of Science. Unit Unit 1 Vocabulary Vocabulary You should be familiar with these terms as you prepare for the final exam. atom biology biosphere cell chemistry community ecosystem environment experiment homeostasis hypothesis molecule observation organ system organelle https://learn.saylor.org/mod/book/tool/print/index.php?id=51885 12/4/24, 8 30 PM Page 6 of 44 :  organism population prediction reproduction science tissue https://learn.saylor.org/mod/book/tool/print/index.php?id=51885 12/4/24, 8 30 PM Page 7 of 44 :  Unit Unit 2: 2: Basic Basic Chemistry Chemistry 2a. 2a. List the the major major components components of of an an atom atom and and their their locations locations What are the three primary subatomic particles? What are the major differences between the various subatomic particles? Where are the various subatomic particles located within an atom? What is an electron shell? What is a subshell? What is an orbital? The universe is made up of matter and energy. Matter (all of the material in the universe) is composed of almost unimaginably small particles called atoms atoms. As tiny as atoms are, even smaller particles make up each atom. We call them subatomic subatomic par particles ticles because they are smaller than atoms. The primary subatomic particles are protons protons, neutrons neutrons, and electrons electrons. Protons and neutrons make up the nucleus of an atom. Electrons Electrons are outside the nucleus. A proton has an electrical charge of +1. A neutron is nearly identical in size to a proton, but it has no charge. An electron is much smaller than a proton or neutron. An electron is also a charged particle. Despite being much smaller than a proton, the charge of an electron is equal in magnitude to the charge of a proton. However, the charge is opposite, so each electron has a charge of -1. Electrons occupy spaces around the nucleus nucleus. These spaces have a hierarchical arrangement. An orbital orbital is a space that can be occupied by electrons. Each orbital can contain up to two electrons. There are different types and shapes of orbitals: s , p , d , and f. There is only one kind of ss orbital orbital, but there are three kinds of pp orbital orbital, five dd orbitals orbitals, and seven ff orbitals orbitals. A collection of orbitals of the same type makes up a subshell subshell, and a collection of subshells makes up a shellshell (also called an energy energy level level). The first shell includes only one subshell (the s subshell), which is made up of only one s orbital. The second shell is made up of two subshells (an s and a p subshell), with the s subshell being made up of one s orbital and the p subshell being made up of three p orbitals. Since different shells contain different numbers of orbitals, each shell has a different maximum number of electrons it can hold. Review the atomic structure and orbitals in Elements and Atoms , More on the Atom , and Protons, Neutrons, and Electrons. 2b. 2b. List the the different different types types of of bonds bonds and and how they lead to to the formation of molecules and and compounds compounds What is a compound? How is a compound different from an element? How are compounds formed? Atoms are the building blocks of elements elements, which are pure substances made up of only one kind of atom. Although there are just more than one hundred different elements, there are countless different substances in the universe. Most of these substances are compounds, not elements. A compound compound is a substance made up of two or more different kinds of atoms. This is the fundamental distinction between an element and a compound. Rather than simply being a mixture of two or more kinds of atoms, compounds are formed when different kinds of atoms interact. This interaction gives the compound different properties compared to the properties of the constituent elements. For example, sodium chloride (table salt) is comprised of the elements sodium and chlorine, but sodium chloride (the compound) is different from each of these elements. The interactions between atoms in a compound are called chemical bonds. There are three major categories of chemical chemical bonds bonds: Ionic Ionic bonds bonds form when one or more electrons from one atom is transferred to another atom, creating a positive ion and a negative ion that are attracted to each other because of their opposite charges. Ions Ions are charged elements. Covalent Covalent bonds bonds form when two different atoms share one or more pairs of electrons which hold the two atoms together more strongly than an ionic bond. Metallic Metallic bonds bonds consist of a "sea" of electrons that move about from one metallic atom to another, holding together many metallic atoms. https://learn.saylor.org/mod/book/tool/print/index.php?id=51885 12/4/24, 8 30 PM Page 8 of 44 :  Molecules Molecules are particles that are bigger than atoms. They are made up of multiple atoms (of the same or different elements) held together by covalent bonds. For example, a molecule of water consists of an oxygen atom which is covalently and separately bonded to two hydrogen atoms. You should appreciate the distinction between atoms, ions, molecules, elements, and compounds. Review this material in Orbitals , More on Orbitals and Electron Configuration , Valence Electrons , Isotopes, Ions, and Molecules , Ionic, Covalent, and Metallic Bonds , Chemical Notation , and Balancing Chemical Equations. 2c. 2c. Describe the the primary primary concepts concepts of thermodynamics thermodynamics as as they they relate relate to to heat, temperature, energy, energy, and and work work What is energy? What is heat? What is temperature? What is work? What are the laws of thermodynamics? Thermodynamics Thermodynamics is the branch of science concerned with energy and energy transfer between objects. Although thermodynamics applies throughout the universe, we study it within biology because organisms are involved in many energy transactions. In other words, organisms are thermodynamic systems. These are fundamental questions of thermodynamics. We can define energy energy as the capacity to do work. Work Work refers to some sort of change. For example, moving an object from one place to another requires work, and energy is required for that work. Heat is energy in the form of movement of particles (atoms, ions, or molecules) within a substance. Heat is energy that is unavailable for performing work. Temperature Temperature is a measure of the average speed of the particles in an object. Temperature and heat are not the same thing. Temperature does not depend on how much matter is present, whereas heat does. For example, a swimming pool has the same temperature as a cup of water from that swimming pool, but the swimming pool contains much more heat than the cup of water because it contains much more matter. Two of the four laws of thermodynamics are important in biology: The First First Law Law of of Thermodynamics Thermodynamics states that energy cannot be created or destroyed, though it can be transferred and transformed. This is also known as the Law Law of of Conservation Conservation of of Energy Energy. The Second Second Law Law of of Thermodynamics Thermodynamics states that every energy transaction increases the entropy entropy (disorder) of the universe. An implication of this second law is that every energy transaction involves some loss of usable energy as heat, so no energetic process (including those occurring in organisms) can ever be perfectly efficient. These thermodynamic concepts are important for understanding living things. Review this material in Energy and Metabolism , More on Energy , The First Law of Thermodynamics , and Gibbs Free Energy. Unit Unit 2 Vocabulary You should be familiar with these terms as you prepare for the final exam. atom chemical bond compound covalent bond electron element energy heat ion ionic bond metallic bond https://learn.saylor.org/mod/book/tool/print/index.php?id=51885 12/4/24, 8 30 PM Page 9 of 44 :  molecule neutron orbital proton shell subshell temperature thermodynamics work https://learn.saylor.org/mod/book/tool/print/index.php?id=51885 12/4/24, 8 30 PM Page 10 of 44 :  Unit Unit 3: 3: Biological Biological Molecules Molecules 3a. 3a. List the the characteristics characteristics of of water water that that make make it it important important to to life life as as we we know know it it What is special about water? What is the electrical charge distribution on a water molecule? Why does the polarity of water make it well suited to its functions in biology? Water Water is so indispensable for life that our primary method for searching for life outside of earth is to search for evidence of water. A water molecule is composed of one oxygen atom that is simultaneously bonded to two hydrogen atoms. The covalent bonds between the oxygen and each hydrogen are polar polar because the sharing of electrons between oxygen and hydrogen is not equal. Because of this unequal sharing, the oxygen atom is partially negatively charged, and each hydrogen atom is partially positively charged. This makes the overall water molecule polar. This gives water several special characteristics: Water molecules can form hydrogen hydrogen bonds bonds with other polar molecules, including other water molecules. Water is less dense in the frozen state than in the liquid state. Because of this, bodies of water freeze from the top down, and thaw during seasonal warming. Water has a high specific specific heat heat capacity capacity, requiring more energy than most substances to change its temperature. This stabilizes the temperature of bodies of water more than landmasses. Water has a high cohesion cohesion. This can create capillary capillary attraction attraction which can lift water through vessels to the tops of the tallest trees. Water is an excellent solvent solvent. The chemistry of life is mostly aqueous solution chemistry. Water has high sur surface face tension tension. This allows small organisms to walk on the surface of water. Water has a high latent latent heat heat of of vaporization vaporization. This means water requires a lot of energy to change its state from liquid to gas. This allows for effective evaporative cooling by sweating. Water exists in all three states (solid, liquid, and gas) within a comparatively narrow range of temperatures that organisms can tolerate. Because of these special characteristics, it is no surprise that life evolved in the water of the ocean. We can think of every living cell as a tiny bag of water and biological molecules. Keep these special properties in mind as you study biology, and be sure to review polarity and how it underlies these properties. Review this material in Water and The Properties of Water. 3b. 3b. Describe Describe the the role role of of acids, bases, bases, and buffers buffers in biological systems What are the definitions of an acid and base? How do buffers work? In aqueous solutions, the hydrogen atom shifts from one water molecule to another. This creates H+ and OH- ions that are very reactive. These ions are equal in pure water, but an imbalance in concentration occurs when certain solutes are added. Acids Acids increase the H+ concentration; bases decrease H+ concentration. Different environments in living organisms have different amounts of acids and bases. For example, the stomach requires high amounts of acid to break down food. The bloodstream is a different environment. Buffers Buffers are chemicals that resist the changes that acids and bases make in a solution of the body environment. Review this material in Acids, Bases, and the pH Scale , pH, pOH, and pKw , and Electrolytes and pH. 3c. 3c. Define pH pH and and the the role of of hydrogen hydrogen ions ions in living systems systems What is the definition of pH? https://learn.saylor.org/mod/book/tool/print/index.php?id=51885 12/4/24, 8 30 PM Page 11 of 44 :  How do acids and bases alter the hydrogen ion concentration in a solution? pH measures the H+ ion concentration in a solution. We define it as the negative negative log log of of H+ H+ concentration concentration. This creates an inverse inverse comparison. When the H+ ion concentration increases, the pH value is low. When the H+ concentration is low, the pH value increases. The pH scale is from zero to 14. Pure water has a pH of seven because the H+ concentration equals the OH- concentration. Acids increase the H+ ion concentration by 10 fold and lowers the pH, while bases decrease the H+ concentration. The pH of the stomach is two while the blood is around seven. Buffers are needed to maintain the pH in both of these environments. Review Hydrogen Atoms in Acids and Bases , which describes the modification of H+ concentrations. 3d. 3d. Recognize Recognize the structure structure of of the the four major major biological macromolecules What are the four classes of biological macromolecules? What are the structural differences between the different classes of biological macromolecules? All organisms feature four major classes of large biological molecules, or macromolecules:  Lipids Lipids are made up of a diverse set of hydrocarbon molecules (containing hydrogen and carbon). This makes them largely partially non- non- polar polar because the covalent bonds in hydrocarbons (between two carbon atoms or between a carbon atom and a hydrogen atom) share electrons equally.  Polysaccharides Polysaccharides are complex carbohydrates made up of carbon, hydrogen, and oxygen in a 1:2:1 ratio, giving them an empirical formula generalized as (CH2O)n.  Proteins Proteins are enormously diverse in structure and function, yet they all feature the substructure of amino amino acids acids. Each amino acid features a central carbon atom simultaneously connected to a hydrogen atom, an amino amino group, a carboxyl carboxyl group, and a variable R group.  Nucleic Nucleic acids acids are informational molecules with a basic structure in which each subunit includes a five-carbon sugar (either ribose or deoxyribose) attached to a phosphate group and a nitrogenous nitrogenous base base. Knowing the chemical structure that underlies these essential biomolecules not only allows you to recognize them. It allows you to understand how they are constructed within cells and how they chemically interact with each other in metabolism and to give rise to structural components of organisms. Review this material in Biological Polymers , Carbohydrates , Lipids , Proteins , and Nucleic Acids. 3e. 3e. Describe Describe the the functions functions of of the the four major biological biological macromolecules macromolecules What are the major functions of the four classes of biological macromolecules? Lipids Lipids are important for storing energy, thermal insulation, and providing protective padding. Phospholipids Phospholipids form the infrastructure of all cell membranes. Lipids also make up natural waxes and oils and many hormones. Some polysaccharides polysaccharides (such as cellulose and chitin) are important for their structural strength, whereas other polysaccharides (such as starch and glycogen) are important for storing energy. Polysaccharides also serve as important identity markers on the surfaces of cells, so they play a role in immunity. Proteins Proteins perform an impressively long list of biological functions. They function as enzymes, structural elements, chemical signals, transporters, and receptors. They also play important roles in cell-to-cell adhesion and immunity. Nucleic Nucleic acids acids include various DNA and RNA molecules. They serve informational purposes. DNA DNA stores the genetic code, and various types of RNA RNA help in the process of interpreting that code to build proteins. Certain RNA's can also function as catalysts. Review these major functions in Lipids , Carbohydrates , Proteins , and Nucleic Acids. Try to make sense of why each macromolecule's basic structure is well suited to its particular function. 3f. 3f. Indicate the monomers monomers and and polymers polymers of of carbohydrates, proteins, and nucleic acids What are the monomers that make up polysaccharides? https://learn.saylor.org/mod/book/tool/print/index.php?id=51885 12/4/24, 8 30 PM Page 12 of 44 :  What are the monomers that make up proteins? What are the monomers that make up nucleic acids? A polymer polymer is a particular category of macromolecule that is built by connecting together many ("poly-" means "many") smaller subunits, called monomers monomers. Only three of the four biological macromolecules we have been studying are polymers. Lipids are not polymers, but the others are. Polysaccharides Polysaccharides are macromolecular carbohydrates. Be careful with the words "polysaccharide" and "carbohydrate". Sometimes these words are used interchangeably, but they should not be since they are different. Carbohydrates Carbohydrates include small and large molecules (macromolecules). Put another way, all polysaccharides are carbohydrates, but not all carbohydrates are polysaccharides. As the name implies, polysaccharides are polymers made up of multiple monosaccharides. Monosaccharides Monosaccharides are monomers monomers, and they can be connected in either a linear or branched arrangement. Proteins Proteins are polymers that are made up of monomers called amino amino acids acids. Unlike polysaccharides, which may be branched, a protein must be a linear (or end-to-end) arrangement of amino acids. Organisms use 20 different kinds of amino acids (in an unlimited number of combinations and orders) to construct their proteins. We can also call a nucleic nucleic acid acid aa polynucleotide polynucleotide. This alternative name indicates it is a polymer made up of many nucleotides nucleotides. In the case of DNA DNA, the monomers are nucleotides that contain the pentose (five-carbon sugar) called deoxyribose. For RNA RNA, the nucleotides contain ribose ribose instead of deoxyribose deoxyribose. Although there are only four commonly used DNA nucleotides (and four commonly used RNA nucleotides), a typical DNA molecule contains millions of nucleotides. So there is an unlimited number of sequences of such nucleotides. Be sure you can match each type of monomer to the type of polymer that can be made from such monomers. In addition to reviewing the various monomers, refresh your memory about how polymers are constructed using dehydration reactions and deconstructed using hydrolysis reactions in Biological Polymers. 3g. 3g. Describe Describe the the four four levels levels of of protein protein structure What are the four levels of protein structure? How is each level distinct? As a polymer, a protein is a large and complex molecule, and proteins have the most complex and most variable shapes among the three classes of biological polymers. Any given protein has its particular function because of its particular shape (also called its conformation conformation). This is why proteins have such diverse functions. Some proteins function as enzymes enzymes, which are biological catalysts catalysts. We can describe protein structure up to four different levels: Primary Primary structure structure refers to the particular sequence of amino acids (both the number and the order) making up a single polypeptide. A polypeptide polypeptide is one continuous strand made up of some number of amino acids connected end-to-end in a particular order. If a protein consists of just one polypeptide, then that "polypeptide" is itself a "protein". Secondary Secondary structure structure refers to repeating patterns found within a polypeptide. The repeating patterns include alpha alpha helices helices (a singular helix) and beta-pleated sheets. Ter Tertiary tiary structure structure refers to the particular three-dimensional structure of a single polypeptide. In other words, the particular shape that a single polypeptide assumes when it bends and folds is called its tertiary structure. Every protein includes at least one polypeptide polypeptide, so every protein features a primary, secondary, and tertiary structure. Only some proteins (called multimeric proteins) are made up of two or more polypeptides. For multimeric proteins, there is a fourth level of structure in addition to the other three levels. Quaternary Quaternary structure structure refers to the particular way in which multiple individual polypeptides (each with their own primary, secondary, and tertiary structures) come together to form the overall shape of a multimeric protein. In this case, "polypeptide" and "protein" are not interchangeable terms. The polypeptides are just parts of the overall protein. Review the section on protein structure in Proteins. Keep in mind that a protein cannot function properly unless it has the correct shape, regardless of its job in the cell. Unit Unit 3 Vocabulary You should be familiar with these terms as you prepare for the final exam. https://learn.saylor.org/mod/book/tool/print/index.php?id=51885 12/4/24, 8 30 PM Page 13 of 44 :  amino acid amino group carbohydrate carboxyl group catalyst cohesion deoxyribose DNA enzyme hydrogen bond latent heat of vaporization lipid monomer monosaccharide multimeric nitrogenous base non-polar nucleic acid nucleotide phospholipid polar polymer polynucleotide polypeptide polysaccharide primary structure protein quaternary structure ribose RNA secondary structure solvent specific heat capacity surface tension tertiary structure https://learn.saylor.org/mod/book/tool/print/index.php?id=51885 12/4/24, 8 30 PM Page 14 of 44 :  Unit Unit 4: 4: Cells Cells and and Cell Cell Membranes Membranes 4a. 4a. Describe and diagram diagram the the structure structure and and function function of aa typical typical biological membrane What is another name for the cell membrane? What types of molecules make up a cell membrane? How does the chemistry of the molecules in a membrane explain why a cell membrane forms? The cell cell is the functional unit of life. Every organism features at least one cell; metabolism metabolism (the chemistry of life) occurs within cells. A membrane membrane separates the cell from its surroundings. Every cell features a cell cell membrane membrane, which is also called the plasma plasma membrane membrane. The plasma membrane is a complex arrangement of several different types of molecules. The chief components are phospholipids phospholipids. Each phospholipid molecule is an amphipathic molecule (polar at one end and non-polar at the other end). This explains why plasma (cell) membranes form. In the presence of water, phospholipids self-assemble into a bilayer bilayer, with the non-polar non-polar tails tails in each monolayer pointing toward the non-polar tails of the other monolayer, and the polar heads of each monolayer pointing toward the watery solution on its side of the membrane (the water interior of the cell for one monolayer, and the water exterior of the cell for the other monolayer). In addition to the phospholipid phospholipid bilayer bilayer, the plasma (cell) membrane features various other macromolecules, including proteins, sterols, and polysaccharides. The plasma (cell) membrane is fundamental to life, so be sure to review its structure (and the structure of an individual phospholipid) in Parts of the Cell Membrane. Also, watch Review of the Cell Membrane and Structure of the Cell Membrane. 4b. 4b. Describe Describe characteristics of a membrane, solutes, and solvents, as well as predict where molecules molecules will will move move and and how how the the mass mass of a cell cell may may change What are the components of a solution? What is the difference between a solvent and a solute? What happens to cell volume when osmosis occurs? A solution solution is a mixture that includes a solvent solvent and a number of solutes solutes. The solvent is the part of the solution that dissolves the solutes; the solutes are the parts the solvent has dissolved. In an aqueous solution, water is the solvent. A cell's plasma membrane forms a barrier between intracellular intracellular fluid fluid and extracellular extracellular fluid fluid (which are both aqueous solutions). The plasma membrane is selectively selectively permeable permeable, which means some particles easily pass through the membrane, while other particles cannot get through. Many solutes are effectively (although not perfectly) prevented from passing through the membrane, so we say the membrane is impermeable impermeable to these solutes. Water, on the other hand, can pass through to a certain degree. Water passes through a plasma membrane using a mechanism called osmosis osmosis, a special type of diffusion diffusion process that is passive passive. The direction and rate of osmosis depend on the relative solute concentrations inside and outside the cell. Water always osmoses to the area that is less watery. This means water always moves away from the compartment that has a higher solute concentration. If the solute concentration of the extracellular fluid is higher than the solute concentration of the intracellular fluid, this means the extracellular fluid is less watery, so water will leave the cell by osmosis, and the cell volume will decrease. If the reverse is true (the gradient gradient is reversed), then water will enter the cell by osmosis, and cell volume will increase. In each case, notice that the water moves toward the less watery compartment. Organisms must regulate their osmotic conditions since changes in osmotic gradients can profoundly damage their cells. Review solutions and osmosis in Passive Transport via Simple Diffusion , Passive Transport and Tonicity, Passive Transport via Osmosis , More on Osmosis , Facilitated Diffusion , Primary Active Transport , Secondary Active Transport , and Bulk Transport. 4c. 4c. Describe Describe characteristics of a cell, cell, and classify the the cell cell as as a prokaryotic, animal, animal, or or plant plant What distinguishes a eukaryotic cell from a prokaryotic cell? Are animal and plant cells eukaryotic or prokaryotic? https://learn.saylor.org/mod/book/tool/print/index.php?id=51885 12/4/24, 8 30 PM Page 15 of 44 :  Although all cells share certain characteristics (for example, every cell has a plasma membrane), biologists recognize two fundamentally different categories of cells: prokaryotic cells and eukaryotic cells. A prokaryotic prokaryotic cell does not feature membrane-bounded organelles; a eukaryotic eukaryotic cell does feature membrane-bounded organelles. A membrane-bounded organelle is an organelle (a tiny organ-like structure within a cell) that is enclosed by its own membrane, separate from the plasma membrane that encloses the entire cell. Membrane-bounded organelles include diverse structures such as the nucleus nucleus, endoplasmic endoplasmic reticulum reticulum, lysosomes, mitochondria, chloroplasts, and others. Only eukaryotic cells feature these membrane-bounded organelles, though a eukaryotic cell might feature only some (but not all) of them. For example, an animal cell (like one in a human body) features most of the membrane-bounded organelles, but it does not feature chloroplasts chloroplasts. A plant plant cell cell, on the other hand, typically includes the membrane-bounded organelles found in an animal cell, plus it also features chloroplasts. A bacterium bacterium, which is a prokaryotic cell, does not feature any of these membrane-bounded organelles. Ensure that you appreciate the differences between these major categories of cell types. Review Prokaryotic Cells , Eukaryotic Cells , and Types of Cells. 4d. 4d. Identify organelles that that are are found in typical typical prokaryotic, prokaryotic, plant, and and animal cells cells What are the names of the various organelles? Are all of the organelles membrane-bounded? What types of cells feature these various organelles? You should recognize several organelles organelles in this course: Ribosome Ribosome - not membrane-bounded; found in prokaryotic and eukaryotic cells Plasma Plasma (cell) (cell) membrane membrane -- found in prokaryotic and eukaryotic cells Cell Cell wall wall - found in most prokaryotic and some eukaryotic cells (though not animal cells) Nucleus Nucleus - membrane-bounded; found only in eukaryotic cells Mitochondrion Mitochondrion - membrane-bounded; found only in most eukaryotic cells Chloroplasts Chloroplasts - membrane-bounded; found only in photosynthetic eukaryotic cells (plants and algae) Golgi Golgi body body - membrane-bounded; found only in eukaryotic cells Central Central vacuole vacuole - membrane-bounded; found only in some eukaryotic cells, including plants and some protists Rough Rough endoplasmic endoplasmic reticulum reticulum - membrane-bounded; found only in eukaryotic cells Smooth Smooth endoplasmic endoplasmic reticulum reticulum - membrane-bounded; found only in eukaryotic cells Lysosome Lysosome - membrane-bounded; found only in eukaryotic cells Peroxisome Peroxisome - membrane-bounded; found only in eukaryotic cells Notice that most of these organelles are membrane-bounded; therefore, they appear only in eukaryotic cells. These cells are structurally more complex than the prokaryotic cells they evolved from. Review the structures of these important organelles in Cell Structure. Pay particular attention to Figure 1. Also, watch Parts of a Cell. 4e. 4e. Indicate Indicate the the functions functions of of the the various various cellular organelles, including including the the nucleus, nucleus, cell membrane, membrane, cell cell wall, wall, mitochondria, mitochondria, chloroplasts, chloroplasts, ribosomes, ribosomes, Golgi body, central central vacuole, vacuole, rough rough endoplasmic reticulum, reticulum, smooth smooth endoplasmic reticulum, reticulum, lysosome, lysosome, and and peroxisome peroxisome What are the major functions of the various types of organelles? What advantage is gained by some organelles being membrane-bounded? https://learn.saylor.org/mod/book/tool/print/index.php?id=51885 12/4/24, 8 30 PM Page 16 of 44 :  One difference between the various organelles is their shapes. However, our primary reason for classifying organelles differently is because they perform different functions, just as different organs in our body perform different functions. Ribosome Ribosome - molecular machines that interpret codes in mRNA to build proteins Plasma Plasma (cell) (cell) membrane membrane - defines the cell and forms the boundary between the contents of the cell and its surroundings Cell Cell wall wall - thicker, more rigid than, and exterior to the plasma membrane; withstands pressure and prevents the cell from bursting Nucleus Nucleus - enclosed by two membranes; houses the DNA Mitochondrion Mitochondrion - enclosed by two membranes; site for cellular respiration Chloroplast Chloroplast - enclosed by two membranes; site for photosynthesis Golgi Golgi body body - receives newly-formed proteins, modifies them, and packages them for transport to the plasma membrane or out of the cell Central Central vacuole vacuole - largely water-filled organelle that can also house pigments and wastes Rough Rough endoplasmic endoplasmic reticulum reticulum - site for synthesis of proteins that the Golgi body will package Smooth Smooth endoplasmic endoplasmic reticulum reticulum - site for synthesis of lipids and storage of calcium ions Lysosome Lysosome - digests materials by subjecting them to enzymes Peroxisome Peroxisome - safely breaks down harmful chemicals in the cell The organelles that are membrane-bounded membrane-bounded form sub-compartments, so they can perform their functions in isolation from the rest of the cellular contents. Before proceeding, be sure you know which functions each organelle performs. Review this material in Parts of a Cell. 4f. 4f. Explain Explain how large signal signal molecules get get their signal into the cell cell What are signal modules? What are receptors? Signal Signal molecules molecules are examples of ligands ligands, because they must bind to other molecules. We call the molecules that signal molecules bind to receptors receptors. When a signal signal binds to a receptor receptor, that binding causes changes in the cell. These changes are the responses to the signal. Some signals are small and non-polar, so they are easily able to pass through a cell's plasma membrane, and they bind to internal receptors. Most signals, however, are too large or too polar to pass through the plasma membrane, so they must bind to receptors on the exterior surface of the cell. Although these signal molecules do not actually enter the cell, they still cause changes inside the cell. This occurs using three primary mechanisms – the difference lies in what kind of receptor receives these signals. Ion-channel-linked Ion-channel-linked receptors receptors are transmembrane proteins that simultaneously serve as signal receptors and ion channels. When a signal molecule binds to this type of receptor, the ion channel either opens or closes its gate. This leads to changes in the flow of ions, which are charged particles. This redistribution of charge causes various responses. G-protein-linked G-protein-linked receptors receptors are transmembrane receptors that are associated with special proteins (G proteins) situated on the part of the protein that is in contact with the interior surface of the membrane. The binding of a signal molecule to the receptor activates (and frees) the G protein. This activation causes various responses. Enzyme-linked Enzyme-linked receptors are transmembrane proteins that simultaneously serve as signal receptors and enzymes. The binding of a signal molecule to the receptor activates the enzymatic portion of the receptor (which faces the interior of the cell). Once activated, the enzyme catalyzes various reactions, which causes various responses. Be sure you understand the functional differences between these three classes of receptors; all three operate by binding to a signal molecule at the exterior surface. Since it helps to look at diagrams to make sense of the differences, review the text and figures in the section on types of receptors of Signaling Molecules and Cellular Receptors. 4g. 4g. Describe the the forms forms of of transport transport across across biological membranes membranes What are the primary categories of transmembrane transport? What is the fundamental difference between these primary categories? https://learn.saylor.org/mod/book/tool/print/index.php?id=51885 12/4/24, 8 30 PM Page 17 of 44 :  Particles pass through biological membranes (including the plasma membrane) by various mechanisms, which we can lump into two primary categories. We can classify transmembrane transmembrane transpor transportt (transport of a particle through a biological membrane) as active active or passive passive. The distinction between the two is the requirement of an external source of energy. Active Active transpor transportt requires an additional (external) source of energy to drive it. ATP is often the energy source, but other energy sources can be used. Since additional energy is applied, active transport can move particles against their gradient gradient (see definition in next paragraph), which causes gradients to become even steeper. Passive Passive transpor transportt does not require additional (external) energy for the transport to occur. The energy that drives passive transport is in the form of a gradient. A gradient is a difference in magnitude. A gradient gradient that drives passive transport can be a concentration concentration gradient gradient (when the concentration of the particle type is higher on one side of the membrane than the other), an electrical electrical gradient gradient (when the charge distribution is different on one side of the membrane than the other), or both. In all cases of passive transport, the transport occurs down down the gradient, such as from the place of higher concentration to the place of lower concentration. Passive transport never occurs in the direction against the gradient. There are important subcategories of passive transport: Simple Simple diffusion diffusion is passive transport of solute particles down the gradient for that type of solute and directly through the phospholipid bilayer of the biological membrane. This can occur only for particles small enough or nonpolar enough to pass through the bilayer. Facilitated Facilitated diffusion diffusion is also diffusion, but it requires the help (facilitation) of a transport protein to get the particle through the membrane. This occurs for particles that are too big or too polar to cross the phospholipid bilayer directly. Osmosis Osmosis is passive transport of solvent particles (not solute particles) down the gradient for solvent particles and through a selectively permeable membrane. In biological systems, the solvent is always water, so biological osmosis is movement of water. These transmembrane transport processes are fundamental to life because organisms must continuously exchange materials with their surroundings to stay alive. Review the categories and subcategories by watching Review of the Cell Membrane and reviewing subunit 4.4. Unit Unit 4 Vocabulary Vocabulary You should be familiar with these terms as you prepare for the final exam. active transport amphipathic aqueous cell membrane cell wall cellular respiration central vacuole chloroplast enzyme-linked receptor eukaryotic extracellular fluid facilitated diffusion g-protein-linked receptor Golgi body intracellular fluid ion-channel-linked receptor ligand lysosome membrane-bounded mitochondrion non-polar nucleus organelle osmosis passive transport peroxisome phospholipid https://learn.saylor.org/mod/book/tool/print/index.php?id=51885 12/4/24, 8 30 PM Page 18 of 44 :  photosynthesis plasma membrane polar prokaryotic receptor ribosome rough endoplasmic reticulum selectively permeable signal simple diffusion smooth endoplasmic reticulum solute solution solvent https://learn.saylor.org/mod/book/tool/print/index.php?id=51885 12/4/24, 8 30 PM Page 19 of 44 :  Unit Unit 5: 5: Enzymes, Enzymes, Metabolism, Metabolism, and and Cellular Cellular Respiration Respiration 5a. 5a. Recognize Recognize and and explain explain the the difference between between matter matter and and energy energy What is energy? How is energy different from matter? Organisms are examples of open thermodynamic systems because organisms must exchange matter and energy with their surroundings. As we reviewed in previous units, matter is the material stuff of the universe. Matter Matter occupies space and has mass. Matter is made up of atoms. Energy Energy is not material. It does not have mass and it does not occupy space. We often describe energy as the capacity to perform work work or bring about some sort of change. There are countless examples. A human performs work by flexing a muscle. A tiny cell within a human performs work by transporting particles into or out of the cell or by oxidizing fuel molecules. There are many different forms of energy (light energy, mechanical energy, heat energy, etc.), and we can broadly classify energy into two categories: Potential Potential energy energy is energy in a stored form. It may be used, but it is not currently being used. The energy in food is an example of chemical potential energy. K Kinetic inetic energy energy is energy that is being used at the moment. A falling object, for example, has kinetic energy. Energy can readily be converted between forms. For example, a book that falls from a shelf converts potential energy into kinetic energy. When someone moves the book back to the shelf, they convert kinetic energy into potential energy. The metabolism of life involves countless interactions between matter and energy and countless conversions between energy forms, so it is important to understand the distinction between matter and energy. Review Energy and Metabolism , More on Energy , and Energy and Thermodynamics. 5b. 5b. Apply Apply the the laws laws of of thermodynamics thermodynamics and and conservation conservation of of matter to metabolism metabolism What are the laws of thermodynamics? How do these laws affect biological processes? Recall that the First Law of Thermodynamics states that energy is conserved (it cannot be created or destroyed; it can only be transferred and transformed). In ordinary chemical reactions (like biochemical reactions), matter is also conserved. Therefore, the overall amount of energy and matter entering the processes of glycolysis and cellular respiration is the same as the overall amount of energy and matter exiting these processes. What has changed are the forms of that energy and matter. Energy enters as the potential chemical energy in the bonds of the glucose molecule. Some of that energy gets released as heat (unavailable for cellular work), and some of that energy ultimately gets stored in the bonds of ATP ATP molecules molecules. ATP is formed when ADP ADP and inorganic phosphate combine. Matter enters as glucose and oxygen and, after many rearrangements of atoms, matter leaves as carbon dioxide and water. Review the principles of thermodynamics in subunit 2.2. Also review Energy and Thermodynamics , Metabolism Part 1 , and Metabolism Part 2. 5c. 5c. Describe the the role role of of enzymes enzymes and and how how they they function function What is an enzyme? What kind of macromolecule makes up an enzyme? What is the function of an enzyme? What is a substrate? Metabolism Metabolism is the chemistry of life. Thousands of chemical reactions occur in a single cell – most of these chemical reactions rely on enzymes. An enzyme enzyme is a protein that serves as a biological catalyst. A catalyst catalyst is a substance that greatly accelerates a chemical reaction, without actually being a reactant in that reaction. In other words, a catalyst (and therefore an enzyme) does not get changed into another substance (a product). The enzyme interacts with the reactants to make it more likely for the reactants to chemically react, turning them into products. We call the reactants of catalyzed reactions substrates substrates. An enzyme operates by temporarily binding to substrates. https://learn.saylor.org/mod/book/tool/print/index.php?id=51885 12/4/24, 8 30 PM Page 20 of 44 :  The rate rate of of the the reaction reaction (its speed) when it is catalyzed by an enzyme is usually at least one million times faster than without the help of an enzyme. This is why enzymes are absolutely vital. Without enzymes, biochemical reactions of metabolism would occur much too slowly to support life. Most importantly, enzymes are reusable since they do not get altered during the reaction – they can continue catalyzing the same sort of reaction until all of the substrate is depleted. Review Energy and Metabolism and Metabolism Part 3 to make sure you are familiar with the basics of enzymes. 5d. 5d. Explain Explain the the role of of cellular respiration What is oxidation? What is reduction? How does cellular respiration accomplish its redox reactions? Any living cell can extract energy from fuel and temporarily store that energy in the form of ATP ATP, or a similar energy currency. This primary processing of fuel is called glycolysis glycolysis. Only certain cells under the right conditions can continue where glycolysis leaves off, allowing much more usable energy to be extracted from the fuel. This additional processing of energy is called cellular cellular respiration respiration. Glycolysis and cellular respiration both extract usable energy from fuel by undergoing oxidation/reduction (or redox redox) reactions. Oxidation Oxidation is the loss of electrons from a particle (like a fuel molecule), whereas reduction is the gain of electrons. Since electrons are not destroyed in chemical reactions, oxidation occurs only if reduction also occurs. When something is oxidized (loses electrons), something else gets reduced (gains electrons). Organisms extract energy from fuel molecules by oxidizing these fuel molecules. During cellular cellular respiration respiration, there is a substance (external to the process) that ultimately accepts the electrons that have been removed from the fuel. For aerobic organisms, that substance is oxygen, and when oxygen accepts these electrons (along with protons) from the fuel molecules, the oxygen gets reduced into water. Cellular respiration is important because it allows for maximal oxidation of fuels, which maximizes the amount of energy that can be extracted and stored as ATP. Review glycolysis and cellular respiration in Introduction to Glycolosis , Cellular Respiration , The Citric Acid Cycle and Oxidative Phosphorylation , Glycolysis , More on Glycolysis , and The Process of Glycolysis. 5e. 5e. Account Account for for the the matter matter inputs and outputs to glycolysis, pyruvate oxidation (preparatory reaction) reaction) the the Krebs/Citric Krebs/Citric Acid Acid Cycle, Cycle, and the electron electron transport chain chain What are the material inputs and outputs for each of these processes? Each component of the oxidation of glucose contributes to a series of reactions that can be summarized by a reaction equation that lists the inputs (reactants) and the outputs (products) of that process. The component processes that comprise the complete oxidation of glucose are glycolysis glycolysis, pyruvate pyruvate oxidation oxidation, the the Citric Citric Acid Acid Cycle Cycle, and oxidative oxidative phosphorylation phosphorylation (including electron electron transpor transportt and chemiosmosis chemiosmosis). Inputs Process Outputs Glucose Pyruvate NAD+ Glycolysis NADH ADP ATP Pyruvate Carbon Dioxide NAD+ Pyruvate Oxidation Acetyl Coenzyme A Coenzyme A NADH Acetyl Coenzyme A Carbon Dioxide https://learn.saylor.org/mod/book/tool/print/index.php?id=51885 12/4/24, 8 30 PM Page 21 of 44 :  NAD+ NADH Citric Acid Cycle FAD FADH2 ADP ATP ADP ATP NADH NAD+ Oxidative Phosphorylation FADH2 FAD O2 H2O It is useful to review illustrations to make sense of these inputs and outputs, so pay careful attention to the figures in The Citric Acid Cycle and Oxidative Phosphorylation. You should also review subunits 5.5 and 5.6. 5f. 5f. Describe Describe the the source source and and fate fate of of energy energy in in glycolysis, pyruvate oxidation oxidation (preparatory (preparatory reaction), reaction), the the Krebs/Citric Krebs/Citric Acid Acid Cycle, Cycle, and and the the electron electron transport chain chain What are the sources of energy and the fates of that energy in glycolysis, pyruvate oxidation, the Citric Acid Cycle, and oxidative phosphorylation? The goal of the oxidation of a fuel (like glucose) is to transfer energy from that fuel into a versatile form of energy storage known as ATP ATP (adenosine (adenosine triphosphate triphosphate)). Many transfers of energy take place during the many reactions that make up glycolysis and cellular respiration. These transfers involve the original fuel (glucose), intermediate fuels, energy-carrying coenzymes (NAD NAD and FAD FAD), and ATP. Due to the third law of thermodynamics, some energy is lost as heat during each transfer. This lost heat energy becomes unavailable to perform work in the cell. During glycolysis glycolysis, energy starts out in the original fuel, glucose. By oxidizing glucose, some usable energy gets transferred into ATP ATP and some into NADH NADH. The intermediate fuel (pyruvate pyruvate pyruvate) that is left over contains usable energy, as well. During the oxidation of pyruvate, some of that usable energy gets transferred to more NADH. This leaves only acetyl acetyl coenzyme coenzyme A A as the remaining fuel, which still contains usable energy. The citric citric acid acid cycle cycle completes the oxidation of the remaining fuel (acetyl coenzyme A), and the usable energy that is extracted gets transferred to more NADH, to more ATP, and to FADH FADH22. The carbon carbon dioxide dioxide that remains from the fuel contains no usable energy (it is spent fuel). Oxidative Oxidative phosphorylation phosphorylation serves to collect all of the usable energy that got transferred to NADH and FADH2 (in the earlier processes) and the usable energy is transferred to even more ATP. The final acceptor of the electron is the molecule oxygen which subsequently changes to water as the final waste product. Refresh your understanding of this complex set of processes by reviewing subunits 5.4, 5.5, and 5.6. Unit Unit 5 Vocabulary You should be familiar with these terms as you prepare for the final exam. acetyl coenzyme A ADP ATP carbon dioxide catalyst cellular respiration chemiosmosis citric acid cycle coenzyme A electron transport energy enzyme FAD https://learn.saylor.org/mod/book/tool/print/index.php?id=51885 12/4/24, 8 30 PM Page 22 of 44 :  FADH2 glucose glycolysis kinetic energy Krebs cycle matter NAD+ NADH oxidation oxidative phosphorylation oxygen potential energy pyruvate pyruvate oxidation reaction rate redox reduction substrate water work https://learn.saylor.org/mod/book/tool/print/index.php?id=51885 12/4/24, 8 30 PM Page 23 of 44 :  Unit Unit 6: 6: Photosynthesis Photosynthesis 6a. 6a. Explain the the role role of of photosynthesis What are the two ecological categories of organisms? What type of organism is capable of photosynthesis? How does photosynthesis relate to nutrient cycling? We can ecologically classify any living organism as an autotroph autotroph or a heterotroph heterotroph. Autotrophs Autotrophs ("self-feeders") are also known producers producers because they produce organic compounds from inorganic materials. They make their own food. Autotrophs require energy to do so, and most autotrophs use light energy in the process of photosynthesis. We call heterotrophs heterotrophs ("feeders on others") consumers consumers because they feed on organic compounds produced by other organisms. Maximally extracting energy from an organic fuel (food) involves the complete oxidation of the fuel (including glycolysis and cellular respiration); this leaves inorganic carbon dioxide. Photosynthesis Photosynthesis reverses these processes by starting with inorganic carbon dioxide and transforming it into organic compounds that can be used as fuel. In this way, photosynthesis is an important part of carbon cycling, because photosynthesis has a reciprocal relationship with glycolysis and cellular respiration. Photosynthesis is of vital importance to organisms, because photosynthesis provides food for photosynthetic organisms (the producers) and the consumers of the world. As you review Overview of Photosynthesis , pay close attention to the summary reaction for photosynthesis (figure 5). Notice that photosynthesis is the reverse of the summary reaction for glycolysis and cellular respiration. 6b. 6b. Describe Describe where where matter matter originates originates and and ends up up during photosynthesis photosynthesis What are the inputs and outputs of photosynthesis? Recall that photosynthesis has a reciprocal rela