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This document contains notes on biology topics, including the levels of biological organization, properties of life, and a description of the scientific method. It consists of definitions and explanations, outlining key concepts within the subject.

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CHAPTER 1: **List the levels of Life's organization and define each entity in life's organization**: - **Atom**: The smallest chemical unit of a type of pure substance (element). - **Molecule**: A group of joined atoms. - **Organelle**: A membrane-bounded structure that has a specific functio...

CHAPTER 1: **List the levels of Life's organization and define each entity in life's organization**: - **Atom**: The smallest chemical unit of a type of pure substance (element). - **Molecule**: A group of joined atoms. - **Organelle**: A membrane-bounded structure that has a specific function within a cell. - **Cell**: The fundamental unit of life. - **Tissue**: A collection of specialized cells that function in a coordinated fashion. - **Organ**: A structure consisting of tissues organized to interact and carry out specific functions. - **Organ system**: Organs connected physically or chemically that function together. - **Organism**: A single living individual. - **Population**: A group of the same species of organism living in the same place and time. - **Community**: All populations that occupy the same region. - **Ecosystem**: The living and nonliving components of an area. - **Biosphere**: The global ecosystem; the parts of the planet and its atmosphere where life is possible. 2. **What is emergent property?** - **Emergent property** refers to new characteristics that arise from the interaction of a system’s components. The whole is greater than the sum of its parts. For example, individual brain cells cannot think, but when they interact in networks, they give rise to consciousness. 3. **List the properties of life**: - Life is organized. - Life requires energy. - Life maintains internal constancy (homeostasis). - Life reproduces, grows, and develops. - Life evolves. 4. **Describe the flow of energy and cycling of materials through an ecosystem**: - **Energy flow**: Energy enters ecosystems as sunlight, which producers (like plants) capture and convert into chemical energy through photosynthesis. Consumers obtain this energy by eating other organisms. Energy is lost as heat at each stage of the energy transfer. - **Cycling of materials**: Nutrients are recycled within ecosystems. Decomposers break down dead organisms and return nutrients to the soil, which are then absorbed by producers. 5. **Define the terms**: - **Energy**: The ability to do work or cause change. - **Nutrient**: A substance that an organism needs for growth, reproduction, and survival. - **Producers**: Organisms that make their own food by extracting energy and nutrients from nonliving sources (e.g., plants). - **Consumers**: Organisms that obtain energy and nutrients by eating other organisms. - **Receptors**: Structures that detect stimuli and help organisms maintain homeostasis. - **Homeostasis**: The process by which a cell or organism maintains internal equilibrium. - **DNA**: The molecule that carries genetic information. - **Traits**: Characteristics inherited from parents through DNA. - **Inheritance**: The transmission of DNA from parents to offspring. - **Reproduction**: The process of producing new organisms. - **Development**: Changes that occur as an organism matures, including growth and specialization. 6. **List the 2 parts of the scientific name and define them**: - **Genus**: The first part of the scientific name, a group of species that are closely related. - **Species**: The second part of the scientific name, which identifies a specific organism within the genus. 7. **How are organisms categorized based on the presence or absence of a nucleus?** - **Prokaryotes**: Organisms that lack a nucleus (e.g., Bacteria, Archaea). - **Eukaryotes**: Organisms that have a nucleus (e.g., animals, plants, fungi, protists). 8. **List the 3 domains of life and define them**: - **Bacteria**: One of the domains of life, consisting of small, prokaryotic, and unicellular organisms. - **Archaea**: Domain of prokaryotic organisms that often live in extreme environments. - **Eukarya**: Domain of organisms with larger, more complex cells that contain nuclei (includes animals, plants, fungi, and protists). 9. **Name the 4 sub-classes of the domain Eukarya**: - **Protista**, **Animalia**, **Fungi**, **Plantae**. 10. **List and define the steps involved in the scientific method**: - **Observation**: Gathering information through the senses or existing knowledge. - **Hypothesis**: A tentative explanation that can be tested. - **Experimentation**: Testing the hypothesis by collecting and interpreting data. - **Conclusion**: Drawing conclusions based on the results of the experiment. - **Peer review and publication**: Sharing findings for scrutiny by other scientists. 11. **Define scientific theory, experiments, variable (independent and dependent), experimental group, and control group**: - **Scientific theory**: A broad explanation for natural phenomena, supported by extensive evidence. - **Experiments**: Procedures to test hypotheses and gather data. - **Independent variable**: The factor that is manipulated during an experiment. - **Dependent variable**: The factor that is measured as a result of changes in the independent variable. - **Experimental group**: The group in which the independent variable is changed. - **Control group**: The group that serves as a baseline for comparison; it does not receive the experimental treatment. 12. **When does a hypothesis become a scientific theory?** - A **hypothesis** becomes a **scientific theory** when it is supported by a large body of evidence through repeated testing and experimentation across different studies and contexts. CHAPTER 2 **What are the basic building blocks of all matter?** - All matter consists of atoms, which are made up of subatomic particles: protons, neutrons, and electrons. 2. **Describe the structure of an atom.** - An atom consists of a nucleus that contains protons (positively charged) and neutrons (neutral), with electrons (negatively charged) orbiting the nucleus in energy shells. 3. **What is the difference between an atom and an element?** - An **atom** is the smallest unit of an element that retains the properties of that element. An **element** is a pure substance that cannot be broken down by chemical means and is composed of only one type of atom. 4. **Define protons, neutrons, and electrons and mention their location in an atom.** - **Protons**: Positively charged particles located in the nucleus. - **Neutrons**: Neutral particles also found in the nucleus. - **Electrons**: Negatively charged particles orbiting the nucleus in energy shells. 5. **Differentiate an element's atomic number from its mass number.** - **Atomic number**: The number of protons in an atom, defining the element. - **Mass number**: The sum of protons and neutrons in an atom's nucleus. 6. **Differentiate an atom from an ion. When does an atom become an ion?** - An **atom** is neutral, with equal numbers of protons and electrons. An **ion** forms when an atom gains or loses electrons, creating a charged particle. A loss of electrons results in a positive ion (cation), and a gain results in a negative ion (anion). 7. **Define the following terms: Electronegativity, Chemical bond, Molecule, Compound, and Mixture.** - **Electronegativity**: An atom's ability to attract electrons in a bond. - **Chemical bond**: The force holding two atoms together in a molecule. - **Molecule**: Two or more atoms bonded together chemically. - **Compound**: A substance made of atoms from two or more different elements bonded together. - **Mixture**: A combination of two or more substances that are not chemically bonded and can be separated physically. 8. **How do atoms interact?** - Atoms interact by forming chemical bonds, either by sharing electrons (covalent bonds), transferring electrons (ionic bonds), or through weaker attractions like hydrogen bonds. 9. **Name and describe the 3 kinds of bonds with examples.** - **Covalent bond**: Atoms share electrons (e.g., H2O). - **Ionic bond**: One atom transfers electrons to another, creating oppositely charged ions (e.g., NaCl). - **Hydrogen bond**: A weak attraction between a hydrogen atom in one molecule and an electronegative atom in another molecule (e.g., between water molecules). 10. **Distinguish a nonpolar covalent bond from a polar covalent bond.** - **Nonpolar covalent bond**: Electrons are shared equally between atoms (e.g., in H2). - **Polar covalent bond**: Electrons are shared unequally, resulting in partial charges (e.g., in H2O). 11. **Why is water essential to life? List and explain the factors that contribute to water's life-giving properties.** - Water is essential to life due to its unique properties: - **Cohesion**: Water molecules stick together, contributing to surface tension. - **Adhesion**: Water molecules stick to other substances, aiding processes like capillary action. - **Solvent**: Water dissolves many substances, facilitating biochemical reactions. - **Temperature regulation**: Water resists temperature changes, helping maintain stable environments. - **Expansion upon freezing**: Ice is less dense than liquid water, allowing it to float and insulate aquatic life. 12. **Define the following terms: Polarity, Hydrophilic, Hydrophobic, Solution, Solute, Solvent, Cohesion.** - **Polarity**: The distribution of electrical charge across a molecule. - **Hydrophilic**: Water-attracting (polar) substances. - **Hydrophobic**: Water-repelling (nonpolar) substances. - **Solution**: A homogeneous mixture of solute and solvent. - **Solute**: The substance that dissolves in a solvent. - **Solvent**: The substance that dissolves a solute. - **Cohesion**: The tendency of water molecules to stick to each other. 13. **All the molecules of life are built with carbon atoms. Explain.** - Carbon is the backbone of organic molecules because it can form four covalent bonds, enabling complex structures like chains and rings, which are essential for building biomolecules like carbohydrates, proteins, lipids, and nucleic acids. 14. **What are functional groups? List all the functional groups with their structure.** - **Functional groups** are specific groups of atoms within molecules that are responsible for the characteristic chemical reactions of those molecules. The key functional groups include: - **Hydroxyl (-OH)** - **Carboxyl (-COOH)** - **Amino (-NH2)** - **Phosphate (-PO4)** - **Carbonyl (C=O)** - **Methyl (-CH3)** 15. **Explain the difference between condensation and hydrolysis with examples.** - **Condensation (Dehydration synthesis)**: A chemical reaction that joins two monomers together, releasing a molecule of water (e.g., forming a peptide bond between amino acids). - **Hydrolysis**: A reaction that breaks down polymers into monomers by adding water (e.g., breaking down starch into glucose). 16. **List the four organic molecules (biomolecules) built on the framework of carbon atoms.** - **Carbohydrates**, **Proteins**, **Lipids**, and **Nucleic acids**. 17. **List the monomers and polymers of the organic molecules.** - **Carbohydrates**: Monomer = Monosaccharides; Polymer = Polysaccharides. - **Proteins**: Monomer = Amino acids; Polymer = Polypeptides. - **Nucleic acids**: Monomer = Nucleotides; Polymer = DNA/RNA. - **Lipids**: No true monomers; some are made from glycerol and fatty acids. 18. **What are the 3 main types of carbohydrates in the living system?** - **Monosaccharides**, **Disaccharides**, and **Polysaccharides**. 19. **Explain the three major types of polysaccharides in the living system.** - **Cellulose**: Provides structural support in plant cell walls. - **Starch**: Stores energy in plants. - **Glycogen**: Stores energy in animals. 20. **List the different kinds of lipids.** - **Triglycerides**, **Phospholipids**, **Steroids**, **Waxes*. 21. **Differentiate between saturated, monounsaturated, and polyunsaturated fatty acids.** - **Saturated fatty acids**: No double bonds between carbon atoms; straight chains. - **Monounsaturated fatty acids**: One double bond in the carbon chain, causing a bend. - **Polyunsaturated fatty acids**: More than one double bond, leading to multiple bends. 22. **What are phospholipids and where are they present?** - **Phospholipids** consist of two fatty acids, a glycerol, and a phosphate group. They are the main components of cell membranes. 23. **What are steroids? Explain with examples.** - **Steroids** are lipids with four fused carbon rings. Examples include **cholesterol** (which regulates membrane fluidity) and **sex hormones** like estrogen and testosterone. 24. **Define proteins.** - **Proteins** are polymers of amino acids that perform a wide variety of functions in cells, including structural support, enzyme activity, and transportation. 25. **Draw the structure of an amino acid.** - The general structure of an amino acid consists of a central carbon atom (C) bonded to an amino group (NH2), a carboxyl group (COOH), a hydrogen atom (H), and an R group (side chain) which varies among different amino acids. 26. **What are the four levels of protein structure?** - **Primary structure**: The sequence of amino acids in a polypeptide chain. - **Secondary structure**: Local folding into structures like alpha helices or beta sheets, stabilized by hydrogen bonds. - **Tertiary structure**: The overall 3D shape of a single polypeptide chain. - **Quaternary structure**: The arrangement of multiple polypeptide chains into a functional protein. 27. **How is a peptide bond formed?** - A **peptide bond** is formed through a dehydration synthesis reaction between the amino group of one amino acid and the carboxyl group of another, releasing a water molecule. 28. **What are the components of a nucleotide?** - **Nucleotides** consist of three components: a phosphate group, a 5-carbon sugar (either deoxyribose or ribose), and a nitrogenous base (adenine, guanine, cytosine, thymine, or uracil). 29. **What are the 2 kinds of nucleic acids?** - **DNA (Deoxyribonucleic acid)** and **RNA (Ribonucleic acid)**. 30. **What are the four bases that are found in nucleotides?** - **Adenine (A)**, **Guanine (G)**, **Cytosine (C)**, and **Thymine (T)** in DNA (or **Uracil (U)** in RNA). **Cell Theory** - **Cell theory** was developed in the mid-1800s and states: - All organisms are composed of one or more cells. - The cell is the fundamental unit of life. - All cells come from preexisting cells. - Additionally, modern cell theory includes the ideas that: - All cells have the same basic chemical composition. - All cells use energy. - All cells contain DNA that is duplicated and passed on as cells divide. 2. **Why are cells too small to be seen with the naked eye?** - Cells are small because a high surface area-to-volume ratio allows them to efficiently exchange materials with their surroundings. For example, oxygen needs to quickly enter cells, and waste needs to be expelled. Smaller cells have a higher ratio of surface area to volume, making these exchanges more efficient. 3. **List and explain the four features common to all cells.** - **Genetic material**: DNA is present in all cells to carry hereditary information. - **Ribosomes**: Structures where protein synthesis occurs. - **Cytoplasm**: The jelly-like substance inside the cell where organelles reside. - **Cell membrane**: The boundary that separates the interior of the cell from its environment and controls what enters and exits. 4. **List the major functions of the plasma membrane.** - Forms a boundary between the cell and its external environment. - Regulates the passage of substances in and out of the cell, helping maintain homeostasis. 5. **What is the difference between the nucleus and a nucleoid?** - **Nucleus**: A membrane-bound organelle found in eukaryotic cells, containing DNA. - **Nucleoid**: A region in prokaryotic cells where the DNA is located, but it is not membrane-bound. 6. **Study the generalized body plan of a prokaryote – Draw, label, and learn the functions of each part.** - In prokaryotes, DNA is located in the **nucleoid**. The **cell membrane** encloses the cell, and the **cytoplasm** contains ribosomes. Some prokaryotes have a **cell wall** for protection, and external structures such as **flagella** or **pili** help with movement and attachment. 7. **List the organelles of eukaryotic cells with their function.** - **Nucleus**: Contains genetic material and controls cell activities. - **Mitochondria**: Produce energy through cellular respiration. - **Endoplasmic reticulum (ER)**: Synthesizes proteins and lipids. - **Golgi apparatus**: Processes, sorts, and ships proteins. - **Lysosomes**: Break down waste materials. - **Chloroplasts** (in plant cells): Carry out photosynthesis. - **Vacuoles**: Store substances and help with waste disposal. - **Cytoskeleton**: Provides structure and helps with cell movement. 8. **Learn the components of the nucleus. Name two important functions of the nucleus in a eukaryotic cell.** - Components: - **Nuclear envelope**: Double membrane surrounding the nucleus. - **Nucleolus**: Produces ribosomes. - **Chromatin**: DNA-protein complex. - Functions: - Houses the cell's genetic material (DNA). - Controls cellular activities by regulating gene expression. 9. **What is an endomembrane system? What are the major organelles of the endomembrane system?** - The **endomembrane system** is a network of membranes inside the cell that work together to modify, package, and transport lipids and proteins. Major components include: - **Nuclear envelope** - **Endoplasmic reticulum (ER)** - **Golgi apparatus** - **Lysosomes** - **Vesicles** - **Plasma membrane** 10. **What is endoplasmic reticulum? Describe the two forms with their function.** - **Endoplasmic Reticulum (ER)**: A network of membranes involved in protein and lipid synthesis. - **Rough ER**: Studded with ribosomes and involved in protein synthesis. - **Smooth ER**: Lacks ribosomes and synthesizes lipids, detoxifies harmful substances. 11. **Golgi apparatus and Vesicles** - **Golgi apparatus**: A stack of membrane sacs that modifies, sorts, and packages proteins and lipids for transport. - **Vesicles**: Small membrane-bound sacs that transport materials within the cell and to the cell membrane for secretion. 12. **Describe the structure and function of Mitochondria.** - **Mitochondria** have a double membrane, with the inner membrane folded into structures called **cristae**. The space inside is called the **matrix**. Mitochondria produce energy for the cell through **cellular respiration**, converting sugar into ATP. 13. **State the endosymbiotic theory and list the evidence that supports endosymbiosis.** - The **endosymbiotic theory** proposes that mitochondria and chloroplasts originated from free-living bacteria that were engulfed by ancestral eukaryotic cells. Evidence includes: - Mitochondria and chloroplasts have their own DNA. - They reproduce independently of the cell. - They have double membranes, suggesting an engulfing event. 14. **Describe the structure and function of Chloroplast.** - **Chloroplasts** have an inner and outer membrane, with internal structures called **thylakoids** arranged in stacks called **grana**. The space around the grana is called the **stroma**. Chloroplasts convert light energy into chemical energy (sugar) through **photosynthesis**. 15. **Name the 3 kinds of Cell Junctions in animals and one kind found in plants.** - **Animal cells**: - **Tight junctions**: Prevent leakage between cells. - **Adhering (anchoring) junctions**: Provide strong mechanical attachments. - **Gap junctions**: Allow the passage of materials between cells. - **Plant cells**: - **Plasmodesmata**: Channels that allow the movement of substances between plant cells. 16. **What are cytoskeletons and name the different kinds of cytoskeletons found in cells?** - The **cytoskeleton** is a network of protein filaments that provide structure and facilitate movement in the cell. The three types are: - **Microfilaments**: Made of actin, involved in cell movement and shape changes. - **Intermediate filaments**: Provide mechanical strength. - **Microtubules**: Serve as tracks for organelle movement and are involved in cell division. 17. **What are cytoskeletons and name the different kinds of cytoskeletons found in cells?** - **Cytoskeleton** is a network of protein tracks and tubules in eukaryotic cells that provides structure, helps with movement, and organizes the contents of the cell. It also plays roles in cell division and transporting organelles. - The three main components are: - **Microfilaments**: Composed of actin, involved in muscle contraction, cell shape changes, and movement. - **Intermediate filaments**: Provide mechanical strength and support for the cell. - **Microtubules**: Made of tubulin, act as "tracks" for moving organelles and vesicles; also form the mitotic spindle during cell division. 18. **What are the 3 kinds of Cell Junctions in animals and one kind found in plants?** - **Cell junctions in animals**: - **Tight junctions**: Prevent leakage of materials between cells (e.g., in the gut lining). - **Adhering (anchoring) junctions**: Provide strong connections between cells or between a cell and the extracellular matrix. - **Gap junctions**: Allow communication between neighboring cells by forming channels that permit the passage of ions and small molecules. - **Cell junction in plants**: - **Plasmodesmata**: Channels between plant cells that allow the passage of water, nutrients, and signaling molecules. 19. **Learn the components of the nucleus. Name two important functions of the nucleus in a eukaryotic cell.** - **Components of the nucleus**: - **Nuclear envelope**: A double membrane that surrounds the nucleus, separating it from the cytoplasm. - **Nucleolus**: A region where ribosomal RNA (rRNA) is synthesized. - **Chromatin**: DNA wrapped around proteins (histones), which forms chromosomes during cell division. - **Functions of the nucleus**: - Stores and protects the cell's genetic material (DNA). - Controls the production of proteins by transcribing DNA into messenger RNA (mRNA). CHAPTER 4 **State two laws of Thermodynamics.** - **First Law of Thermodynamics**: Energy cannot be created or destroyed, only transformed from one form to another. - **Second Law of Thermodynamics**: Energy transformations increase the disorder (entropy) of the universe, and energy is always lost as heat in these transformations. 2. **Define the following terms – Energy, Entropy, Kinetic energy, and Potential energy.** - **Energy**: The ability to do work or cause change. - **Entropy**: A measure of disorder or randomness in a system. - **Kinetic energy**: Energy of motion. - **Potential energy**: Stored energy available to do work. 3. **Explain endergonic and exergonic reactions with examples.** - **Endergonic reactions**: Require an input of energy to build complex molecules (e.g., photosynthesis). - **Exergonic reactions**: Release energy by breaking down molecules (e.g., cellular respiration). 4. **What is activation energy?** - **Activation energy** is the minimum energy required to initiate a chemical reaction. 5. **What are enzymes? List the factors that contribute to enzyme-substrate specificity.** - **Enzymes** are biological catalysts that speed up chemical reactions by lowering activation energy. - Factors affecting enzyme-substrate specificity include the shape of the enzyme's active site and its chemical compatibility with the substrate. 6. **List the factors that have an effect on enzyme activity.** - **Temperature**, **pH**, **substrate concentration**, **enzyme concentration**, and the presence of **inhibitors** or **activators** all influence enzyme activity. 7. **Define metabolic pathway, anabolic pathway, catabolic pathway, and cyclic pathways.** - **Metabolic pathway**: A series of chemical reactions occurring within a cell. - **Anabolic pathway**: Builds complex molecules from simpler ones (energy required). - **Catabolic pathway**: Breaks down complex molecules into simpler ones (energy released). - **Cyclic pathway**: A series of reactions where the final product regenerates the initial substrate. 8. **Explain the mechanisms by which enzyme activity is regulated to control the cell’s metabolism.** - Enzyme activity is regulated through **feedback inhibition**, **competitive inhibition**, and **noncompetitive inhibition**. Cells also use **allosteric regulation** and **temperature/pH changes** to control enzyme activity. 9. **Understand “redox” reactions OR Explain oxidation-reduction reactions.** - **Redox reactions** involve the transfer of electrons from one molecule (oxidation) to another (reduction). Oxidation is the loss of electrons, while reduction is the gain of electrons. These reactions are often coupled. 10. **What is the electron transfer chain?** - The **electron transfer chain** is a series of proteins embedded in a membrane that transfer electrons through redox reactions, releasing energy in small steps. This energy is used to form ATP. 11. **Define cofactors and coenzymes.** - **Cofactors**: Non-protein molecules (e.g., metal ions) that assist enzyme function. - **Coenzymes**: Organic cofactors (e.g., vitamins) that aid enzyme function. 12. **Types of Diffusion and Passive Transport.** - **Diffusion**: The movement of molecules from an area of higher concentration to lower concentration. - **Simple diffusion**: Movement of small, nonpolar molecules through the membrane. - **Facilitated diffusion**: Movement of larger or polar molecules through a transport protein. - **Passive Transport**: The movement of substances across a membrane without using energy, following the concentration gradient. Includes both simple and facilitated diffusion. 13. **Understand the importance of osmosis to all cells, including hypo-, hyper-, and isotonic solutions.** - **Osmosis** is the diffusion of water across a selectively permeable membrane. - **Hypotonic**: Water enters the cell, causing it to swell (may burst). - **Hypertonic**: Water exits the cell, causing it to shrink. - **Isotonic**: Water moves in and out at equal rates, maintaining cell stability. 14. **Study Active Transport using Calcium Pump and Sodium-Potassium Pump.** - **Active transport** requires energy (ATP) to move substances against their concentration gradient. - **Calcium pump**: Moves calcium ions across the membrane using ATP. - **Sodium-Potassium pump**: Exchanges sodium (Na⁺) and potassium (K⁺) ions across the cell membrane, essential for nerve and muscle function. 15. **Study about Endocytosis and Exocytosis.** - **Endocytosis**: The process by which cells engulf materials from their environment by forming vesicles. - **Exocytosis**: The process where cells expel materials by merging vesicles with the plasma membrane.

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