Atoms and Molecules in Chemistry PDF

ATOM - An atom is the fundamental building block of matter. It is the smallest unit of an element that retains the chemical properties of that element. Atoms are composed of three main subatomic particles: protons, neutrons, and electrons. Atoms are electrically neutral because they have an equal nu...

ATOM - An atom is the fundamental building block of matter. It is the smallest unit of an element that retains the chemical properties of that element. Atoms are composed of three main subatomic particles: protons, neutrons, and electrons. Atoms are electrically neutral because they have an equal number of protons and electrons, resulting in overall zero net charge. The mass of an atom is primarily determined by the combined masses of its protons and neutrons, while its size is determined by the distribution of its electrons. PARTS OF THE ATOMS Protons Protons are positively charged particles found in the nucleus (central core) of the atom. The number of protons in the nucleus determines the element's identity and is referred to as the atomic number. ▪ The proton is a composite particle, which means it is made up of other particles, namely two up quarks and one down quark, held together by the strong force. Neutrons Neutrons are neutral particles also found in the nucleus. They add mass to the atom but do not significantly affect its chemical properties. The number of neutrons can vary within atoms of the same element, resulting in isotopes, which are atoms of the same element with different numbers of neutrons. 1.675 x 10^-27 kg 1.00867 amu Electrons Electrons are negatively charged particles that orbit the nucleus in energy levels or electron shells. Electrons are responsible for an atom's chemical behavior because they participate in chemical reactions and interactions with other atoms. The arrangement of electrons in shells determines the atom's chemical reactivity and bonding capabilities. Mass = 9.1 x 10^-31 kg 1 amu (atomic mass unit) = 1/12 mass of carbon - 12 atom Mass = 0.000549 amu MOLECULES A molecule is a group of atoms held together by chemical bonds. It is the smallest unit of a compound that retains the chemical properties of that compound. Molecules can  consist of atoms of the same element or atoms of different elements bonded together. COVALENT BONDS Covalent bonds form when atoms share electrons to achieve a more stable electron configuration. This type of bond is common between nonmetals. Covalent bonds can be further classified into: Single Bonds: In a single covalent bond, two atoms share one pair of electrons. Double Bonds: Two atoms share two pairs of electrons, forming a double covalent bond. Triple Bonds: Three pairs of electrons are shared, creating a triple covalent bond. IONIC BONDS Ionic bonds occur when atoms transfer electrons from one to another, resulting in charged particles called ions. These ions are held together by electrostatic attractions between their opposite charges. Ionic bonds typically form between a metal and a nonmetal. METALLIC BONDS Metallic bonds occur when atoms lose some of their electrons to form a "sea" of electrons that are free to move throughout the metal. These bonds are responsible for the characteristic properties of metals, such as their high melting and boiling points, ductility and malleability. HYDROGEN BOND Hydrogen Bonds are the weak chemical bonds between a hydrogen atom and a highly electronegative atom such as nitrogen, oxygen, or fluorine. These bonds are relatively weak compared to covalent or ionic bonds and are formed between molecules rather than atoms. They play an important role in the properties of many biomolecules such as DNA and proteins. BASIC CELLULAR BIOLOGY Basic cellular biology is the foundational study of the fundamental unit of life: the cell. Cells are the microscopic building blocks that comprise all living organisms, from the simplest single-celled organisms to complex multicellular beings. Understanding cellular biology provides insights into how organisms function, develop, and maintain their internal environments. It encompasses a diverse range of topics, including cell structure and organelles, cellular processes like metabolism and energy production, cell division and growth, and the intricate molecular interactions that underlie the intricate machinery of life. CELL Cells are the basic structural and functional units of life. They are the smallest entities  that can carry out all the functions necessary for an organism's survival. Cells are the building blocks of all living organisms, from simple single-celled organisms like bacteria to complex multicellular organisms like plants and animals, including humans. CELLULAR STRUCTURE Cell Membrane (Plasma Membrane): The cell membrane is a semi-permeable lipid bilayer that surrounds the cell, separating its internal contents from the external environment. It regulates the passage of substances in and out of the cell, maintaining cellular integrity and facilitating communication with the surroundings. Nucleus: The nucleus houses the cell's genetic material, including DNA, in the form of chromosomes. It serves as the control center of the cell, orchestrating essential functions such as DNA replication, transcription, and the regulation of gene expression. Cytoplasm: The cytoplasm is the gel-like substance that fills the space between the cell membrane and the nucleus. It contains various organelles, structures, and molecules necessary for cellular processes, including metabolism and protein synthesis. Endoplasmic Reticulum (ER): The ER is a network of membranes involved in protein synthesis, folding, and transport. It consists of rough ER (with ribosomes attached, involved in protein synthesis) and smooth ER (involved in lipid metabolism and detoxification). Golgi Apparatus (Golgi Complex): The Golgi apparatus modifies, sorts, and packages proteins and lipids for transport within the cell or secretion to the extracellular environment. It consists of flattened sacs called cisternae. Mitochondria: Mitochondria are often referred to as the "powerhouses" of the cell because they produce energy through cellular respiration. They generate adenosine triphosphate (ATP), the cell's primary energy currency. Lysosomes: Lysosomes contain enzymes that break down waste materials, cellular debris, and foreign substances through processes called autophagy and phagocytosis. They are crucial for cellular recycling and maintenance Peroxisomes: Peroxisomes contain enzymes that break down fatty acids and detoxify harmful substances, producing hydrogen peroxide as a byproduct.  They play a role in lipid metabolism and oxidative processes. Cytoskeleton: The cytoskeleton is a network of protein filaments (microtubules, microfilaments, and intermediate filaments) that provide structural support, maintain cell shape, and facilitate cellular movement and transport. Centrioles are cylindrical structures involved in cell division and the organization of microtubules. Centrosomes are regions near the nucleus that contain centrioles and help coordinate cell division. CELLULAR FUNCTION Cellular functions are the processes and activities that occur within cells to maintain life and support the overall functioning of organisms. crucial for comprehending how living organisms operate at the molecular level. These processes collectively ensure that cells can obtain energy, synthesize and break down molecules, maintain internal balance, and carry out specialized functions necessary for the survival and growth of organisms. BASIC CELL CHEMISTRY 1. Atomic and Molecular Interactions: Cells engage in complex interactions between atoms and molecules. Chemical reactions within cells involve the rearrangement of atoms to form new compounds. 2. Electrochemical Balance: Cells maintain a balance of ions and charges across their membranes, which is crucial for processes like nerve signaling and muscle contraction. METABOLISM Anabolism and Catabolism: Metabolism includes anabolic processes (building up molecules) and catabolic processes (breaking down molecules). These processes are driven by enzymes and are essential for energy production and the synthesis of biomolecules. Energy Production: Cells generate energy through metabolic pathways like glycolysis, the citric acid cycle (Krebs cycle), and oxidative phosphorylation, which produce adenosine triphosphate (ATP). Cellular Respiration: Cellular respiration is a series of metabolic reactions that convert nutrients, such as glucose, into ATP. It includes glycolysis, the citric acid cycle, and the electron transport chain ORGANIC AND INORGANIC COMPOUND Organic Compounds: Cells contain a wide variety of organic compounds, including carbohydrates (sugars), lipids (fats), proteins (amino acids), and nucleic acids (DNA and RNA). These biomolecules have diverse functions, such as energy storage, structural  support, and information storage. Inorganic Compounds: Inorganic compounds like water, salts (ions), and minerals are essential for cellular processes. Water is a universal solvent, participating in chemical reactions and providing a medium for cellular activities. Ions and minerals are involved in nerve signaling, muscle contraction, and other vital functions. Enzymes and Catalysts Enzymes: Enzymes are proteins that act as biological catalysts, accelerating chemical reactions within cells. Enzymes are highly specific and play a central role in metabolic pathways, breaking down or building up molecules as needed. Catalysis: Enzymes lower the activation energy required for a reaction, facilitating chemical transformations without being consumed in the process. CELL PROLIFERATION Cell proliferation refers to the regulated process by which cells divide and multiply to produce new daughter cells. This fundamental biological mechanism plays a pivotal role in growth, development, tissue repair, and the maintenance of homeostasis within organisms. Precisely controlled, cell proliferation involves intricate molecular signaling pathways that govern when and how cells transition from quiescence to division. CELL CYCLE The cell cycle is a series of ordered events that a cell undergoes as it grows, prepares for division: divides, and produces two new daughter cells. It encompasses the stages from the birth of a new cell (cell birth) to its own division into two new cells (cell division) and includes the phases in between when the cell carries out various activities to ensure accurate replication and distribution of genetic material. The cell cycle is crucial for growth, development, tissue repair, and maintaining a balance of cell numbers in organisms. It consists of distinct phases: INTERPHASE This is the phase between cell divisions, where the cell grows, carries out its normal functions, and duplicates its DNA. Interphase is further divided into three sub-phases: G1 Phase (Gap 1): The cell grows and carries out its normal functions, preparing for DNA synthesis. S Phase (Synthesis): DNA replication occurs, resulting in the duplication of the cell's genetic material. G2 Phase (Gap 2): The cell continues to grow and prepares for cell division. MITOSIS Mitosis is the process by which the nucleus of the cell divides into two identical nuclei, each with the same number of chromosomes as the original cell. Mitosis is crucial for cell growth and tissue repair. It consists of several phases: Prophase, Metaphase, Anaphase, and Telophase. CYTOKINESIS Following mitosis, cytokinesis occurs, where the cytoplasm of the cell is divided into two, resulting in the formation of two distinct daughter cells.