FULL-HANDOUT-GEN-BIO-1-23.docx

**LESSON 1: CELL STRUCTURE AND FUNCTIONS** **CELLS ** - Cells are made up of one or more cells - Cells are the basic unit of life - All cells arise from pre-existing cells. **Types of Cells** 1. **Prokaryotic** 2. **Eukaryotic** \ **Prokaryotes** Have no nucle...

**LESSON 1: CELL STRUCTURE AND FUNCTIONS** **CELLS ** - Cells are made up of one or more cells - Cells are the basic unit of life - All cells arise from pre-existing cells. **Types of Cells** 1. **Prokaryotic** 2. **Eukaryotic** \ **Prokaryotes** Have no nucleus and is comprised of bacterial and archaea.   Single-celled organisms that are the earliest and most primitive forms of life on Earth. Some prokaryotes, such as cyanobacteria, are photosynthetic organisms capable of photosynthesis. Many prokaryotes are extremophiles and can live and thrive in various types of extreme environments **Eukaryotes** Have a nucleus. Both uni-cellular and multi-cellular organism. Eukaryotes are thought to have evolved between about 1.7 billion and 1.9 billion years ago.  **The Three (3) Major Parts of the Cell** 1. **Nucleus** The nucleus is the control center of the cell, containing DNA and gene regulation. It also directs the synthesis of ribosomes proteins. 2. **Cell Membrane** A double layered thin barrier, surrounding the cell to control the entry and the exit of substances 3. **Cytoplasm** The fluid that fills a cell wherein it is the site of many metabolic reactions. The cytoplasm  also provides structure to the cell.  **What is an Organelle?** - Organelles (little organs) are the subcellular structures inside a cell that perform specific jobs or functions within the cell. **Types of Organelles** **MEMBRANE-BOUND ORGANELLES** - found in eukaryotic cells, are cellular structures that are bound by a membrane to keep their internal fluids separate from the cytoplasm of the rest of the cell. **NON MEMBRANE-BOUND ORGANELLES** - are cytoplasmic structures that are not bound by a membrane but have more solid structures that are not fluid-filled, so they have no need for a membrane. **Membrane -Bound Organelles** **Nucleus** - The "control center" of both plant and animal cells that controls growth and reproduction, and it also stores the cell's DNA. It is the largest organelle in a cell that contains the chromosomes (thread-like structures). **Nucleolus** - a smaller structure within the nucleus, that is made up of RNA and proteins.  Its primary function is to produce and assemble the cell\'s ribosomes.  **Nuclear Membrane** - also known as the nuclear envelope, is a double layer that encloses the cell\'s nucleus, where the chromosomes reside.  The nuclear membrane serves to separate the chromosomes from the cell\'s cytoplasm and provides the structural framework of the nucleus. **Endoplasmic Reticulum (E.R.)** An organelle attached to the nucleus that occurs in plants and animals is made up of flattened sacs called cisternae. It is a very important manufacturing site for lipids (fats) and many proteins.  **Two Components of Endoplasmic Reticulum (E.R.)** **1.Smooth Endoplasmic Reticulum** - mainly composed of tubules and lacks ribosomes.   - makes and stores lipids and steroids.   **  2. Rough Endoplasmic Reticulum** - mainly composed of cisternae and has ribosomes. - functions in the synthesis  (making) of proteins **Golgi apparatus** -has a stack-like structure which is found in both plant and animal cells. -responsible for transporting, modifying, and packaging proteins and lipids that are received from the endoplasmic reticulum.  **Lysosomes** are spherical sacs found in animal cells that contain digestive enzymes used to break down biomolecules (carbohydrates, lipids, proteins...) to recycle food particles and to capture bacteria. **Mitochondria ** known as the "powerhouse of the cell", are the ones responsible for aerobic respiration, and production of energy knows as adenosine triphosphate (ATP),  which is needed to power the cell.  **Chloroplast** found in plant cells, is the one responsible for photosynthesis. Converts light energy into sugars that can be used by cells for photosynthesis.  **Vacuole** the storage structure of the cell that stores water and nutrients, including storing and getting rid of waste products.  Vacuoles are found in both plant and animal cells but are larger in plant cells.  **Peroxisome** An organelle that contains enzymes to oxidize organic substances like fats, and  helps break down toxic materials. It uses oxygen to break down molecules.  **NON-MEMBRANE-BOUND ORGANELLES** **Cell Wall** The outer layer of plant cells that helps keep everything inside the cell protected. Furthermore, it provides  structural support and maintenance of cell shape. **Centrioles** Organizing center of microtubules in animal cells.  Helps the cell divide during mitosis and meiosis. They move chromosomes  around by forming fibers called "spindles" during cell division.  **Ribosomes** Small organelles that build long chains of amino acids for the cell. Ribosomes are found in both plant and animal cells and are known as the "protein builders" of the cell.   **Cytoskeleton** Maintains cell's shape, secure organelles on specific positions, allows cytoplasm and vesicles to move within the cell, and enables unicellular organisms to move independently. ** Flagella** are slender, thread-like structures that primarily functions as the cellular locomotion.  **Flagella (plural)** **Flagellum (singular)** **Cilia** hair-like structures responsible for cellular locomotion, movement of particles along extracellular surface of plasma membrane, and filtration. **LESSON 2: PROKARYOTIC AND EUKARYOTIC CELLS** BIOTIC COMPONENTS OF THE ENVIRONMENT INCLUDE ALL FORMS OF LIFE FROM MINUTE BACTERIA TO TOWERING GIANT SEQUOIAS. HOWEVER, AT THE MICROSCOPIC LEVEL, ALL LIVING ORGANISMS ARE MADE UP OF THE SAME BASIC UNIT -- THE CELL. **THERE ARE DIFFERENT FEATURES IN PROKARYOTIC AND EUKARYOTIC CELLS** **WHAT IS PROKARYOTIC CELLS?** The term "prokaryote" is derived from the Greek word "pro", (meaning: before) and "karyon" (meaning: kernel). It translates to "before nuclei." Prokaryotes are one of the most ancient groups of living organisms on earth, with fossil records dating back to almost 3.5 billion years ago. Prokaryotic cells are comparatively smaller and much simpler than eukaryotic cells. The other defining characteristic of prokaryotic cells is that it does not possess membrane-bound cell organelles such as a nucleus. Reproduction happens through the process of binary fission. A prokaryotic cell is a primitive type of cell that is characterized by the absence of a nucleus. Furthermore, prokaryotes do not possess membrane-bound cellular organelles. Prokaryotes are exclusively unicellular. **WHAT IS EUKARYOTIC CELLS?** The term "Eukaryotes" is derived from the Greek word "eu", (meaning: good) and "karyon" (meaning: kernel), therefore, translating to "good or true nuclei." Eukaryotes are more complex and much larger than prokaryotes. They include almost all the major kingdoms except kingdom monera. Structurally, eukaryotes possess a cell wall, which supports and protects the plasma membrane. The cell is surrounded by the plasma membrane and it controls the entry and exit of certain substances. The nucleus contains DNA, which is responsible for storing all genetic information. The nucleus is surrounded by the nuclear membrane. Within the nucleus exists the nucleolus, and it plays a crucial role in synthesising proteins. Eukaryotic cells also contain mitochondria, which are responsible for the creation of energy, which is then utilized by the cell. Present in only plant cells, chloroplasts are the subcellular sites of photosynthesis. The endoplasmic reticulum helps in the transportation of materials. Besides these, there are also other [[cell organelles]](https://byjus.com/biology/cell-organelles/) that perform various other functions and these include ribosomes, lysosomes, Golgi bodies, cytoplasm, chromosomes, vacuoles and centrosomes. **WHAT ARE THEIR DIFFERENCES?** **What is the difference between Prokaryotic and Eukaryotic cells?** The defining characteristic feature that distinguishes between prokaryotic and eukaryotic cell is the nucleus. In prokaryotic cells, the true nucleus is absent, moreover, membrane-bound organelles are present only in eukaryotic cells. Another major difference between prokaryotic and eukaryotic cells is that prokaryotic cells are exclusively unicellular, while the same does not apply to eukaryotic cells. **LESSON 3: TYPES OF CELLS AND CELL MODIFICATION** - All living things exhibit certain characteristics, the characteristics of life. Living things are made up of cells. - They metabolize, grow and develop, respond to stimulus, adapt to their environment and reproduce. Life on Earth exhibits organization. - Different tissues can be grouped further and form organs. The organs form organ systems that make the body\'s function more complex and efficient. - The organ systems will then form the whole organism. All living things exhibit organization, whether they are unicellular or multicellular organisms. **FOUR MAIN TYPES OF CELL** 1. Epithelial cells 2. Connective tissue cells 3. Muscle cells 4. Nerve cells **EPITHELIAL TISSUE** - This type of tissue is commonly seen outside the body as coverings or as linings of organs and cavities. Epithelial tissues are characterized by closely joined cells with tight junctions (i.e., a type of cell modification). Being tightly packed, tight junctions serve as barriers or pathogens, mechanical injuries, and fluid loss. **CELLS THAT MAKE UP EPITHELIAL TISSUE CAN HAVE DISTINCT ARRANGEMENTS** ###### **Cuboidal** - ###### for secretion ###### **Simple columnar** - brick-shaped cells; for secretion and active absorption 3. **Simple Squamous** 4. **Stratified squamous** - multilayered and regenerates quickly; for protection 5. ###### Stratified Columnar 6. **Pseudo-stratified columnar** - a single layer of cells; may just look stacked because of varying height; for lining of respiratory tract; usually lined with cilia (i.e., a type of cell modification that sweeps the mucus) ###### **Transitional** **CONNECTIVE TISSUE** - ##### **BLOOD** - - ##### **CARTILAGE** - - ##### **BONE** - **MUSCLE TISSUE** - **IN VERTEBRATES, THESE MUSCLE CAN BE CATEGORIZED INTO THE FOLLOWING:** 1. **SKELETAL** - Striated; voluntary movements. It is attached to our bones by tendons throughout our body. 2. **CARDIAC** - Striated with intercalated disk for synchronized heart contraction; involuntary. This is exclusively found in the heart. 3. **SMOOTH** - Not striated; involuntary. It lines the walls of various internal organs like digestive tract and blood vessels.  **NERVOUS TISSUE** These tissues are composed of nerve cells called neurons and glial cells that function as support cells. These neurons sense stimuli and transmit electrical signals throughout the animal body. Neurons connect to other neurons to send signals. The dendrite is the part of the neuron that receives impulses from other neurons while the axon is the part where the impulse is transmitted to other neurons. **CELL MODIFICATION** **MODIFICATION OF CELL SURFACE** **5 TYPES OF APICAL SURFACE** **CILIA**- small hair-like protuberances on the outside of eukaryotic cells. They are primarily responsible for locomotion. **2 TYPES OF CILIA** **FLAGELLA**- A whip-like modification that acts like propeller and its primarily for locomotion. **MICROVILLI**- Non-motile finger-like protrusions that function to increase the cell surface area and the efficiency of absorption. **PSEUDOPODS**- "false feet". Enable the organism to make temporary and irregular lobes. Use for movement and engulf prey. - Cell wall for plant cell. - Glycoprotein for animal cell **BASAL MODIFICATION** -Specialize structured found on the basal surface of the cell. Facilitates stable adhesion of basal cells to basement membrane. **DESMOSOMES** - are responsible for strong adhesion in epithelia and cardiac muscle. **HEMIDESMOSOMES** - Attach a cell to extracellular structures such as protein fibers in the basement membrane. **LATERAL MODIFICATION** - Also known as *cell junctions.* Specialized structure that serves as intercellular connection between two adjacent cells. **TIGHT JUNCTIONS** - Held two adjacent cell tightly, prevents leakage of materials between cells and act as a water seal. #### **ADHERING JUNCTIONS** - Fastens cells to one another and provides a strong mechanical attachment to adjacent cell. #### **GAP JUNCTIONS** - communication junctions". Allows direct flow of molecules between cells and connect two cells directly from the cytoplasm.  **LESSON 4: CELL CYCLE** **PHASES OF THE CELL AND THEIR CENTRAL POINTS** 1. **INTERPHASE** - is the active part of the cell cycle, including G1, S, and G2 phases, where cells grow, replicate DNA, and prepare for mitosis. It\'s not a dormant stage, as cells in interphase are busy synthesizing proteins, transcribing DNA,and processing signals. It\'s the \"daily living\" or metabolic phase of a cell. - Interphase is the phase where the cell prepares for division. It consists of **three stages:** **G1 PHASE (GAP 1)** **S PHASE (SYNTHESIS)** **G2 PHASE (GAP 2)** **PHASES OF THE CELL AND THEIR CENTRAL POINTS** **MITOSIS** -  **PHASES OF MITOSIS** 1. - The first stage of mitosis where chromosomes become visible, and the mitotic spindle begins to form. ##### CENTRAL POINTS: - - - - 2. ##### **METAPHASE** - The stage where chromosomes align at the cells equatorial plane, also known as the metaphase plate. ##### CENTRAL POINT: - - 3. ##### **ANAPHASE** - The stage where sister chromatids are pulled apart toward opposite poles of the cell. ##### CENTRAL POINT: - - 4. **TELOPHASE** - The final stage of mitosis where chromosomes de- condense and nuclear envelopes reform around each set of chromosomes. ##### CENTRAL POINT: - - **MEIOSIS** **MEIOSIS I** Cells enter meiosis from interphase, similar to mitosis, and replicate DNA. In humans, there are 46 chromosomes and 46 pairs of chromatids **PHASES OF MEIOSIS I** 1. - ##### CENTRAL POINTS: - **Chromosome Condensation:** Chromosomes become visible as they condense. - **Synapsis:** Homologous chromosomes pair up to form tetrads (bivalents), allowing crossing over to occur. - **Crossing Over:** Exchange of genetic material between non-sister chromatids of homologous chromosomes, leading to genetic recombination. - **Formation of the Synaptonemal Complex**: A protein structure that helps stabilize the homologous chromosome pairs. - **Nuclear Envelope Breakdown:** The nuclear envelope disintegrates to allow spindle fibers to access chromosomes. 2. ##### **METAPHASE I:** - ##### CENTRAL POINTS: - - 3. ##### **ANAPHASE I:** - ##### CENTRAL POINTS: - **Homologous Chromosome Separation:** Homologous chromosomes (each still consisting of two chromatids) are pulled to opposite poles of the cell. - **Reduction in Chromosome Number:** This step reduces the chromosome number by half. 4. ##### **TELOPHASE I:** - ##### ##### ##### ##### CENTRAL POINTS: - **Formation of Two New Nuclei:** Two new nuclear envelopes form around each set of chromosomes at opposite poles. - **Cytokinesis:** The cell divides into two daughter cells, each with half the chromosome number but still composed of two chromatids. - 1. **PROPHASE II:** - Chromosomes condense and become visible again. The nuclear envelope dissolves, and spindle fibers begin to form. At this stage, each cell has a haploid number of chromosomes (in humans, 23 chromosomes or 23 pairs of chromatids). - 1. ##### **METAPHASE II:** - Chromosomes line up at the metaphase plate in the center of the cell. Spindle fibers attach to the centromeres of each chromosome. ##### CENTRAL POINTS: - - 2. ##### **ANAPHASE II:** - ##### CENTRAL POINTS: - - 3. ##### **TELOPHASE II:** - ##### CENTRAL POINTS: - - ##### CENTRAL POINTS: - **Chromosome Condensation**: Chromosomes condense again. - **Nuclear Envelope Breakdown**: The nuclear envelope disintegrates in each of the two daughter cells. - Cytokinesis is the physical process of cell division, which divides the cytoplasm of a parental cell into two daughter cells. It occurs concurrently with two types of nuclear division called mitosis and meiosis, which occur in animal cells. - Cytokinesis is the final stage of cell division, where the cytoplasm of the cell divides to form two separate daughter cells. - In animal cells, a cleavage furrow forms and pinches the cell membrane inwards until the cell is divided into two daughter cells. - In plant cells, a cell plate forms in the center of the cell and develops into a new cell wall that separates the daughter cells ##### **DISORDERS AND DISEASES THAT OCCURS WHEN A CELL MALFUNCTIONS DURING CELL CYCLE** ##### CANCER ##### GENETIC DISORDER ###### Examples: - Down Syndrome: Caused by an extra copy of chromosome 21 (trisomy 21). - Turner Syndrome: Caused by the complete or partial absence of one X chromosome in females. - Klinefelter Syndrome: Caused by an extra X chromosome in males (XXY) 3. - These diseases are caused by dysfunction in mitochondria, the energy-producing organelles in cells. Some mitochondrial diseases are related to defects in cell division**.** 4. ##### CELL CYCLE DISORDER - ###### Disorders resulting from specific defects in cell cycle regulation and checkpoint controls. Examples: 5. ##### PROGARIA AND RELATED DISORDER - These are rare genetic disorders that cause premature aging and result from defects in the cell cycle and DNA repair mechanisms. ###### Examples: Caused by mutations in the LMNA gene, leading to abnormal nuclear envelope proteins and premature aging. 6. ANEUPLOIDY SYNDROMES - Disorders cause by abnormal numbers of chromosomes resulting from errors in mitosis or meiosis. EXAMPLE: **PATAU SYNDROME**: caused by an extra copy of chromosome 13 (trisomy 13). **EDWARD SYNDROME**: caused by an extra copy of chromosome 18 (trisomy 18). **LESSON 5: STRUCTURAL COMPONENTS OF CELL MEMBRANE** **Cell Membrane** (\"**plasma membrane**\", \"**cytoplasmic membrane**\", \"**plasmalemma\"**) \- the outer covering of a cell \- responsible for controlling entry and exit of material from the cell. \- is described as a fluid mosaic where various macromolecules are embedded in the phospholipid bilayer **Fluid Mosaic Model** The fluid mosaic model is the accepted structural model of the cell membrane. It describes how the cell membrane is made of different components, free moving in the membrane. **Major Components of Cell Membrane** **1. Phospholipids** **2. Proteins** **3. Carbohydrates** **4. Cholesterol** **Phospholipids** are the primary building blocks of the cell membrane. They are amphipathic molecules, meaning they have both hydrophilic (water-loving) and hydrophobic (water-hating) parts. **Phospholipid Bilayer** - a double layer of phospholipid molecules arranged with their hydrophilic heads facing outward and their hydrophobic tails facing inward. This creates a barrier that separates the cell\'s internal environment from the external surroundings. **Phospholipid Molecule** - consists of a hydrophilic head group (usually containing a phosphate group) and two hydrophobic fatty acid tails. The hydrophilic head interacts with the aqueous environment, while the hydrophobic tails create a barrier within the membrane. **Hydrophilic Head**: The water-loving head of a phospholipid molecule is polar and interacts with water molecules. It is typically composed of a glycerol backbone and a phosphate group. **Hydrophobic Tails**: The water-hating tails of a phospholipid molecule are nonpolar and do not interact with water. They are composed of fatty acid chains. **Proteins** - they are embedded within the phospholipid bilayer and contribute to the structure, function, and communication of the cell. **2 Types of Proteins** **Integral proteins** - embedded within the phospholipid bilayer, these proteins serve various functions including: **Transport**: Facilitating the movement of substances into and out of the cell **Cell signaling**: Receiving and transmitting signals from the environment. **Enzymes**: Catalyzing chemical reactions within the cell. **Peripheral proteins** - attached to the outer or inner surface of the membrane, these proteins are involved in a variety of functions such as cell recognition and structural support. **Surface proteins** - proteins located on the outer surface of the membrane, involved in cell-to-cell communication and recognition. **Globular proteins** - are spherical proteins that play various roles in the cell membrane, including enzymes, transport proteins, receptors, hormones, and structural proteins. **Alpha-Helix protein** - A common secondary structure of proteins found in the cell membrane. \- Characterized by a helical shape formed by hydrogen bonds between amino acids. - Alpha-helices often play a role in transmembrane proteins, allowing them to span the phospholipid bilayer and interact with both the intracellular and extracellular environments. **Protein channel (transport protein)** - a type of integral protein that forms a pore through the membrane, allowing specific molecules to pass through. **Carbohydrates** - are attached to the outer surface of the cell membrane and are involved in cell recognition, adhesion, and communication. \- Plays a crucial role in identifying and interacting with other cells, as well as in protecting the cell surface. **Types of Carbohydrates** **Glycolipids** - Lipids with attached carbohydrate chains, involved in cell recognition and adhesion. **Glycoproteins** - Proteins with attached carbohydrate chains, also involved in cell recognition and adhesion. **Cholesterol** - a type of lipid found in the cell membrane. \- Plays a crucial role in maintaining the membrane\'s structure, fluidity, and permeability. **LESSON 6: CELL TRANSPORT** **What is cell transport?** The movement of a substance across the cell membrane. **2 MAIN PROCESSES OF CELL TRANSPORT** 1. **Passive transport processes** - the molecules are moved within and across the cell membrane and thus transporting through the concentration gradient, without using ATP (energy) 2. **Active transport processes** - the molecules are moved across the cell membrane, pumping the molecules against the concentration gradient using ATP (energy).  **PASSIVE TRANSPORT** - **Simple Diffusion** - **Osmosis** - **Facilitated\ Diffusion** **SIMPLLE DIFFUSION** **It is a process where the molecules move directly through the cell membrane from an area of higher concentration to an area of lower concentration without any assistance. It typically applies to small, nonpolar molecules like oxygen and carbon dioxide.**  **OSMOSIS** It is the passage of water from a region of high water concentration through a semi-permeable membrane to a region of low water concentration. Water moves in or out of a cell until its concentration is the same on both sides of the plasma membrane. **FACILITATED DIFFUSION** This process involves the movement of molecules across the cell membrane with the help of transport proteins. It allows larger or polar molecules, like glucose or ions, to pass through the membrane without expending energy, moving from higher to lower concentration areas. **ACTIVE TRANSPORT** - Pump - Primary - Secondary - Vesicle - Exocytosis - Endocytosis - Pinocytosis - Phagocytosis - Receptor-mediated **PUMP** **[Primary Active Transport]** - this type of transport directly uses energy, usually from ATP, to move the molecules across the membrane. **[Secondary Active Transport]** - this type does not directly use ATP. Instead, it relies on the energy created by primary active transport. It uses the gradient established by primary transport to move other substances. **VESICLE** **[Exocytosis]** - "exo" means "external." It is a process where vesicles fuse with the cell membrane to release their contents outside the cell. This is essential for processes like secretion of hormones, neurotransmitters, or waste **[Endocytosis]** - "endo" means "internal or within." It is the process where the cell membrane engulfs materials from the outside, forming vesicles that carry the material into the cell. **3 MAIN FORMS OF ENDOCYTOSIS** 1. Pinocytosis 2. Phagocytosis 3. Receptor-mediated **PINOCYTOSIS** Also called as **" cell drinking "**. \- It is when the plasma membrane folds inward and engulfs droplets of interstitial fluid that contain dissolved solutes that can be used by the cell. \- The cell undergoing pinocytosis is called a pinocyte. **PHAGOCYTOSIS** \- Also called as **" cell eating "**. \- In phagocytosis a large particle is engulfed by the newly formed vesicle and this vesicle fuses with a lysosome, which is a membranous vesicle that contains digestive enzymes that break down the particle into its component molecules. \- A cell undergoing phagocytosis is known as a phagocyte. RECEPTOR -- MEDIATED Involves using receptors on the outside of the plasma membrane.