Exam 2 Study Guide PDF

**[EXAM 2 STUDY GUIDE]** [**Cells as Building Blocks**: ] **[Fundamental Characteristics of Cells]**: Despite their diversity, all cells share basic features 1. DNA is used to direct the synthesis of proteins through transcription & translation 2. They are too small to be seen with the nak...

**[EXAM 2 STUDY GUIDE]** [**Cells as Building Blocks**: ] **[Fundamental Characteristics of Cells]**: Despite their diversity, all cells share basic features 1. DNA is used to direct the synthesis of proteins through transcription & translation 2. They are too small to be seen with the naked eye 3. A plasma membrane **[How Cells Are Studied]** **Microscopy**: Microscopes are essential tools for studying cells due to their small size. Different types of microscopes provide different views and levels of detail. 1. **Light Microscopes**: Use visible light that passes through lenses. Used to view living organisms, but staining may be needed to view cellular components. 2. **Fluorescence Microscopes**: Fluorescence microscopy uses light of specific wavelengths (i.e., colors) together with complicated specimen preparation to visualize subcellular structures 3. **Electron Microscopes**: Use beams of electrons for higher magnification and resolution than light microscopes. Cannot view live cells (preparation kills cells). **[Comparing Prokaryotic and Eukaryotic Cells]** **Prokaryotic Cells**: **Domains**: Bacteria and Archaea. - Simpler structure, lack a nucleus and membrane-bound organelles. - Key features include: plasma membrane, cytoplasm, DNA (in the nucleoid region), and ribosomes. - Prokaryotes have cell walls (made of peptidoglycan in bacteria), sometimes with capsules, and use **flagella** for movement. **Eukaryotic Cells**: **Domains**: Animals, plants, fungi, and protists. - More complex, with a membrane-bound nucleus and organelles (e.g., mitochondria, chloroplasts). - Larger than prokaryotic cells, ranging from 10-100 μm in size. - Adaptations such as specialized organelles help manage the large size and complex functions of eukaryotic cells. **[Eukaryotic Cells Overview]** **Eukaryotic Cell Structure:** Eukaryotic cells, both animal and plant, have a complex structure compared to prokaryotic cells. These cells contain organelles, which are specialized structures within the cell that perform specific functions. This allows for various cellular processes to occur simultaneously. Some shared properties of eukaryotic cells: 1. The most fundamental shared property of eukaryotic cells is that they are "compartmentalized" into a variety of organelles, each with a specialized structure, composition, and function---why? - Order & Efficiency -- Each compartment carries out specific activities in the cell and the segregation of activities to distinct compartments enhances the order & efficiency of those activities 2. Eukaryotic cells contain a complex intracellular skeletal system called the cytoskeleton 3. Eukaryotic cells [of multicellular organisms] are surrounded by extracellular substances 4. Eukaryotic cells [of multicellular organisms] form a variety of cell junctions - "Cell junctions" refers to sites of contact between adjacent cells **Key Components of Eukaryotic Cells:** 1. **Plasma Membrane**: Composed of a phospholipid bilayer with embedded proteins, the plasma membrane regulates the passage of substances in and out of the cell. It also contains cholesterol and carbohydrates, which provide structural support and facilitate cell recognition. 2. **Cytoplasm**: The cytoplasm is the cell's internal fluid, consisting of organelles suspended in an **aqueous solution within which organelles reside** called cytosol. It also contains water, ions, and various organic molecules, including proteins, sugars, and fatty acids. Many metabolic reactions, like protein synthesis, take place here. - **The Endomembrane System**: This includes the [nuclear envelope, ER, Golgi apparatus, vesicles, and plasma membrane]. These structures work together to produce, modify, package, and transport proteins to the lysosome and plasma membrane. 3. **Nucleus**: The nucleus is the control center of the cell, containing DNA organized into chromosomes. - The DNA is wrapped around proteins and is condensed into chromatin. DNA directs transcription and protein synthesis. The nucleus has two phospholipid bilayers called the nuclear envelope. - Nuclear pores allow for large or polar molecules to enter and exit the nucleus (this is how mRNA leaves the nucleus to be translated). - The outer membrane of the nucleus is covered in ribosomes. The perinuclear space of the nuclear envelope is continuous with the lumen of the rough ER. 4. **Endoplasmic Reticulum (ER)**: - an extensive network of membranes organized in folds & stacks called cisternae - ER membrane organization creates a tubular intracellular compartment -- the inside is called the ER lumen **Rough ER:** Studded with ribosomes, it synthesizes and modifies proteins. - Proteins synthesized on ER-bound ribosomes are transported into the ER lumen as they are produced - Site where proteins transported by the endomembrane system are produced - Site of protein modification (by enzymes) with carbohydrates (resulting in "glycoproteins") - Initiates transport of proteins toward their final destination by vesicular transport - Proteins exported from the ER in vesicles travel first to the Golgi apparatus 5. **Golgi Apparatus**: Functions as the "shipping & receiving center" of the cell - This organelle modifies, sorts, and packages proteins and lipids for distribution within the cell or secretion outside the cell. - The Golgi apparatus consists of a stack of flattened membranous sacs called cisternae & associated vesicles - Like the ER, Golgi membranes are organized forming intracellular compartments called the Golgi lumen 6. **Lysosomes**: Found in animal cells, lysosomes contain digestive enzymes that break down cellular waste, old organelles, and foreign invaders. - Lysosome function is dependent on the endomembrane system, which delivers hydrolytic enzymes to lysosomes that then breakdown/digest substances within the organelle **Phagocytosis entails:** 1. The internalization of extracellular substances (e.g., food for the cell) in vesicles 2. The fusion between the vesicles with a lysosome, whereupon the hydrolytic enzymes break down the substance 1. The encapsulation of a dysfunctional organelle into an intracellular vesicle 2. The fusion between the vesicle with a lysosome, where the hydrolytic enzymes break down the dysfunctional organelle 7. **Transport Vesicles**: transport proteins and other cargo through the cells \(1) Bud a vesicle from the membrane of one compartment 8. **Mitochondria**: Known as the cell's powerhouses, mitochondria generate ATP (energy) through cellular respiration using glucose. 1. All eukaryotic organisms have multiple mitochondria per cell 2. Mitochondria contain an abundance of proteins that synthesize ATP, most of which are associated with the inner membrane 3. The cristae folds increase the amount of inner membrane, which in turn increases the number of proteins & amount of ATP production 4. They contain their own circular DNA that contains several genes that encode proteins essential for ATP production 5. Mitochondria also contain their own ribosomes to synthesize proteins 9. **Chloroplasts (Plant Cells)**: Chloroplasts are responsible for photosynthesis, converting light energy into chemical energy stored as glucose. 1. They have their own DNA and ribosomes, similar to mitochondria. 2. contain membranous system of flattened, interconnected sacs called thylakoids 3. Thylakoids contain a molecule called chlorophyll, which along with the many proteins is responsible for producing glucose from solar E **Endosymbiosis**: - **Endosymbiotic Theory**: This theory suggests that mitochondria and chloroplasts originated as separate prokaryotic organisms. Ancient host cells engulfed aerobic bacteria and cyanobacteria, which then developed symbiotic relationships. Over time, these bacteria became specialized as mitochondria (aerobic bacteria) and chloroplasts (photosynthetic bacteria) within the host cells. - This explains why mitochondria and chloroplasts have their own DNA and ribosomes, which are similar to those found in bacteria. 10. **Vacuoles (Plant Cells)**: The central vacuole functions as a storage site for water & organic compounds---it has a phospholipid bilayer membrane 11. **Cell Cytoskeleton**: A network of protein fibers within the cytoplasm, the cytoskeleton maintains cell shape, anchors organelles, and facilitates movement. It consists of: 1. **Actin Filaments**: The thinnest filaments involved in cell movement and division. [Functions:] **Cell structure,** cell shape, and cell movement 2. **Intermediate Filaments (IFs)**: Provide structural support and anchor organelles. 3. **Microtubules (MTs)**: Thick, hollow tubes that move organelles and chromosomes during cell division and makeup structures like cilia and flagella. **[Differences Between Plant and Animal Cells:]** **Plant Cells**: - Have a rigid *cell wall* made of cellulose. - Contain *chloroplasts*, which perform photosynthesis. - Have a large *central vacuole* that helps maintain turgor pressure. **Animal Cells**: - Contain *centrioles* and *lysosomes*, which are absent in plant cells. - Do not have cell walls or chloroplasts. [**Intercellular Junctions**:] 1. **Tight Junctions**: In animal cells, these create a watertight seal, preventing leakage of materials, like those found in epithelial cells lining organs. 2. **Desmosomes**: These structures connect adjacent animal cells, giving tissues like skin and muscle their strength. 3. **Gap Junctions**: Gap junctions form pores that allow communication between animal cells by enabling the exchange of ions and small molecules. 4. **Plasmodesmata**: Similar to gap junctions, these are channels that connect plant cells, allowing for the transport of nutrients and communication. **[Membrane Structure and Function]** 1\. Composition, structure, & general properties (review w/ elaboration) Fundamental structure = phospholipid bilayer - Membranes are composed of phospholipids + proteins - Membrane proteins attach (or "bind") the ECM & cytoskeleton - Membrane proteins are classified based on how they are physically associated with the membrane - **Integral proteins** -- integrated into the phospholipid bilayer - **Transmembrane proteins**Proteins that cross the bilayer - **Peripheral proteins** -- associated by binding to integral proteins - Integral proteins are synthesized & integrated into membrane by ER-bound ribosomes. After synthesis at the ER, integral proteins are transported to the plasma membrane by vesicular transport - - - Cell-cell recognition - Intercellular joining - Attachment to the cytoskeleton and extracellular matrix (ECM) - Transport - Enzymatic activity - Signal transduction 2\. Movement of molecules across membranes **Cellular life is dependent on the exchange of numerous molecules across its membranes (plasma membrane & organelle membranes)** **[Passive Transport]: Movement of molecules across membranes driven by the laws of diffusion** 1. [Diffusion:] refers to the tendency of molecules to spread out evenly within an available space (gases & liquids) from high to low concentrations 2. [Osmosis: ] \(1) Diffusion of water across a semi-permeable membrane MEMBRANE on either side Solutions are classified based on their solute concentrations **During osmosis, water moves from hypotonic to hypertonic to become isotonic again** 3. [Facilitated Diffusion]: Large polar molecules & ions transit membranes through transmembrane proteins a. A channel protein: Provide an open channel/pore to facilitate the diffusion of molecules b. A carrier protein: Undergo shape changes (aka, conformational changes) to facilitate the diffusion of molecules c. [NOTE]: In both cases, molecules move according to laws of diffusion **[Active Transport:] Movement of molecules across membranes AGAINST or UP their concentration gradient** 2 KEY REQUIREMENTS: 1. Protein transporter pump 2. ATP A good example is a sodium-potassium pump Note that the pump has different conformations (shapes) in each position Conformational changes alter the affinity of the pump for sodium and potassium Conformational changes are driven by energy from ATP **Bulk Transport of Large Molecules/Structures across the Plasma Membrane by Vesicular Transport** [Two directions]: \(1) Out of cell = Exocytosis Exocytosis: Transport of large molecules OUT of cell by vesicular transport \(2) Into cell = Endocytosis **[Cellular Energy and Respiration]** [ATP: The Cell's Energy Currency] Key Idea: Adenosine triphosphate (ATP) is the primary energy-supplying molecule in cells. Structure: ATP contains three components:              Adenine (a nitrogenous base)              Ribose (a five-carbon sugar)              **Three phosphate groups connected in a series**, making ATP high energy **            ATP Hydrolysis:** Removal of a phosphate group from ATP releases energy, converting it to ADP (adenosine diphosphate). This energy powers cellular processes. **[CELL RESPIRATION]** **1.** ** Glycolysis: The First Step in Glucose Breakdown**                   **Location**: Cytoplasm of prokaryotic and eukaryotic cells.             **Overview**: Glycolysis converts one molecule of glucose (6-carbon) into two molecules of pyruvate (3-carbon). **            Process:
First Phase**: Uses energy (ATP) to split glucose into two molecules of pyruvate.**
Second Phase**: Produces ATP and NADH.              **Products**: **2 Pyruvate** molecules, **2 ATP**, **2 NADH**             **Importance**: Glycolysis occurs in the absence of oxygen and is the sole source of ATP for cells like mature red blood cells.   **2.** **Citric Acid Cycle (Krebs Cycle)** **Location**: Mitochondrial matrix in eukaryotic cells. **Process**:          The 2 Pyruvate from glycolysis are converted into **acetyl CoA**, which enters the cycle.          Produces **1 CO₂, 1 ATP (or equivalent), 4 NADH, and 1 FADH₂** from each pyruvate          Functions as a **closed loop** with the regeneration of starting compounds. **Significance**: Extracts energy from acetyl CoA, releasing high-energy electrons. **From 2 pyruvate Generates**: 2 ATP, 8 NADH, 2 FADH **NADH and FADH are coenzymes that can transfer elections**  important during oxidative phosphorylation   **3.** **Oxidative Phosphorylation** **Location**: Inner mitochondrial membrane (eukaryotes) **Process**:          Electrons are transferred through the **electron transport chain (ETC)** complexes, losing energy.          This energy is used to pump H⁺ ions, creating an electrochemical gradient.          **The proton gradient allows** H⁺ ions to flow through ATP synthase, regenerating ATP from ADP. **Oxygen's Role**: Acts as the final electron acceptor, forming water with hydrogen ions to keep the gradient moving **Importance**: Responsible for **90% of ATP production** during aerobic respiration. ** ** **[Fermentation and Anaerobic Cellular Respiration]**   **Fermentation**          **Definition**: A process where NADH donates electrons to an organic molecule, regenerating NAD⁺ for glycolysis in the absence of oxygen. **Types**: 1.   **Lactic Acid Fermentation**: Converts pyruvate into lactic acid (e.g., in muscle cells during oxygen shortage). 2.   **Alcohol Fermentation**: Converts pyruvate into ethanol and CO₂ (e.g., by yeast in brewing).   **Anaerobic Respiration**   **Definition**: Uses an inorganic molecule (other than oxygen) as the final electron acceptor in the ETC.             **Example**: **Sulfate-reducing bacteria** use sulfate to regenerate NAD⁺ and produce hydrogen sulfide (H₂S). [ ]**Key Questions for Review** 1. What are the inputs and outputs of glycolysis, and what happens to the pyruvate produced? 2. How do the citric acid cycle and oxidative phosphorylation contribute to ATP production in aerobic respiration? 3. What differentiates fermentation from aerobic respiration in terms of final electron acceptors and ATP yield? **[Photosynthesis]** **Definition:** A process used by certain organisms (photoautotrophs) to convert solar energy into chemical energy in the form of glucose (food). **Importance:** Directly or indirectly provides energy for almost all living organisms on Earth and releases oxygen into the atmosphere. **Relevance:** Every food product humans consume can be traced back to photosynthesis. **[Overview of Photosynthesis]** **Key Components Needed:** **Reactants:** Sunlight, water (H₂O), and carbon dioxide (CO₂). **Products:** Glucose (C₆H₁₂O₆) and oxygen (O₂). **Summary:** Organisms like plants, algae, and some bacteria use photosynthesis to produce carbohydrates and oxygen. Humans, as heterotrophs, rely on autotrophs for their energy needs. **[Main Structures Involved in Photosynthesis]** **Chloroplasts:** Organelles where photosynthesis occurs, containing chlorophyll and other pigments. **Key Structures:** **Thylakoids:** Membrane-bound compartments within chloroplasts that contain chlorophyll. Stacks of thylakoids form a granum. **Stroma:** The fluid surrounding the thylakoids where the Calvin cycle occurs. **Stomata:** Small openings in the leaves that allow gas exchange (CO₂ and O₂). **[The Two Stages of Photosynthesis]** **1. Light-Dependent Reactions:** **Location:** Thylakoid membrane. **Purpose:** Convert solar energy into chemical energy in the form of ATP and NADPH. **Process:** - Light hits chlorophyll, exciting an electron. - Water molecules are split, producing O₂ as a byproduct. - Electrons travel through the electron transport chain, creating an electrochemical gradient. - ATP and NADPH are produced. **Photosystems I and II:** Complexes in the thylakoid membrane where light energy is absorbed and transferred to electrons. **Photon Absorption:** A photon excites an electron, causing it to be transferred to an electron acceptor. Water splits to replace lost electrons, releasing O₂. **Electron Transport Chain:** Transfers excited electrons, pumping H⁺ ions and creating an electrochemical gradient. **2. Calvin Cycle (Light-Independent Reactions):** **Purpose:** Converts CO₂ into carbohydrate molecules like glucose using the energy stored in ATP and NADPH. **Location:** Occurs in the stroma of chloroplasts. **Significance:** Provides the carbon backbone needed to form carbohydrate molecules, ultimately sustaining nearly all living organisms. **[Stages of the Calvin Cycle]** 1\. **Fixation Stage:** **Enzyme:** RuBisCO catalyzes a reaction between CO₂ and RuBP (ribulose bisphosphate). **Process:** Combines CO₂ with RuBP to form a six-carbon compound, which immediately splits into two three-carbon molecules (3-PGA). **Key Term:** **Carbon Fixation** --- CO₂ is converted from its inorganic form to an organic molecule. 2\. **Reduction Stage:** **Energy Input:** ATP and NADPH from the light-dependent reactions are used to convert 3-PGA into G3P **Key Reaction:** Reduction involves gaining electrons (supplied by NADPH). **Output:** One G3P molecule exits the cycle to form carbohydrates like glucose. 3\. **Regeneration Stage:** **Regeneration:** The remaining G3P molecules are used to regenerate RuBP with the help of ATP. **Cycle Continuation:** The regenerated RuBP allows the Calvin Cycle to continue fixing CO₂. **Key Points to Remember:** It takes **six turns** of the Calvin Cycle to produce one glucose molecule, fixing six CO₂ molecules. **Process:** ATP and NADPH provide energy to convert CO₂ into GP3 molecules, which are used to make glucose after 6 turns of the Calvin Cycle. **[Light Energy and Pigments]** **Chlorophyll a:** The main pigment involved in photosynthesis, absorbs blue and red light, reflects green. **[FOCUS HEAVILY ON THESE SPECIFIC TOPICS ]** 1. **Cell Structure and Function** **Basic Building Blocks:** Cells are the fundamental building blocks of the human body. **Characteristics of Cells:** All cells share certain traits, such as DNA, a plasma membrane, and typically being too small to see without a microscope. **Prokaryotic vs. Eukaryotic Cells:** Understand the structural differences between these types of cells. **Prokaryotic Cells:** Lack a nucleus but have ribosomes. 2. **Structures & Functions:** **Plasma Membrane:** Regulates the passage of substances in and out of cells. **Cytoskeleton:** Provides cell structure, enables movement, and assists with cell division. Actin filaments are key in cell movement. **Nucleus:** Controls cellular activities via the endomembrane system and contains DNA. **Endoplasmic Reticulum (ER):** The rough ER is involved in protein synthesis and modification, while the smooth ER synthesizes lipids. **Golgi Apparatus:** Modifies and packages proteins and lipids for secretion or transport. **Lysosomes:** Responsible for digesting cellular waste and foreign invaders. They also play a role in autophagy. They do not synthesize proteins 3. **Microscope Types:** **Electron Microscope:** Provides higher magnification by using beams of electrons. (Question 3) 4. **Cellular Processes** **Transport Mechanisms:** Movement across cell membranes includes diffusion, osmosis, active transport, and bulk transport (endocytosis and exocytosis). **Types of Membrane Proteins:** Integral proteins, carrier proteins, and channel proteins play roles in transporting substances across membranes. **Membrane Structure:** Described by the "fluid mosaic model." **Cell Junctions:** Tight junctions, gap junctions, and desmosomes facilitate communication and structural integrity in animal cells. 5. **Energy and Metabolism** **Mitochondria and ATP Production:** Mitochondria are the site of ATP production via cellular respiration. **Cellular Respiration:** A multistep process involving glycolysis (in the cytoplasm), the Citric Acid Cycle (in the mitochondrial matrix), and oxidative phosphorylation (involving the electron transport chain). **Glycolysis:** Produces 2 ATP, 2 NADH, and 2 pyruvate. **Citric Acid Cycle:** Occurs in the mitochondrial matrix and produces molecules for the electron transport chain. **Oxidative Phosphorylation:** Uses the movement of hydrogen ions to generate ATP. Oxygen is the final electron acceptor that makes H2O. **Role of NADH in Cellular Respiration:** Donates electrons to the electron transport chain. **ATP Function:** ATP releases energy when a phosphate group is hydrolyzed and removed. **Fermentation:** Allows cells to produce ATP in the absence of oxygen. Lactic acid is a byproduct in muscle cells. 6. **Photosynthesis** **Photosynthesis Overview:** Takes place in chloroplasts and includes light-dependent reactions (in the thylakoids) and the Calvin Cycle (in the stroma). **Light-dependent reactions:** Take place in the thylakoid membrane, where water is split to release O₂ and provide electrons. **Role of Water in Photosynthesis:** Provides electrons for Photosystem II and releases oxygen. **Calvin Cycle (Light-Independent):** Occurs in the chloroplast stroma, where G3P is produced and used to form glucose. Requires six turns of the cycle to make one glucose molecule. **Role of Pigments:** Chlorophyll a is primarily responsible for absorbing light. **Products of Photosynthesis:** Oxygen and glucose are the main products. 7. **Evolutionary Perspectives and Theories** **Endosymbiotic Theory:** Explains the origin of mitochondria and chloroplasts. 8. **Plant Cell Structures:** Unique structures in plant cells include chloroplasts, the central vacuole, and cell walls. **Intercellular Junctions in Plants:** Plasmodesmata in plant cells enable communication.