Unit 2 Honors Biology Lecture Notes PDF

Honors Biology Lecture note pack for Unit 2: Cell Structure and Function Lesson 2.1, Cell Structure and Function Cell theory was the first unifying theory of biology. No matter if we are discussing a prokaryote or a eukaryote, the cell theory applies to all life...

Honors Biology Lecture note pack for Unit 2: Cell Structure and Function Lesson 2.1, Cell Structure and Function Cell theory was the first unifying theory of biology. No matter if we are discussing a prokaryote or a eukaryote, the cell theory applies to all life forms. - Can you recall the 3 parts of the cell theory? Why are most cells small? - Surface area-to-volume ratio - The volume of a cell determines its metabolic activity relative to time. - The surface area of a cell determines the number of substances that can enter or leave the cell. Prokaryotes - What is a prokaryote? What do they have in common with eukaryotes? What is unique about them? Prokaryotic cells vs. Eukaryotic cells - Bacteria and archaea are prokaryotic cells. - All other forms of life are composed of eukaryotic cells. - Similarities between prokaryotic and eukaryotic cells → Plasma membrane → Ribosomes → One or more chromosomes - Differences… → Prokaryotes ▪ A nucleoid region ▪ Non-membrane bound organelles ▪ A single circular strand of DNA ▪ Use plasmids to transfer genetic information between individuals (more on this later) ▪ Small (1 μ m – 10 μ m) → Eukaryotes ▪ Membrane-bound organelles ▪ A nucleus ▪ Multiple strands of linear DNA ▪ Larger in size (10 μm – 100 μ m) - Bacteria cell walls contain peptidoglycans: a polymer consisting of sugars (“-glycan”) and amino acids (“peptido”). - Some bacteria have a slime layer of polysaccharides, called the capsule. Eukaryotes - A eukaryote is an organism consisting of a cell or cells in which the genetic material is DNA in the form of chromosomes contained within a distinct nucleus. - Eukaryotes include all living organisms other than the prokaryotes (eubacteria and archaebacteria). - Do you recall the theory for how eukaryotes evolved? Endosymbiont Theory - Theory explains how eukaryotic cells likely evolved from prokaryotic cells Page 1 of 9  o Endo = within o Symbiont = symbiosis (close, beneficial relationship between 2+ organisms - Evidence: 1. Both mitochondria and chloroplasts have double membranes 2. Both mitochondria and chloroplasts have their own ribosomes and DNA in the form of circular chromosomes 3. Both mitochondria and chloroplasts can reproduce on their own, independently of cell division - Eukaryotes are often compared to cities – Eukaryopolis, if you will. - There’s a reason for this as all internal parts can be separated based on their function: → “Control center”: nucleus and ribosomes → “Day to day function”: Endomembrane system → “Energy production”: mitochondria and chloroplasts → “Framework and support”: cell membrane and cytoskeleton “Control Center” Nucleus - True or false: the largest organelle. __________________________ - Location of most of the cell’s DNA - Where DNA replication and transcription occurs - It contains the nucleolus, where ribosomes are assembled from RNA and proteins - True or false: the nucleus has a single membrane. ____________________ - How do things enter and exit the nucleus? _______________________ Ribosomes - What is the function of ribosomes? ______________________________________________________ - True or false: ribosomes are membrane bound. ____________________ Where is rRNA produced?! ___________________________ - Cells that must synthesize large amounts of protein have a large number of ribosomes. EX. A human pancreas cell producing digestive enzymes contains millions of ribosomes - Why do cells with high rates of protein synthesis have a prominent nucleolus? _____________________________________________ - Some ribosomes are free ribosomes while others are bound. - Free and bound are structurally identical, and can alternate between both locations. Free ribosomes are suspended in the cytoplasm and typically involved in making proteins that function within the cytoplasm. (EX. Enzymes that start the process of glycolysis). Bound ribosomes are attached to the RER and associated with proteins packed in certain organelles or exported from the cell (membrane and secreted proteins). “Day to Day Function” – The Endo Membrane System - “Endo-” as within - Thus, this system involves the membranes within the eukaryotic cell. - Some of these membranes are physically connected (ex. nuclear membrane and ER membrane) while some are related by the transfer of membrane segments by tiny vesicles (sacs made of membrane). - These membranous organelles work together in the synthesis, storage, and export of molecules. - The endomembrane system includes the nuclear envelope (but not the nucleus), endoplasmic reticulum (ER), Golgi apparatus, lysosomes, vacuoles, and the plasma membrane. Endoplasmic Reticulum (ER) - There are two kinds of ER - smooth and rough. - Why are they named so? - Can you recall their functions? Page 2 of 9  - Note: endoplasmic means “within the cytoplasm” and reticulum means “tiny net”. - Smooth ER (SER) is involved in a variety of diverse metabolic processes. Contains enzymes important in the synthesis of lipids, oils, phospholipids, and steroids. Other enzymes help process drugs, alcohol, and other potentially harmful substances. ▪ EX. Liver has a large amount of smooth ER Storage of calcium ions. ▪ EX. In muscle cells, a specialized SER membrane pumps calcium ions into the ER to stimulate muscle contraction. - Rough ER (RER) → Makes additional membrane for itself → Folds and modifies proteins destined for secretion out of the cell or membrane-bound Golgi Apparatus - “Molecular warehouse and finishing factory” for products manufactured by the ER - Products travel in transport vesicles from the ER to the Golgi. - One side of the Golgi functions as a receiving dock (cis face) for the product and the other as a shipping dock (trans face). - Products are modified as they go from one side of the Golgi to the other. “The journey of a protein” - Step 1: the polypeptide is threaded into the lumen of the RER. The polypeptide undergoes post-translational modification which includes folding and chemical modification (more on this later), converting into a protein. - Step 2: Proteins are packaged into transport vesicles and transported the Golgi Apparatus to be further modified. → Note: the transport vesicle buds off from the RER membrane and then fuses with the Golgi’s membrane. Thus, all membranes are interchangeable and connected! - Step 3: the transport vesicle merges with the Golgi apparatus membrane where the protein is further modified and packaged. - Step 4: Proteins are packaged into a secretory vesicle. The secretory vesicle buds off from the Golgi and then fuses with the cell membrane. - Step 5: the protein content is secreted from the cell. Lysosomes - Do you remember the function of lysosomes? - Where do they originate from? ______________________________ - A membranous sac containing digestive enzymes. - Lysosomes help digest food particles engulfed by a cell. A food vacuole binds with a lysosome, forming a phagosome. The enzymes in the lysosome digest the food. The nutrients are then released into the cell. - Lysosomes also help remove or recycle damaged parts of a cell. Damaged organelle is enclosed in a membrane vesicle. Lysosome fuses with the vesicle, dismantles its contents, and breaks down the damaged organelle. Vacuoles - Vesicles of various sizes that have a variety of functions. Storage of waste products and toxic compounds; some may deter herbivores. Structure for plant cells (large central vacuole) - water creates turgor pressure which keeps the plant upright. Reproduction – flower & fruit vacuoles contain pigments which attract pollinators and aid seed dispersal. Catabolism - digestive enzymes in seeds’ vacuoles hydrolyze stored food for early growth. Contractile vacuoles in freshwater protists remove excess water entering the cell due to solute imbalance. ▪ https://www.youtube.com/watch?v=9Ynm5ZOW59Q Page 3 of 9 “Energy Production” Mitochondria - Remember, molecules are first broken down in the cytosol by lysosomes. - The monomers are then transported to the mitochondria to be converted into ATP. - What kind of cell might you expect a lot of mitochondria? - Can you remember all the parts of a mitochondrion? - What is the purpose of the cristae (inner membrane folds)? Plastids - Plant and algae cells contain plastids that can differentiate into a variety of organelles. Ex. Chromoplasts make and store red, yellow, and orange pigments for things like flowers and fruits. - Of all the plastids, chloroplasts, of course, we are most familiar with. - Can you remember all the parts? “Framework and Support” Cytoskeleton - Supports and maintains cell shape - Holds organelles in position - Moves organelles - Involved in cytoplasmic streaming - Interacts with extracellular structures to anchor cell in place - We know its function, but what is it made of? → - Do you recall the 3 types of fibers and which is smallest/largest? → → → Microfilaments - Usually in bundles - Made from the protein actin (monomer) - Functions: Help entire cell or parts of cell to move ▪ Ex. muscle cells = contraction Determine and stabilize cell shape Create cleavage furrow during cell division Intermediate filaments - >50 different kinds in six molecular classes (based on AA sequence) - Tough, ropelike protein assemblages - More permanent than other filaments and do not show dynamic instability - Two major structural functions: → Anchor cell structures in place → Resist tension, maintain rigidity Microtubules - Thickest (largest diameter) of the 3 filament types - Long, hollow, unbranched cylinders formed from dimers of the protein tubulin - Functions: Form rigid internal skeleton in some cells Act as framework for ▪ Spindle formation during cell division ▪ Extracellular projections such as cilia and flagella Page 4 of 9  ▪ Motor proteins to move in cell – “highway systems” of the cell; Kinesin protein walking on microtubule: https://safeyoutube.net/w/ZOQr - Like microfilaments, they also show dynamic instability → Polymerization leads to stability; depolymerization leads to instability and collapse Movement - Cilia: short, present by the hundreds, move with stiff power strokes - Flagella: longer, occur singly or in pairs, movement is snakelike Extracellular Structure Support - Many things are found outside of the cell which play essential roles in protecting, supporting, or attaching cells to each other. - In eukaryotes, the extracellular matrix (ECM) is found outside of the plasma membrane and is made up of two components: A fibrous macromolecule called collagen A gel-like medium made up of proteoglycans - Role of the ECM in animal cells: → Hold cells together in tissues, contributing to physical properties of cartilage, skin, and other tissues ▪ Proteins, like integrin (pictured right), connect the extracellular matrix to the plasma membrane. → Filter materials passing between different tissues (ex. Kidney) → Orient cell movement during embryonic growth and tissue repair ▪ For cell movement, the protein changes shape and detaches from the collagen. - Is the cell wall of a plant considered an extracellular structure? - The plant cell wall has three major roles: 1. Provides support for the cell and limits volume by remaining rigid. 2. Acts as a barrier to infection. 3. Contributes to form during growth and development. Cell Junctions - Cell junctions are specialized structures that protrude from adjacent cells and “glue” them together. - Three major types of animal cell junctions: → Tight junctions → Desmosomes (anchoring) → Gap junctions - Tight junctions: prevent leakage of extracellular fluid across a layer of cells → Commonly found in cells that form linings (ex. intestines) - Desmosomes (anchoring junctions): anchor cells together but allow materials to move in the matrix. → Commonly found in tissues that are prone to constant mechanical stress (ex. skin, heart tissue) - Gap junctions: are direct connections between the cytoplasm of two cells. → Allow various molecules, ions, and electrical impulses to directly pass through the cells. → Commonly found in nerves and cardiac and smooth muscles - Plant cells have only one type of cell junction, called plasmodesmata. → Plasmodesmata channels allow movement of water, ions, small molecules, hormones, and some RNA and proteins. Page 5 of 9 Lesson 2.2, Cell membrane permeability and transport What is the fluid mosaic model? - Membranes are composed of a bilayer of phospholipids with embedded and attached proteins and other molecules, in a structure termed the fluid mosaic model. Mosaic = a surface of small pieces; referring to the various parts (e.g. proteins) embedded in the membrane “Fluid” because most molecules can are free to move around Factors that affect cell membrane fluidity - Membranes differ in phospholipid composition which alters membrane fluidity. → Length of fatty acid chains ▪ Short tails = phospholipids stack poorly, increases fluidity ▪ Long tails = decreases fluidity → Degree of saturation (of fatty acid chains) ▪ More sat. fatty acids = less fluidity ▪ Less saturated fatty acids (more double bonding) = more fluidity → Presence of cholesterol ▪ Cholesterol acts as a bi-directional regulator of membrane fluidity High temperatures = stabilizes membrane & raises melting point Low temperatures = prevents clustering, increasing fluidity Structures found in the cell membrane - Cell membranes also contain different types of proteins: Peripheral membrane proteins are partially embedded in the bilayer. Anchored membrane proteins have lipid components that anchor them in the bilayer. Transmembrane (Integral) proteins extend through the bilayer on both sides, and may have different functions in its external and transmembrane domains. - Carbohydrates located on the outside of the cell membrane serve as recognition sites. Glycolipid: carbohydrate bonded covalently to a lipid Glycoprotein: one or more carbohydrate chains covalently bonded to a protein ▪ Carbs are usually oligosaccharides (2-10 monosaccharides) Proteoglycan: one or more carbohydrate chains covalently bonded to a protein ▪ Carbs are often polysaccharides (>10 monosaccharides) - Cell membranes are selectively permeable. What does this mean? - Two processes of transport: Passive transport does not require metabolic energy. Active transport requires input of metabolic energy. PASSIVE TRANSPORT - Two ways molecules move passively: Simple diffusion Facilitated diffusion - Simple diffusion Random movement of particles towards equilibrium. Speed of diffusion depends on four factors 1. Diameter of the molecules: smaller molecules diffuse faster 2. Temperature of the solution: higher temperatures lead to faster diffusion Page 6 of 9  3. The concentration gradient in the system: the greater the concentration gradient in a system, the faster a substance will diffuse 4. Molecular charge: non-polar molecules tend to diffuse better than polar. - Osmosis is a special form of simple diffusion in which water moves across a semi-permeable membrane. - Tonicity of the solutions will determine rate of diffusion. - There are 3 types of tonicities: A hypertonic solution has a higher solute concentration compared to that of another solution. A hypotonic solution has a lower solute concentration compared to that of another solution. Isotonic solutions have equal solute concentrations. - Important terms for animal cells: Crenation or Crenated: cells in a hypertonic solution undergo shrinkage and acquire a notched or scalloped surface. Lysis or Lysed: the disintegration of a cell by rupture of the cell wall or membrane. - Important terms for plant cells: Plasmolysis or Plasmolysed: contraction of a plant cell as a result of loss of water from the cell. ▪ The rigid cell wall prevents the cell from immediate collapse. Turgid: swollen and distended. ▪ Pressure on cell wall prevents cell from bursting. ▪ Pressure built up is termed turgor pressure ▪ Turgor pressure is the internal pressure against the cell wall as a result of water entering the cells (osmosis). Water Potential - Water potential is the potential energy of water to move from one solution to another. → Highest water potential is zero (pure water). → High water potential = more water than solutes = hypotonic → Low water potential = less water than solutes = hypertonic - The more negative the number becomes, the less water potential (less energy) that solution has. - Pressure potential: often zero or the value you will solve for can be a positive or negative value, more on this shortly. - Solute potential: always negative Adding solutes decreases the solute potential (and water potential). As you add solutes to solution, there is less water molecules available to move away from that solution and your potential to add more solutes also decreases. Page 7 of 9  - This time, let’s see how pressure potential can change. Passive Transport: Facilitated diffusion - Facilitated diffusion requires a facilitator – a protein embedded into the cell membrane which allows diffusion of molecules to occur. Facilitated diffusion is more specific It can increase the rate of diffusion (especially for polar or charged molecules). - Because facilitated diffusion requires help from proteins, is it possible that the rate of diffusion can be limited? Yes: facilitated diffusion can become saturated. This occurs when all carrier molecules are occupied. - Two general types of integral membrane proteins are involved in facilitated diffusion Channel proteins quickly shuttle specific molecules across the membrane. Carrier proteins are opened by the binding of specific substances, allowing one or more molecules to cross the membrane. - Ion channels are specific channel proteins which open or close in response to an ion stimulus. The ion stimulus is often referred to as a ligand. ▪ “Ligand-gated ion channels” open when an ion binds, causing the channel to change shape (opening or closing the channel). A “voltage-gated channel” opens or closes in response to a change in the voltage across the membrane (as a result of ion concentration differences). - A glucose transporter is a type of carrier protein in mammalian cells. Glucose molecules (the ligand in this case) bind to the carrier protein and cause the protein to change shape, releasing glucose on the other side of the membrane. ▪ (2 min) http://www.pol2e.com/at05.02.html Page 8 of 9  - Aquaporins are specific protein channels that allow large amounts of water to move along its concentration gradient. ACTIVE TRANSPORT - Requires the input of energy to move substances against their concentration gradients. Substances moves in the direction of the cell’s needs, usually by means of a specific carrier protein and usually against its concentration gradient (hence why energy is required). - Active transport example: Sodium-Potassium Pump: An integral membrane protein that uses ATP to pump Na+ out of a cell and K+ in. ▪ Found in all animal cells - Movement of large molecules How do macromolecules which are too large or too charged pass through biological membranes? ▪ Vesicles via endocytosis or exocytosis. - Three types of endocytosis bring molecules into the cell: 1. Phagocytosis 2. Pinocytosis 3. Receptor–mediated endocytosis In all three, the membrane invaginates, or folds around the molecules and forms a vesicle. The vesicle then separates from the membrane. - In phagocytosis (“cellular eating”), part of the membrane engulfs a large particle or cell. A food vacuole (phagosome) forms and usually fuses with a lysosome, where contents are digested. - In pinocytosis (“cellular drinking”), vesicles also form. However, vesicles are smaller and bring in fluids and dissolved substances, as in the endothelium near blood vessels. - Receptor–mediated endocytosis Used to capture specific macromolecules (ex. viruses; cholesterol) Receptors on the cell bind to specific molecules (ligands), causing the pit to invaginate, forming a vesicle. The receptors are integral membrane proteins located in regions called coated pits. The contents of the vesicle are then either released or digested and then used by the cell. - Exocytosis Moves materials out of the cell. Vesicle membrane fuses with plasma membrane and contents are released into the extracellular environment. Exocytosis is important in the secretion of substances made in the cell. Review questions - By what movement would a small, nonpolar molecule enter a cell? - By what movement would a large, nonpolar molecule enter a cell? - By what movement would a small polar molecule enter a cell? - By what movement would a large polar molecule enter a cell? Page 9 of 9