AP Biology Notes Outline Enduring Understanding 2.B

L. Carnes

Big Idea 2: Biological systems utilize free energy and molecular building blocks

to grow, to reproduce and to maintain dynamic homeostasis.

Enduring Understanding 2.B: Growth, reproduction and dynamic homeostasis require that cells create and

Maintain internal environments that are different from their external environments.

Learning Objectives: Essential Knowledge 2.B.1: Cell membranes are selectively permeable due to their structure.

– (2.10) The student is able to use representations and models to pose scientific questions about the properties of cell membranes and selective permeability based on molecular structure.

– (2.11) The student is able to construct models that connect the movement of molecules across membranes with membrane structure and function.

Essential Knowledge 2.B.2: Growth and dynamic homeostasis are maintained by the constant movement of molecules across membranes. – (2.12) The student is able to use representations and models to analyze situations or solve problems qualitatively and quantitatively to investigate whether

dynamic homeostasis is maintained by the active movement of molecules across membranes.

Essential Knowledge 2.B.3: Eukaryotic cells maintain internal membranes that partition the cell into specialized regions. – (2.13) The student is able to explain how internal membranes and organelles contribute to cell functions. – (2.14) The student is able to use representations and models to describe differences in prokaryotic and eukaryotic cells.

Required Readings: Textbook Ch. 6 (pp. 98-111; 122) Textbook Ch. 7

Practicing Biology Homework Questions: Questions #22-27

Essential Knowledge 2.B.1: Cell membranes are selectively permeable due to their structure.

Cell membranes separate the internal environment of the cell from the external environment. The specialized structure of the membrane described in the fluid mosaic model allows the cell to be selectively permeable, with dynamic homeostasis maintained by the constant movement of molecules across the membrane. Selective permeability is a direct consequence of membrane structure, as describe by the fluid mosaic model. Cell membranes consist of a structural framework of phospholipid molecules, embedded proteins, cholesterol, glycoproteins and glycolipids. Proteins determine most of the membrane’s specific functions. The fluid mosaic model describes the membrane as a fluid structure with various proteins embedded in or attached to a double layer of phospholipids. Membranes are NOT sheets of molecules locked rigidly in place – most lipids and some proteins can drift about laterally (in the plane of the membrane).

– Integral proteins have nonpolar regions that completely span the hydrophobic interior of the membrane. Peripheral proteins are loosely bound to the surface of the membrane.

– Cholesterol molecules are embedded in the interior of the bilayer to stabilize the membrane. Phospholipids move along the plane of the membrane rapidly – while some proteins are kept in place by the cytoskeleton. Other proteins drift slowly.

– The external surface of the plasma membrane also has carbohydrates attached to it, forming the glycocalyx – which is very important for cell-to-cell recognition.

Phospholipids are the most abundant lipid in the plasma membrane. Phospholipids give the membrane both hydrophilic and hydrophobic properties.

• Hydrophilic heads are oriented toward the aqueous external or internal environments.

• Hydrophobic fatty acid tails face each other within the interior of the membrane itself.

Embedded proteins can be hydrophilic, with charged and polar side groups, or hydrophobic, with nonpolar side groups.

Some functions of membrane proteins:

Transport – protein spans membrane to provide a channel selective for a particular solute. Enzyme Activity – protein built into membrane may be an enzyme w/ its active site exposed to substances in the adjacent solution. Signal Transduction – membrane protein may have a binding site w/ a specific shape that fits the shape of a chemical messenger…such as a hormone. The external messenger may cause a conformational change in the protein that relays the message to the inside of the cell. Intercellular Joining – Membrane proteins of adjacent cells may be hooked together in various kinds of junctions. Cell-cell recognition- some glycoproteins (proteins w/ short chain of sugars) serve as identification tags that are specifically recognized by other cells. Attachment – elements of cytoskeleton may be bonded to membrane proteins, a function that helps maintain cell shape and fixes the location of some membrane proteins.

A cell must exchange materials with its surroundings, a process controlled by the plasma membrane. Plasma membranes are selectively permeable, regulating the cell’s molecular traffic:

• Small, uncharged polar molecules and small nonpolar molecules, such as N2, freely pass across the membrane.

• Hydrophilic substances such as large polar molecules and ions move across the membrane through embedded channel and transport proteins.

• Water moves across membranes and through channel proteins called aquaporins.

Transport proteins allow passage of hydrophilic substances. across the membrane. Some transport proteins, called channel proteins, have a hydrophilic channel that certain molecules or ions can use as a tunnel. Channel proteins called aquaporins facilitate the passage of water. Other transport proteins, called carrier proteins, bind to molecules and change shape to shuttle them across the membrane. A transport protein is specific for the substance it moves – i.e. FORM FITS FUNCTION!!!

Why are cell membranes selectively permeable? The answer is the phospholipid bilayer. – Lipid bilayers are generally impermeable to ions and polar molecules. – The arrangement of hydrophilic heads and hydrophobic tails of the lipid bilayer prevent polar solutes (ex. amino acids,

nucleic acids, carbohydrates, proteins, and ions) from diffusing across the membrane, but generally allows for the passive diffusion of hydrophobic molecules.

– Nonpolar molecules cross the lipid bilayer easily and without any aid because they are hydrophobic and can dissolve through the membrane.

– The hydrophobic region inside of the lipid bilayer prevents polar molecules from dissolving through it without the aid of proteins.

– This affords the cell the ability to control the movement of these substances via transmembrane protein complexes such as pores, channels and gates.

The cell wall is the tough, usually flexible but sometimes fairly rigid layer that surrounds some types of cells. Cell walls provide a structural boundary, as well as a permeability barrier for some substances to the internal environments. It is located outside the cell membrane and provides these cells with structural support and protection, in addition to acting as a filtering mechanism. A major function of the cell wall is to act as a pressure vessel, preventing over-expansion when water enters the cell. Cell walls are found in plants, bacteria, fungi, algae, and some archaea. Animals and protozoa do not have cell walls. The material in the cell wall varies between species, and can also differ depending on cell type and developmental stage. Plant cell walls are made of cellulose and are external to the cell membrane. The cell wall protects the plant cell, maintains its shape, and prevents excessive uptake of water.

Fungal cell walls are made of chitin. The fungal cell wall is a dynamic structure that protects the cell from changes in osmotic pressure and other environmental stresses, while allowing the fungal cell to interact with its environment. The structure and biosynthesis of a fungal cell wall is unique to the fungi, and is therefore an excellent target for the development of anti-fungal drugs.

Prokaryotic cell walls may contain peptidoglycan (gram +) or may not (gram -). Penicillins and cephalosporins interfere with the linking of the interpeptides of peptidoglycan. Gram-positive bacteria, with no membrane outside the peptidoclycan cell wall, are more susceptible to these antibiotics.

Essential Knowledge 2.B.2: Growth and dynamic homeostasis are maintained by the constant movement of molecules across membranes.

Passive transport does not require the input of metabolic energy because spontaneous movement of molecules occurs from high to low concentrations; examples of passive transport are osmosis, diffusion, and facilitated diffusion. Active transport requires metabolic energy and transport proteins to move molecules from low to high concentrations across a membrane. Active transport establishes concentration gradients vital for dynamic homeostasis, including sodium/potassium pumps in nerve impulse conduction and proton gradients in electron transport chains in photosynthesis and cellular respiration. The processes of endocytosis and exocytosis move large molecules from the external environment to the internal environment and vice versa, respectively.

http://www.wiley.com/college/boyer/0470003790/animations/membrane_transport/membrane_transport.htm Passive Transport: Passive Transport is the diffusion of a substance across a semi-permeable membrane from an area of high concentration to an area of low concentration WITHOUT the use of energy. Passive transport plays a primary role in the import of resources and the export of wastes. Diffusion is the tendency for molecules to spread out evenly into the available space. Although each molecule moves randomly, diffusion of a population of molecules may exhibit a net movement in one direction. At dynamic equilibrium, as many molecules cross one way as cross in the other direction. Substances diffuse down their concentration gradient, the difference in concentration of a substance from one area to another. No work must be done to move substances down the concentration gradient. The diffusion of a substance across a biological membrane is passive transport because it requires no energy from the cell to make it happen. There are two (2) types of diffusion: (1) Dialysis: the PASSIVE movement of particles across a semi-permeable membrane from an area of high concentration to an area of low concentration (no energy); and (2) Osmosis: the PASSIVE movement of water molecules across a semi-permeable membrane from an area of high solute concentration to an area of low solute concentration (no energy). Tonicity is the ability of a solution to cause a cell to gain or lose water:

• Isotonic solution: Solute concentration is the same as that inside the cell; no net water movement across the plasma membrane

• Hypertonic solution: Solute concentration is greater than that inside the cell; cell loses water • Hypotonic solution: Solute concentration is less than that inside the cell; cell gains water

a) ANIMAL CELL – fares best in an isotonic environment because it

does not have a cell wall…unless it has special adaptations to offset the osmotic uptake or loss of water.

b) PLANT CELL – turgid and generally fair best in a hypotonic environment…tendency for water uptake is balanced by the elastic cell wall pushing back on the cell.

ARROW INDICATES WATER MOVEMENT WHEN CELL IS FIRST PLACED IN THE SOLUTION!!!

Hypertonic or hypotonic environments create osmotic problems for organisms. Osmoregulation, the control of water balance, is a necessary adaptation for life in such environments. The protist Paramecium, which is hypertonic to its pond water environment, has a contractile vacuole that acts as a pump.

Cell walls help maintain water balance.

A plant cell in a hypotonic solution swells until the wall opposes uptake; the cell is now turgid (firm).

If a plant cell and its surroundings are isotonic, there is no net movement of water into the cell; the cell becomes flaccid (limp), and the plant may wilt.

In a hypertonic environment, plant cells lose water; eventually, the membrane pulls away from the wall, a usually lethal effect called plasmolysis.

http://highered.mcgraw-hill.com/sites/9834092339/student_view0/chapter38/animation_-_osmosis.html

In facilitated diffusion, transport proteins speed the passive movement of molecules across the plasma membrane. Channel proteins provide corridors that allow a specific molecule or ion to cross the membrane. Facilitated diffusion is still passive transport because the solute moves down its concentration gradient. Types of channel proteins include:

• Aquaporins, for facilitated diffusion of water • Ion channels that open or close in response to a stimulus (gated

channels) a) Transport protein forms a channel through which water molecules or a

specific solute can pass. b) Transport protein alternates between two conformations, moving a solute

across the membrane as the shape of the protein changes…can transport in either direction…but net movement MUST BE DOWN CONCENTRATION GRADIENT!

Active Transport: Active Transport uses free energy to move molecules AGAINST their concentration gradients via proteins imbedded in the cell membrane. Active transport is a process where free energy (often provided by ATP) is used by proteins embedded in the membrane to “move” molecules and/or ions across the membrane and to establish and maintain concentration gradients. Active transport allows cells to maintain concentration gradients that differ from their surroundings.

http://highered.mcgraw-hill.com/olc/dl/120068/bio03.swf The sodium-potassium pump is one type of active transport system. This transport system pumps ions against steep concentration gradients. The pump oscillates between two conformational states in a pumping cycle that translocates three Na

+ ions out of the cell for

every two K+ ions pumped into the cell.

ATP powers the changes in conformation by phosphorylating the transport proteins. BOTH Na

+ and K

+ are moving AGAINST

concentration gradients!

How Ion Pumps Maintain Membrane Potential: Membrane potential is the voltage difference across a membrane. Voltage is created by differences in the distribution of positive and negative ions. Two combined forces, collectively called the electrochemical gradient, drive the diffusion of ions across a membrane:

• A chemical force (the ion’s concentration gradient) • An electrical force (the effect of the membrane potential on the ion’s movement)

An electrogenic pump is a transport protein that generates voltage across a membrane. The sodium-potassium pump is the major electrogenic pump of animal cells. The main electrogenic pump of plants, fungi, and bacteria is a proton pump. http://highered.mcgraw-hill.com/olc/dl/120068/bio05.swf

Cotransport is coupled transport by a membrane protein. Cotransport occurs when active transport of a solute indirectly drives transport of another solute. Plants commonly use the gradient of hydrogen ions generated by proton pumps to drive active transport of nutrients into the cell.

http://highered.mcgraw-hill.com/olcweb/cgi/pluginpop.cgi?it=swf::535::535::/sites/dl/free/0072437316/120068/bio04.swf::Cotransport Bulk Transport Across Membranes: Bulk transport across the plasma membrane occurs by exocytosis and endocytosis. Small molecules and water enter or leave the cell through the lipid bilayer or by transport proteins. Large molecules, such as polysaccharides and proteins, cross the membrane in bulk via vesicles. Bulk transport requires energy. http://highered.mcgraw-hill.com/olc/dl/120068/bio02.swf a) Phagocytosis – pseudopodia engulf a particle and package it in a vacuole. b) Pinocytosis – Droplets of extracellular fluid are incorporated into the cell in small

vesicles. c) Receptor-Mediated Endocytosis – coated pits form vesicles when specific

molecules (ligands) bind to receptors on the cell surface. In exocytosis, transport vesicles migrate to the membrane, fuse with it, and release their contents.

In endocytosis, the cell takes in macromolecules by forming vesicles from the plasma membrane. Endocytosis is a reversal of exocytosis, involving different proteins. There are three types of endocytosis:

• In phagocytosis (cellular eating) a cell engulfs a particle in a vacuole, the vacuole fuses with a lysosome to digest the particle.

• In pinocytosis (cellular drinking), molecules are taken up when extracellular fluid is “gulped” into tiny vesicles.

• In receptor-mediated endocytosis, binding of ligands to receptors triggers vesicle formation. A ligand is any molecule that binds specifically to a receptor site of another molecule.

Essential Knowledge 2.B.3: Eukaryotic cells maintain internal membranes that partition the cell into specialized regions.

Eukaryotic cells maintain internal membranes that partition the cell into specialized regions so that cell processes can operate with optimal efficiency by increasing beneficial interactions, decreasing conflicting interactions and increasing surface area for chemical reactions to occur. Each compartment or membrane-bound organelle localizes reactions, including energy transformation in mitochondria and production of proteins in rough endoplasmic reticulum. All organisms are made of cells. The cell is the simplest collection of matter that can live. Cell structure is correlated to cellular function. All cells are related by their descent from earlier cells. The basic structural and functional unit of every organism is one of two types of cells: prokaryotic or eukaryotic. Eukaryotic cells have internal membranes that compartmentalize their functions. Protists, fungi, animals, and plants all consist of eukaryotic cells. Only organisms of the domains Bacteria and Archaea consist of prokaryotic cells. Basic features of all cells:

• Plasma membrane • Semifluid substance called cytosol • Chromosomes (carry genes) • Ribosomes (make proteins)

Eukaryotic cells are characterized by having

• DNA in a nucleus that is bounded by a membranous nuclear envelope • Membrane-bound organelles • Cytoplasm in the region between the plasma membrane and nucleus • Eukaryotic cells are generally much larger than prokaryotic cells

A eukaryotic cell has internal membranes that partition the cell into organelles. Plant and animal cells have most of the same organelles-

• Not in Animal Cells: chloroplasts | central vacuole | tonoplast | cell wall | plasmodesmata • Not in Plant Cells: lysosomes | centrioles | flagella

Organelles: A Demonstration of Emergent Properties: All biological systems are composed of parts that interact with each other. These interactions result in characteristics not found in the individual parts alone. In other words, “THE WHOLE IS GREATER THAN THE SUM OF ITS PARTS.” This phenomenon is referred to as emergent properties. All biological systems from the molecular level to the ecosystem level exhibit properties of biocomplexity and diversity. Together, these two properties provide robustness to biological systems, enabling greater resiliency and flexibility to tolerate and respond to changes in the environment. At the cellular level, organelles interact with each other and their environment as part of a coordinated system that allows cells to live, grow and reproduce. The myriad of interactions of different parts at the subcellular level determine the functioning of the entire cell, which would not happen with the activities of individual organelles alone. Internal membranes facilitate cellular processes by minimizing competing interactions and by increasing surface area where reactions can occur. Membranes and membrane-bound organelles in eukaryotic cells localize (compartmentalize) intracellular metabolic processes and specific enzymatic reactions. Archaea and Bacteria generally LACK internal membranes and organelles and have a cell wall.

The Nucleus (Figure 6.10) Structure: The Eukaryotic cell’s genetic instructions are housed in the nucleus and carried out by the ribosomes. The nucleus contains most of the DNA in a eukaryotic cell. Ribosomes use the information from the DNA to make proteins Function: The nucleus contains most of the cell’s genes and is usually the most conspicuous organelle. The nuclear envelope encloses the nucleus, separating it from the cytoplasm. The nuclear membrane is a double membrane; each membrane consists of a lipid bilayer. Pores regulate the entry and exit of molecules from the nucleus. The shape of the nucleus is maintained by the nuclear lamina, which is composed of protein. Within the nucleus is chromatin – consisting of DNA & proteins. When the cell prepares to divide, individual chromosomes become visible as chromatin condenses. The Nucleolus functions in ribosome synthesis – it is the site of rRNA synthesis. The Endomembrane System The endomembrane system regulates protein traffic and performs metabolic functions in the cell. Internal membranes facilitate cellular processes by minimizing competing interactions and by increasing surface area where reactions can occur. Components of the endomembrane system (these are either continuous or connected via transfer by vesicles):

• Nuclear envelope • Endoplasmic reticulum • Golgi apparatus • Lysosomes • Vacuoles • Plasma membrane

Arrows show some of the pathways of the membrane migration. Nuclear envelope is connected to rough ER…which is confluent with smooth ER. Membrane produced by the ER flows in the form of transport vesicles to the Golgi, which in turn pinches off vesicles that give rise to lysosomes & vacuoles. Lysosomes A lysosome is a membranous sac of hydrolytic enzymes that can digest macromolecules. Lysosomal enzymes can hydrolyze proteins, fats, polysaccharides, and nucleic acids. Some types of cell can engulf another cell by phagocytosis; this forms a food vacuole. A lysosome fuses with the food vacuole and digests the molecules. Lysosomes also use enzymes to recycle the cell’s own organelles and macromolecules, a process called autophagy. Programmed destruction of cells (apoptosis) by their own lysosomal enzymes is important in the development of many multicellular organisms (such as tadpoles into frogs). This even occurs in the hands of human embryos (which are webbed until lysosomes digest the tissue between the fingers). The Golgi Complex (Figure 6.13) The Golgi apparatus consists of flattened membranous sacs called cisternae which are not physically connected. The functions of the Golgi apparatus include:

Modifies products of the ER

Manufactures certain macromolecules

Sorts and packages materials into transport vesicles

Consists of stacks of flattened sacs (cisternae) which are not physically connected.

A Golgi stack receives & dispatches transport vesicles and products they contain.

Ribosomes (Figure 6.11) Ribosomes are particles made of two interacting parts: ribosomal RNA and protein. These cellular components interact to become the site of protein synthesis where the translation of genetic instructions yields specific polypeptides. In eukaryotic cells, ribosomes are found both in the CYTOSOL and attached to the ROUGH ER. Ribosomes carry out protein synthesis in two locations:

1. In the cytosol (free ribosomes)…Proteins produced on free ribosomes are delivered to the cytosol. EXAMPLE: A protein produced on a free ribosome may be delivered to the cytosol where it ultimately becomes a structural protein in the cell (cytoskeleton or motor protein). Or, it may become an enzyme that mediates various cellular processes. Or, it may be released into the nucleus where it becomes a transcription factor.

2. On the outside of the endoplasmic reticulum or the nuclear envelope (bound ribosomes)…Proteins produced on the

attached ribosomes are delivered to the ER. EXAMPLE: a particular protein produced on an attached ribosome may be excreted from the cell as an intercellular messenger/hormone/signaling molecule. Or, it may be integrated into the cell membrane as a surface receptor or transmembrane protein to function in transport.

Smooth & Rough ER (Figure 6.12) The endoplasmic reticulum (ER) accounts for more than half of the total membrane in many eukaryotic cells. The ER membrane is continuous with the nuclear envelope. There are two distinct regions of ER:

1. Smooth ER, which lacks ribosomes (functions to synthesize lipids, metabolize carbohydrates, detoxify poisons, and store calcium).

2. Rough ER, with ribosomes studding its surface (functions to compartmentalize the cell, serves as mechanical support, provides site-specific protein synthesis with membrane-bound ribosomes. Has bound ribosomes, which secrete glycoproteins (proteins covalently bonded to carbohydrates). Distributes transport vesicles, proteins surrounded by membranes. Is a membrane factory for the cell. • Biological Example: Many specialized cells secrete proteins produced by ribosomes attached to rough ER: Cells in

pancreas secrete the protein insulin (a hormone) into the bloodstream. Secretory proteins depart from the ER

wrapped in vesicles that bud like bubbles from the ER.

Pathway of Protein-Based Secretion: After leaving the ER wrapped in the membranes of vesicles, many transport proteins travel to the Golgi apparatus. Here, products of the ER are modified and stored and then sent to other destinations. Not surprisingly, the Golgi apparatus is especially extensive in cells specialized for secretion. As they are being synthesized, secretory proteins enter the endoplasmic reticulum. From the ER, vesicles transport these proteins to the cis-medial-trans Golgi. Secretory vesicles then bud from the Golgi trans face and move along cytoskeletal filaments to eventually fuse with the plasma membrane. Products of the ER are usually modified during their transition from the cis pole to the trans pole of the Golgi. Before the Golgi stack dispatches the final products by budding vesicles from the trans face, it sorts these products and targets them for various parts of the cell.

Mitochondria & Chloroplasts Mitochondria and chloroplasts change energy from one form to another. Mitochondria are the sites of cellular respiration, a metabolic process that generates ATP. Chloroplasts, found in plants and algae, are the sites of photosynthesis. Mitochondria and chloroplasts are not part of the endomembrane system; have a double membrane; have proteins made by free ribosomes; and contain their own DNA. Mitochondria are in nearly all eukaryotic cells. They have a smooth outer membrane and an inner membrane folded into cristae. The inner membrane creates two compartments: intermembrane space and mitochondrial matrix. Some metabolic steps of cellular respiration are catalyzed in the mitochondrial matrix. Cristae present a large surface area for enzymes that synthesize ATP. The chloroplast is a member of a family of organelles called plastids. Chloroplasts contain the green pigment chlorophyll, as well as enzymes and other molecules that function in photosynthesis. Chloroplasts are found in leaves and other green organs of plants and in algae. Chloroplast structure includes: thylakoids, membranous sacs, stacked to form a granum, and stroma, the internal fluid. A Living Unit is GREATER than the SUM of its PARTS Cells rely on the integration of structures and organelles in order to function. For example, a macrophage’s ability to destroy bacteria involves the whole cell, coordinating components such as the cytoskeleton, lysosomes, and plasma membrane The large cell is a macrophage – it helps defend against infection by ingesting bacteria (the smaller cells) into phagocytic vesicles.

• The macrogphage crawls along the surface and grabs bacteria using pseudopodia. Actin filaments interact with other elements of the cytoskeleton in these movements.

• After engulfing the bacteria, they are destroyed by lososomes. The elaborate endomembrane system produces the lysosomes.

• The digestive enzymes of the lysosomes and proteins of the cytoskeleton are all made on ribosomes. • The synthesis of these proteins is programmed by genetic messages dispatched from the DNA. • All of these processes require energy – which mitochondria supply in the form of ATP.

CELLULAR FUNCTIONS ARISE FROM CELLULAR ORDER – the cell is a living unit greater than the sum of its parts!!!