Chapter 3 Cells PDF

Chapter 3 Cells and How They Work Cecie Starr | Beverly McMillan © Cengage Learning 2016  3.1 What Is a Cell? Cell theory – Every organism is composed of one or more cells...

Chapter 3 Cells and How They Work Cecie Starr | Beverly McMillan © Cengage Learning 2016  3.1 What Is a Cell? Cell theory – Every organism is composed of one or more cells – The cell is the smallest unit with properties of life – Cells come from pre-existing cells Cell structure - All living cells have three things in common. 1. An outer plasma membrane - the outer covering that encloses the cell’s internal parts, so that cell activities can go on apart from events that may be taking place outside the cell. Substances can enter or leave the cells by moving across the membrane. 2. Cytoplasm - everything between the plasma membrane and the region of DNA. It consists of a thick, jellylike fluid called the cytosol, and various other components. 3. DNA - Cells contain DNA. Cells also contain molecules that can copy or “read” the genetic instructions DNA carries. © Cengage Learning 2016  Cell Classification There are two basic kinds of cells 1. Prokaryotic - (meaning “before the nucleus”)  Nothing separates DNA from other internal cell parts  Bacteria are prokaryotic cells. 2. Eukaryotic (“true nucleus”)  Cells that have their DNA inside a nucleus are called eukaryotic cells.  Most cells have large surface area compared to their volume. Membrane encloses cells and organelles. The nucleus is one of numerous organelles (“little organs”) in eukaryotic cells. Organelles are compartments or sacs. © Cengage Learning 2016  Most cells have a large surface area compared  A few cellsto their e.g., volume the yolks of chicken eggs are large, but most cells are so small that they can only be seen with a microscope.  The surface-to-volume ratio is responsible for the small size of cells. This ratio is a physical relationship.  As the linear dimensions of a three-dimensional object increase, the volume of the object increases faster than its surface area does (Figure 3.2).  For instance, if a round cell grew like an inflating balloon so that its diameter increased to 4 times the starting girth, the volume inside the cell would be 64 times more than before, but the cell’s surface would be just 16 times larger.  The cell would not have enough surface area to allow nutrients to flow inward rapidly, or for wastes © Cengage Learning 2016  Formula for volume of a cube is V = S3 and formula for surface area of a cube is SA = 6S2 Where, S = length of one side 1” cube 2” cube 4” cube Volume: 1 8 64 Surface area: 6 24 96 The relationship of surface to volume influences the size of cells. Here boxes represent cells. If the linear dimensions of a box double, the volume increases 8 times but the surface area increases only 4 times. As in the text example, if the linear dimensions increase by 4 times, the volume is 64 times greater but the surface area is only 16 times larger. © Cengage Learning 2016  Different shapes and sizes of human cells © Cengage Learning 2016  In cell membranes, phospholipids are arranged in a bilayer Watery cytoplasm flui d head one layer of lipids tail s one layer of s lipids © Cengage Learning 2016 Figure 3.4 p43  3.2 Organelles of a Eukaryotic Cell The interior of a cell is divided into organelles, each with one or more special functions. In every eukaryotic cell, at any given moment, a vast number of chemical reactions are going on. Many of the reactions would conflict if they occurred in the same cell compartment. Chemical reactions take place in organelles. In eukaryotic cells, organelles solve this problem. Outer membrane separates interior of organelle from rest of cytoplasm. Membrane controls types of substances that enter and leave. It also controls the types and amounts of substances that enter or leave the organelle. For example, organelles called lysosomes contain enzymes that break down various unwanted substances. Chemical reactions take place in organelles. Ribosomes and centrioles do not have a membrane. Organelles also may serve as “way stations” for operations that occur in steps. For example, proteins are assembled and modified in steps involving several organelles. © Cengage Learning 2016  nuclear Nucleus envelope Keeps DNA away Cytoskele nucleolus from potentially ton Structurally DNA in damaging supports, nucleoplasm reactions in gives shapemicrotubules cytoplasm Ribosomes to cell; microfilament (attached to rough moves s ER and free in cell and intermediat cytoplasm) Sites its parts e filaments of protein Rough synthesisER Mitochondrion Modifies new Energy polypeptide chains powerhouse; produces ATP by Smooth ER cellular Makes lipids, Centrioles degrades fats, respiration Special centers inactivates toxins that produce and Golgi Body organize Modifies, sorts, microtubules ships proteins and Plasma lipids for export or Membrane for insertion into Controls the kinds cell membranes Lysosome and amounts of Digests, recycles substances materials moving into and out of cell © Cengage Learning 2016 Figure 3.5 p44 © Cengage Learning 2016  3.3 How Do We See Cells? Microscopy - Use of a microscope to view objects, including cells, that are not visible to the unaided eye. It has allowed us to learn a great deal about cells. A photograph of an image formed by a microscope is called a micrograph. Types of microscopes – Compound light Limited to magnification of 2,000 times or less. – Scanning electron: With a scanning electron microscope, a beam of electrons is directed back and forth across a specimen thinly coated with metal. The metal emits some of its own electrons, and then the electron energy is converted into an image of the specimen’s surface on a television screen. – Transmission electron: It uses a magnetic field as the “lens” that bends a stream of electrons and focuses it into an image. © Cengage Learning 2016 © Cengage Learning 2016  3.4 The Plasma Membrane: A Double Layer of Lipids Plasma membrane is composed of lipids and proteins – The plasma membrane encloses a cell, but it isn’t a solid wall between a cell’s cytoplasm and the fluid outside. It has a fluid quality, something like cooking oil. It is also extremely thin. – The structure of plasma membrane is described as a “mosaic” of proteins and different kinds of lipids like, phospholipids & glycolipids. In human cells and other animal cells, the lipid is called cholesterol. Plasma membrane proteins are embedded in the bilayer or attach to its outer or inner surface. – The plasma membrane controls movement of substances in and out. Therefore, it is said to be selectively permeable. Proteins in cell membranes carry out many functions – Many of them are enzymes (speed up chemical reactions in cells). Other membrane proteins are receptors; they are like docks for signaling molecules, such as hormones, that trigger changes in cell activities. © Cengage Learning 2016  Cell’s plasma membrane consists of lipids and proteins. Most of the lipids are phospholipids. This diagram also shows examples of membrane proteins. Biologists refer to the membrane’s mix of lipids and proteins as a ©“mosaic.” Cengage Learning 2016 3.4 The Plasma Membrane: A Double Layer of Lipids A Oxygen, carbon dioxide, B Glucose and other large, small nonpolar molecules, polar, water-soluble and some molecules of molecules, and ions (e.g., water cross a lipid bilayer H+, Na+, K+, Cl–, Ca++) freely. cannot cross on their own. lipid bilayer Cell membranes are selectively permeable. © Cengage Learning 2016 Figure 3.8 p47  3.5 100 Trillion of Your Closest Friends Only about 10% of your cells are human. The other 90 percent, roughly 100 trillion cells that account for several pounds of your body weight, are bacteria that live in the digestive system and on the skin. A few of the resident bacteria cause illness if our defenses don’t keep them in check. The rest are helpful or harmless. No two people have exactly the same array, in part because the mix depends on our diet, age, physical surroundings, health issues, and other factors. Many species of bacteria are represented in our bodies. In a project called the Belly Button Biodiversity Project, researchers in North Carolina are studying the 4,000-plus species of bacteria they have collected from swabs of volunteers’ navels. Learning about bacteria in the body leads to medical insights. – Example: mix of skin bacteria changes with high blood sugar. © Cengage Learning 2016  3.6 The Nucleus Like a master control center, the nucleus contains and protects the cell’s DNA, the genetic material. Nucleus encloses the DNA of a eukaryotic cell. – DNA contains instructions for building cell’s proteins. The proteins in turn determine cell structure and function. In a human cell there are forty-six DNA molecules that together would be more than 6 feet long if they were stretched out end to end. The nucleus has several key functions. It prevents DNA from getting tangled up with structures in the cytoplasm. When a cell divides, its DNA molecules must be copied so that each new cell receives a full set. If the DNA is separate, it is easier to copy and organize these hereditary instructions. Outer membranes of the nucleus are a boundary where the movement of substances to and from the cytoplasm can be controlled. © Cengage Learning 2016  A nuclear envelope encloses the nucleus  Unlike the cell itself, the nucleus has two outer lipid bilayers, one pressed against the other. This double-membrane system is called a nuclear envelope (Figure 3.11).  The envelope surrounds the fluid part of the nucleus (the nucleoplasm), and many proteins are embedded in its layers.  The outer portion of the nuclear envelope merges with the membrane of ER.  Threadlike bits of protein attach to the inner surface of the nuclear envelope. They anchor DNA molecules to the envelope and help keep them organized.  Proteins that span both bilayers have a wide variety of functions. Some are receptors or transporters. Others form pores. The pores are passageways. They allow small ions and molecules dissolved in the watery fluid inside and outside the nucleus to cross the nuclear membrane. © Cengage Learning 2016  Nucleolus  It is the more dense mass that appear inside the nucleus. Each mass is a nucleolus.  It is the construction site where some proteins and RNAs are combined to make the parts of ribosomes.  These subunits eventually will cross through nuclear pores to the cytoplasm.  There, they will briefly join up to form ribosomes.  These organelles are “workbenches” where amino acids are assembled into proteins. © Cengage Learning 2016  The nucleus of an animal cell contains the cell’s DNA. The microscope image on the right shows the nucleus of a liver cell. © Cengage Learning 2016  The nuclear envelope is a double membrane with pores. A This view of a cell’s nuclear envelope shows pores that form channels through it. B This micrograph image reveals that each pore is a cluster of membrane proteins. They selectively allow certain substances to move into and out of the nucleus. The sketch of the nuclear envelope in C shows the envelope’s structure. © Cengage Learning 2016  DNA and Chromosomes DNA is organized in chromosomes  Chromatin – It is made up of cell’s DNA and proteins associated with it.  Chromosome – Double-stranded DNA molecule that carries genetic information.  When cell is preparing to divide it makes a copy of its DNA. © Cengage Learning 2016  a grainy, threadlike a chromosome a chromosome molecule of DNA that that has been (two has been duplicated, strands, with duplicated then proteins) (two DNA twisted and © Cengage Learning 2016 molecules folded  3.7 The Endomembrane System The endomembrane system consists of membrane bound organelles with different structures and functions. It modifies protein, build lipids and package completed molecules.  Endoplasmic reticulum - The ER is a flattened channel that starts at the nuclear envelope and snakes through the cytoplasm.  Lipid assembly and processing of polypeptide chains into proteins occurs here.  May be rough or smooth.  Rough ER is studded with ribosomes.  Smooth ER has no ribosomes and curves through the cytoplasm like flat connecting pipes.  A ribosome is a platform for building a cell’s proteins.  In liver cells, smooth ER inactivates certain drugs and harmful byproducts of metabolism. In skeletal muscle cells, a type of smooth ER called sarcoplasmic reticulum stores and releases calcium ions essential for muscles to contract. © Cengage Learning 2016  Golgi Bodies. Functions  Enzymes inside finish the synthesis of proteins and lipids.  Package completed molecules in vesicles for shipment to specific locations. A vesicle is a tiny sac that moves through the cytoplasm or takes up positions in it. Vesicles have a range of roles in cells from transport of substances to digestion of substances. – Lysosome: Enzymes digest unwanted substances – Peroxisome: Enzymes digest fatty acids and amino acids The pancake at the top of a Golgi body is the organelle’s “shipping- gate” for molecules to be exported. Vesicles form there as patches of the membrane bulge out and then break away into the cell’s cytoplasm. © Cengage Learning 2016  3.8 Mitochondria: The Cell’s Energy Factories ATP is the fuel for most cell activities. ATP forms during reactions that break down organic compounds to carbon dioxide and water. These reactions occur in a mitochondrion (plural: mitochondria). Only eukaryotic cells contain mitochondria. A mitochondrion has a double-membrane system.  The outer membrane faces the cell’s cytoplasm.  The inner one generally folds back on itself, accordion-fashion ‫األكورديون‬. ATP forms in the mitochondria – Formation requires oxygen – Occurs in an inner compartment Mitochondria have their own DNA known as mtDNA © Cengage Learning 2016  outer membrane outer compartm inner ent compartment inner membrane Mitochondria form ATP. Sketch and transmission electron micrograph of a mitochondrion. Reactions inside mitochondria produce ATP, the major energy carrier in cells. Figure 3.14 p52 © Cengage Learning 2016  3.9 The Cell’s Skeleton - Cytoskeleton Cytoskeleton – A system of interconnected fibers, threads, and lattices in the cytosol. Different proteins form these parts, which collectively give cells their shape, organization, and ability to move. Components of the cytoskeleton  Microtubules - the largest cytoskeleton elements. They spatially organize the interior of the cell, and also help move cell parts.  Microfilaments – these often reinforce some parts of a cell, such as the plasma membrane.  Intermediate filaments - add strength much as steel rods strengthen concrete pillars. Intermediate filaments also anchor the filaments of two proteins, called actin and myosin, which interact in muscle cells and enable the muscle to contract. © Cengage Learning 2016  Cell Movement Structures Some types of cells move about by flagella (singular: flagellum) or cilia (singular: cilium) In both structures, nine pairs of microtubules ring a central pair. A system of spokes and links hold “9+2 array’ together. Flagella – Whip-like. Arranged in spokes-like manner and provide structure. – Propel sperm Cilia - Cilia are shorter than flagella, and there may be more of them per cell. In the respiratory tract, thousands of mucus laden ciliated cells capture dust or other undesirable material. The microtubules of cilia and flagella arise from centrioles. © Cengage Learning 2016  microtubules microfilaments intermediate filaments Microtubules and filaments make up the cytoskeleton. a The cytoskeleton of a pancreas cell. b The flagellum of a sperm cell. c Cilia in an airway in the lungs. © Cengage Learning 2016  Sketch and micrograph of a flagellum. Like a cilium, it contains a ring of nine pairs of microtubules plus one pair at its core. © Cengage Learning 2016  3.10 How Diffusion and Osmosis Move Substances Concentration refers to the number of molecules of a substance in a certain volume of fluid. Gradient means that the number of molecules in one region is not the same as in another. Hence, a concentration gradient is a difference in the number of molecules or ions of a given substance in two neighboring regions. Mechanisms for moving substances across cell membrane Diffusion – It is the net movement of like molecules or ions down a concentration gradient - from a high concentration to a low concentration. In living organisms, the diffusion of a substance across a cell membrane is called passive transport. Passive transport does not require energy. Molecules diffuse faster when gradient is steep. © Cengage Learning 2016  Diffusion and Osmosis (cont’d.) Osmosis - Diffusion of water across a semipermeable membrane in response to solute concentration gradients. Tonicity is the concentration of solutes in a solution.  Isotonic (iso- means “same”) - solute concentrations in the fluids on either side of a cell membrane are the same and there is no net flow of water in either direction across the membrane.  Hypotonic fluid has fewer solutes.  Hypertonic fluid has more solutes. © Cengage Learning 2016  dye A dye dye B Substances diffuse down a concentration gradient. A. A drop of dye enters a bowl of water. Gradually the dye molecules disperse evenly through the molecules of water. B. The same thing happens with the water molecules. If red dye and yellow dye are added to the same bowl, each substance will move (diffuse) down its own concentration gradient. Stepped Art © Cengage Learning 2016 Figure 3.17 p54  hypotonic hypertonic solution (few solution (more solute solute molecules) molecules) in in first second compartment compartment membra B The fluid volume rises in A Initially, the netwo the second compartment as compartments have equal water follows its concentration volumes of fluid, but the gradient and diffuses solute concentration across into it. the membrane differs. © Cengage Learning 2016 © Cengage Learning 2016  3.11 Other Ways Substances Cross Cell Membranes There are several ways by which substances can move into and out of a cell. Transporter proteins – Help solutes cross membranes – Specific to a solute eg. Protein for amino acid transport will not transport glucose. – Provide a channel Passive transport process – Also called facilitated diffusion. No use of energy. Active transport – Cell uses energy to move solutes against concentration gradients using ‘membrane pumps’. © Cengage Learning 2016  B. Passive Transport A solute moves across bilayer through interior of passive transporter; movement is driven by concentration gradient. A B C Fluid outside cell Cytoplasm energy A. C. Active Transport D. Solute pumped out Diffusion - Active transporter uses against its concentration A energy (often, ATP) to gradient. substance pump a solute through simply bilayer against its diffuses concentration across gradient. © lipid Cengage Learning 2016  Vesicles Transporter proteins can only move small molecules and ions into or out of cells. To bring in or expel larger molecules or particles, cells use vesicles that form through endocytosis and exocytosis. In endocytosis, a cell takes in substances. In exocytosis, a cell sends out substances. Phagocytosis - When endocytosis brings organic matter into the cell, the process is called phagocytosis, or “cell eating.” © Cengage Learning 2016  A Endocytosis A vesicle brings substances in bulk into the cell. B Exocytosis A vesicle ejects substances in bulk from the cell. © Cengage Learning 2016  END OF THE CHAPTER © Cengage Learning 2016  3.12 Focus on Human Impact: A Watery Disaster for Cells  Waterborne diseases can pose serious problems in places where public sanitation is poor or previously safe water supplies become contaminated.  One such disease, cholera, is caused by a bacterium, Vibrio cholerae. It produces a toxin that affects transport proteins in the plasma membranes of cells in the small intestine.  Their toxin causes cells to pump out various ions, and other dissolved substances follow. As these substances leave, cells lose their water by osmosis.  Main symptom is massive watery diarrhea.  Can drain entire body’s water in one day.  Treatment involves rehydration with water and electrolytes, followed by antibiotics. © Cengage Learning 2016  3.13 Metabolism: Doing Cellular Work Chemical reactions in cells are called metabolism. – Fueled by ATP (adenosine triphosphate). – Some release energy and some require it A molecule of ATP consists of the five-carbon sugar ribose to which adenine (a nucleotide base) and three phosphate groups are attached. ATP’s stored energy is contained in the bond between the second and third phosphate groups. Cells must constantly renew ATP supply through ATP/ADP cycle Two main metabolic pathways i. Anabolism puts together small molecules. Anabolic pathways assemble complex carbohydrates, proteins, and other large molecules. The energy stored in their bonds is a major reason why we can use these substances as food. ii. Catabolism breaks down large molecules. Catabolic reactions disassemble complex carbohydrates, proteins, and similar molecules, releasing their components for use by cells. © Cengage Learning 2016  ATP provides energy for cell activities. A Structure of ATP. B ATP connects energy-releasing reactions with energy-requiring ones. In the ATP/ADP cycle, the transfer of a phosphate group turns ATP into ADP, then back again to ATP. © Cengage Learning 2016 Figure 3-23 p58  Metabolic Reactions Reactant - Any substance that takes part in a metabolic reaction Intermediate - Substance formed between beginning and end of metabolic pathway Product - Substance present at the end of a reaction or pathway. Many metabolic pathways advance step by step from reactants to products: enzyme 1 enzyme 2 enzyme 3 Reactant intermediate intermediate product © Cengage Learning 2016  Enzymes Essential part of metabolic reactions Most enzymes are proteins – All are catalysts Enzyme and its substrate interact at the enzyme’s active site The body controls the activities of enzymes © Cengage Learning 2016  two substrate molecules substrate s contactin e g active activ site site of enzyme substrate s briefly Enzymes and substrates fit together bind physically. tightly to When substrate molecules contact an enzyme enzyme’s active site active site, they bind to the site for a product brief time and a product molecule molecule forms. enzyme When the product molecule is unchange released, the enzyme goes back to its d by the previous shape. reaction The reaction it catalyzed does not change the enzyme © Cengage Learning 2016 in any way. Figure 3.24 p59  3.14 How Cells Make ATP Cellular respiration makes ATP –  To make ATP, cells break apart carbohydrates, especially glucose, as well as lipids and proteins.  The reactions remove electrons from intermediate compounds, then energy from the electrons powers the formation of ATP.  Human cells typically form ATP by cellular respiration which can be summarized into the following 3 steps. Step 1: glycolysis (splitting Sugar) breaks down glucose into pyruvate (a glucose molecule is broken into two molecules of pyruvate). Step 2: the Krebs cycle produces energy-rich transport molecules (The pyruvate molecules formed by glycolysis move into a mitochondrion. Step 3: electron transport produces many ATP molecules © Cengage Learning 2016  GLUCOSE ADP Energy ADP in (2 ATP) PGAL: INTERMEDIATES DONATE PHOSPHATE TO ADP, MAKING 4 To second set of Figure Glycolysis splits Pyruvate reactions glucose molecules and forms NET ENERGY YIELD: 2 a small amount of ATP. PGAL (for phosphoglyceraldehyde) © Cengage Learning 2016 © Cengage Learning 2016  3.15 Summary of Cellular Respiration Visual summary - See Figure 3.27 on next slide. The aerobic pathway delivers enough energy to build and maintain a large, active, multicellular organism such as a human. In many types of cells, the third stage of reactions forms thirty- two ATP. When we add these to the final yield from the preceding stages, the total harvest is thirty-six ATP from one glucose molecule. This is a very efficient use of our cellular resources! Actual amount may vary depending on cell conditions for instance, if a cell requires a particular intermediate elsewhere and pulls it out of the reaction sequence. © Cengage Learning 2016  glucos Cytoplas e A mThe first stage, glycolysis, occurs in the cell’s cytoplasm. Enzymes 4 ATP 2 Glycolysi convert a glucose molecule to 2 (2 net) pyruvate for a net yield of 2 ATP. ATP s During the reactions, 2 NAD+ pick up 2 2 electrons and hydrogen atoms, so 2 NADH form. NADH pyruvate Mitochondri B onThe second stage, the Krebs cycle and a few steps before it, Krebs 6 CO2 occurs inside mitochondria. The 2 Cycle 2 pyruvates are broken down to CO2, ATP which leaves the cell. During the reactions, 8 NAD+ and 2 FAD pick up electrons and hydrogen atoms, 8 NADH, 2 so 8 NADH and 2 FADH 2 form. 2 FADH2 C The third and final stage, the ATP also form. electron transport chain, occurs inside mitochondria. 10 NADH and 2 oxyge Electron FADH2 donate electrons and 32 n Transport hydrogen ions at electron transfer ATP chains. Electron flow through the Chain chains sets up H+ gradients that drive ATP formation. Oxygen Figure 3.27 p62 accepts electrons at the end of the chains. © Cengage Learning 2016  3.16 Other Energy Sources Glucose from carbohydrates is the body’s main energy source, but fats and proteins also can supply this sugar. Other kinds of cells tend to store excess glucose as fat, mostly in the form of triglycerides. These lipids build up in the cells of body fat (called adipose tissue), which occurs in the buttocks and other locations beneath the skin. The body doesn’t store excess proteins but dismantles them into amino acids. A cell may use leftover carbons to make fats or carbohydrates. Therefore, carbohydrates, fats, and proteins supply raw materials for making ATP. Excess glucose is stored as glycogen. Another source is lactate fermentation - Sudden, strenuous exercise may call on cells in skeletal muscles (which attach to bones) that use an ATP- forming mechanism called lactate fermentation. The process converts pyruvate from glycolysis to lactic acid. It does not use oxygen and produces ATP quickly but not for long. Muscles feel sore when lactic acid builds up in them. © Cengage Learning 2016  3.17 Focus on Our Environment: A Way with Arsenic The element arsenic occurs naturally in some soil and rock. It is a powerful poison. When arsenic atoms enter cells, they disrupt the Krebs cycle and electron transport chain - ATP production stops, and cell dies. This effect has made arsenic a useful ingredient (in carefully regulated amounts) in some anticancer drugs, wood preservatives, and insecticides. On the other hand, murderers have used killer doses of arsenic to dispatch their victims for thousands of years. More often, people are exposed to low doses of arsenic in tainted food, water, or industrial emissions. To help poor families in Bangladesh Dr. Abul Hussam built a low- cost device to filter arsenic from water. © Cengage Learning 2016 © Cengage Learning 2016