Parts of the Cell

4.4 Eukaryotic cells are partitioned into functional compartments There are four life processes in eukaryotic cells that depend upon structures and organelles Manufacturing Breakdown of molecules Energy processing Structural support, movement, and communication Teaching Tips 1. Some instructors have found that challenging students to come up with analogies for the many eukaryotic organelles is a highly effective teaching method. Students may wish to construct one inclusive analogy between a society or factory and a cell or construct separate analogies for each organelle. As with any analogy, it is important to list the similarities and exceptions. Copyright © 2009 Pearson Education, Inc.

4.4 Eukaryotic cells are partitioned into functional compartments Manufacturing involves the nucleus, ribosomes, endoplasmic reticulum, and Golgi apparatus The nuclear DNA directs protein synthesis by first transcribing DNA into mRNA. The mRNA reaches the ribosomes, which translate the genetic message into a protein. The entire process of transcription and translation requires enzymes, whose synthesis was also directed by DNA. The endoplasmic reticulum and Golgi apparatus further process the proteins. Teaching Tips 1. Some instructors have found that challenging students to come up with analogies for the many eukaryotic organelles is a highly effective teaching method. Students may wish to construct one inclusive analogy between a society or factory and a cell or construct separate analogies for each organelle. As with any analogy, it is important to list the similarities and exceptions. Copyright © 2009 Pearson Education, Inc.

4.4 Eukaryotic cells are partitioned into functional compartments Breakdown of molecules involves lysosomes, vacuoles, and peroxisomes Breakdown of an internalized bacterium by a phagocytic cell would involve all of these Lysosomes, vacuoles, and peroxisomes involve digestion by hydrolytic enzymes of unwanted materials within the cell, resulting in products that are used by the cell as food. Teaching Tips 1. Some instructors have found that challenging students to come up with analogies for the many eukaryotic organelles is a highly effective teaching method. Students may wish to construct one inclusive analogy between a society or factory and a cell or construct separate analogies for each organelle. As with any analogy, it is important to list the similarities and exceptions. Copyright © 2009 Pearson Education, Inc.

4.4 Eukaryotic cells are partitioned into functional compartments Energy processing involves mitochondria in animal cells and chloroplasts in plant cells Although mitochondria and chloroplasts are enclosed by membranes, they are not part of the endomembrane system. Teaching Tips 1. Some instructors have found that challenging students to come up with analogies for the many eukaryotic organelles is a highly effective teaching method. Students may wish to construct one inclusive analogy between a society or factory and a cell or construct separate analogies for each organelle. As with any analogy, it is important to list the similarities and exceptions. Copyright © 2009 Pearson Education, Inc.

4.4 Eukaryotic cells are partitioned into functional compartments Structural support, movement, and communication involve the cytoskeleton, plasma membrane, and cell wall Teaching Tips 1. Some instructors have found that challenging students to come up with analogies for the many eukaryotic organelles is a highly effective teaching method. Students may wish to construct one inclusive analogy between a society or factory and a cell or construct separate analogies for each organelle. As with any analogy, it is important to list the similarities and exceptions. Copyright © 2009 Pearson Education, Inc.

Pili Nucleoid Ribosomes Plasma membrane Bacterial chromosome Cell wall Capsule Figure 4.3 A structural diagram of a typical prokaryotic cell. Module 4.3 mentions how antibiotics can specifically target prokaryotic but not eukaryotic cells. This might be a good time to discuss the evolution of antibiotic resistance. Teaching tips and ideas for related lessons can be found at http://www.pbs.org/wgbh/evolution/educators/lessons/lesson6/act1.html. Flagella

NUCLEUS: Nuclear envelope Chromosomes Smooth endoplasmic reticulum Nucleolus Rough endoplasmic reticulum Lysosome Centriole Ribosomes Figure 4.4A An animal cell. Peroxisome Golgi apparatus CYTOSKELETON: Microtubule Plasma membrane Intermediate filament Mitochondrion Microfilament

NUCLEUS: Rough endoplasmic reticulum Nuclear envelope Chromosome Ribosomes Nucleolus Smooth endoplasmic reticulum Golgi apparatus CYTOSKELETON: Central vacuole Microtubule Chloroplast Intermediate filament Cell wall Plasmodesmata Microfilament Figure 4.4B A plant cell. Mitochondrion Peroxisome Plasma membrane Cell wall of adjacent cell

Hydrophilic head Phosphate group Symbol Hydrophobic tails Figure 4.5A Phospholipid molecule. Hydrophobic tails

Outside cell Hydrophilic heads Hydrophobic region of protein tails Inside cell Proteins Figure 4.5B Phospholipid bilayer with associated proteins. Hydrophilic region of protein

Nucleus Double-layer membrane with pores. Connected to ER. Ribosomes made in a part called the nucleolus.

Two membranes of nuclear envelope Nucleus Nucleolus Chromatin Pore Figure 4.6 TEM (left) and diagram (right) of the nucleus. Endoplasmic reticulum Ribosomes

4.9 The endoplasmic reticulum is a biosynthetic factory There are two kinds of endoplasmic reticulum—smooth and rough Smooth ER lacks attached ribosomes Rough ER lines the outer surface of membranes They differ in structure and function However, they are connected Student Misconceptions and Concerns 1. Students can have trouble relating many cell organelles to their diverse functions. They may not realize that Modules 4.6–4.13 introduce the primary organelles in the order that they function in the production and release of secretory proteins. Products and information generally move from the central nucleus to the rough ER, through the more peripherally located Golgi apparatus and the secretory vesicles, and finally to the outer plasma membrane. Emphasizing the flow from center to periphery in this process will help students to remember the function of individual organelles as they recall the steps of the sequence. 2. Conceptually, some students seem to benefit from the well-developed cell-factory analogy developed in the text. The use of this analogy in lecture might help to anchor these relationships. As mentioned before, challenge students to find exceptions in the analogy, an exercise that promotes critical thinking. Teaching Tips 1. If you continue the factory analogy, the addition of a molecular tag by the Golgi apparatus is like adding address labels in the shipping department of a factory. Copyright © 2009 Pearson Education, Inc.

Nuclear envelope Ribosomes Smooth ER Rough ER Figure 4.9A Smooth and rough endoplasmic reticulum.

4.9 The endoplasmic reticulum is a biosynthetic factory Smooth ER is involved in a variety of diverse metabolic processes (ex: synthesis of many types of lipids) Smooth ER processes include synthesis of lipids, metabolism of carbohydrates, and detoxification of drugs and poisons. Student Misconceptions and Concerns 1. Students can have trouble relating many cell organelles to their diverse functions. They may not realize that Modules 4.6–4.13 introduce the primary organelles in the order that they function in the production and release of secretory proteins. Products and information generally move from the central nucleus to the rough ER, through the more peripherally located Golgi apparatus and the secretory vesicles, and finally to the outer plasma membrane. Emphasizing the flow from center to periphery in this process will help students to remember the function of individual organelles as they recall the steps of the sequence. 2. Conceptually, some students seem to benefit from the well-developed cell-factory analogy developed in the text. The use of this analogy in lecture might help to anchor these relationships. As mentioned before, challenge students to find exceptions in the analogy, an exercise that promotes critical thinking. Teaching Tips 1. If you continue the factory analogy, the addition of a molecular tag by the Golgi apparatus is like adding address labels in the shipping department of a factory. Copyright © 2009 Pearson Education, Inc.

4.9 The endoplasmic reticulum is a biosynthetic factory Rough ER makes additional membrane for itself and proteins destined for secretion (these proteins are transported in vesicles) Secreted proteins are important to the multicellular individual. For example, hormones, antibodies, and enzymes are glycoproteins that have significant impacts on homeostasis, protection, or metabolism. Student Misconceptions and Concerns 1. Students can have trouble relating many cell organelles to their diverse functions. They may not realize that Modules 4.6–4.13 introduce the primary organelles in the order that they function in the production and release of secretory proteins. Products and information generally move from the central nucleus to the rough ER, through the more peripherally located Golgi apparatus and the secretory vesicles, and finally to the outer plasma membrane. Emphasizing the flow from center to periphery in this process will help students to remember the function of individual organelles as they recall the steps of the sequence. 2. Conceptually, some students seem to benefit from the well-developed cell-factory analogy developed in the text. The use of this analogy in lecture might help to anchor these relationships. As mentioned before, challenge students to find exceptions in the analogy, an exercise that promotes critical thinking. Teaching Tips 1. If you continue the factory analogy, the addition of a molecular tag by the Golgi apparatus is like adding address labels in the shipping department of a factory. Copyright © 2009 Pearson Education, Inc.

4 3 1 2 Transport vesicle buds off Ribosome Secretory protein inside trans- port vesicle 3 Sugar chain 1 Figure 4.9B Synthesis and packaging of a secretory protein by the rough ER. Glycoprotein 2 Polypeptide Rough ER

Golgi Receives proteins in vesicles from the ER. Modifies proteins- adds sugar chains to “mark” them for a certain destination. Puts the proteins back into vesicles and sends them out.

4.11 Lysosomes are digestive compartments within a cell A lysosome is a membranous sac containing digestive enzymes The enzymes and membrane are produced by the ER and transferred to the Golgi apparatus for processing The membrane serves to safely isolate these potent enzymes from the rest of the cell Student Misconceptions and Concerns 1. Students can have trouble relating many cell organelles to their diverse functions. They may not realize that Modules 4.6–4.13 introduce the primary organelles in the order that they function in the production and release of secretory proteins. Products and information generally move from the central nucleus to the rough ER, through the more peripherally located Golgi apparatus and the secretory vesicles, and finally to the outer plasma membrane. Emphasizing the flow from center to periphery in this process will help students to remember the function of individual organelles as they recall the steps of the sequence. 2. Conceptually, some students seem to benefit from the well-developed cell-factory analogy developed in the text. The use of this analogy in lecture might help to anchor these relationships. As mentioned before, challenge students to find exceptions in the analogy, an exercise that promotes critical thinking. Teaching Tips 1. As noted in Module 4.11, lysosomes help to recycle damaged cell components. Challenge your students to explain why this is adaptive. Recycling, whether in human society or in our cells, can be an efficient way to reuse materials. The recycled components, which enter the lysosomes in a highly organized form, would require a much greater investment to produce from “scratch.” Copyright © 2009 Pearson Education, Inc.

4.11 Lysosomes are digestive compartments within a cell One of the several functions of lysosomes is to remove or recycle damaged parts of a cell The damaged organelle is first enclosed in a membrane vesicle Then a lysosome fuses with the vesicle, breaking down the damaged organelle Student Misconceptions and Concerns 1. Students can have trouble relating many cell organelles to their diverse functions. They may not realize that Modules 4.6–4.13 introduce the primary organelles in the order that they function in the production and release of secretory proteins. Products and information generally move from the central nucleus to the rough ER, through the more peripherally located Golgi apparatus and the secretory vesicles, and finally to the outer plasma membrane. Emphasizing the flow from center to periphery in this process will help students to remember the function of individual organelles as they recall the steps of the sequence. 2. Conceptually, some students seem to benefit from the well-developed cell-factory analogy developed in the text. The use of this analogy in lecture might help to anchor these relationships. As mentioned before, challenge students to find exceptions in the analogy, an exercise that promotes critical thinking. Teaching Tips 1. As noted in Module 4.11, lysosomes help to recycle damaged cell components. Challenge your students to explain why this is adaptive. Recycling, whether in human society or in our cells, can be an efficient way to reuse materials. The recycled components, which enter the lysosomes in a highly organized form, would require a much greater investment to produce from “scratch.” Animation: Lysosome Formation Copyright © 2009 Pearson Education, Inc.

Vacuoles Functions: storage, maintaining water balance, holding pigments, etc. Membrane-bound.

Chloroplast Nucleus Central vacuole Figure 4.12A Central vacuole in a plant cell. Ask your students to identify organelles in animal cells that are not involved in the synthesis of proteins (other than mitochondria). (Vacuoles and peroxisomes are not involved in protein synthesis.)

Nucleus Contractile vacuoles Figure 4.12B Contractile vacuoles in Paramecium, a single-celled organism. Contractile vacuoles

Mitochondria Convert sugar (glucose) into ATP (adenosine triphosphate)- small energy packets. This is called cellular respiration. Have two membranes (inner and outer)

Mitochondrion Outer membrane Intermembrane space Inner membrane Figure 4.14 The mitochondrion. Inner membrane Cristae Matrix

Chloroplasts Use the sun’s energy to create glucose from carbon dioxide and water (photosynthesis)

Chloroplast Stroma Inner and outer membranes Granum Intermembrane Figure 4.15 The chloroplast. Granum Intermembrane space

Mitochondrion Engulfing of photosynthetic prokaryote Some cells of aerobic prokaryote Chloroplast Host cell Figure 4.16 Endosymbiotic origin of mitochondria and chloroplasts. Mitochondrion Host cell

The cytoskeleton is composed of three kinds of fibers 4.17 The cell’s internal skeleton helps organize its structure and activities The cytoskeleton is composed of three kinds of fibers Microfilaments (actin filaments) support the cell’s shape and are involved in motility Intermediate filaments reinforce cell shape and anchor organelles Microtubules (made of tubulin) shape the cell and act as tracks for motor protein A specialized arrangement of microtubules in eukaryotes is responsible for the beating of flagella (human sperm) and cilia (cells of the human respiratory tract). Student Misconceptions and Concerns 1. Students often regard the cytosol as little more than a watery fluid that suspends the organelles. The diverse functions of thin, thick, and intermediate filaments are rarely appreciated before college. Module 4.17 describes the dynamic and diverse functions of the cytoskeleton. Teaching Tips 1. Analogies between the infrastructure of human buildings and the cytoskeleton are limited by the dynamic nature of the cytoskeleton. Few human structures have a structural framework that is routinely constructed, deconstructed, and then reconstructed in a new configuration on a regular basis. (Tents are often constructed, deconstructed, and then reconstructed repeatedly, but typically rely upon the same basic design.) Thus, caution is especially warranted when using such analogies Copyright © 2009 Pearson Education, Inc.

Receptor for motor protein Vesicle ATP Receptor for motor protein Motor protein (ATP powered) Microtubule of cytoskeleton (a) Microtubule Vesicles 0.25 µm Campbell, Neil, and Jane Reece, Biology, 8th ed., Figure 6.21 Motor proteins and the cytoskeleton. (a) Motor proteins that attach to receptors on vesicles can “walk” the vesicles along microtubules or, in some cases, microfilaments; Vesicles containing neurotransmitters migrate to the tips of nerve cell axons via the mechanism in (a). (b)