critical thinking questions cell organelles

Critical Thinking in Science

• Part 1: Introduction to Experimental Design
• Part 2: The Story of Pi
• Part 3: Experimenting with pH
• Part 4: Water Quality
• Part 5: Change Over Time

Part 6: Cells

• Part 7: Microbiology and Infectious Disease
• About the Author

Introduction:

This lesson introduces students to organelles, cells, and characteristics of the kingdoms. Students will begin their investigation at the organelle level and work up to the kingdom level. After students have created a study guide to cells, they will plan and complete an experiment to increase their knowledge and experience.

Learning Outcomes:

• Students will define the structure and function of each cell organelle.
• Students will identify organelles in cell samples.
• Students will use cell samples to identify major characteristics of the kingdoms.
• Students will organize observations to create a study guide.
• Students will increase their inquiry skills.
• Students will use experimental data to make conclusions.
• Students will present their finding to the class.

Curriculum Alignment:


1.01 Identify and create questions and hypotheses that can be answered through scientific investigations.

1.02 Develop appropriate experimental procedures for:

• Given questions.
• Student generated questions.

1.04 Analyze variables in scientific investigations:

• Identify dependent and independent.
• Use of a control.
• Manipulate.
• Describe relationships between.
• Define operationally.

1.05 Analyze evidence to:

• Explain observations.
• Make inferences and predictions.
• Develop the relationship between evidence and explanation.

1.06 Use mathematics to gather, organize, and present quantitative data resulting from scientific investigations:

• Measurement.
• Analysis of data.
• Prediction models.

1.08 Use oral and written language to:

• Communicate findings.
• Defend conclusions of scientific investigations.
• Describe strengths and weaknesses of claims, arguments, and/or data

6.02 Analyze structures, functions, and processes within animal cells for:

• Capture and release of energy.
• Feedback information.
• Dispose of wastes.
• Reproduction.
• Specialized needs.

6.04 Conclude that animal cells carry on complex chemical processes to balance the needs of the organism.

• Cells grow and divide to produce more cells.
• Cells take in nutrients to make the energy for the work cells do.
• Cells take in materials that a cell or an organism needs.

Classroom Time Required:

Approximately 280 minutes, divided as describes below. Students can also complete some of the research on their own to decrease the required time.

Materials Needed:

• Microscopes (1 microscope for every two students is best)
• Various slides from the Animal, Plant, Fungi, Bacteria, and Protista Kingdoms.
• Electron Microscope images of cell organelles
• Copies of Organelle chart, Organelle Function Checklist, Cell chart, and Kingdom Chart

Research materials:

• internet, books, encyclopedias, articles, text book, etc.
• Grids for cell counting- print small grids on overheads and cut into small sections for the students
• Green Algae- from outdoor water sample or aquarium store
• Petri dishes for algae growth- determine how many each group needs
• Substances to adjust pH for students
• pH paper to determine pH and monitor
• slides and cover-slips for wet mounts
• Graph paper, large paper for posters (if necessary)

Technology Resources:

Computer, Projector, student computers with internet access if possible

Pre-Activities/ Activities:

Pre-activity:.

Students should be introduced to proper microscope use and techniques. They should also understand the importance of scientific drawings and their accuracy.

• What are cells? (Time: 20 minutes)
• Assess prior knowledge: Ask the students to describe cells, give examples of cells, and draw a picture of a cell.
• Students should then pair up with their neighbors and compare their answers to the above questions.
• As a class, share student ideas on cells.
• Cells have Organelles (Time: 50 minutes)
• The students will begin by looking at the cell organelles.
• Find Electron Microscope images of the following organelles: Nucleus, Mitochondria, Chloroplast, Golgi Body/Apparatus, Cell Wall, Cell Membrane, Lysosome, Endoplasmic Reticulum, Ribosome, Vacuole, Vesicle, Cytoplasm
• Print these images for each student. Make sure they are small enough to fit in the square on the paper.
• Give each student 6 copies of the Organelle Chart Worksheet (See Worksheet 1). (Or 3 pages front to back) Each student should also receive a small, printed electron microscope image for each organelle.
• Discuss what an electron microscope is and why it is important to use this tool when studying the structure of an organelle.
• Students should complete each organelle chart by:
• Writing the name of the organelle at the top of the paper
• Describe the function of the organelle in the provided space
• Paste the organelle image in the electron microscope image square
• Create a drawing of the organelle- this should look like the “cartoon” images students often see
• In order for students to accurately complete the organelle pages you can either:
• Create a Power point of the cell organelle functions, electron microscope images, and “cartoon” drawing to use with the class.
• Provide the students access to computers to research these things on their own.
• Provide the students with appropriate research materials (books, articles, etc.) to find the answers.
• The students will complete the charts after viewing cell samples and determining the characteristics of the Kingdoms.
• Organelle Function Overview (Time: 20 minutes)
• Students will complete the Organelle job checklist to more clearly define the role of these organelles in the cell (See Worksheet 2).
• Organelles in Cells (Time: 2-50 minutes class periods)
• The students will use the microscope to view various cell samples and identify the visible organelles.
• Each sample will be drawn under low power (for cell to cell structure) and high power (cell detail/organelles) (See Worksheet 3).
• Students should color their drawings and label the important details.
• Students will identify the organelles that were visible.
• You will need to help the students identify the organelles that were present but NOT visible with the microscope.
• Students should be provided with 2 samples from each of the following kingdoms: Animal, Plant, Fungi, and Bacteria. Tell students which samples belong to which kingdom.
• Using Cells Samples to define Kingdom Characteristics (Time: 30 minutes)
• Students will use their cell worksheets to characterize the Animal, Plant, Fungi, and Bacteria kingdoms.
• Students will complete the Kingdom Chart for these four kingdoms (See Worksheet 4).
• Option 2: Why are Archaebacteria in a separate kingdom? (Time: 20 minutes)
• Ask students to research the defining characteristics of this kingdom and determine why it is its own kingdom.
• Option 3: What is the Protista kingdom? (Time: 40 minutes)
• Give students several examples of members of the Protista kingdom:
• Animal-like: Paramecium, amoeba
• Fungi-like: mildew, molds
• Plant-like: Euglena, diatoms, Green Algae, Red Algae, Brown Algae
• Ask students to define the major characteristics of this kingdom using these examples.
• Students should determine that this kingdom is the “left over” kingdom. Its members are similar to the other kingdoms, but don’t fit all of the characteristics.
• (Time: 2 days to plan and gather materials, 30 minutes/day for 5 days to complete experiment, 1 day to organize results)
• Students will design and complete their own experiment to determine the effect of pH on algae growth. First, you must review the Algae Growth Experiment Directions (See Worksheet 5) with the students. Explain how cell counts are completed and even demonstrate it for the class (See Worksheet 6).
• When students are designing their experiment it is good to give them several good ideas of household chemicals that could be used to make various pH solutions for the experiment. Some groups may use acids and bases and some may focus on a small range in either the acids or bases.
• Students will use the experimental design graphic organizer (See Worksheet 7) to plan their experiment.
• Ask students to show you their experimental plan, procedure, and materials list before they begin.
• You may need to adjust time for this depending on the class.
• (Time: 1 to 2 class periods)
• After students have completed their experiments, organized their data, and graphed their results, students will create a poster display to explain their experiment and results. These can be displayed and presented to the class if desired. A rubric is provided, but should be adjusted according to your requirements.

Assessment:

See evaluation section.

Modifications:

• EDGO can be edited for any motor skill deficiencies by making it larger, or making it available to be typed on.
• All basic modifications can be used for these activities.
• The experiment can be adjusted as necessary.

Critical Vocabulary:

• Prokaryotic
• Multi-cellular
• Unicellular
• Cell Organelles (nucleus, endoplasmic reticulum, ribosome, vacuole, vesicle, lysosome, golgi body, mitochondria, chloroplast, cell wall, and cell membrane)
• Kingdoms (Animal, Plant, Fungi, Protista, Bacteria, and Archaebacteria)

This lesson is part of the Critical Thinking in Science Unit. This lesson should be used while teaching Goal 6 of the North Carolina Standards of Learning (cells). Students are observing a variety of samples using the microscope so it is important to have several slide examples for each kingdom. This lesson focuses on the student’s ability to research and gather observations to create their own study guide of information on organelles, cells, and kingdoms. The ability to use scientific observations and research is important for students. It helps them to organize and apply knowledge. Students also have a chance to experiment with the needs of living things. The students will gain considerable knowledge by planning, performing, analyzing, and presenting their experiment.

Supplemental Files: 

Address: Campus Box 7006. Raleigh, NC 27695 Telephone: 919.515.5118 Fax: 919.515.5831 E-Mail: [email protected]

50 Critical Thinking Questions

21. Why is it advantageous for the cell membrane to be fluid in nature?

22. Why do phospholipids tend to spontaneously orient themselves into something resembling a membrane?

23. How can a cell use an extracellular peripheral protein as the receptor to transmit a signal into the cell?

24. Discuss why the following affect the rate of diffusion: molecular size, temperature, solution density, and the distance that must be traveled.

25. Why does water move through a membrane?

26. Both of the regular intravenous solutions administered in medicine, normal saline and lactated Ringer’s solution, are isotonic. Why is this important?

27. Describe two ways that decreasing temperature would affect the rate of diffusion of molecules across a cell’s plasma membrane.

28. A cell develops a mutation in its potassium channels that prevents the ions from leaving the cell. If the cell’s aquaporins are still active, what will happen to the cell? Be sure to describe the tonicity and osmolarity of the cell.

29. Where does the cell get energy for active transport processes?

30. How does the sodium-potassium pump contribute to the net negative charge of the interior of the cell?

31. Glucose from digested food enters intestinal epithelial cells by active transport. Why would intestinal cells use active transport when most body cells use facilitated diffusion?

32. The sodium/calcium exchanger (NCX) transports sodium into and calcium out of cardiac muscle cells. Describe why this transporter is classified as secondary active transport.

33. Why is it important that there are different types of proteins in plasma membranes for the transport of materials into and out of a cell?

34. Why are both chloroplasts and mitochondria found in plant cells? What are the purposes of both?

Biology Part I Copyright © 2022 by LOUIS: The Louisiana Library Network is licensed under a Creative Commons Attribution 4.0 International License , except where otherwise noted.

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Critical Thinking Questions

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• What materials can easily diffuse through the lipid bilayer, and why?
• Why is receptor-mediated endocytosis said to be more selective than phagocytosis or pinocytosis?
• What do osmosis, diffusion, filtration, and the movement of ions away from like charge all have in common? In what way do they differ?
• Explain why the structure of the ER, mitochondria, and Golgi apparatus assist their respective functions.
• Compare and contrast lysosomes with peroxisomes: name at least two similarities and one difference.
• Explain in your own words why DNA replication is said to be “semiconservative”?
• Why is it important that DNA replication take place before cell division? What would happen if cell division of a body cell took place without DNA replication, or when DNA replication was incomplete?
• Briefly explain the similarities between transcription and DNA replication.
• Contrast transcription and translation. Name at least three differences between the two processes.
• What would happen if anaphase proceeded even though the sister chromatids were not properly attached to their respective microtubules and lined up at the metaphase plate?
• What are cyclins and cyclin-dependent kinases, and how do they interact?
• Explain how a transcription factor ultimately determines whether or not a protein will be present in a given cell?
• Discuss two reasons why the therapeutic use of embryonic stem cells can present a problem.

3.2 The Cytoplasm and Cellular Organelles

Learning objectives.

By the end of this section, you will be able to:

• Describe the structure and function of the cellular organelles associated with the endomembrane system, including the endoplasmic reticulum, Golgi apparatus, and lysosomes
• Describe the structure and function of mitochondria and peroxisomes
• Explain the three components of the cytoskeleton, including their composition and functions

Now that you have learned that the cell membrane surrounds all cells, you can dive inside of a prototypical human cell to learn about its internal components and their functions. All living cells in multicellular organisms contain an internal cytoplasmic compartment, and a nucleus within the cytoplasm. Cytosol , the jelly-like substance within the cell, provides the fluid medium necessary for biochemical reactions. Eukaryotic cells, including all animal cells, also contain various cellular organelles. An organelle (“little organ”) is one of several different types of membrane-enclosed bodies in the cell, each performing a unique function. Just as the various bodily organs work together in harmony to perform all of a human’s functions, the many different cellular organelles work together to keep the cell healthy and performing all of its important functions. The organelles and cytosol, taken together, compose the cell’s cytoplasm . The nucleus is a cell’s central organelle, which contains the cell’s DNA ( Figure 3.2.1 ).

Organelles of the Endomembrane System

A set of three major organelles together form a system within the cell called the endomembrane system. These organelles work together to perform various cellular jobs, including the task of producing, packaging, and exporting certain cellular products. The organelles of the endomembrane system include the endoplasmic reticulum, Golgi apparatus, and vesicles.

Endoplasmic Reticulum

The endoplasmic reticulum (ER) is a system of channels that is continuous with the nuclear membrane (or “envelope”) covering the nucleus and composed of the same lipid bilayer material. The ER can be thought of as a series of winding thoroughfares similar to the waterway canals in Venice. The ER provides passages throughout much of the cell that function in transporting, synthesizing, and storing materials. The winding structure of the ER results in a large membranous surface area that supports its many functions ( Figure 3.2.2 ).

Endoplasmic reticulum can exist in two forms: rough ER and smooth ER. These two types of ER perform some very different functions and can be found in very different amounts depending on the type of cell. Rough ER (RER) is so-called because its membrane is dotted with embedded granules—organelles called ribosomes, giving the RER a bumpy appearance. A ribosome is an organelle that serves as the site of protein synthesis. It is composed of two ribosomal RNA subunits that wrap around mRNA to start the process of translation, followed by protein synthesis. Smooth ER (SER) lacks these ribosomes.

One of the main functions of the smooth ER is in the synthesis of lipids. The smooth ER synthesizes phospholipids, the main component of biological membranes, as well as steroid hormones. For this reason, cells that produce large quantities of such hormones, such as those of the female ovaries and male testes, contain large amounts of smooth ER. In addition to lipid synthesis, the smooth ER also sequesters (i.e., stores) and regulates the concentration of cellular Ca ++ , a function extremely important in cells of the nervous system where Ca ++ is the trigger for neurotransmitter release. The smooth ER additionally metabolizes some carbohydrates and performs a detoxification role, breaking down certain toxins.

In contrast with the smooth ER, the primary job of the rough ER is the synthesis and modification of proteins destined for the cell membrane or for export from the cell. For this protein synthesis, many ribosomes attach to the ER (giving it the studded appearance of rough ER). Typically, a protein is synthesized within the ribosome and released inside the channel of the rough ER, where sugars can be added to it (by a process called glycosylation) before it is transported within a vesicle to the next stage in the packaging and shipping process: the Golgi apparatus.

The Golgi Apparatus

The Golgi apparatus is responsible for sorting, modifying, and shipping off the products that come from the rough ER, much like a post-office. The Golgi apparatus looks like stacked flattened discs, almost like stacks of oddly shaped pancakes. Like the ER, these discs are membranous. The Golgi apparatus has two distinct sides, each with a different role. One side of the apparatus receives products in vesicles. These products are sorted through the apparatus and then they are released from the opposite side after being repackaged into new vesicles. If the product is to be exported from the cell, the vesicle migrates to the cell surface and fuses to the cell membrane, and the cargo is secreted ( Figure 3.2.3 ).

Some of the protein products packaged by the Golgi include digestive enzymes that are meant to remain inside the cell for use in breaking down certain materials. The enzyme-containing vesicles released by the Golgi may form new lysosomes, or fuse with existing, lysosomes. A lysosome is an organelle that contains enzymes that break down and digest unneeded cellular components, such as a damaged organelle. (A lysosome is similar to a wrecking crew that takes down old and unsound buildings in a neighborhood.) Autophagy (“self-eating”) is the process of a cell digesting its own structures. Lysosomes are also important for breaking down foreign material. For example, when certain immune defense cells (white blood cells) phagocytize bacteria, the bacterial cell is transported into a lysosome and digested by the enzymes inside. As one might imagine, such phagocytic defense cells contain large numbers of lysosomes.

Under certain circumstances, lysosomes perform a more grand and dire function. In the case of damaged or unhealthy cells, lysosomes can be triggered to open up and release their digestive enzymes into the cytoplasm of the cell, killing the cell. This “self-destruct” mechanism is called autolysis , and makes the process of cell death controlled (a mechanism called “apoptosis”).

External Website

Watch this video to learn about the endomembrane system, which includes the rough and smooth ER and the Golgi body as well as lysosomes and vesicles. What is the primary role of the endomembrane system?

Organelles for Energy Production and Detoxification

In addition to the jobs performed by the endomembrane system, the cell has many other important functions. Just as you must consume nutrients to provide yourself with energy, so must each of your cells take in nutrients, some of which convert to chemical energy that can be used to power biochemical reactions. Another important function of the cell is detoxification. Humans take in all sorts of toxins from the environment and also produce harmful chemicals as byproducts of cellular processes. Cells called hepatocytes in the liver detoxify many of these toxins.

Mitochondria

A mitochondrion (plural = mitochondria) is a membranous, bean-shaped organelle that is the “energy transformer” of the cell. Mitochondria consist of an outer lipid bilayer membrane as well as an additional inner lipid bilayer membrane ( Figure 3.2.4 ). The inner membrane is highly folded into winding structures with a great deal of surface area, called cristae. It is along this inner membrane that a series of proteins, enzymes, and other molecules perform the biochemical reactions of cellular respiration. These reactions convert energy stored in nutrient molecules (such as glucose) into adenosine triphosphate (ATP), which provides usable cellular energy to the cell. Cells use ATP constantly, and so the mitochondria are constantly at work. Oxygen molecules are required during cellular respiration, which is why you must constantly breathe it in. One of the organ systems in the body that uses huge amounts of ATP is the muscular system because ATP is required to sustain muscle contraction. As a result, muscle cells are packed full of mitochondria. Nerve cells also need large quantities of ATP to run their sodium-potassium pumps. Therefore, an individual neuron will be loaded with over a thousand mitochondria. On the other hand, a bone cell, which is not nearly as metabolically-active, might only have a couple hundred mitochondria.

Peroxisomes

Like lysosomes, a peroxisome is a membrane-bound cellular organelle that contains mostly enzymes ( Figure 3.2.5 ). Peroxisomes perform a couple of different functions, including lipid metabolism and chemical detoxification. In contrast to the digestive enzymes found in lysosomes, the enzymes within peroxisomes serve to transfer hydrogen atoms from various molecules to oxygen, producing hydrogen peroxide (H 2 O 2 ). In this way, peroxisomes neutralize poisons such as alcohol. In order to appreciate the importance of peroxisomes, it is necessary to understand the concept of reactive oxygen species.

Reactive oxygen species (ROS) such as peroxides and free radicals are the highly reactive products of many normal cellular processes, including the mitochondrial reactions that produce ATP and oxygen metabolism. Examples of ROS include the hydroxyl radical OH, H 2 O 2 , and superoxide (O 2 − ). Some ROS are important for certain cellular functions, such as cell signaling processes and immune responses against foreign substances. Free radicals are reactive because they contain free unpaired electrons; they can easily oxidize other molecules throughout the cell, causing cellular damage and even cell death. Free radicals are thought to play a role in many destructive processes in the body, from cancer to coronary artery disease. Peroxisomes, on the other hand, oversee reactions that neutralize free radicals. Peroxisomes produce large amounts of the toxic H 2 O 2 in the process, but also contain enzymes that convert H 2 O 2 into water and oxygen. These byproducts are safely released into the cytoplasm. Like miniature sewage treatment plants, peroxisomes neutralize harmful toxins so that they do not wreak havoc in the cells. The liver is the organ primarily responsible for detoxifying the blood before it travels throughout the body, and liver cells contain an exceptionally high number of peroxisomes. Defense mechanisms such as detoxification within the peroxisome and certain cellular antioxidants serve to neutralize many of these molecules. Some vitamins and other substances, found primarily in fruits and vegetables, have antioxidant properties. Antioxidants work by being oxidized themselves, halting the destructive reaction cascades initiated by the free radicals. Sometimes though, ROS accumulate beyond the capacity of such defenses. Oxidative stress is the term used to describe damage to cellular components caused by ROS. Due to their distinctive unpaired electrons, ROS can set off chain reactions where they remove electrons from other molecules, which then become oxidized and reactive; they do the same to other molecules, causing a chain reaction. ROS can cause permanent damage to cellular lipids, proteins, carbohydrates, and nucleic acids. Damaged DNA can lead to genetic mutations and even cancer. A mutation is a change in the nucleotide sequence in a gene within a cell’s DNA, potentially altering the protein coded by that gene. Other diseases believed to be triggered or exacerbated by ROS include Alzheimer’s disease, cardiovascular diseases, diabetes, Parkinson’s disease, arthritis, Huntington’s disease, and schizophrenia, among many others. It is noteworthy that these diseases are largely age-related. Many scientists believe that oxidative stress is a major contributor to the aging process.

Aging and the … Cell: The Free Radical Theory The free radical theory on aging was originally proposed in the 1950s, and still remains under debate. Generally speaking, the free radical theory of aging suggests that accumulated cellular damage from oxidative stress contributes to the physiological and anatomical effects of aging. There are two significantly different versions of this theory: one states that the aging process itself is a result of oxidative damage, and the other states that oxidative damage causes age-related diseases and disorders. The latter version of the theory is more widely accepted than the former. However, many lines of evidence suggest that oxidative damage does contribute to the aging process. Research has shown that reducing oxidative damage can result in a longer lifespan in certain organisms such as yeast, worms, and fruit flies. Conversely, increasing oxidative damage can shorten the lifespan of mice and worms. Interestingly, a manipulation called calorie-restriction (moderately restricting the caloric intake) has been shown to increase life span in some laboratory animals. It is believed that this increase is at least in part due to a reduction of oxidative stress. However, a long-term study of primates with calorie-restriction showed no increase in their lifespan. A great deal of additional research will be required to better understand the link between reactive oxygen species and aging.

The Cytoskeleton Much like the bony skeleton structurally supports the human body, the cytoskeleton helps the cells to maintain their structural integrity. The cytoskeleton is a group of fibrous proteins that provide structural support for cells, but this is only one of the functions of the cytoskeleton. Cytoskeletal components are also critical for cell motility, cell reproduction, and transportation of substances within the cell. The cytoskeleton forms a complex thread-like network throughout the cell consisting of three different kinds of protein-based filaments: microfilaments, intermediate filaments, and microtubules ( Figure 3.2.6 ). The thickest of the three is the microtubule , a structural filament composed of subunits of a protein called tubulin. Microtubules maintain cell shape and structure, help resist compression of the cell, and play a role in positioning the organelles within the cell. Microtubules also make up two types of cellular appendages important for motion: cilia and flagella. Cilia are found on many cells of the body, including the epithelial cells that line the airways of the respiratory system. Cilia move rhythmically; they beat constantly, moving waste materials such as dust, mucus, and bacteria upward through the airways, away from the lungs and toward the mouth. Beating cilia on cells in the female fallopian tubes move egg cells from the ovary towards the uterus. A flagellum (plural = flagella) is an appendage larger than a cilium and specialized for cell locomotion. The only flagellated cell in humans is the sperm cell that must propel itself towards female egg cells.

A very important function of microtubules is to set the paths (somewhat like railroad tracks) along where the genetic material can be pulled (a process requiring ATP) during cell division, so that each new daughter cell receives the appropriate set of chromosomes. Two short, identical microtubule structures called centrioles are found near the nucleus of cells. A centriole can serve as the cellular origin point for microtubules extending outward as cilia or flagella or can assist with the separation of DNA during cell division. Microtubules grow out from the centrioles by adding more tubulin subunits, like adding additional links to a chain.

In contrast with microtubules, the microfilament is a thinner type of cytoskeletal filament (see Figure 3.2.6 b ). Actin, a protein that forms chains, is the primary component of these microfilaments. Actin fibers, twisted chains of actin filaments, constitute a large component of muscle tissue and, along with the protein myosin, are responsible for muscle contraction. Like microtubules, actin filaments are long chains of single subunits (called actin subunits). In muscle cells, these long actin strands, called thin filaments, are “pulled” by thick filaments of the myosin protein to contract the cell.

Actin also has an important role during cell division. When a cell is about to split in half during cell division, actin filaments work with myosin to create a cleavage furrow that eventually splits the cell down the middle, forming two new cells from the original cell.

The final cytoskeletal filament is the intermediate filament. As its name would suggest, an intermediate filament is a filament intermediate in thickness between the microtubules and microfilaments (see Figure 3.2.6 c ). Intermediate filaments are made up of long fibrous subunits of a protein called keratin that are wound together like the threads that compose a rope. Intermediate filaments, in concert with the microtubules, are important for maintaining cell shape and structure. Unlike the microtubules, which resist compression, intermediate filaments resist tension—the forces that pull apart cells. There are many cases in which cells are prone to tension, such as when epithelial cells of the skin are compressed, tugging them in different directions. Intermediate filaments help anchor organelles together within a cell and also link cells to other cells by forming special cell-to-cell junctions.

Chapter Review

The internal environment of a living cell is made up of a fluid, jelly-like substance called cytosol, which consists mainly of water, but also contains various dissolved nutrients and other molecules. The cell contains an array of cellular organelles, each one performing a unique function and helping to maintain the health and activity of the cell. The cytosol and organelles together compose the cell’s cytoplasm. Most organelles are surrounded by a lipid membrane similar to the cell membrane of the cell. The endoplasmic reticulum (ER), Golgi apparatus, and lysosomes share a functional connectivity and are collectively referred to as the endomembrane system. There are two types of ER: smooth and rough. While the smooth ER performs many functions, including lipid synthesis and ion storage, the rough ER is mainly responsible for protein synthesis using its associated ribosomes. The rough ER sends newly made proteins to the Golgi apparatus where they are modified and packaged for delivery to various locations within or outside of the cell. Some of these protein products are enzymes destined to break down unwanted material and are packaged as lysosomes for use inside the cell.

Cells also contain mitochondria and peroxisomes, which are the organelles responsible for producing the cell’s energy supply and detoxifying certain chemicals, respectively. Biochemical reactions within mitochondria transform energy-carrying molecules into the usable form of cellular energy known as ATP. Peroxisomes contain enzymes that transform harmful substances such as free radicals into oxygen and water. Cells also contain a miniaturized “skeleton” of protein filaments that extend throughout its interior. Three different kinds of filaments compose this cytoskeleton (in order of increasing thickness): microfilaments, intermediate filaments, and microtubules. Each cytoskeletal component performs unique functions as well as provides a supportive framework for the cell.

Interactive Link Questions

Processing, packaging, and moving materials manufactured by the cell.

Review Questions

Critical thinking questions.

Explain why the structure of the ER, mitochondria, and Golgi apparatus assist their respective functions.

The structure of the Golgi apparatus is suited to its function because it is a series of flattened membranous discs; substances are modified and packaged in sequential steps as they travel from one disc to the next. The structure of the Golgi apparatus also involves a receiving face and a sending face, which organize cellular products as they enter and leave the Golgi apparatus. The ER and the mitochondria both have structural specializations that increase their surface area. In the mitochondria, the inner membrane is extensively folded, which increases surface area for ATP production. Likewise, the ER is elaborately wound throughout the cell, increasing its surface area for functions like lipid synthesis, Ca++ storage, and protein synthesis.

Compare and contrast lysosomes with peroxisomes: name at least two similarities and one difference.

Peroxisomes and lysosomes are both cellular organelles bound by lipid bilayer membranes, and they both contain many enzymes. However, peroxisomes contain enzymes that detoxify substances by transferring hydrogen atoms and producing H2O2, whereas the enzymes in lysosomes function to break down and digest various unwanted materials.

Kolata, G. Severe diet doesn’t prolong life, at least in monkeys. New York Times [Internet]. 2012 Aug. 29 [cited 2013 Jan 21]; Available from:

http://www.nytimes.com/2012/08/30/science/low-calorie-diet-doesnt-prolong-life-study-of-monkeys-finds.html?_r=2&ref=caloricrestriction&

This work, Anatomy & Physiology, is adapted from Anatomy & Physiology by OpenStax , licensed under CC BY . This edition, with revised content and artwork, is licensed under CC BY-SA except where otherwise noted.

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Critical Thinking Questions

28 . Compare and contrast a human somatic cell to a human gamete.

29 . What is the relationship between a genome, chromosomes, and genes?

30 . Eukaryotic chromosomes are thousands of times longer than a typical cell. Explain how chromosomes can fit inside a eukaryotic nucleus.

31 . Briefly describe the events that occur in each phase of interphase.

32 . Chemotherapy drugs such as vincristine (derived from Madagascar periwinkle plants) and colchicine (derived from autumn crocus plants) disrupt mitosis by binding to tubulin (the subunit of microtubules) and interfering with microtubule assembly and disassembly. Exactly what mitotic structure is targeted by these drugs and what effect would that have on cell division?

33 . Describe the similarities and differences between the cytokinesis mechanisms found in animal cells versus those in plant cells.

34 . List some reasons why a cell that has just completed cytokinesis might enter the G 0 phase instead of the G 1 phase.

35 . What cell-cycle events will be affected in a cell that produces mutated (non-functional) cohesin protein?

36 . Describe the general conditions that must be met at each of the three main cell-cycle checkpoints.

37 . Compare and contrast the roles of the positive cell-cycle regulators negative regulators.

38 . What steps are necessary for Cdk to become fully active?

39 . Rb is a negative regulator that blocks the cell cycle at the G 1 checkpoint until the cell achieves a requisite size. What molecular mechanism does Rb employ to halt the cell cycle?

40 . Outline the steps that lead to a cell becoming cancerous.

41 . Explain the difference between a proto-oncogene and a tumor-suppressor gene.

42 . List the regulatory mechanisms that might be lost in a cell producing faulty p53.

43 . p53 can trigger apoptosis if certain cell-cycle events fail. How does this regulatory outcome benefit a multicellular organism?

44 . Name the common components of eukaryotic cell division and binary fission.

45 . Describe how the duplicated bacterial chromosomes are distributed into new daughter cells without the direction of the mitotic spindle.

Biology 2e for Biol 111 and Biol 112 Copyright © by Mary Ann Clark; Jung Choi; and Matthew Douglas is licensed under a Creative Commons Attribution 4.0 International License , except where otherwise noted.

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Approaches to Cell Biology Teaching: Questions about Questions

• Deborah Allen
• Kimberly Tanner

Search for more papers by this author

Questions! Questions! Questions! When a teacher is teaching students of any age, on any topic, questions are the teacher's best friend. As a teacher, do you ask questions of your students? When do you ask questions? Are they oral questions or written questions? For what purposes do you ask questions? Do you write out in advance the questions you ask? What kinds of questions do you tend to ask? What kinds of answers do you tend to get? What do you predict would happen in your classroom if you changed the kinds of questions that you ask? How could you collect data on and analyze your questioning patterns and the impact of different kinds of questions on your students' learning? What criteria could you use to assess the effectiveness of your questions?

There are many questions to be asked about the pedagogical practice of questioning. Questions provide insight into what students at any age or grade level already know about a topic, which provides a beginning point for teaching. Questions reveal misconceptions and misunderstandings that must be addressed for teachers to move student thinking forward. In a classroom discussion or debate, questions can influence behaviors, attitudes, and appreciations. They can be used to curb talkative students or draw reserved students into the discussion, to move ideas from the abstract to the concrete, to acknowledge good points made previously, or to elicit a summary or provide closure. Questions challenge students' thinking, which leads them to insights and discoveries of their own. Most important, questions are a key tool in assessing student learning. When practiced artfully, questioning can play a central role in the development of students' intellectual abilities; questions can guide thinking as well as test for it.

Although many teachers carefully plan test questions used as final assessments of students' degree of experience with the course material, much less time is invested in oral questions that are interwoven in our teaching. Analysis of the kinds of questions we ask, whether they are oral or written, and the nature of the answers they elicit is even rarer. Given the important role of questions in teaching and learning, a method for collecting evidence about our own questioning strategies and a framework within which to analyze them has the potential to transform our teaching. Such a framework can be found in Bloom's (1956) Taxonomy of the Cognitive Domain, a classification system for cognitive abilities and educational objectives developed by educational psychologist Benjamin Bloom and his four colleagues (M. Englehart, E. Furst, W. Hill, and D. Krathwohl). Since its inception, Bloom's Taxonomy has influenced curriculum development, the construction of test questions, and our understanding of learning outcomes ( Kunen et al. , 1981 ; Kottke and Schuster, 1990 ). It has helped educators to match the questions they ask with the type of thinking skills they are trying to develop, and to otherwise formulate or clarify their instructional objectives.

Bloom's Taxonomy is based on the premise that there are distinct thinking behaviors that we engage in that are important in the process of learning. Bloom and colleagues grouped these behaviors into six categories that ascend in their level of complexity: from knowledge, comprehension, and application at the lower levels to analysis, synthesis, and evaluation at the higher levels. This scheme orders the six categories into a hierarchy such that cognition at each level encompasses, builds on, and is more difficult than that at the levels below it. In turn, these categories provide a framework for classifying questions that prompt students to engage in these different thinking behaviors, and thus a tool for reflecting on our own questioning strategies used in teaching.

The utility of Bloom's Taxonomy in helping to distinguish the cognitive level needed to answer a given question becomes clearer when the categories in the hierarchy are more fully described. These descriptions (a composite of descriptions found in Bloom et al. , 1956 ; Uno, 1998 ; and Granello, 2000 ) are provided next in their ascending order in the hierarchy. 1

Knowledge : Recalling or recognizing previously learned ideas or phenonema (including definitions, principles, criteria, conventions, trends, generalizations, sequences, classifications and categories, and structures) in the approximate form in which they were learned. Questions asked to prompt or assess a student's thinking behavior at this lowest level in the hierarchy require only factual recall (“regurgitation”), are easy to formulate, and typically incorporate verbs or phrases such as Define, Describe, State, Name, How much is, How did , or What is .

Comprehension : Understanding the literal meaning of a communication, usually demonstrated by the ability to paraphrase or summarize, to predict consequences or effects, or to translate from one form to another. Questions linked to this level of Bloom's Taxonomy require students to show more in-depth understanding and typically use the verbs or phrases Explain, Summarize, Translate, Extrapolate, What is the main idea of , or Give an example of .

Application : Selecting and using information (such as rules, methods such as experimental approaches, and theories) in a new and concrete context (including solving problems and performing tasks). At this level, questions ask students to use what they know without telling them how to use it, and, in addition to Apply , use verbs such as Use, Demonstrate, Compute, Solve , or Predict.

Analysis : Breaking a concept, statement, or question into its components (e.g., assumptions, hypotheses, and evidence) and explaining the relationships between the components and the organizational structures and principles involved. Analysis includes the ability to distinguish relevant information from irrelevant information and facts from inferences, and to recognize fallacies in reasoning. Questions that assess students at this level ask them to Compare, Contrast, Categorize, Discriminate, Question ,or Relate . Such questions could ask either for discrimination of the key elements in a written communication and their interrelationships or for reconstruction of the process by which something was done. Analysis of experimental data requires functioning at this level.

Synthesis : Integrating and combining ideas to form a new product, pattern, plan, communication, or structure (including those for abstract relationships, such as classification schemes); solving problems involving creativity or originality. Questions that ask students to function at this cognitive level typically use the verbs Design, Develop , or Propose .

Evaluation : Using a specific set of internal or external criteria or standards to arrive at a reasoned judgment (decision, appraisal, or critique) about the value of material for a given purpose. Questions used to assess an individual's level of competency in this category are typically open ended, with more than one correct answer or more than one path to an answer. They use verbs such as Judge, Appraise, Rate, Defend, Revise , or Assess . Critical appraisal of research papers, particularly when the findings are controversial or inconsistent with previous findings, falls under this category.

1If you want to assess your understanding of Bloom's Taxonomy after reading theseinitial descriptions, the first paragraph of this article may be used as part of a practice quiz. Referring to each question aboutquestioning in the first paragraph of this article, can you identify the level of Bloom's Taxonomy at which the answerer would need to becompetent to answer the question? For answers to this practice quiz, see Appendix A .

For a more in-depth assessment of your understanding of Bloom's Taxonomy, you may want to take the Bloom's Quiz in Appendix B.

For further clarification of these categories, Table 1 provides not only a synopsis of words and phrases that often begin questions within each category, but also concrete example questions in each category that can be used to prompt thinking behaviors in students at each level of the hierarchy. Three topical areas in the life sciences—neurobiology, virology, and biological taxonomy—are used to demonstrate not only the distinctions in Bloom's categories, but also the hierarchical nature of the classification scheme.

a First column is a list of words that often begin questions at that level. Second column gives three questions, one for each topical area in the life sciences–neurobiology, virology, and biological taxonomy. These questions are used to demonstrate not only distinctions in Bloom's categories, but also the hierarchical nature of the classification scheme. We assume for these questions that, for the application level and above, the context is new to individuals answering the question

Although Bloom's Taxonomy is a widely accepted classification system, it has its full share of critics. Some critics have questioned its validity because of its behaviorally specified goals—that is, because it requires individuals to demonstrate mental processes in observable ways, including task performance ( Pring, 1971 ). Many critics have suggested that although research supports the basic hierarchical structure of the classification system, the hierarchy falls down at the synthesis and evaluation levels, that these are instead two divergent processes that operate at the same level of complexity ( Seddon, 1978 ). Other critics have pointed out that Bloom's Taxonomy fails to acknowledge past history or context. For example, if a sophisticated appraisal of a research paper emerges from a student discussion, an exam question that then asks students to evaluate these same research findings will require them to function at the lower knowledge or comprehension level, to simply recall and restate the outcomes of an evaluative discussion. Finally, as Nordvall and Braxton ( 1996 ) have pointed out, the knowledge and comprehension levels of Bloom's Taxonomy do not acknowledge that some types of information are more difficult to remember and understand. For example, most students find it easier to briefly describe three major functional types of RNA than to explain the details of how RNA is transcribed or translated. However, most educators agree that although the research on the validity of Bloom's Taxonomy is not necessarily conclusive, this taxonomy is a useful tool for making a distinction between lower-level and higher-order knowing and thinking (commonly referred to as critical thinking) and for improving our teaching.

Bloom's Taxonomy has provided a particularly useful way to investigate the congruence between course and curricular objectives and the content that is actually taught and assessed. Bloom and colleagues pointed out the utility of their model in this regard when they introduced it in the 1950s. Along with the classification system, they presented a content analysis of the types of questions that college faculty were typically asking on their course exams. They found that 70-95% of the questions that students encountered on these undergraduate exams required them to think only at the lower levels of knowledge and comprehension. Many researchers subsequently found that even 40 yr after the original publication of Bloom's Taxonomy, the typical college-level objective test question continued to assess predominantly the lower-order thinking levels ( Gage and Berliner, 1992 ; Evans, 1999 ). With the advent of the National Education Standards and Project 2061 ( American Association for the Advancement of Science, 1993 ; National Research Council, 1996 ) and the host of reform proposals in science education (e.g., National Science Foundation 1996 ), we are all striving to develop critical thinking and scientific inquiry skills in students of all ages. To do so, we should ensure that our pedagogy in general and our questioning strategies in particular extend to the analytic, synthetic, and evaluation levels of Bloom's Taxonomy. Laboratory experiences clearly have the potential to foster intellectual development (problem solving, analysis, and evaluation); however, a content analysis of 10 manuals commonly used in undergraduate chemistry laboratory courses revealed that 8 of the 10 manuals focused on questions that challenged learners to think predominantly at the three lower levels of Bloom's Taxonomy ( Domin, 1999 ). Clearly, we have a long way to go to achieve our goal.

The point of raising these findings is not to chastise the authors of these exams and manuals. Questions at the lower levels have appropriate and legitimate uses (remember that Bloom and colleagues considered knowledge and comprehension to be foundational to more complex cognitive processes). At the very least, such questions can verify student preparation and comprehension before teachers move on to materials and strategies that promote development of the higher-order thinking skills. Rather, the point is that the assessments and questions that we use in our teaching not only drive what we teach and how we teach it, but also what students learn (this concept is informally described as “what you measure is what you get,” or WYMIWYG; Hummel and Huitt, 1994 ). If our course assessments require predominantly lower-level thinking, such thinking is likely to be all that we will get from our students. In other words, asking a predominance of lower-level questions on exams or as part of classroom question-answer dialogues may fixate student thinking at this level and waste opportunities for us to develop students' more complex intellectual capabilities ( Napell, 1976 ). Conversely, if we make more forays into developing effective and appropriate questions and assessments aimed at the higher-order thinking levels in Bloom's Taxonomy, there is at least a chance that we will also be teaching more at these levels and that students will have the opportunity to develop thinking behaviors at these levels. Using Bloom's Taxonomy (or some other validated taxonomy) to perform a careful content analysis of our instructional objectives—and of questions embedded in activities, assessments, and other student experiences—can therefore help to make us conscious of the potential misalignment between what we think our objectives are and the messages we send to students through our questions. Bloom's Taxonomy, not unlike assays routinely used in the laboratory to assess the quality and quantity of proteins, cells, or nucleic acids, can serve as a tool to measure the quantity and quality of the questions we ask in our teaching.

That said, in thinking about your own teaching, we hope you will consider again, deeply, the questions that we began with: As a teacher, do you ask questions of your students? When do you ask questions? For what purposes do you ask questions? What kinds of questions do you tend to ask? What kinds of answers do you tend to get? What do you predict would happen in your classroom if you changed the kinds of questions that you ask? And perhaps most important, how could you begin to collect data on and analyze your questioning patterns? We encourage you to share your experiences with and insights on answering these questions about questions.

APPENDIX B Understanding Bloom's Taxonomy: Quiz

As you develop familiarity with the categories in Bloom's Taxonomy, it can be useful to analyze questions, decide where you might place them in the categories, and explain why. As such, we have provided this Bloom's Quiz, a collection of questions to use in probing your understanding of and insights into Bloom's Taxonomy. As described in this article, all questions used in teaching occur in a context, including the pedagogical structure in which they are presented and their relationship to the discussion of other concepts and topics. That said, these questions are relatively free of contextual information. We challenge you to think about which category or categories they most often fit into and why you place them there. We have provided answers that represent the category in which we think the question would most often fit, and in some cases we have described gray areas where the question may fit well into more than one category. We hope that in your analysis of the questions you clarify your thinking about the taxonomy and perhaps find more gray areas yourself. That said, enjoy thinking about the questions and consider doing a similar analysis on questions that you ask in your classrooms and laboratories.

BLOOM'S QUIZ

Suggested answers follow the questions.

Design an experiment to test the hypothesis that some prostate cancer cells thrive after elimination of the influence of androgens because estrogen activates genes normally controlled by an androgen receptor.

What factors might influence the contribution that industrial carbon dioxide emissions make to global temperature levels?

How are proteins destined for export from a cell typically modified prior to secretion?

Which of the following is not an event that occurs during the first division of meiosis: replication of DNA, pairing of homologous chromosomes, formation of haploid chromosome complements, crossing over, or separation of sister chromatids?

Do the authors' data support their hypotheses and conclusions? Why or why not?

Should embryos “left over” from in vitro fertilization procedures be used as sources of stem cells for biomedical research?

Construct a concept map with the following title: Regulation of the Cell Cycle.

How does the generalized life cycle of an animal differ from that of a plant?

Suggested Answers

Analysis : However, if these factors were previously discussed in class or presented in a reading assigned to students, this question involves only comprehension.

Comprehension

This question intentionally brings out gray areas in trying to fit short questions to Bloom's categories without awareness of the context. According to the explanations provided in the text, the question could be at the analysis level; it requires the answerer to break down a communication about experimental findings into its components and explain their interrelationships. However, the question can take another context if, for example, it is asked in the context of peer review of a manuscript or of a student lab report. In this context, the methodology of the experiment may be open to question, or the authors may have taken an overly optimistic or confident viewpoint in interpreting their data. The answer would then require some critical appraisal ( evaluation ) and a knowledge of the standards used in communicating about experimental findings in a particular discipline.

Evaluation : The answerer could find many written opinions on this issue through a quick search on the Internet. If other opinions were discussed or read previously and the answerer merely recapitulates another person's opinion, this question involves only comprehension .

Synthesis , if the person constructing the map has not seen one before on this topic. A concept map is a collection of boxes, lines, and words used to represent understanding of major themes and ideas on a subject and how these ideas are interrelated. Maps are typically put together by placing key concepts related to the subject in the boxes, then arranging the boxes in a scheme that indicates hierarchies of importance or specificity (for example, with the “bigger ideas” at the top and a progression toward increasingly more specific concepts toward the bottom of the map). Lines drawn between boxes (propositional linkages) are used to indicate relatedness of concepts. A word or phrase above the linkage (usually a verb or an adverb) is used to indicate the nature of the relationship.

Comprehension : Some people might argue that the level for this question is analysis if the answerer has not previously been told what the differences are (or read the typical introductory biology textbook treatment of animal versus plant cell cycles). Our opinion is that the cycles do not have to be broken into their components for the major differences to be evident.

• American Association for the Advancement of Science (AAAS). ( 1993 ). Benchmarks for Science Literacy , Washington, DC: AAAS. Available online at http://www.project2061.org/tools/benchol/bolframe.htm (Project 2061 web site). Google Scholar
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LINKS TO WEB SITES ON BLOOM'S TAXONOMY

• Division of Instructional Development, Office of Instructional Resources, University of Illinois at Urbana-Champaign. Levels and Types of Questions . http://www.oir.uiuc.edu/did/booklets/question/quest1.html Google Scholar
• Krumme, G. University of Washington. Major Categories in the Taxonomy of Educational Objectives . http://faculty.washington.edu/krumme/guides/bloom.html Google Scholar
• Learning Skills Program, Counselling Services, University of Victoria. Bloom's Taxonomy . http://www.coun.uvic.ca/learn/program/hndouts/bloom.html Google Scholar
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• David J. Baumler ,
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Submitted: 19 July 2002 Revised: 30 July 2002 Accepted: 6 August 2002

© 2002 by The American Society for Cell Biology

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2.3: The Cytoplasm and Cellular Organelles

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• Whitney Menefee, Julie Jenks, Chiara Mazzasette, & Kim-Leiloni Nguyen
• Reedley College, Butte College, Pasadena City College, & Mt. San Antonio College via ASCCC Open Educational Resources Initiative

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By the end of the section, you will be able to:

• Describe the structure and function of the cellular organelles associated with the endomembrane system, including the endoplasmic reticulum, Golgi apparatus, and lysosomes
• Describe the structure and function of mitochondria and peroxisomes
• Explain the three components of the cytoskeleton, including their composition and functions

Now that you have learned that the cell membrane surrounds all cells, you can dive inside of a prototypical human cell to learn about its internal components and their functions. All living cells in multicellular organisms contain an internal cytoplasmic compartment, and a nucleus within the cytoplasm. Cytosol , the jelly-like substance within the cell, provides the fluid medium necessary for biochemical reactions. Eukaryotic cells, including all animal cells, also contain various cellular organelles. An organelle (“little organ”) is one of several different types of specialized structures in the cell, each performing a unique function. Just as the various bodily organs work together in harmony to perform all of a human’s functions, the many different cellular organelles work together to keep the cell healthy and performing all of its important functions. The organelles and cytosol, taken together, compose the cell’s cytoplasm . The nucleus is a cell’s central organelle, which contains the cell’s DNA (Figure \(\PageIndex{1}\)).

Organelles of the Endomembrane System

A set of three major organelles together form a system within the cell called the endomembrane system. These organelles work together to perform various cellular jobs, including the task of producing, packaging, and exporting certain cellular products. The organelles of the endomembrane system include the endoplasmic reticulum, Golgi apparatus, and vesicles.

Endoplasmic Reticulum

The endoplasmic reticulum (ER) is a system of channels that is continuous with the nuclear membrane (or “envelope”) covering the nucleus and composed of the same lipid bilayer material. The ER can be thought of as a series of winding thoroughfares similar to the waterway canals in Venice. The ER provides passages throughout much of the cell that function in transporting, synthesizing, and storing materials. The winding structure of the ER results in a large membranous surface area that supports its many functions (Figure \(\PageIndex{2}\)).

Endoplasmic reticulum can exist in two forms: rough ER and smooth ER. These two types of ER perform some very different functions and can be found in very different amounts depending on the type of cell. Rough ER (RER) is so-called because its membrane is dotted with embedded granules—organelles called ribosomes, giving the RER a bumpy appearance. A ribosome is an organelle that serves as the site of protein synthesis. Smooth ER (SER) lacks these ribosomes.

One of the main functions of the smooth ER is in the synthesis of lipids. The smooth ER synthesizes phospholipids, the main component of biological membranes, as well as steroid hormones. For this reason, cells that produce large quantities of such hormones, such as those of the female ovaries and male testes, contain large amounts of smooth ER. In addition to lipid synthesis, the smooth ER also sequesters (i.e., stores) and regulates the concentration of cellular Ca ++ , a function extremely important in cells of the nervous system where Ca ++ is the trigger for neurotransmitter release. The smooth ER additionally metabolizes some carbohydrates and performs a detoxification role, breaking down certain toxins.

In contrast with the smooth ER, the primary job of the rough ER is the modification of proteins destined for the cell membrane or for export from the cell. For this protein synthesis, many ribosomes attach to the ER (giving it the studded appearance of rough ER). Typically, a protein is synthesized within the ribosome and released inside the channel of the rough ER, where sugars can be added to it (by a process called glycosylation) before it is transported within a vesicle to the next stage in the packaging and shipping process: the Golgi apparatus.

The Golgi Apparatus

The Golgi apparatus is responsible for sorting, modifying, and shipping off the products that come from the rough ER, much like a post-office. The Golgi apparatus looks like stacked flattened discs, almost like stacks of oddly shaped pancakes. Like the ER, these discs are membranous. The Golgi apparatus has two distinct sides, each with a different role. One side of the apparatus receives products in vesicles from the ER. These products are modified as needed and sorted as they move through the apparatus, and then they are released from the opposite side after being repackaged into new vesicles. If the product is to be exported from the cell, the vesicle migrates to the cell surface and fuses to the cell membrane, and the cargo is secreted via exocytosis (Figure \(\PageIndex{3}\)).

Some of the protein products packaged by the Golgi will function in a membrane-bound organelle inside the cell. For example, when the Golgi packages digestive enzymes that are meant to remain inside the cell for use in breaking down certain materials into a vesicle, that vesicle may become a new lysosome, or it may fuse with an existing lysosome. A lysosome is an organelle that contains enzymes that break down and digest unneeded cellular components, such as a damaged organelle. A lysosome is similar to a wrecking crew that takes down old and unsound buildings in a neighborhood. Autophagy (“self-eating”) is the process of a cell digesting its own structures. Lysosomes are also important for breaking down foreign material. For example, when certain immune defense cells (white blood cells) phagocytize bacteria, the bacterial cell is transported into a lysosome and digested by the enzymes inside. As one might imagine, such phagocytic defense cells contain large numbers of lysosomes.

Under certain circumstances, lysosomes perform a more grand and dire function. In the case of damaged or unhealthy cells, lysosomes can be triggered to open up and release their digestive enzymes into the cytoplasm of the cell, killing the cell. This “self-destruct” mechanism is called autolysis , and makes the process of cell death controlled (a mechanism called “apoptosis”).

Organelles for Energy Production and Detoxification

In addition to the jobs performed by the endomembrane system, the cell has many other important functions. Just as you must consume nutrients to provide yourself with energy, so must each of your cells take in nutrients, some of which convert to chemical energy that can be used to power biochemical reactions. Another important function of the cell is detoxification. Humans take in all sorts of toxins from the environment and also produce harmful chemicals as byproducts of cellular processes. Cells called hepatocytes in the liver detoxify many of these toxins.

Mitochondria

A mitochondrion (plural = mitochondria) is a membranous, bean-shaped organelle that is the “energy transformer” of the cell. Mitochondria consist of an outer lipid bilayer membrane as well as an additional inner lipid bilayer membrane (Figure \(\PageIndex{4}\)). The inner membrane is highly folded into winding structures with a great deal of surface area, called cristae. It is along this inner membrane that a series of proteins, enzymes, and other molecules perform the biochemical reactions of cellular respiration. These reactions convert energy stored in nutrient molecules (such as glucose) into adenosine triphosphate (ATP), which provides usable cellular energy to the cell. Cells use ATP constantly, and so the mitochondria are constantly at work. Oxygen molecules are required during cellular respiration, which is why you must constantly breathe it in. One of the organ systems in the body that has high demands for ATP is the muscular system because ATP is required to sustain muscle contraction. As a result, muscle cells are packed full of mitochondria. Nerve cells also need large quantities of ATP to run their sodium-potassium pumps. Therefore, an individual neuron will be loaded with over a thousand mitochondria. On the other hand, a bone cell, which is not nearly as metabolically-active, might only have a couple hundred mitochondria.

Peroxisomes

Like a lysosome, a peroxisome is a membrane-bound cellular organelle that contains mostly enzymes (Figure \(\PageIndex{5}\)). Peroxisomes perform a couple of different functions, including lipid metabolism and chemical detoxification. In contrast to the digestive enzymes found in lysosomes, the enzymes within peroxisomes serve to transfer hydrogen atoms from various molecules to oxygen, producing hydrogen peroxide (H 2 O 2 ). In this way, peroxisomes neutralize free radicals that are produced during many normal cellular processes. Free radicals are reactive because they contain free unpaired electrons typically associated with oxygen (so they are also called reactive oxygen species). Free radicals can easily oxidize other molecules throughout the cell, causing cellular damage and even cell death.

AGING AND THE CELL: The Free Radical Theory

The free radical theory on aging was originally proposed in the 1950s, and still remains under debate. Generally speaking, the free radical theory of aging suggests that accumulated cellular damage from oxidative stress contributes to the physiological and anatomical effects of aging. There are two significantly different versions of this theory: one states that the aging process itself is a result of oxidative damage, and the other states that oxidative damage causes age-related disease and disorders. The latter version of the theory is more widely accepted than the former. However, many lines of evidence suggest that oxidative damage does contribute to the aging process. Research has shown that reducing oxidative damage can result in a longer lifespan in certain organisms such as yeast, worms, and fruit flies. Conversely, increasing oxidative damage can shorten the lifespan of mice and worms. Interestingly, a manipulation called calorie-restriction (moderately restricting the caloric intake) has been shown to increase life span in some laboratory animals. It is believed that this increase is at least in part due to a reduction of oxidative stress. However, a long-term study of primates with calorie-restriction showed no increase in their lifespan. A great deal of additional research will be required to better understand the link between reactive oxygen species and aging.

The Cytoskeleton

Much like the bony skeleton structurally supports the human body, the cytoskeleton helps the cells to maintain their structural integrity. The cytoskeleton is a group of fibrous proteins that provide structural support for cells, but this is only one of the functions of the cytoskeleton. Cytoskeletal components are also critical for cell motility, cell reproduction, and transportation of substances within the cell.

The cytoskeleton forms a complex thread-like network throughout the cell consisting of three different kinds of protein-based filaments: microfilaments, intermediate filaments, and microtubules (Figure \(\PageIndex{6}\)). The thickest of the three is the microtubule , a structural filament composed of subunits of a protein called tubulin. Microtubules maintain cell shape and structure, help resist compression of the cell, and play a role in positioning the organelles within the cell. Microtubules also make up two types of cellular appendages important for motion: cilia and flagella (seen previously in this chapter). Cilia are found on many cells of the body, including the epithelial cells that line the airways of the respiratory system. Cilia move rhythmically; they beat constantly, moving waste materials such as dust, mucus, and bacteria upward through the airways, away from the lungs and toward the mouth. Beating cilia on cells lining the female fallopian tubes move egg cells from the ovary towards the uterus. A flagellum (plural = flagella) is an appendage larger than a cilium and specialized for cell locomotion. The only flagellated cell in humans is the sperm cell that must propel itself towards female egg cells.

A very important function of microtubules is to set the paths (somewhat like railroad tracks) along which the genetic material can be pulled (a process requiring ATP) during cell division, so that each new daughter cell receives the appropriate set of chromosomes. Two short, identical microtubule structures called centrioles are found near the nucleus of cells. A centriole can serve as the cellular origin point for microtubules extending outward as cilia or flagella or can assist with the separation of DNA during cell division. Microtubules grow out from the centrioles by adding more tubulin subunits, like adding additional links to a chain.

In contrast with microtubules, the microfilament is a thinner type of cytoskeletal filament (see Figure \(\PageIndex{6.b}\)). Actin, a protein that forms chains, is the primary component of these microfilaments. Actin fibers, twisted chains of actin filaments, constitute a large component of muscle tissue and, along with the protein myosin, are responsible for muscle contraction. Like microtubules, actin filaments are long chains of single subunits (called actin subunits). In muscle cells, these long actin strands, called thin filaments, are “pulled” by thick filaments of the myosin protein to contract the cell.

Actin also has an important role during cell division. When a cell is about to split in half during cell division, actin filaments work with myosin to create a cleavage furrow that eventually splits the cell down the middle, forming two new cells from the original cell.

The final cytoskeletal filament is the intermediate filament. As its name would suggest, an intermediate filament is a filament intermediate in thickness between the microtubules and microfilaments (see Figure \(\PageIndex{6.c}\)). Intermediate filaments are made up of long fibrous subunits of a protein called keratin that are wound together like the threads that compose a rope. Intermediate filaments, in concert with the microtubules, are important for maintaining cell shape and structure. Unlike the microtubules, which resist compression, intermediate filaments resist tension—the forces that pull apart cells. There are many cases in which cells are prone to tension, such as when epithelial cells of the skin are compressed, tugging them in different directions. Intermediate filaments help anchor organelles together within a cell and also link cells to other cells by forming special cell-to-cell junctions.

Concept Review

The internal environmental of a living cell is made up of a fluid, jelly-like substance called cytosol, which consists mainly of water, but also contains various dissolved nutrients and other molecules. The cell contains an array of cellular organelles, each one performing a unique function and helping to maintain the health and activity of the cell. The cytosol and organelles together compose the cell’s cytoplasm. Most organelles are surrounded by a lipid membrane similar to the cell membrane of the cell. The endoplasmic reticulum (ER), Golgi apparatus, and lysosomes share a functional connectivity and are collectively referred to as the endomembrane system. There are two types of ER: smooth and rough. While the smooth ER performs many functions, including lipid synthesis and ion storage, the rough ER is mainly responsible for protein synthesis using its associated ribosomes. The rough ER sends newly made proteins to the Golgi apparatus where they are modified and packaged for delivery to various locations within or outside of the cell. Some of these protein products are enzymes destined to break down unwanted material and are packaged as lysosomes for use inside the cell.

Cells also contain mitochondria and peroxisomes, which are the organelles responsible for producing the cell’s energy supply and detoxifying certain chemicals, respectively. Biochemical reactions within mitochondria transform energy-carrying molecules into the usable form of cellular energy known as ATP. Peroxisomes contain enzymes that transform harmful substances such as free radicals into oxygen and water. Cells also contain a miniaturized “skeleton” of protein filaments that extend throughout its interior. Three different kinds of filaments compose this cytoskeleton (in order of increasing thickness): microfilaments, intermediate filaments, and microtubules. Each cytoskeletal component performs unique functions as well as provides a supportive framework for the cell.

Review Questions

Q. Choose the term that best completes the following analogy: Cytoplasm is to cytosol as a swimming pool containing chlorine and flotation toys is to ________.

A. the walls of the pool

B. the chlorine

C. the flotation toys

D. the water

Q. The rough ER has its name due to what associated structures?

A. Golgi apparatus

B. ribosomes

C. lysosomes

D. proteins

Q. Which of the following is a function of the rough ER?

A. production of proteins

B. detoxification of certain substances

C. synthesis of steroid hormones

D. regulation of intracellular calcium concentration

Q. Which of the following is a feature common to all three components of the cytoskeleton?

A. They all serve to scaffold the organelles within the cell.

B. They are all characterized by roughly the same diameter.

C. They are all polymers of protein subunits.

D. They all help the cell resist compression and tension.

Q. Which of the following organelles produces large quantities of ATP when both glucose and oxygen are available to the cell?

A. mitochondria

B. peroxisomes

Critical Thinking Questions

Q. Explain why the structure of the ER, mitochondria, and Golgi apparatus assist their respective functions.

A. The structure of the Golgi apparatus is suited to its function because it is a series of flattened membranous discs; substances are modified and packaged in sequential steps as they travel from one disc to the next. The structure of Golgi apparatus also involves a receiving face and a sending face, which organize cellular products as they enter and leave the Golgi apparatus. The ER and the mitochondria both have structural specializations that increase their surface area. In the mitochondria, the inner membrane is extensively folded, which increases surface area for ATP production. Likewise, the ER is elaborately wound throughout the cell, increasing its surface area for functions like lipid synthesis, Ca ++ storage, and protein synthesis.

Q. Compare and contrast lysosomes with peroxisomes: name at least two similarities and one difference.

A. Peroxisomes and lysosomes are both cellular organelles bound by lipid bilayer membranes, and they both contain many enzymes. However, peroxisomes contain enzymes that detoxify substances by transferring hydrogen atoms and producing H 2 O 2 , whereas the enzymes in lysosomes function to break down and digest various unwanted materials.

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OpenStax Anatomy & Physiology (CC BY 4.0). Access for free at  https://openstax.org/books/anatomy-and-physiology

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2.3.11: Critical Thinking Questions

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Does physical exercise involve anabolic and/or catabolic processes? Give evidence for your answer.

Name two different cellular functions that require energy that parallel human energy-requiring functions.

Explain in your own words the difference between a spontaneous reaction and one that occurs instantaneously, and what causes this difference.

Describe the position of the transition state on a vertical energy scale, from low to high, relative to the position of the reactants and products, for both endergonic and exergonic reactions.

Imagine an elaborate ant farm with tunnels and passageways through the sand where ants live in a large community. Now imagine that an earthquake shook the ground and demolished the ant farm. In which of these two scenarios, before or after the earthquake, was the ant farm system in a state of higher or lower entropy?

Energy transfers take place constantly in everyday activities. Think of two scenarios: cooking on a stove and driving. Explain how the second law of thermodynamics applies to these two scenarios.

Do you think that the E A for ATP hydrolysis is relatively low or high? Explain your reasoning.

With regard to enzymes, why are vitamins necessary for good health? Give examples.

Explain in your own words how enzyme feedback inhibition benefits a cell.

• Introduction
• 1.1 The Science of Biology
• 1.2 Themes and Concepts of Biology
• Chapter Summary
• Review Questions

Critical Thinking Questions

• Test Prep for AP ®  Courses
• 2.1 Atoms, Isotopes, Ions, and Molecules: The Building Blocks
• Science Practice Challenge Questions
• 3.1 Synthesis of Biological Macromolecules
• 3.2 Carbohydrates
• 3.4 Proteins
• 3.5 Nucleic Acids
• 4.1 Studying Cells
• 4.2 Prokaryotic Cells
• 4.3 Eukaryotic Cells
• 4.4 The Endomembrane System and Proteins
• 4.5 The Cytoskeleton
• 4.6 Connections Between Cells and Cellular Activities
• 5.1 Components and Structure
• 5.2 Passive Transport
• 5.3 Active Transport
• 5.4 Bulk Transport
• Art Connection Questions
• 6.1 Energy and Metabolism
• 6.2 Potential, Kinetic, Free, and Activation Energy
• 6.3 The Laws of Thermodynamics
• 6.4 ATP: Adenosine Triphosphate
• 6.5 Enzymes
• 7.1 Energy in Living Systems
• 7.2 Glycolysis
• 7.3 Oxidation of Pyruvate and the Citric Acid Cycle
• 7.4 Oxidative Phosphorylation
• 7.5 Metabolism Without Oxygen
• 7.6 Connections of Carbohydrate, Protein, and Lipid Metabolic Pathways
• 7.7 Regulation of Cellular Respiration
• 8.1 Overview of Photosynthesis
• 8.2 The Light-dependent Reaction of Photosynthesis
• 8.3 Using Light Energy to Make Organic Molecules
• 9.1 Signaling Molecules and Cellular Receptors
• 9.2 Propagation of the Signal
• 9.3 Response to the Signal
• 9.4 Signaling in Single-Celled Organisms
• 10.1 Cell Division
• 10.2 The Cell Cycle
• 10.3 Control of the Cell Cycle
• 10.4 Cancer and the Cell Cycle
• 10.5 Prokaryotic Cell Division
• 11.1 The Process of Meiosis
• 11.2 Sexual Reproduction
• 12.1 Mendel’s Experiments and the Laws of Probability
• 12.2 Characteristics and Traits
• 12.3 Laws of Inheritance
• 13.1 Chromosomal Theory and Genetic Linkages
• 13.2 Chromosomal Basis of Inherited Disorders
• 14.1 Historical Basis of Modern Understanding
• 14.2 DNA Structure and Sequencing
• 14.3 Basics of DNA Replication
• 14.4 DNA Replication in Prokaryotes
• 14.5 DNA Replication in Eukaryotes
• 14.6 DNA Repair
• 15.1 The Genetic Code
• 15.2 Prokaryotic Transcription
• 15.3 Eukaryotic Transcription
• 15.4 RNA Processing in Eukaryotes
• 15.5 Ribosomes and Protein Synthesis
• 16.1 Regulation of Gene Expression
• 16.2 Prokaryotic Gene Regulation
• 16.3 Eukaryotic Epigenetic Gene Regulation
• 16.4 Eukaryotic Transcriptional Gene Regulation
• 16.5 Eukaryotic Post-transcriptional Gene Regulation
• 16.6 Eukaryotic Translational and Post-translational Gene Regulation
• 16.7 Cancer and Gene Regulation
• 17.1 Biotechnology
• 17.2 Mapping Genomes
• 17.3 Whole-Genome Sequencing
• 17.4 Applying Genomics
• 17.5 Genomics and Proteomics
• 18.1 Understanding Evolution
• 18.2 Formation of New Species
• 18.3 Reconnection and Rates of Speciation
• 19.1 Population Evolution
• 19.2 Population Genetics
• 19.3 Adaptive Evolution
• 20.1 Organizing Life on Earth
• 20.2 Determining Evolutionary Relationships
• 20.3 Perspectives on the Phylogenetic Tree
• 21.1 Viral Evolution, Morphology, and Classification
• 21.2 Virus Infections and Hosts
• 21.3 Prevention and Treatment of Viral Infections
• 21.4 Other Acellular Entities: Prions and Viroids
• 22.1 Prokaryotic Diversity
• 22.2 Structure of Prokaryotes
• 22.3 Prokaryotic Metabolism
• 22.4 Bacterial Diseases in Humans
• 22.5 Beneficial Prokaryotes
• 23.1 The Plant Body
• 23.4 Leaves
• 23.5 Transport of Water and Solutes in Plants
• 23.6 Plant Sensory Systems and Responses
• 24.1 Animal Form and Function
• 24.2 Animal Primary Tissues
• 24.3 Homeostasis
• 25.1 Digestive Systems
• 25.2 Nutrition and Energy Production
• 25.3 Digestive System Processes
• 25.4 Digestive System Regulation
• 26.1 Neurons and Glial Cells
• 26.2 How Neurons Communicate
• 26.3 The Central Nervous System
• 26.4 The Peripheral Nervous System
• 26.5 Nervous System Disorders
• 27.1 Sensory Processes
• 27.2 Somatosensation
• 27.3 Taste and Smell
• 27.4 Hearing and Vestibular Sensation
• 27.5 Vision
• 28.1 Types of Hormones
• 28.2 How Hormones Work
• 28.3 Regulation of Body Processes
• 28.4 Regulation of Hormone Production
• 28.5 Endocrine Glands
• 29.1 Types of Skeletal Systems
• 29.3 Joints and Skeletal Movement
• 29.4 Muscle Contraction and Locomotion
• 30.1 Systems of Gas Exchange
• 30.2 Gas Exchange across Respiratory Surfaces
• 30.3 Breathing
• 30.4 Transport of Gases in Human Bodily Fluids
• 31.1 Overview of the Circulatory System
• 31.2 Components of the Blood
• 31.3 Mammalian Heart and Blood Vessels
• 31.4 Blood Flow and Blood Pressure Regulation
• 32.1 Osmoregulation and Osmotic Balance
• 32.2 Excretion Systems
• 32.3 The Kidneys and Osmoregulatory Organs
• 32.4 Nitrogenous Wastes
• 32.5 Hormonal Control of Osmoregulatory Functions
• 33.1 Innate Immune Response
• 33.2 Adaptive Immune Response
• 33.3 Antibodies
• 33.4 Disruptions in the Immune System
• 34.1 Reproduction Methods
• 34.2 Fertilization
• 34.3 Human Reproductive Anatomy and Gametogenesis
• 34.4 Hormonal Control of Human Reproduction
• 34.5 Fertilization and Early Embryonic Development
• 34.6 Organogenesis and Vertebrate Formation
• 34.7 Human Pregnancy and Birth
• 35.1 The Scope of Ecology
• 35.2 Biogeography
• 35.3 Terrestrial Biomes
• 35.4 Aquatic Biomes
• 35.5 Climate and the Effects of Global Climate Change
• 36.1 Population Demography
• 36.2 Life Histories and Natural Selection
• 36.3 Environmental Limits to Population Growth
• 36.4 Population Dynamics and Regulation
• 36.5 Human Population Growth
• 36.6 Community Ecology
• 36.7 Behavioral Biology: Proximal and Ultimate Causes of Behavior
• 37.1 Ecology of Ecosystems
• 37.2 Energy Flow through Ecosystems
• 37.3 Biogeochemical Cycles
• 38.1 The Biodiversity Crisis
• 38.2 The Importance of Biodiversity to Human Life
• 38.3 Threats to Biodiversity
• 38.4 Preserving Biodiversity

• All cells come from pre-existing cells.
• All living organisms are composed of one or more cells.
• A cell is the basic unit of life.
• A nucleus and organelles are found in prokaryotic cells.

What are the advantages and disadvantages of light microscopes? What are the advantages and disadvantages of electron microscopes?

• Advantage: In light microscopes, the light beam does not kill the cell. Electron microscopes are helpful in viewing intricate details of a specimen and have high resolution. Disadvantage: Light microscopes have low resolving power. Electron microscopes are costly and require killing the specimen.
• Advantage: Light microscopes have high resolution. Electron microscopes are helpful in viewing surface details of a specimen. Disadvantage: Light microscopes kill the cell. Electron microscopes are costly and low resolution.
• Advantage: Light microscopes have high resolution. Electron microscopes are helpful in viewing surface details of a specimen. Disadvantage: Light microscopes can be used only in the presence of light and are costly. Electron microscopes uses short wavelength of electrons and hence have lower magnification.
• Advantage: Light microscopes have high magnification. Electron microscopes are helpful in viewing surface details of a specimen. Disadvantage: Light microscopes can be used only in the presence of light and have lower resolution. Electron microscopes can be used only for viewing ultra-thin specimens.

Mitochondria are observed in plant cells that contain chloroplasts. Why do you find mitochondria in photosynthetic tissue?

• Mitochondria are not needed but are an evolutionary relic.
• Mitochondria and chloroplasts work together to use light energy to make sugars.
• Mitochondria participate in the Calvin cycle/light-independent reactions of photosynthesis.
• Mitochondria are required to break down sugars and other materials for energy.

In what situation(s), would the use of a light microscope be ideal? Why?

• A light microscope is used to view the details of the surface of a cell, as it cannot be viewed in detail by the transmission microscope.
• A light microscope allows visualization of small cells that have been stained.
• A standard light microscope is used to view living organisms with little contrast to distinguish them from the background, which would be harder to see with the electron microscope.
• A light microscope reveals the internal structures of a cell, which cannot be viewed by transmission electron microscopy.

The major role of the cell wall in bacteria is protecting the cell against changes in osmotic pressure: pressure caused by different solute concentrations in the environment. Bacterial cells swell, but do not burst, in low solute concentrations. What happens to bacterial cells if a compound that interferes with the synthesis of the cell wall is added to an environment with low solute concentrations?

• Bacterial cells will shrink due to the lack of cell wall material.
• Bacterial cells will shrink in size.
• Bacterial cells may burst due to the influx of water.
• Bacterial cells remain normal; they have alternative pathways to synthesize cell walls.

There is a lower limit to cell size. What determines how small a cell can be?

• The cell should be large enough to escape detection.
• The cell should be able to accommodate all the structures and metabolic activities necessary to survival.
• The size of the cell should be large enough to reproduce itself.
• The cell should be large enough to adapt to the changing environmental conditions.
• Plants remain exposed to changes in temperature and thus require rigid cell walls to protect themselves.
• Plants are subjected to variations in osmotic pressure, and a cell wall helps them against bursting or shrinking.
• Plant cells have a rigid cell wall to protect themselves from grazing animals.
• Plant cells have a rigid cell wall to prevent the influx of waste material.

Bacteria do not have organelles, yet the same reactions that take place on the mitochondria inner membrane, the phosphorylation of ADP to ATP, and chloroplasts, photosynthesis, take place in bacteria. Where do these reactions take place?

• These reactions take place in the nucleoid of the bacteria.
• These reactions occur in the cytoplasm present in the bacteria.
• These reactions occur on the plasma membrane of bacteria.
• These reactions take place in the mesosomes.

What are the structural and functional similarities and differences between mitochondria and chloroplasts?

• Similarities: double membrane, inter-membrane space, ATP production, contain DNA. Differences: Mitochondria have inner folds called cristae; chloroplast contains accessory pigments in thylakoids, which form grana and a stroma.
• Similarities: DNA, inter-membrane space, ATP production, and chlorophyll. Differences: Mitochondria have a matrix and inner folds called cristae; chloroplast contains accessory pigments in thylakoids, which form grana and a stroma.
• Similarities: double membrane and ATP production. Differences: Mitochondria have inter-membrane space and inner folds called cristae; chloroplast contains accessory pigments in thylakoids, which form grana and a stroma.
• Similarities: double membrane and ATP production. Differences: Mitochondria have inter-membrane space, inner folds called cristae, ATP synthase for ATP synthesis, and DNA; chloroplast contains accessory pigments in thylakoids, which form grana and a stroma.

Is the nuclear membrane part of the endomembrane system? Why or why not? 

• The nuclear membrane is not a part of the endomembrane system, as the endoplasmic reticulum is a separate organelle of the cell.
• The nuclear membrane is considered a part of the endomembrane system, as it is continuous with the Golgi body.
• The nuclear membrane is part of the endomembrane system, as it is continuous with the rough endoplasmic reticulum.
• The nuclear membrane is not considered a part of the endomembrane system, as the nucleus is a separate organelle.
• These proteins move through the Golgi apparatus and enter in the nucleus.
• These proteins go through the Golgi apparatus and remain in the cytosol.
• The proteins do not go through the Golgi apparatus and move into the nucleus for processing.
• The proteins do not go through the Golgi apparatus and remain free in the cytosol.

What are the similarities and differences between the structures of centrioles and flagella?

• Centrioles and flagella are made of microtubules but show different arrangements.
• Centrioles are made of microtubules but flagella are made of microfilaments, and both show the same arrangement.
• Centrioles and flagella are made of microfilaments. Centrioles have a 9 + 2 arrangement.
• Centrioles are made of microtubules and flagella are made of microfilaments, and both have different structures.

Inhibitors of microtubule assembly, vinblastine for example, are used for cancer chemotherapy. How does an inhibitor of microtubule assembly affect cancerous cells?

• The inhibitors restrict the separation of chromosomes by the mitotic spindle.
• The inhibition of microtubules interferes with the synthesis of proteins.
• The inhibitors bind the microtubule to the nuclear membrane.
• The inhibitors interfere with energy production.
• Cilia are made of microfilaments and flagella of microtubules.
• Cilia are helpful in the process of engulfing food. Flagella are involved in the movement of the organism.
• Cilia are short and found in large numbers on the cell surface whereas flagella are long and fewer in number.
• Cilia are found in prokaryotic cells and flagella in eukaryotic cells.
• bone cells and cartilage cells
• muscle cells and skin cells
• nerve cells and muscle cells
• secretory cells and muscle cells

If there is a mutation in the gene for collagen, such as the one involved in Ehlers-Danlos syndrome, and the individual produces defective collagen, how would it affect coagulation?

• The syndrome affects the clotting factors and platelet aggregation.
• The syndrome leads to hyper-coagulation of blood.
• Coagulation is not affected because collagen is not required for coagulation.
• The syndrome occurs due to the breakdown of platelets.

How does the structure of a plasmodesma differ from that of a gap junction?

• Gap junctions are essential for transportation in animal cells, and plasmodesmata are essential for the movement of substances in plant cells.
• Gap junctions are found to provide attachment in animal cells, and plasmodesmata are essential for attachment of plant cells.
• Plasmodesmata are essential for communication between animal cells, and gap junctions are necessary for attachment of cells in plant cells.
• Plasmodesmata help in transportation and gap junctions help in attachment, in plant cells.

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Autophagy and machine learning: Unanswered questions

Affiliations.

• 1 Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA; Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA; Department of Electrical Engineering and Computer Science, University of Michigan, Ann Arbor, MI 48109, USA; Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA.
• 2 Department of Electrical Engineering and Computer Science, University of Michigan, Ann Arbor, MI 48109, USA.
• 3 Department of Computer Science, University of Virginia, Charlottesville, VA 22903, USA.
• 4 Department of Electrical Engineering and Computer Science, University of Michigan, Ann Arbor, MI 48109, USA; Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA.
• 5 Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA; Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA. Electronic address: [email protected].
• PMID: 38801963
• DOI: 10.1016/j.bbadis.2024.167263

Autophagy is a critical conserved cellular process in maintaining cellular homeostasis by clearing and recycling damaged organelles and intracellular components in lysosomes and vacuoles. Autophagy plays a vital role in cell survival, bioenergetic homeostasis, organism development, and cell death regulation. Malfunctions in autophagy are associated with various human diseases and health disorders, such as cancers and neurodegenerative diseases. Significant effort has been devoted to autophagy-related research in the context of genes, proteins, diagnosis, etc. In recent years, there has been a surge of studies utilizing state of the art machine learning (ML) tools to analyze and understand the roles of autophagy in various biological processes. We taxonomize ML techniques that are applicable in autophagy context, comprehensively review existing efforts in this route, and outline principles to consider in biomedical context. In recognition of recent groundbreaking advances in deep learning community, we discuss new opportunities in interdisciplinary collaborations and seek to engage autophagy and computer science researchers to promote autophagy research with joint efforts.

Keywords: Lysosome; Macroautophagy; Stress.

Copyright © 2024. Published by Elsevier B.V.

Publication types

Critical Thinking Questions

What materials can easily diffuse through the lipid bilayer, and why?

Why is receptor-mediated endocytosis said to be more selective than phagocytosis or pinocytosis?

What do osmosis, diffusion, filtration, and the movement of ions away from like charge all have in common? In what way do they differ?

Explain why the structure of the ER, mitochondria, and Golgi apparatus assist their respective functions.

Compare and contrast lysosomes with peroxisomes: name at least two similarities and one difference.

Explain in your own words why DNA replication is said to be “semiconservative”?

Why is it important that DNA replication take place before cell division? What would happen if cell division of a body cell took place without DNA replication, or when DNA replication was incomplete?

Briefly explain the similarities between transcription and DNA replication.

Contrast transcription and translation. Name at least three differences between the two processes.

What would happen if anaphase proceeded even though the sister chromatids were not properly attached to their respective microtubules and lined up at the metaphase plate?

What are cyclins and cyclin-dependent kinases, and how do they interact?

Explain how a transcription factor ultimately determines whether or not a protein will be present in a given cell?

Discuss two reasons why the therapeutic use of embryonic stem cells can present a problem.

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Access for free at https://openstax.org/books/anatomy-and-physiology/pages/1-introduction

• Authors: J. Gordon Betts, Kelly A. Young, James A. Wise, Eddie Johnson, Brandon Poe, Dean H. Kruse, Oksana Korol, Jody E. Johnson, Mark Womble, Peter DeSaix
• Publisher/website: OpenStax
• Book title: Anatomy and Physiology
• Publication date: Apr 25, 2013
• Location: Houston, Texas
• Book URL: https://openstax.org/books/anatomy-and-physiology/pages/1-introduction
• Section URL: https://openstax.org/books/anatomy-and-physiology/pages/3-critical-thinking-questions

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