Teacher Notes for

Structure and Functionof Molecules and Cells

Ingrid Waldron, Department of Biology, University of Pennsylvania, 2018[1]

In this analysis and discussion activity, students learn how the function of molecules and cells is related totheir structure (including shape, constituent components, and relationships between components). Students analyze multiple examples of the relationship between structure and function in diverse proteins and eukaryotic cells.In addition, students learn that cells are dynamic structures with constant activity, students learn about emergent properties, and students engage in argument from evidence to evaluate three alternative claims concerning the relationship between structure and function.

This activity is aligned with Next Generation Science Standards for high school students and would also be suitable for students in a non-majors college biology course. Some of the questions in this activity are also included in "Structure and Function of Cells, Organs and Organ Systems" (available at which is aligned with Next Generation Science Standards for middle school students.

Before students begin this activity, they should have a basic understanding of proteins and the functions of organelles in animal and plant cells. For this purpose, you may want to:

  • use the activity "Understanding the Functions of Proteins and DNA", available at
  • have students explore the animation, "Inside a Cell" available at

Learning Goals

In accord with the Next Generation Science Standards[2]:

  • Students learn the following Disciplinary Core Ideas, LS1.A:

"… specialized cells within organisms help them perform the essential functions of life."

"… proteins… carry out most of the work of cells."

"Multicellular organisms have a hierarchical structural organization, in which any one system is made up of numerous parts and is itself a component of the next level."

  • Students engage in recommended Scientific Practices, including "constructing explanations" and engaging in "argument from evidence".
  • This activity focuses on the Crosscutting Concept: Structure and function. "The functions and properties of natural and designed objects and systems can be inferred from their overall structure, the way their components are shaped and used, and the molecular substructures of its various materials."
  • This activity helps to prepare students to meet Performance Expectation HS-LS1-1, "Construct an explanation based on evidence for how the structure of DNA determines the structure of proteins which carry out the essential functions of life through systems of specialized cells."

Specific Learning Goals include:

  • The structure of aprotein is related to the function of the protein.
  • Analysis of the different components and relationships between components helps us to understand the function of cells. This activity reinforces student learning about the functions of different types of organelles and the ways that different types of organelles work together to accomplish cell functions.
  • Different types of eukaryotic cells have different shapes and different amounts of specific types of organelles, corresponding to their different functions in different eukaryotic organisms (e.g. animals vs. plants) or in different types of cells in a human body.
  • Cells are highly dynamic with constant activity at the molecular level, organelle level, and whole cell level.
  • Students analyze an example that illustrates emergent properties; an emergent property is only observed in a larger structure and not observed in its component parts (e.g., cells are alive, but the molecules within them are not alive).

Instructional Suggestions and Background Information

To maximize student participation and learning, I suggest that you have your students work individually or in pairs to complete groups of related questions and then have a class discussion after each group of related questions. In each discussion, you can probe student thinking and help them develop a sound understanding of the concepts and information covered before moving on to the next group of related questions.

A key is available upon request to Ingrid Waldron (). The following paragraphs provide additional instructional suggestions, links for recommended videos, and biological information – some for inclusion in your class discussions and some to provide you with relevant background that may be useful for your understanding and/or for responding to student questions.

When you introduce the concept that structure is related to function, you may want to

  • explain that this relationship applies at multiple levels from molecules to organisms
  • explain that structure includes not only overall shape, but the makeup of and relationships between constituent parts
  • introduce familiar examples such as the different shapes of different types of teeth and the hard enamel surface of teeth
  • explain that the relationship between structure and functionis a result of natural selection.

Collagen is a triple helix which forms long, cable-like fibers that provide tensile strength to ligaments (which connect two bones) and tendons (which connect muscle to bone). Collagen is also found in skin and some other tissues. Porin proteins provide channels for small molecules like water and amino acids to cross the cell membrane. For more information on these proteins and motor proteins, see pages 3-4 below.

Question 1 in the Student Handout requires students to know that proteins are polymers of amino acids which have a very different structure from sugars and thus will not fit in the active site of the enzyme that breaks down maltose. Indeed, the matching between the active site of an enzyme and the substrate is very precise, so different enzymes are required to break down maltose (a disaccharide derived from the digestion of starch), lactose (the disaccharide in milk), and sucrose (the disaccharide in fruits and some vegetables), despite the relatively modest differences between these disaccharides (see figure on next page). The specificity of the active site depends not only on the shape of the active site, but also on which specific amino acids surround the active site. If a person's body produces little or no lactase (the enzyme that breaks down lactose), he or she will have trouble digesting the sugar in milk and suffer the symptoms of lactose intolerance when he or she drinks too much milk. Additional information about lactose intolerance is available in "Understanding the Functions of Proteins and DNA", available at .

With respect to question 2,you may want to introduce the importance of changes in shape by asking students to imagine trying to run if they could not bend any of their joints. The figure below outlines howthe motor protein, kinesin, swivels to step along the microtubule. You may want to show your students an animation of kinesin in action ( or

( ) Microtubules are made up of tubulin

proteins (alpha and beta-tubulin dimers). Microtubules stiffen the cell by resisting compression forces.

The dynamism of molecules in cells is further illustrated by evidence that the other three labeled protein molecules shown on page 1 of the Student Handout can change shape as part of their function (and the other type of protein shown, but not labeled, is tubulin which can polymerize to form growing microtubules).

  • The shape of the active site of an enzyme can change when the substrate molecule binds to the active site of the enzyme; this change can enhance binding and facilitate the reaction (illustrated in the top right-hand figure on this page).
  • Collagen can bend when muscle contraction or external forces act on a ligament, tendon or skin.
  • Many porin molecules are gated channels; this means that the channel opens or closes in response to a chemical or electrical signal (illustrated in the schematic diagram shown on the next page). (Many membrane transport proteins do not have an open channel like that observed in porin proteins; instead they are carrier proteins that change shape to move an ion or molecule across the membrane; see figure on next page.)

Gated Channel

( / Carrier protein

(

Activity at the molecular level can be extremely rapid. Some enzymes catalyze 25,000 or more reactions per second.Kinesin can take roughly 100 steps per second.

You may want to discuss two additional examples of the relationship between structure and function in molecules if your students have the necessary background. If your students are familiar with DNA replication, you may want to talk about how the DNA double helixstructure is well-suited for the function of carrying genetic information that needs to be copied precisely for cell reproduction and organism reproduction (see and If your students are familiar with the relationship between the structure and function of ATP, you maywant to include that example also (see ).

In your discussion about how the parts of the cell help to carry out the variousactivities of life (question 3 in the Student Handout) you may want to point out how different parts of the cell cooperate to accomplish important functions (as described in the key). Also, you may want to include other activities of life (e.g. reproduction) if your students have the relevant background knowledge.

Emergent properties are only observed in a larger structure and not observed in its component parts. (This concept is sometimes worded as "The whole is greater than the sum of its parts.") The emergent property of lifeis only observed when the molecules in a cell are organized in the specific structures needed to carry out the activities of life (not when randomly mixed in a test tube). Thus, the organization of constituent parts plays a crucial role in producing emergent properties.Students sometimes have difficulty understanding emergent properties, and you may want to use an analogy. For example, the meaning of a sentence is an emergent property that depends on the meaning of the words in the sentence and the relationships between words. The meaning cannot be understood by a reductionist analysis which determines, for example, how many letters of each type are contained in the sentence. Similarly, many biological phenomena can only be understood if researchers investigate at higher (larger) levels of analysis and not just at the molecular level.

This activity focuses on eukaryotic cells in plants and animals. If your students are learning about prokaryotic cells, you may want to discuss with them how eukaryotic and prokaryotic cells have different internal structure, but both types of cells carry out the activities of life. In part, this is because eukaryotic and prokaryotic cells share multiple important structural similarities (e.g. plasma membrane, ribosomes, and many identical or similar molecules).

The differences between plant and animal cells are best understood in the context of differences in how plants and animals obtain food. For example, plants’ ability to photosynthesize means that plants do not require the mobility that many animals need to obtain food, so the rigidity of cell walls and the weight of the water in the central vacuole are not significant disadvantages for plant cells. This illustrates that the adaptive value of a given characteristic varies, depending on the other characteristics of an organism.

You may want to show your students a video of sperm swimming (available at ). Notice that some of these sperm move quite rapidly, reflecting selection for characteristics that contribute to being the first sperm to reach an egg and fertilize it. The figure on the next page shows how small human sperm are relative to a humanegg. The egg is a large cell with a lot of cytoplasm; once the egg has been fertilized, this large amount of cytoplasm is useful to supply the cytoplasm for the multiple cells that are produced by the cell divisions in early development before the developing embryo implants in the wall of the uterus.

(Figure from Krogh, Biology -- A Guide to the Natural World, Fifth Edition)

An epithelium that consists of a single layer of flattened epithelial cells(also known as a simple squamous epithelium) is observed in the walls of capillaries and also the walls of the alveoli in the lungs. In both cases transport across the epithelium depends on diffusion, which is reasonably rapid over very short distances but very slow over any substantial distance. Thus, it is advantageous to have a minimal barrier to diffusion.[3] The flattened epithelial cells also reflect the fact that the cells of capillaries and alveoli have minimal metabolic activity, so there is minimal need for cytoplasm.

In mammals (which have high metabolic rates) the oxygen-carrying capacity of the red blood cell is maximized by ejecting the nucleus, mitochondria and ribosomes as the red blood cell matures. Each red blood cell contains about 300 million hemoglobin molecules. Also, the absence of mitochondria prevents the red blood cells from using up the oxygen they are carrying to cells throughout the body. Although the absence of nucleus, mitochondria and ribosomes maximizesthe oxygen-carrying capacity of red blood cells, this also results in little capacity for repair;this is one reason why the average lifespan of a red blood cell is only about four months. Notice that a red blood cell is considered to be alive even though it cannot carry out all the activities of life (e.g. growth and reproduction; new red blood cells are produced by stem cells in the bone marrow).

To help your students appreciate the dynamism of cells, I recommend that you show your students a time lapse video of a phagocytic cell (neutrophil) chasing a bacterium (available at or In this video, the phagocytic cell uses chemical information to pursue a bacterium and then eat it. This video shows the dynamic changes in shape as the phagocytic cell moves.The figure on the next page gives some more information about how phagocytic white blood cells move from the blood toconsume bacteria or other microorganisms by phagocytosis. After the phagocytic white blood cell has engulfed the

(continued)

microorganism, the phagosome merges with a lysosome which produces nitric oxide and hydrogen peroxide to kill the microorganism and digestive enzymes to break down the microorganism to components the cell can use or the body can dispose of. I recommend that you link your discussion of flexible cell shape (question 9) to changes in shape for multiple kinds of protein molecules (e.g. motor proteins and changes in shape of the active site of enzymes, see pages 3-4 of these notes).

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(

The rough endoplasmic reticulum and Golgi apparatus process proteins that will be secreted from the cell or embedded in cell membranes. In accord with the principle that structure is related to function, these organelles are abundant in both pancreatic cells that secrete protein enzymes and the cells in the epithelium that lines the inner surface of the small intestine (these cells synthesize digestive enzymes which are embedded in the cell membrane on the side of the cell that faces the lumen of the small intestine). In discussing question 10, I suggest that you point outhow different organelles cooperate to produce proteins for secretion:

  • the nucleus provides instructions and the ribosomes synthesize proteins that are processed in the rough endoplasmic reticulum and Golgi complex
  • motor proteins move vesicles containing these proteins by walking along the microtubules of the cytoskeleton
  • mitochondria provide the energy needed for protein synthesis. (ATP is required both to provide the energy to link amino acids with their corresponding tRNA molecules and to provide the energy for recharging the GTP which provides the energy for forming polypeptide bonds.)

(You may also want to point out how chloroplasts and mitochondria cooperate to provide energy in a form that the plant cells can use (see "Using Models to Understand Photosynthesis", available at ).)

For an excellent dynamic animation showing how different parts of the cell cooperate, see (with narration) or (without narration).This animation is relatively complex, so you may want to:

  • Show just part of it. For example, you may want to show roughly the second half, beginning with microtubules and transport vesicles, continuing through exocytosis of secreted proteins and membrane proteins, and ending with a white blood cell squeezing between the endothelial cells of a capillary to exit the capillary.
  • Use the version without the narration (which is very detailed) and instead give a student-friendly narration. To prepare a student-friendly narration you may want to use the relevant section from

Question 11 challenges students to develop a scientific argument to support one of three claims concerning the relationship between structure and function of molecules and cells. If you feel that your students will benefit from a more structured version of this question with scaffolding, please see the version of question 11 presented on the last page of these Teacher Notes. If you decide to use this more structured version of question 11, you may want to have a discussion after the students have completed the first row in the table in order to make sure they are on the right track. If you feel that either version of this question is too challenging for your students, you can substitute the following easier alternative:

11. Write an argument to support the claim that "The structure of a molecule or cell is related to its function." Give specific examples and explain how each example supports this claim.

If your students are not familiar with scientific argumentation, you will probably want to introduce them to the idea that,in a scientific argument, a claim is supported by observable evidence with justificationto explain how the evidence is relevant to the claim. (In question 11, the justification is referred to as "reasoning".)Criteria for evaluating a scientific argument include: