Exam Review: Biological Molecules (PDF)

Exam review: Unit 1: Biological Molecules Activity 1: Importance of Water Pieces Coming Together A lot of what we will work on in this course will be building on things you’ve seen in past courses. For example, in Grade 10, you learned that organs are made of tissues and specialized cells and that chemicals react in predictable ways. Now in Grade 12 we focus on the microscopic layer (zoomed in) and macroscopic layer (zoomed out): biological molecules, cells and populations. This is important to know because a lot of what we will work on in this course will be building off of things you’ve seen in past courses. Water has significant cultural importance to Indigenous communities in Canada. Water is the source of life and needs to be respected. For the Indigenous peoples in Canada, there is a reciprocal and unique relationship with water. Indigenous water activist Autumn Peltier, who grew up in Wiikwemkoong First Nation on Ontario's Manitoulin Island, spoke before the UN General Assembly for the launch of the International Decade for Action on Water for Sustainable Development in 2018. “Water is a basic human right. Everyone deserves access to clean drinking water, no matter what our race or colour is or how rich or poor we are,” Autumn said. (https://www.cbc.ca/kidsnews/post/watch-teen-activist-autumn-peltier-demands-clean-drinking-w ater-for-all) In 2019, she was named Chief Water Commissioner for the Anishinabek Nation, which means she speaks on behalf of 40 First Nations in Ontario. Water has significant cultural importance to Indigenous communities in Canada. Water is the source of life and needs to be respected. For the Indigenous peoples in Canada, there is a reciprocal and unique relationship with water. Indigenous water activist Autumn Peltier, who grew up in Wiikwemkoong First Nation on Ontario's Manitoulin Island, spoke before the UN General Assembly for the launch of the International Decade for Action on Water for Sustainable Development in 2018. “Water is a basic human right. Everyone deserves access to clean drinking water, no matter what our race or colour is or how rich or poor we are,” Autumn said. (https://www.cbc.ca/kidsnews/post/watch-teen-activist-autumn-peltier-demands-clean-drinking-w ater-for-all) In 2019, she was named Chief Water Commissioner for the Anishinabek Nation, which means she speaks on behalf of 40 First Nations in Ontario. Remember that between non-metals, electrons are usually shared in a covalent bond. Some elements, like carbon and hydrogen share electrons almost equally. We describe this as non-polar. Since water contains hydroxyl functional groups which are polar, we can say that water is polar. One of the important things about functional groups is that they determine how they interact with each other. Do they attract, or do they repel? Is this a strong attraction or weak attraction? This will determine if a substance is a liquid because it melts easily, or a solid because the molecules are attracted tightly together. Or if it’s hard or soft. Soluble or insoluble. Watch one of the two videos about the water. In particular, look for different properties of water and how they are explained by and connected to the attractive force between water molecules. Polarity and Intermolecular Forces of Attraction In addition to hydrogen bonding, there are other intermolecular forces of attraction. These attractive forces can be organized on a scale from weakest to strongest. Summary This Activity introduced the big idea that certain molecules are important to biology and their structure affects their function. Specifically, - water has a functional group that gives it specific properties. - other functional groups gives molecules different properties depending on the type of intermolecular force of attraction they make. Activity 2: Carbohydrates Nutrition and Macromolecules From our perspective as consumers in a food chain, we must ingest all the nutrients we require. These essential nutrients are found in a variety of different foods that are part of a balanced diet. Our body can convert these essential nutrients into other important biological molecules. The most important nutrients for us are carbohydrates. They are found in almost every food we eat and without them we would quickly run out of energy. Various foods have distinct flavours and textures because they contain different types of carbohydrates. They are found in almost every food we eat and without them we would quickly run out of energy. Various foods have distinct flavours and textures because they contain different types of carbohydrates. How all biological molecules are used by cells and the body depends on the structure of those molecules. The functional groups that make up different biological molecules are related to the types of intermolecular forces of attraction that are made between those molecules. Also, the shape and size of the molecule is important. There are four main types of nutrients that we require in large amounts. For this reason they are called macronutrients. They are also unique among other nutrients because they are made of smaller molecules, called monomers, put together to make larger ones, called polymers. There is a wide variety of different carbohydrates so it’s sometimes difficult to describe them as a group with similar characteristics. However, as you have seen, all carbohydrates share a similar chemical composition: molecules composed of carbon, hydrogen and oxygen. The name carbohydrate also reminds us of this composition: when we say something is hydrated we understand that it is full of water. That makes carbohydrates molecules with a simple formula of CH2O, or any other number of those three atoms in a similar ratio: 1 C : 2 H : 1 O. Structures of Carbohydrates In some cases, the carbon, hydrogen and oxygen can be arranged differently with the same number of atoms. Notice that each of these carbohydrates has the same number of each element. They can all be summarized as C6H12O6. However, the way the functional groups are organized is different. We describe these three carbohydrates as isomers. Because they have different structures they have different properties. Activity 3: Proteins: Bulking up Cells Amino Acids' Properties Proteins are found in a wide variety of foods. The muscle tissue in the meat and fish that people eat is rich in protein. So are beans, seeds, milk products, eggs and nuts. In the previous Activity we learned that proteins are made up of amino acids. One of the amazing things about proteins is that they are made of the same 20 amino acids in almost all living things. Some species are able to synthesize these amino acids from smaller molecules. In humans, we can made 11 of the 20 amino acids in our cells. The other 9 amino acids must come from our diet and are called essential amino acids. In the image below, you see the chemical structure of the nine essential amino acids. Arginine is essential only for infants: as we grow up we produce the enzymes needed to produce arginine on our own. Look at the chemical structures of the essential amino acids. Notice that some functional groups are similar on each amino acid while some are different. Likewise, the polarity of the different parts of the amino acids is similar for some amino acids but not for others. The properties and chemical structures of the 20 amino acids are important in our understanding of how proteins are used. Amino acids with polar or ionic functional groups make stronger intermolecular forces of attraction. They can also be described as being hydrophilic. On the other hand, amino acids with non-polar functional groups make weaker intermolecular forces of attraction. They can also be described as being hydrophobic. Amino Acids: Coming Together Amino acids have a common chemical structure. A molecule that has a carbon in the centre with four different groups bonded to it. To the left of the central carbon is an amino group with a red box around it, bonded above the central carbon is an R group with a red box around it, to the right of the central carbon is a carboxyl group with a red box around it, and bonded below the central carbon a hydrogen. by Study.com The "R" Group in this molecule represents one of twenty different side chains, one for each amino acid. When amino acids combine, they are always bonded to connect the carboxyl group of one amino acid to the amino group of the next: Glycine has hydrogen for its R group side chain. A red box extends from the OH part of the carboxyl group of the left glycine over to one of the H from the amino group of the right glycine. Below this is an arrow pointing down. Beside the arrow is shown -H2O which came from the OH and H of the two glycine molecules. Below the arrow is the combined dipeptide showing the peptide bond between the carboxyl group of the first glycine and the amino group of the second glycine. The connection between amino acids is called a peptide bond. The amino acids link up into a linear chain of amino acids similar to how monosaccharides link up in carbohydrates. In carbohydrates this structure is called a polysaccharide, so similarly in protein we use the term, polypeptide. This structure is also called the primary structure. This primary structure then folds in different ways to make secondary structures and finally a whole 3D tertiary structures. For many proteins, the tertiary structure gives the protein the shape needed for it to function. Uses of Proteins Proteins have a wide variety of functions. They can work together in their quaternary structure. Some proteins will only function when they combine with other protein subunits. Examples of these type of proteins include microtubules, enzymes, actin, myosin, and hemoglobin. Actin and myosin are especially interesting as they can change shape to allow parts of cells or whole organisms to move. A change in the folding of a protein, in this case from α-helices to β-sheets, can cause a protein to cause a disease. Chemical Signaling in the Body One of the functions of proteins is as signaling molecules in the body. The signals can travel from one cell to another, or across the whole human body through the bloodstream. A good example of this is the body’s biochemical response to stress. Watch the following video to get an overview of how chemical signals affect cells and parts of the body. These signals belong to two main systems in the body: the endocrine system and the nervous system. Hormones, like adrenaline, are chemical signals produced by glands in the endocrine system. Neurotransmitters, like dopamine, are chemical signals produced by neurons in the nervous system. In both systems, proteins are involved in chemical signaling. The molecular signal itself can be a protein or amino acid. Also, the receptor of the chemical signal is a protein. Where and how hormones and neurotransmitters act on cells depends on the polarity of the chemical signal molecule. Hydrophobic chemical signals include modified amino acids, like the hormone thyroxine, and also lipids molecules called steroids. We will explore lipids further in the next Activity. Hydrophilic chemical signals include proteins and modified amino acids Activity 4: Lipids: Essential Fats Lipids as an Energy Source The most energy-dense nutrients belong to the lipid category of macronutrients. Whereas carbohydrates can be oxidized to produce 4 calories of energy per gram, lipids can be oxidized to produce a hefty 9 calories per g. For humans, of the over twenty different fatty acids in food, there are only two essential fatty acids that we have to get from our diet. In this case, these two fatty acids are used for biological processes, like cell membrane structure and making hormones, not energy production. In an experiment performed by an academic researcher from University of Amsterdam, Johannes Romijn, the energy production from either fats (including lipids) or carbohydrates was measured during different exercise intensities: 25 % oxygen demand for light exercise, 65 % oxygen demand for moderate exercise, and 85 % oxygen demand for strenuous exercise. In this experiment the independent variable was the exercise intensity. The dependent variable was the source and amount of energy production. An easy way to quickly identify the variables is by thinking of the experiment as a cause-and-effect relationship. The cause is always the independent variable, and the effect is the dependent variable. Clearly, in this experiment the energy production is affected by the intensity of the exercise, not the other way around. Hydrophobic Interactions Lipids are the first macronutrient we are studying that are predominantly non-polar molecules. The molecule of oleic acid, for example, is made of a long chain of 18 carbon atoms. Carbon and hydrogen share electrons relatively equally so it’s true to describe this section of oleic acid as non-polar or hydrophobic. Yet oleic acid also has a polar, hydrophilic, carboxyl group to the left. Clearly our current definitions aren’t adequate to describe the whole molecule. Instead, we can use the term amphipathic to describe a molecule with both polar and non-polar functional groups. We’ve already seen amphipathic molecules when we looked at the folding of polypeptide chains. Hydrophobic amino acids come together because of hydrophobic interactions and dispersion forces between non-polar side chains. Hydrophilic amino acids tend to attract to each other, or watery environments. Hydrophobic amino acids, tend to be excluded from this attraction and stay together because of weaker dispersion forces Hydrophilic amino acids come together because of stronger dipole-dipole, hydrogen bonding, and ionic-dipole interactions between polar and charged side chains. The hydrophilic amino acids also make strong intermolecular forces of attraction with water so they are located around a core of hydrophobic amino acids. Many lipid molecules are also amphipathic. Let’s take a closer look at the molecules that tend to stay close to the interface between oil and water. Uses of Lipids Just like for proteins with their many possible structures, the different shapes of the different types of lipids means that there are many important biological uses of lipids. Lipids are the building blocks of cell membranes, which is a big deal. Also. lipids play an important role in energy storage, insulation, communication and cell division. Structures of Lipids Lipid molecules are slightly more difficult to describe than other macronutrients. They aren’t considered to be polymers because the smaller molecules that are used to put them together don’t repeat in long chains like in carbohydrates or proteins. Instead, lipids are divided into different categories based on similar molecular shape. The examples of unsaturated fatty acids you have seen so far are called cis fatty acids because the carbon chain is arranged on the same side of the double bond. As a result, the molecules make a concave shape at the double bond. This kink in the shape is important in the increased fluidity between these fatty acid molecules. There is, however, a chemical method of arranging the double bond such that the molecule makes a zigzag shape. This type of fatty acid is called a trans fatty acid. This video summarizes the differences between these isomers. Functions of Lipids An easy way to remember some of the functions of lipids in cells is with the mnemonic, SHIPS: S - Storage and Source of energy H - Hormonal roles I - Insulation P - Protection S - Structural components Fluid Mosaic Model of Membranes The amphipathic property of many lipid molecules is interesting, especially when many of these molecules group together. Let’s explore this further now because it’s an important concept for how cells are organized. Phospholipids containing two fatty acid chains come together but form a different shape. Phospholipids make a structure called the phospholipid bilayer. Phospholipid bilayers are found in the membranes in the cell. Membranes define the compartments of the cell. These include the cell membrane and cell organelles: the nucleus, endoplasmic reticulum, vacuoles, lysosomes, golgi apparatus, mitochondria and chloroplasts. Membranes help to control what molecules are located on either side of them. These membranes are described best as a fluid mosaic. These components can move laterally through the membrane. The following video, by Dr. Mark Cooper, Associate Professor, Department of Zoology, University of Washington, shows fish epidermal cells moving at the edge of epithelial tissue. Within the cells, other membrane structures like lysosomes and elongated mitochondria also are moving. To close a wound, epidermal cells spread from intact epithelial tissue. The term fluid is appropriate because the different components, especially the phospholipids, can move past each other and freely. It allows membranes to bend and stretch in response to their environment. Modeling Cell Membranes Using imaging tools like the one showing fish epidermal cells have helped Biologists put together a generalized model of a typical membrane. A model of a fluid mosaic membrane could look something like this: The term mosaic is also appropriate because membranes are made of different components. Even within the bilayer of the same membrane, there are different components in inner and outer layers of phospholipids. side-by-side images of uniform grey backgrounds. On the left image are dozens of randomly distributed hexagonally shaped structures. On the right image are dozens of randomly distributed star shaped structures along with a few circular shapes. A membrane is composed of mostly phospholipids (yellow) interspersed with cholesterol and various types of proteins. The surface of the membrane is also covered in protruding molecules carbohydrate in the form of glycolipids and glycoproteins. Summary This Activity explored the big idea that the structure of biological molecules is important to their cellular functions. Specifically, - lipids have a variety of different structures; - lipids have a variety of uses in cells; - membranes are composed of many parts that help it to function. Activity 5: Nucleic Acids Energy in Food Chains When we think of calories, the energy in food, carbohydrates and lipids come to mind. Each of these is like a large deposit of energy to our cells. The amount of this energy generated is often too great for any one particular biological process. Instead, cells deal with smaller packages of energy. Just like in a coffee shop, individual sugar packets are more convenient than a large bag of sugar. This smaller package of energy comes in the form of a nucleic acid called adenosine triphosphate, or ATP for short. In autotrophs, like plants, sunlight energy is captured first as ATP. Most of this energy is used by the autotroph in its daily biological processes, such as growing new tissue like cellulose or storing energy in the form of amylose or fatty acids. As matter is passed to heterotrophs in the next trophic level in the food chain only about 5-20 % of the original energy the autotroph received is passed on. In the consumers, enzymes convert the energy consumed into ATP. In nature, populations are constantly changing. The number of individuals can increase or decrease. The environmental conditions can improve or worsen. How organisms interact with each other can be beneficial, neutral or deleterious. The population density can become more dense or less. Yet, on average, viable food chains share similar characteristics. These food chains can be described in the form of ecological pyramids. A comparison of average aquatic and terrestrial food chains. In all cases, the autotroph is on the bottom trophic level of the pyramid. Heterotrophs are organized above the autotroph in order of trophic level. Nucleic acid structures ATP is an example of a nucleotide the monomer of nucleic acids. Out of all the macronutrients, the monomer of nucleic acids is the most complex: each nucleotide is a monomer composed of three parts: one or more phosphate functional groups, a 5-carbon sugar, and a nitrogenous base. There are five common nitrogenous bases: guanine, adenine, cytosine, thymine and uracil. Two of the nitrogenous bases are purines and three are pyrimidines. ATP is made of the purine adenine. Similar to the R-group side chain of amino acids, these nitrogenous bases give nucleic acids important properties. Like proteins, polymer forms of nucleic acids can make 3D structures as a result of intermolecular forces of attraction. Unlike proteins, though, nucleic acids have more predictable rules for which nitrogenous bases are attracted to each other. Let’s explore the sizes of different combinations of nitrogenous bases by building those molecules. It was discovered that nitrogenous bases pair up in molecules like DNA. We can describe these pairing nitrogenous bases as complementary. In 1950, Erwin Chargaff studied the composition of the four nucleotides found in DNA. In Chargaff’s time, it was hypothesized that all four nucleotides combined together to make a “tetranucleotide”, a structure of each nucleotide bonded together in a ring. In order for this to happen there would need to be equal amounts of each nucleotide. As you saw earlier, nucleotides including ATP are made of a phosphate, 5-carbon sugar and a nitrogenous base. The 5-carbon sugar molecule comes in one of two varieties: ribose and deoxyribose. Deoxyribose is used to make polymers of deoxyribonucleotides, also called DNA. Ribose, on the other hand is used to make polymers of ribonucleotides, also called RNA. Ribose is also used to make monomers, like ATP, and dinucleotides that perform other functions for the cell. In proteins, amino acids are connected between their amino group and carboxyl group to make a peptide bond. Similarly, nucleotides are connected between their phosphate group and a hydroxyl group on the 5-carbon sugar to make a phosphodiester bond. Notice that the phosphate between the two nucleotides connects the 3rd carbon on the sugar with the 5th carbon on the next sugar. In DNA and RNA, nucleotides always connect this way. In other nucleic acids, like dinucleotides, cyclic AMP (cAMP), and ATP, the phosphate is connected differently to the ribose sugar. First, it’s important to realize that both DNA and RNA can exist as either single strands of one polymer or double strands made of two polymers. Single stranded This RNA molecule is folded in such a way so that the bottom of the molecule can attach to other RNA molecules. The top right end is shaped to attach to an amino acid. When two strands come together, though, they always line up and connect with one strand inverted compared to the other. This orientation is called antiparallel. The two strands are linear in the foreground but twisted in a double helix in the background. On each strand is highlighted the sugar-phosphate backbone on the outer edge of the double helix. In the middle of the double helix, complementary base pairs are shown making hydrogen bonds. Second, whether DNA or RNA stay as single strands or pair up in double strands depends on a variety of factors RNA world The examples of RNA you have seen so far are involved in making proteins. But, as Canadian molecular biologist Sidney Altman discovered, RNA is used in a surprising variety of functions. It’s used as the genetic molecule in many viruses. Even though there are only 4 nucleotides available compared to 20 amino acids for proteins, RNA can perform a wide variety of chemical reactions. It can also be used to turn off genes. Controlling genes happens naturally and is also being considered as a way of treating certain diseases. Summary In summary, this Activity explored the big idea that the structure of biological molecules is important to their cellular functions. Specifically, - nucleic acids are made of three-part monomers; - nucleic acids have a variety of uses in cells; - energy in the form of ATP is used in biological processes Activity 6: Putting it together Size in Cells In our daily lives we develop an understanding of the sizes of different objects we see and use. It’s easy for you to compare two objects, say a pillow and a smartphone. With a bit of thought, you could confidently estimate how many times bigger the pillow is compared to the phone or even your room. It’s the same thing with cells. Different components of the cell have different sizes compared to one another. It is possible to estimate how many mitochondria could fit in the diameter of a nucleus. In human cells, it’s about 6. Understanding this cellular scale will be important as we start to look at different technologies for viewing parts of the cell. Viewing Inside Cells Biochemists have many tools available to help them to see different objects in and around cells. Some tools work well with living, or in vivo, samples. Others require special techniques only available in a lab. These samples are termed in vitro. Each tool has its advantages for the size of the structures being studied. Activity 7: Making Connections Informed Choices One of the reason that Scientists conduct experiments is to test hypotheses in order to make informed recommendations to people, companies, governments and non-government organizations. Indeed, the best choices we can make in our lives involve considering the best available evidence. You can think of making choices as a natural extension of scientific experiments: a hypothesis is made, then evidence is collected and analysed for similarities and differences. Every part of a food system involves choices. For example, Health Canada provides recommendations to Canadians regarding choices we can make about the food we eat. They publish the Canada Food Guide that is regularly updated and is based on some of the best nutritional research. Many recommendations look at overall health, rather than just counting food energy in the form of calories. Identifying Macronutrients in Food Nutrition fact labels can help us to make informed choices about the products we eat. The Canadian Food Inspection Agency is responsible for making sure that food manufacturers produce labels with similar content and layout. It helps consumers to compare products in a fair test. Among the details on a food label is the quantitative amount of three macronutrients: carbohydrates, lipids and proteins. Qualitatively, macronutrients can be identified using colour indicator chemical tests. This video shows some of the tests that can identify the presence of carbohydrates, lipids and proteins in food. As you watch the video, notice the colours of the different indicators depending on whether or not each macronutrient is present. Unit 2: Energy in the Cell Activity 1: Biochemical Reactions Energy in Reactions In Biology there are several types of energy that are important to understand. As you learn more about Biology in future years you will learn about more types of energy. For now, these are the most common types of energy important to this course: Light used by many autotrophs is a form of electromagnetic energy. You will remember that visible light is the middle portion of the electromagnetic spectrum Heat is also known as thermal energy. Potential energy is the energy stored in the bonds of biological molecules. For example, when we say that energy is transferred from a molecule of glucose to ATP, what is happening is that the potential energy is transferred from the bonds in glucose to the bonds in ATP. Kinetic energy is the energy of a moving object. A good example of this is how ATP is used by a motor protein to move a vesicle along a microtubule in a cell. The reactions that occur in the body are collectively known as metabolism. In everyday life we also use the term metabolism to describe how quickly a person can burn food. In this Activity we are looking at the types of reactions, not the speed of those reactions. That being said, all metabolic reactions involve changes of energy. Metabolism can be further divided into two groups: anabolic - a reaction that makes a larger molecule from smaller ones reactions and catabolic - a reaction that makes smaller molecules from a larger one. Interestingly, one common biochemical reaction is neither anabolism nor catabolism. It is isomerization. Even though it looks like individual functional groups are being oxidized or reduced, the total number of carbon, hydrogen and oxygen atoms in the molecule does not change. Prove it to yourself and count the numbers of each atom! Common Biochemical Reactions 1. Dehydration Synthesis and Hydrolysis 2. Phosphorylation and Hydrolysis 3. Phosphorylation and Decarboxylation 4. Oxidation and Reduction 5. Dehydration Synthesis and Hydrolysis Summary This Activity explored the big idea that how biological molecules interact is important to cellular processes. Specifically, - biochemical reactions involve energy changes; - biochemical reactions can be grouped based on the type of change to the biological molecules or functional groups. Activity 2: Exploring Different Attitudes Spontaneous Changes/Thermodynamics We have seen that metabolic reactions involve changes in energy: anabolism requires energy while catabolism releases energy. Different types of reactions follow predictable patterns and can be grouped using this definition. Yet, considering if a reaction occurs needs more information. As you read this next section look for details about the amount of energy needed to activate a reaction. You will use this information later in this Activity. We know from experience that paper can burn in a combustion reaction that releases large amounts of energy. Only two reactants are needed for this reaction: paper and oxygen. Yet, we constantly keep paper exposed to the oxygen in air. The reactants are there but combustion does not happen spontaneously. In order to get the reaction to start, an energy source, like a flame, is needed. On the other hand, the classic elementary school volcano demo involves a double displacement reaction Scientists who study energy changes have noticed that, in general, catabolism is a spontaneous process. Disorder is more natural than large, organized structures. The paper is more organized on a molecular level than the ashes it makes when burned. Likewise, the volcano demo creates a disorganized chemical mess. As we know, the paper will burn if it gets hot enough, like with the help of a flame. The thermal energy added is sufficient to start the combustion reaction. The energy released from this catabolic reaction is enough to keep the paper burning until the paper is used up. In the volcano demo, the room temperature is sufficient to both start and continue the double displacement reaction until the reactants are used up. The difference in spontaneity, therefore, is the amount of energy needed to activate the first molecules to react. In cells, most biochemical reactions are not spontaneous. In other words, even if the two reacting molecules are present in the same location in the cell, they won’t react without being activated. If the reaction requires energy we describe it as an endergonic reaction. It is the opposite of exergonic reactions. Let's connect some of the biochemical reactions we learned about in the previous Activity to energy change. As you learned in the first Unit, enzymes are a special group of proteins. They help to speed up biochemical reactions. Specifically, they help make non-spontaneous processes become spontaneous by reducing the amount of energy needed to activate the first molecules to react. For example, in cellular respiration, glucose can combine with oxygen to release large amounts of energy. Enzyme Structures The biochemists that study enzymes use the term substrate instead of reactant in biochemical reactions. This may seem like a strange distinction, but it helps biochemists describe biochemical reactions differently from how chemists describe chemical reactions. We will use the term substrate here for this reason. All enzymes are composed of a specialized region called the active site. The active site is where the biochemical reaction occurs. It’s formed by the tertiary or quaternary structure of the enzyme. The shape of the active site is important to how it functions. Also, interestingly, the shape of the active site changes before, during and after a biochemical reaction. We describe these changes as the induced fit of an active site with its substrate. Watch this video to see how the shape of the active site changes. It’s important to note that enzymes do not get used up in a reaction. After the products are made, the enzyme is ready to react again with new substrate. Check your understanding with the interactive below. Drag each word as it appears on the left and drop it in the box at its proper location. Click the submit button to check your answers. Rates of Enzyme Activity In the previous video we could see that the rate of an enzyme reacting generally increases with a factor like temperature. This should make sense because this pattern is true for many other physical and chemical changes. Increased thermal energy means that the molecules involved in the change come together and collide more often and with more energy. In addition to changes in temperature, protein structure is sensitive to changes in pH. Notice that for most species only a narrow pH range is suitable for life. Remember that some amino acids have hydrophilic R-groups. They are able to interact with each other and water molecules to make strong intermolecular forces of attraction. They are also able to interact with acids and bases in the surroundings. In order to protect the shape of proteins and enzymes, organisms have evolved adaptations to prevent denaturation. Cells contain a lot of water. Water can absorb large amounts of energy before increasing its temperature, so cells use water to absorb heat instead of their proteins. We will explore other temperature control adaptations later in the course. Enzymes Involved in Diseases Enzymes are essential to the proper running of our body’s physiological processes. If something goes wrong with one of these enzymes this often leads to a disease. One of the reasons Biologists study enzymes is to learn more about diseases caused by enzyme malfunctions. As more is understood about how enzymes work, including details about their active sites, Biologists hope to be able to find treatments for patients with these diseases Targeted Control of Enzymes Denaturation is one way to turn off enzyme activity. For example, in the digestive system, different organs have different pH values. The mouth is around pH 7, the stomach pH 2, and the small intestines around pH 8. Enzymes in each organ function best at the pH of the organ. As food moves through the digestive system, enzymes can move as well. Salivary amylase, for example, can move into the stomach where it becomes inactive because the highly acidic environment denatures it. New saliva is made to replace the lost enzymes. From an energy perspective, however, this method of inactivating enzymes is not very efficient: energy and resources are used to make new enzymes. A more targeted control of enzymes involves activating or inhibiting the enzyme without destroying it. There are many different methods of activating or inhibiting an enzyme. Each of them describe an elegant way in which nature makes subtle changes to the molecule. Use the following diagrams to explore and enhance your understanding of enzyme activation and inhibition. Activity 3: Cellular Transport Membrane Components Refer back to your graphic organizer from Unit 1, Activity 4 about lipids, and recall that cell membranes are made of many components: phospholipids, proteins, carbohydrates, and cholesterol. These components work together to allow the membrane to function: - to protect the cell from its environment, - to select which substances can enter or leave the cell, - to allow cell-to-cell communication, - to perform specific biochemical reactions. In this Activity we will focus on the membrane’s ability to select which substances can enter or leave the cell. This selectivity of the membrane means that it is semi-permeable to substrates: impermeable to some but permeable to others. Selectivity allows the cell to establish an internal environment that is suitable for biological processes to occur. Membranes are also important in maintaining this internal environment, or homeostasis. This internal balance is sometimes called an equilibrium. However, in many cases, homeostasis does not mean that the equilibrium is the same between the inside and exterior of the cell. Spontaneous Movement of Molecules It’s important, at this time, to remember that many of the cellular processes we are looking at in this Unit involve the interaction of molecules. Often it’s convenient to use words like “need’ or “want” to describe the action of these molecules. But this is not an accurate way to interpret molecular interactions. Instead, it’s better to describe the movement of molecules in terms we will learn about in this Activity. We have seen earlier that biochemical reactions either use or release energy. It is also true that, in general, order and organization decreases over time. In Biology, many biochemical processes and structures work against this disorganization: cells are far more complex and precisely arranged than a puddle of biological molecules. It takes energy to work against disorder. Diffusion is an important process that cells use, especially in the movement of carbon dioxide and oxygen in lungs. Water is another molecule that can move in a similar way, though this is called osmosis. This process is shown in the animation below. Notice how the water moves across the semipermeable membrane, but the salt doesn't? The volume of water on the right side went up as the water moved from an area of higher concentration of water to an area of lower concentration of water. Types of Cellular Transport In the video about osmosis you saw that both diffusion and osmosis were examples of passive transport. Both processes involve molecules moving from an area of higher concentration to lower concentration. We can also say more simply that the molecules are moving along their concentration gradient. Water moves towards the side of the membrane with greater solute concentration. The concentration of solutes on either side can be described qualitatively as: - hypertonic - a solution with greater solute concentration than inside a cell, - hypotonic - a solution with lesser solute concentration than inside a cell, or - isotonic - a solution with equal concentration of solutes as inside a cell. Other biological molecules are too large or too hydrophilic to pass through the semi-permeable membrane. Instead, proteins in the phospholipid bilayer allow for them to pass through facilitated transport. The following video from St. Olaf College summarizes the main methods of cellular transport. The video will autorun so you do not need to click the navigation buttons when they appear. Rate of Cellular Transport The rate of cellular transport is different depending on the type of transport. You will use details about different forms of cellular transport to interpret and analyse the following graphs. Membranes and Homeostasis There are many ways that cellular transport across membranes is important to homeostasis. So far in this Activity you have seen how membranes are important in plants to absorb water through roots and in Grade 11 you learned how diffusion is important to how the lungs exchange gases. In both of these cases passive transport is used by cells. However, homeostasis often uses active transport in order to maintain the correct balance of biological molecules inside and outside of cells. Most cells move sodium ions out and potassium ions in. The process works against a concentration gradient so energy in the form of ATP is used to drive this movement. The following flowchart summarizes this process. The sodium-potassium pump is an example of primary transport. The imbalance of ions sets up a concentration gradient. Those ions can then use special facilitated transporter proteins that move another substance. This transport is called secondary transport. The animation below, from St. Olaf College, shows a simplified process at the sodium-potassium pump, but remember that the pump actually moves Na+ ions separately from K+ ions. Summary This Activity explored the big idea that how biological molecules interact is important to cellular processes. Specifically, - membranes control which substances can pass into or out of a cell; - moving substances with their concentration gradient does not require energy; - moving substances against a concentration gradient uses energy. Activity 4: Photosynthesis Leaf Structure The main photosynthetic organ in vascular plants is the leaf. The two main reactants of photosynthesis are controlled through specialized structures in the leaf. CO2 is allowed into the air spaces of the spongy mesophyll by stomata. Stomata open and close to balance the intake of CO2 with water loss through transpiration. H2O is transported by passive transport through xylem from the roots. As water is consumed in photosynthesis, or lost through transpiration, the decrease in the relative amount of water in the leaf drives osmosis of water from the roots. The overall chemical equation for photosynthesis is: 6 H2O + 6 CO2 + energy→ 6 O2 + C6H12O6 In autotrophs like plants, however, photosynthesis is made up of smaller reactions that are performed in different locations in the cells in a leaf. Energy Before we examine photosynthesis up close we need to remind ourselves of two important forms of energy. Light energy is an obvious form of energy to consider in any discussion of photosynthesis. In addition to chemical potential energy in molecules, concentration gradients store potential energy. You will remember in the previous Activity that we saw that diffusion is an example of passive transport as it leads to an increase in disorder. If a membrane separates a concentration gradient then the molecules on the more concentrated side have the potential to move down the concentration gradient. As we learned in the last Activity, how they get across the membrane depends on the type of molecule. Electromagnetic Spectrum In order for the energy in light to be converted into other forms of energy it must first be absorbed. In the late 19th century, German physiologist Theodor Engelmann first studied the effect of different colours of light on photosynthesis. It was known at the time that aquatic plants produced bubbles of oxygen gas in the presence of light. Also, it was known that aerobic organisms could survive from the oxygen produced by plants. Engelmann’s simple yet effective experiment is summarized in the following video. Engelmann concluded that the red and purple colours were absorbed. These wavelengths of light were used in photosynthesis to produce oxygen, thereby attracting the mobile bacteria. The green and yellow wavelengths of light, however, were not used to produce oxygen and must have been reflected. The dominant green colour in many photosynthesizing plants is caused by a pigment called chlorophyll. Also interestingly, Engelmann noticed that the bacteria were most densely distributed around the chloroplasts of the spirogyra. We will further examine the role of chlorophyll and chloroplasts later in this Activity. Steps in a Process A few decades after Engelmann’s experiment with algae and light, British physiologist Frederick Blackman began an experiment using Elodea, an aquatic plant. Blackman was able to measure the rate of photosynthesis by counting the number of oxygen bubbles produced over a period of time. He kept the colour of the light constant as white. Instead he changed the intensity of the light by moving the light closer to the Elodea. He also kept the amount of CO2 dissolved in the water constant and low. Through manipulation of light intensity and CO2 variables, Blackman also concluded that photosynthesis must proceed in two separate and coupled reactions: light-dependent reactions and light-independent reactions. Blackman theorized that at moderate light intensities, the "light" reaction limits or "paces" the entire process. In other words, at these intensities the light-independent reaction is capable of handling all the intermediate substances produced by the light reaction. With increasing light intensities, however, a point is eventually reached when the light-independent reaction is working at maximum capacity. Any further illumination is ineffective, and the process reaches a steady rate. We now know more about the chemicals that are produced by the light-dependent reactions. These products are also reactants in the light-independent reactions. Watch one of the two following videos to learn more about these coupled reactions. This will give you an overview of the steps in photosynthesis. At the end of this Activity you will be mapping out the steps of photosynthesis in a flowchart. Metabolic Processes Involving Membranes The light-dependent reactions occur in chloroplasts. Chloroplasts have interesting structures in that they have multiple membranes. A chloroplast structure is defined by many membranes. In addition to an outer phospholipid bilayer, they also have an inner bilayer membrane as well as folded membranes called thylakoids. The thylakoids look like discs and they’re called a granum when they’re stacked together. The interior of the chloroplast is a fluid-like gel called the stroma. It’s similar to the cytoplasm of a cell and contains enzymes, substrates and chloroplast DNA. Chlorophyll comes in two forms: chlorophyll a and chlorophyll b. They differ slightly in their structure, but for the purpose of this course we don’t need to differentiate them. We can see from the structure that chlorophyll is mostly non-polar. It is therefore able to make intermolecular forces of attraction with phospholipids in the thylakoid membranes. There, dozens of chlorophyll molecules collect with other lipids and proteins in structures called photosystems. There are two photosystems important to know: Photosystem I (PS I) - the pigment and protein complex that is responsible for producing NADPH, and Photosystem II (PS II) - the pigment and protein complex that is responsible for producing the proton gradient required to produce ATP. As the name suggests, the photosystems absorb light. They both absorb light at the same time, but remember that PS I and PS II are also coupled reactions within the light-dependent reactions. Enzymatic Reactions The light-independent reactions also occur in the chloroplasts. However, unlike the light-dependent reactions, the light-independent reactions occur in the stroma. As we saw earlier, the stroma is a gel-like fluid that contains enzymes and substrates for different reactions. The light-independent reactions are sometimes called the Calvin Cycle after Melvin Calvin who first discovered the sequence of steps. There are 3 main phases in the Calvin Cycle: - carbon fixation in which CO2 is combined with a 5-carbon molecule called ribulose-1, 5-bisphosphate, or RuBP, - reduction of 3-phosphoglycerate, or 3PG, to the carbohydrate glyceraldehyde-3-phosphate, or G3P, - regeneration of RuBP from G3P. Summary This Activity introduced the big idea that certain molecules are important to biology and their structure affects their function. Specifically, the thylakoid membranes contain molecules that use light energy to produce products for the light-independent reactions; - energy is converted from light energy to potential energy in the proton gradient and then to potential energy in biological molecules; and - the rate of photosynthesis is controlled by many factors. Activity 5: Cellular Respiration Biochemical Reactions Cellular respiration is used by all organisms. Autotrophs store carbohydrates and lipids using G3P from the light-independent reactions. Later, perhaps in response to an improvement in growing conditions, they tap into those stored energy sources. Heterotrophs similarly convert macronutrients they consume or have stored into ATP. Just like in the light-dependent reactions, many organisms create a proton gradient that ATP synthase can use to phosphorylate ADP Dozens of enzymes catalyze these reactions. For example, a cysteine amino acid in the active site of the enzyme glyceraldehyde-3-dehydrogenase is involved in both a reduction and phosphorylation reaction. Watch this animation from St. Olaf College. Using a proton gradient to produce ATP happens in both photosynthesis and cellular respiration. Even the overall chemical equation for aerobic cellular respiration reminds us of photosynthesis: C6H12O6 + 6 O2 → 6 H2O + 6 CO2 + energy Energy for Movement The primary purpose of cellular respiration is to produce ATP as needed for cells. If we think of food as fuel then how energy is stored and released from fuel is similar in many ways to energy transfer in food. When burning wood, heat is used to start the fire and it is also produced. In this video from the Genetic Science Learning Centre, we can see how ATP is also used to start cellular respiration and it is a product. For example, a lynx burns a lot of energy when it is chasing prey. Its muscle cells demand ATP so mitochondria convert potential energy into kinetic energy. Predators like the lynx only run for short periods of time before they slow down and their energy stores are depleted: either they have caught their prey, or the prey escaped. Similarly, we become aware of the limitation to using our muscles as they tire during strenuous or repetitive work. Perhaps our muscles shake as we try to do one more push-up. Or maybe we find we just can’t run any further so we stop to catch our breath. These are changes that we seem to do involuntarily. Our muscle cells continue to produce ATP to move, only we change the way it is made. Steps in a Process Early experiments of cellular respiration focused on the consumption of oxygen gas and the production of carbon dioxide. Many biologists believed respiration to be a variation of combustion. Heat is evidence of energy production in cells. In one experiment, the amount of oxygen used and carbon dioxide made by guinea pigs was found to be equal to the gases used and made from the burning of carbon. Yet other experiments showed that the amount of oxygen used by living organisms to burn different types of food did not follow any logical patterns. Indeed, experiments with yeast showed that they could produce carbon dioxide even in the absence of oxygen. The process of producing energy in yeast and other microbes is called fermentation. Fermenting microorganisms have the ability to change food and drinks and so are used to make a range of foods including pickles, yogurt, alcohol, bread and cheese. As we saw for photosynthesis, cellular respiration must include different reactions: some that involve oxygen, and some that do not. Enzymes play an important role. Later research has identified that cellular respiration of glucose involves reactions that occur in the cytoplasm and some that occur in mitochondria in eukaryotic cells. This first process is called glycolysis. It occurs in the cytoplasm and produces a molecule called pyruvate. 2 ATP molecules are produced per glucose molecule by substrate-level phosphorylation. From there, pyruvate can undergo different reactions depending on which species it’s in and also the amount of oxygen available to the cell. Glycolysis itself is composed of 10 individual reactions which you can see here: Some steps in cellular respiration are aerobic, while others are anaerobic. For most eukaryotes, oxygen is one of the requirements of life. Much more ATP is produced using aerobic processes helping to provide energy for more complex forms of life. Glycolysis doesn’t require oxygen but is the first step in glucose metabolism for both aerobic and anaerobic respiration. The fermentation done by microorganisms involves anaerobic respiration. Smaller eukaryotic and prokaryotic organisms can survive longer in low oxygen conditions, and many have adapted to produce energy without any oxygen. Under these anaerobic conditions all the energy produced from glucose is only made in glycolysis. The 2 NADH molecules are recycled back to NAD+. In this way the NAD+ can be used again for a new round of glycolysis with a new molecule of glucose. Cells have evolved two different methods of recycling NADH. In general, most eukaryotes and certain bacteria perform lactate fermentation whereas certain fungi, like yeast, and other bacteria perform alcoholic fermentation. These two processes are summarized in the animation below by Thomas E. Schultz of the College of Science and Engineering at Central Michigan University. Mitochondrial Reactions Mitochondria, like chloroplasts, have an interesting structure. In addition to an outer phospholipid bilayer, they also have an inner bilayer membrane that is folded into cristae. The interior of the mitochondrion is a fluid-like gel called the matrix. It’s similar to the cytoplasm of a cell or stroma of a chloroplast, and contains enzymes, substrates and mitochondrial DNA. Aerobic respiration occurs in the mitochondria. Again, as in the chloroplast performing photosynthesis, the folded membrane increases the surface area and therefore helps to increase the rate of cellular respiration. Aerobically, pyruvate can undergo further reactions. These reactions produce significantly more ATP for cells than anaerobic processes. After glycolysis there are 2 further steps in aerobic respiration: the citric acid cycle and the electron transport chain. As both these steps occur in mitochondria, pyruvate must first be transported across the mitochondrial membrane. Some biochemists view this as a separate step, between glycolysis and the citric acid cycle, called pyruvate oxidation. For our purposes in this course we don’t need to worry about this distinction. The first reactions in the citric acid cycle include the movement of pyruvate into the mitochondrion. A mitochondrion structure is defined by many membranes. In the process, pyruvate with its 3 carbons becomes a 2-carbon functional group, acetyl. Coenzyme A helps to deliver acetyl to the next enzyme in the citric acid cycle. The sulfhydryl group in coenzyme A binds to the acetyl group. For this reason we often see the chemical formula of acetyl-CoA showing this sulfide bond. At this time, it’s worth noting that fatty acids and, under some circumstances, amino acids can also be used as sources of energy. Amino acids undergo deamination reactions in the liver. Those products are then converted into substrates for the citric acid cycle, including acetyl-CoA. Fatty acids are also taken into mitochondria and converted to acetyl-CoA. From an aerobic energy perspective, all roads lead to the citric acid cycle. At this point, most of the chemical potential energy from glucose and other biological molecules has been converted to the two electron carriers: NADH and FADH2. These two molecules next move to the electron transport chain. As the name suggests, electrons are moved, first from NADH and FADH2 to integral membrane proteins. The terminal electron acceptor is oxygen. Finally, in the last step of aerobic respiration oxygen is used. The oxygen that we know is so essential to life plays the important role of accepting the electrons to combine with H+ ions making water. The amount of ATP produced for each glucose molecule is actually a bit less than the theoretical amounts shown here. Membranes are a bit leaky, allowing protons to pass back from the intermembrane space back into the matrix. The energy lost here is given off as heat, which is an important method of producing body heat. An easy number to remember is 30 ATP produced per glucose molecule: 2 ATP from glycolysis, 2 ATP from the citric acid cycle, and about 26 ATP from oxidative phosphorylation Rate of Cellular Respiration The reactions in cellular respiration are performed by a series of enzymes in a pathway. Enzymes in this type of pathway are often controlled using a process called feedback inhibition. In general, products from some of the steps of aerobic respiration inhibit cellular respiration. High levels of ATP, NADH, acetyl-CoA and citrate all inhibit enzymes earlier in the pathway. As ATP is consumed through other cellular processes inhibition stops and cellular respiration proceeds. Furthermore, certain molecules stimulate aerobic respiration, including high levels of O2, ADP and AMP (adenosine monophosphate). Summary This Activity explored the big idea that how biological molecules interact is important to cellular processes. Specifically, - the cells can convert the energy stored in the bonds of carbon biological molecules into ATP with or without oxygen; - in anaerobic respiration, byproducts of ATP production are recycled; - in aerobic respiration, energy in biological molecules is converted to potential energy in the proton gradient and then potential energy in ATP. Unit 3: Genetics Activity 1: Processes in Molecular Genetics The Hereditary Molecule We take it for granted these days that DNA is the molecule that carries our genes. It is so prevalent in popular culture that it’s hard to imagine a time when it was needed to be shown that DNA was the hereditary molecule. As recently as 100 years ago, when biochemists separated nucleic acids, they could find no reactions that these macromolecules performed. It was known that nucleic acids usually came with large amounts of protein. Since proteins were known to do a wide variety of biological processes it was assumed that anything to do with heredity must also involve proteins. You can see more about the early ideas and experiments about DNA in the animation of this interactive Organization of DNA DNA is organized differently in prokaryotes and eukaryotes. Because prokaryotes lack a nucleus, their DNA is organized in a nuclear region within the cytoplasm. Their entire genome is organized in a circular chromosome. In order to save on space, the chromosome is twisted up on itself. Circular chromosomes can twist up upon themselves when they are pulled in a process called supercoiling. Some prokaryotes also have smaller circular pieces of DNA called plasmids, although these generally don’t carry essential genes. The genome in eukaryotes can be organized on one or many different chromosomes. Because of these differences in DNA organization, the way that DNA is copied and used also differs. We will explore processes involving DNA later in this Activity. In all organisms, the nucleotides in each strand are connected by phosphodiester bonds. Biochemists number the carbons in the sugar part of the nucleotide with an apostrophe called “prime”, so the phosphodiester bond is made from the dehydration synthesis between a hydroxyl on the 3’ carbon of deoxyribose and the phosphate group on the 5’ carbon. You can see how this works in the following video showing dehydration synthesis between two nucleotides. The double helix structure of DNA was correctly identified by Watson, Crick, Wilkins and Franklin as having an antiparallel orientation. It would be like writing one line in a paragraph rightside up and the next one upside down. It is only in this way that the nucleotides can be correctly orientated to make hydrogen bonds between the strands. We describe the two strands in terms of the functional group that could be used to make a new phosphodiester bond: either the 3’ hydroxyl or the 5’ phosphate. As we will see in this Activity, the orientation of nucleotides is important to the code in DNA, much like it is important to know which way to read a sentence in order to understand its meaning. Look back to your graphic organizer from Unit 1, Activity 5 on Nucleic Acids, to see how each nucleotide makes hydrogen bonds with only one other nucleotide: A pairs with T and G pairs with C. We describe this base pairing as complementary base pairing because the second nucleotide completes the pair with the first. Genotype to Phenotype Soon after the double helix structure was published scientists began to work on discovering how DNA worked in cells. It was known that the proteins produced by cells is a heritable trait, and so Crick continued research into protein synthesis. With the understanding that DNA was the heritable molecule Crick proposed a theory he called the Central Dogma: DNA makes an intermediate molecule that is used to make protein. Early work hypothesized that this intermediate molecule was made of RNA. Three different RNA molecules play an important role in translation. As you explore each type of RNA at the Genetic Science Learning Centre, look to see how each of them interact with one another. tRNA and rRNA are found only in the cytoplasm. mRNA is found in both the nucleus of eukaryotes, where DNA is, and the cytoplasm, where protein synthesis occurs. Today we call transcription the process of making mRNA molecules in order to make the primary structure of proteins. The process of protein synthesis is called translation. Both transcription and translation consist of three steps: initiation, elongation, and termination. As we explore these two processes you will need to organize the details of the three steps. Transcription, in its simplest form, involves only one enzyme, RNA polymerase, and ribonucleotides as substrates to build the copied RNA strand. There are two sections in the DNA sequence that help RNA polymerase to identify where to initiate transcription and where to terminate it. A section of DNA rich in A and T nucleotides is the initiation site called the promoter. From there, RNA polymerase moves in the 3’ to 5’ direction reading the DNA and building the RNA strand. Only one of the two strands is used to make RNA. The strand that is read in the 3’ to 5’ direction is called the template, or coding, strand. The other strand is not read so it's the non-template, or non-coding, strand. The hydrogen bonds are separated between the DNA strands so that the non-template strand is unzipped from the template strand. Just like between DNA strands in the double helix, the RNA is built so that it is antiparallel to the DNA template. This means that the RNA strand is synthesized in the 5’ to 3’ direction. Transcription ends at a sequence in the DNA called the terminator. In prokaryotes, transcription occurs in the nuclear region of the cytoplasm. In eukaryotes, however, transcription occurs in the nucleus. The RNA strand produced by RNA polymerase is called pre-mRNA at this point because it needs to be modified before it moves through pores in the nuclear membrane into the cytoplasm. The cytoplasm contains enzymes that are designed to hydrolyze DNA and RNA molecules as part of the cell’s natural protection from the genetic information from pathogens. RNAase enzymes can begin to digest RNA from either the 5’ or 3’ end. In order to protect the cell’s own RNA from these enzymes, the pre-RNA is modified with a modified nucleotide “cap” on the 5’ end and a long chain of adenosine nucleotides, or polyadenylate tail, on the 3’ end. The cap changes the shape of the RNA molecule so it can’t fit the active site of RNAase. The polyadenylate tail serves to protect the important information within the code of the RNA from RNAase by saturating their active sites with expendable, non-coding, RNA. In eukaryotes, RNA is modified a third way in the nucleus. The way that genes are organized is that the information containing the code for the gene is broken up with sections of nucleotides which do not code for the gene. The section of the gene containing the code is called an exon with the in between sections that do not code for the gene are called introns. Special enzymes called spliceosomes work to remove introns. Similar to ribosomes, spliceosomes are made of RNA combined with proteins. For the purpose of this course, we do not need to focus on the details of this process. Once the cap and polyadenylate tail are added, and the introns are spliced out, the finished mRNA is transported to the cytoplasm. After transcription mRNA binds to a ribosome to start translation. In prokaryotes, because both transcription and translation occur in the cytoplasm, it is common for these two processes to be coupled. Ribosomes and RNA polymerase are located close together near the nuclear region. Eukaryotes, on the other hand, separate the two processes with only translation occurring in the cytoplasm. Furthermore, ribosomes in eukaryotes are sometimes free in the cytoplasm or attached on the membrane of the rough endoplasmic reticulum. In both eukaryotes and prokaryotes the ribosome is made up of two subunits that combine together to make a functional ribosome, similar to how certain proteins function in a quaternary structure made of tertiary structures connected together. The smaller of the two subunits binds to the cap on the 5’ end of the mRNA and begins moving towards the 3’ direction in search of its initiation sequence. Ribosomes look at three-nucleotide long blocks called codons. For most organisms, the same codon is used to initiate translation, similar to how a capital letter is used to start a sentence in most languages. Each of the 20 amino acids are coded through the 64 codons. Special enzymes in the cell match the correct amino acid to the tRNA that corresponds to its correct codon. In this way the DNA is translated to protein using a codon “dictionary.” Once a start codon is found, a tRNA binds to the mRNA. A three-nucleotide sequence on the tRNA, called the anticodon, is complementary to the codon on the mRNA. The larger ribosomal subunit then connects to the small subunit-mRNA-tRNA complex. Now the ribosome is complete and can catalyze the synthesis of a polypeptide chain. The ribosome has three sites that are important for elongation in translation: the E-site, the P-site and the A-site. The mRNA is found in all three sites. The tRNA for the start codon during initiation is bound to the mRNA at the P-site. New tRNAs are added to the A-site but only if their anticodon is complementary to the codon in the mRNA in the A-site. Sometimes, to simplify how we explain the process of translation the E-site is not mentioned. Proteins made in the rough endoplasmic reticulum are sent in vesicles to the Golgi apparatus to undergo further modifications and proper tertiary structure formatting. In this way the genotype coded in the DNA is converted to a phenotype that is caused by the proteins that leave the Golgi apparatus. Genetic Continuity Also after the double helix structure was published scientists began to work on discovering how DNA was copied in cells. There were three main hypotheses for how this might happen. In conservative replication the parent DNA double helix is used to make an exact copy of itself but it is not changed in the process. This is similar to how a photocopier works. In dispersive replication the parent DNA is broken up into smaller bits that are later put back together. Some parts of the new double helices are made of the parent strands in between new sections of DNA. In semi-conservative replication the parent DNA double helix separated into single strands. Each single strand is used to make a complementary daughter strand. The new double helixes are made of a parent strand and a daughter strand. Matthew Meselson and Franklin Stahl tested this hypothesis using E. coli bacteria grown in nutrients composed of an isotope of nitrogen. At the start of the experiment the nitrogen in the nitrogenous bases of the bacterial DNA is tagged with heavier N-15. See how the DNA made after the first and second generation of replication change in their weight after the bacteria are moved to ordinary light N-14 nutrients. The process of replication is similar in a lot of ways to transcription. Again there are three main steps to this process: initiation, elongation and termination. There are a few more enzymes and proteins involved in replication which isn’t surprising given that in replication two strands are copied. As the helicase moves around the chromosome it opens up the double helix to create a replication fork that exposes the nucleotides to enzymes. Replication ends when the two replication forks meet. In eukaryotes, there are usually multiple origins of replication along each chromosome because the genome is often significantly larger than in prokaryotes Again, replication ends when two replication forks meet. In transcription the role of separating DNA strands and making RNA are both performed by RNA polymerase. On the other hand, in replication these roles are separated. To prevent the nucleotides from reannealing after being separated by helicase single stranded binding proteins attach to the single stranded portion of the DNA until it is copied. Just like in transcription, the main polymerases in replication, primase and DNA polymerase III, read the DNA template in the 3’ to 5’ direction. New nucleotides are added in the 5’ to 3’ direction. However, in replication both strands of DNA are copied so that adds a few extra steps. One strand is synthesized quickly and is called the leading strand. The other strand is made slowly so it’s called the lagging strand. Telomeres There are over 20,000 genes in the human genome across each of our 23 pairs of chromosomes. The genes are organized in the chromosomes away from the telomere ends or the centromere towards the middle. The centromere serves as the attachment point for spindle fibres during cell division. Telomeres, on the other hand, don’t have a direct function in the day-to-day processes in the cell. Their length, however, is important and has been correlated to a variety of health indicators ranging from aging to cancer. The length of telomeres is maintained by a special polymerase called telomerase. Changes in the ability of telomerase can lead to changes in the rest of the cell. Summary This Activity explored the big idea that the cells use DNA in important cellular processes. Specifically, - the structure of DNA is important in understanding how it is used; - DNA is transcribed into mRNA that is then translated in protein synthesis; - DNA is copied semi-conservatively. Activity 10: Changes in Molecular Genetics Gene Expression When transcription and translation of a gene is started we say that the gene is being expressed. In this way we can say that certain cell signals alter gene expression. Genes play an important role in how cells respond to their environment. They are affected by cell-to-cell communication. Interestingly, gene expression can also be changed because of environmental conditions. Human skin colour is an interesting example of this kind of response. See how the pigments of our skin are influenced by both genetics and the environment in this video. Protein Shapes Look back at your graphic organizer from Unit 1, Activity 3 on Proteins. Remember that amino acids differ from each other with their R-group. In addition to its length we also saw how some side chains are hydrophobic and some are hydrophilic. Among the hydrophilic amino acids, R-groups can be uncharged, positively charged, or negatively charged. When Evolutionary Biologists look at genetic differences among species they compare the amino acid sequences of a protein that is homologous. In this way small changes on the evolutionary level can be used to assemble an evolutionary tree Species with fewer differences in amino acid sequence are more closely related than those with more differences. In the figure above we can see that monkeys like chimpanzees, Rhesus and E. Patas have fewer differences in their cytochrome c proteins compared to humans. This makes sense given that primates are more closely related to humans than other mammals or other chordates. Still, for all species that use an electron transport chain to produce ATP, cytochrome c must be able to function in a homologous way. The question then is, shouldn’t all cytochrome c proteins have the same amino acid sequence in their primary structure? The answer to this is “perhaps”. We have seen the importance of shape. Indeed, for an important protein involved in energy metabolism any significant changes in the amino acid sequence could be lethal. However, if a substitution of one amino acids for one with similar properties occurs there is a chance that the protein could still fold into its proper tertiary structure. We can see this where at position #11 hydrophobic I (isoleucine) is substituted for hydrophobic V (valine), or at position #12 where hydrophilic M (methionine) is substituted for hydrophobic Q (glutamine) in the non-primate animals. Changing Genes When we think of the word mutation often the first thing that comes to mind is a monster in a summer blockbuster movie. From a genetic perspective, though, a mutation is just a change in the genetic information of a cell. They can be somatic mutations that happen to our somatic cells or germline mutations that occur in gametes that can be passed to the next generation. We are already familiar with many common mutations in genes. Some have a harmful, or deleterious, effect while others are neutral. Variation among individuals in a population is created by these sorts of mutations. Explore some of these examples from Genetic Science Learning Center. Practice good Initiative skills and look to see how the DNA is changed. Also, look to see how mutations in one species can have similar effects in mutations in homologous genes. Single nucleotide mutations, also called point mutations, can be caused by internal or external factors. External factors include radiation, like radioactivity, X-rays or UV light, and chemicals called mutagens, like tar in cigarettes or polycyclic aromatic hydrocarbons from burned fatty meat. Point mutations are sometimes called single nucleotide polymorphisms, particularly for point mutations that have no deleterious effect on a person’s phenotype. Internal factors involve mistakes by the enzymes responsible for DNA replication. DNA polymerase III has an error rate of inserting a wrong nucleotide once in about 10,000 nucleotides. This causes the double helix to bulge out because the bases can’t properly hydrogen bond there. Recall that towards the end of replication DNA polymerase I proofreads the daughter strands for errors like this and fixes it by putting in the correct nucleotide. Every once in awhile, though, an error stays and is passed to daughter cells after the next round of cell division. And if that error occurs when gametes are formed it might be passed on to the next generation. Point mutations include single nucleotide deletions, insertions, and substitutions. The effects of these type of points mutations depends on where in the gene they occur. Genes are made of introns and exons. Exon sections combine to include a critical portion such as the active site in enzymes. Amino acids with similar R-groups may not significantly change the shape of the protein. Even within the codons, mutations in different nucleotides in each triplet can have different effects. Watch the following video to see how the structure of genes determines the effect of different point mutations. Controlling Gene Expression One of the puzzles that Biologists needed to work out was how specialized cells become differentiated. Do specialized cells receive a different set of genetic instructions during specialization from stem cells? Or do specialized cells just read different instructions from the whole genome? Chromosomal studies of different cell types shows that each somatic cell type has a complete set of 46 diploid chromosomes. Take the example of a firefly’s ability to produce flashes of light. Each somatic cell in the firefly has a full set of genetic instructions in its chromosomes. However, only specialized cells in its abdomen are able to make luciferase, the enzyme responsible for the flashes. Look to see how gene expression is controlled in fireflies in this video from Genetic Science Learning Center. The way that cells turn off and on genes happens in different ways. In this section we will examine operons, transcription factors, and epigenetics. Many prokaryotic genes are organized in groups called operons that are related to a metabolic pathway or cellular processes. The genes in the operon can be induced (turned on) or repressed (turned off) depending on how the genes are used by cells at a given time. For example, E. coli bacteria are able to synthesize the amino acid tryptophan. This anabolic pathway is the product of genes in the trp operon. In order to be energy efficient the amount of tryptophan a cell needs to synthesize is controlled through a negative feedback loop. We can describe this control of gene expression in a feedback diagram. The expression of the genes in the trp operon is repressed by high tryptophan levels. In this case, tryptophan binds to a repressor molecule and the two molecules together act to prevent transcription of the operon. For this reason tryptophan is called a corepressor. Another way to describe control of gene expression is by making a decision tree. Here, the two choices are clearly shown as options and a series of steps branch out from each choice. We can see a decision tree for another operon in E. coli: the lac operon. This catabolic pathway allows cells to metabolize lactose disaccharides. In order to be energy efficient the enzymes needed for lactose metabolism are only expressed when a cell encounters lactose in its environment. The expression of the genes in the lac operon is induced by the presence of lactose. Lactose binds to a repressor and the two molecules together can no longer inhibit RNA polymerase from transcribing the operon. For this reason lactose is called an inducer. Both types of operon involve a protein molecule called a repressor that prevents RNA polymerase from transcribing. They bind to a section of DNA called the operator that’s between the promoter and the first gene in the operon. In eukaryotes gene expression is more varied. Similar to repressors in operons, transcription factors can alter gene expression. Transcription factors also include activators or enhancers that have positive effects on gene expression. Transcription factors also bind to regions of DNA to help or inhibit RNA polymerase. These regions have different names, such as regulatory region and switch. To see how transcription factors work, first get familiar with the anatomy of a gene by exploring the interactive. Then watch the following video to learn about activators and repressors of gene expression. Eukaryotic genes can also be changed at the chromosomal level. Recall that eukaryotic chromosomes are made of DNA wrapped around histones. When chromatin fibers are opened up then the DNA can be read. Here, two modifications can affect gene expression: methylation of nucleotides and modification of histone shape through acetylation. Interestingly, these changes are influenced by environmental factors, like nutrition and stress, and can lead to changes in phenotype that can be inherited. Because these changes are not part of the DNA code they are called epigenetic changes. Regulatory Genes Significant research has recently helped to further scientific understanding of how gene expression can be changing in specialized cell types. One puzzling question that has recently been answered had to do with the production of proteins in certain unrelated organs. For example, animals express the pitx1 gene in their jaw, pituitary and pelvis. Mutations in this gene only affected these parts of the body. So, what is the connection between these body parts and this gene? The answer has to do with general instructions instead of specific instructions. The Pitx1 protein is involved in building structures in the body. The type of structure it helps to build depends on which cell type it’s in. Explore how changes in regulatory genes and the switches that control them in this video Summary This Activity explored the big idea that gene expression can change. Specifically, - changes in the sequence of DNA can have beneficial, neutral or deleterious effects; - transcription can be enhanced or inhibited by changes in a cell’s environment; - changes in chromosome structure can also change gene expression. Decisions in Gene Expression In this Activity we have explored some of the ways that gene expression can change. All of these methods involve natural changes in DNA and chromosomes, even if they are caused by human activity. Research about the role of DNA in the past 30 years has focused on these changes. Increased or decreased gene expression is now being linked to a variety of health outcomes, like diseases, wellbeing, and aging. The role of methylation seems to play an important role in how cells use DNA. It has been linked to: - aging, - cancer, - embryonic development, - amount of exercise, - atherosclerosis, - the immune system (such as B-cells), - memory. Unit 4: Homeostasis Activity 1: Homeostasis 1 Homeostasis In the previous Activity we saw how biotic interactions lead to changes in population growth. Organisms respond to their environment to get energy or to avoid the negative effects of predation, competition, herbivory and parasitism. The Touch Me Not plant, Mimosa pudica, for example, responds when its leaves are touched by a herbivore. Closed leaves look less nutritious to herbivores. The movement is caused by specialized cells at the base of the leaves. Those cells use a sodium-potassium pump to maintain homeostasis. This gives the leaf its shape as its tissues are full of water. When touched, the leaves open potassium channels allowing potassium to diffuse out of the cells. Water follows the potassium ions by diffusion leading the leaves to become limp. As we will see later in this Activity, the movement of sodium and potassium ions is also important to how animals send signals through the body. Being able to respond to the environment is important to organisms on a cellular level: enzymes in cells require a suitable environment for optimal, or ideal, activity. A correct balance in ion concentration, pH, level of nutrients and waste, and temperature are all important physiological conditions. Recall that loss in homeostasis leading to significant changes in pH or temperature can cause proteins to denature and therefore cells to be unable to perform important cellular processes. Responding to Stimuli Animals can respond to stimuli much faster than the Touch Me Not plant. Human neurons, for example, can carry electrical signals at speeds ranging from 0.6 m/s to about 120 m/s. At this time it’s important for us to see that neurons can communicate in two different ways: electrical signals and chemical signals. We will explore the similarities and differences in these signals later in this Activity. Let’s try this simple investigation to explore how our speed in responding to a stimulus can change. Sometimes our response is deliberate and we are aware of our actions. Other times our response any behaviour that results from a stimulus. eems faster, reflexive, and automatic. We are not fully aware of our response until after it happens. Feedback Pathways We have seen in earlier Activities that homeostasis is about changes that lead to a balance in physiological conditions. Processes that lead away from homeostasis are called positive feedback, while processes that lead back to to homeostasis are called negative feedback. In this case, positive and negative describes the direction a change takes compared to homeostasis. For example, when there is a decrease in oxygen levels in the blood, the body responds by increasing the respiratory rate. This causes an increase in gas exchange at the lungs and thereby blood oxygen levels increase. We describe this as negative feedback because the response brings the blood oxygen levels back to homeostasis. A good way to illustrate this is through how animals regulate their internal body temperatures. Thermoregulation involves the same three steps we have seen to describe feedback: receptor, integrator and effector. Multiple responses increase the complexity and details of the feedback diagram. Look for ⊕ and ⊝ symbols in the feedback diagram that add important details. In the feedback diagram for thermoregulation one of the responses is shivering. Activating our muscles to use metabolic processes to produce ATP for movement is typical of a group of animals called endotherms. In fact, an interesting adaptation in endotherms is that their mitochondrial membranes are leakier to the proton gradient established in the electron transport chain. A portion of the potential energy stored in the proton gradient is converted to heat. Metabolic activity increases with colder environmental temperatures. In some cultures, a midday nap helps people to lower their metabolic activity during the hottest time of the day. Endotherms include mammals and birds. Another group of animals are called ectotherms and includes fish, reptiles, amphibians and most invertebrates. The metabolic rate at different temperatures of endotherms shows a different pattern compared to ectotherms. Endotherms have a temperature range in which their metabolic activities do not change. Ectotherms do not rely on heat produced from protons leaking across their mitochondrial membranes. Their body heat comes from the environment and so their rate of metabolic activity increases with temperature. Coordinating Responses Thermoregulation in all animals involves the nervous system. In humans, the nervous system is organized in two main groups: 1. the central nervous system which contains interneurons in the brain and spinal cord, and 2. the peripheral nervous system. In both divisions of the nervous system, neurons send and receive signals although their shapes are slightly different depending on their role. Watch this video, then choose one of the following visuals to explore this further. The receptors from the feedback diagram are located in the sensory pathway of the peripheral nervous system. We can also describe these neurons as afferent neurons as they function before the interneurons. The effectors from the feedback diagram is located in the motor pathway. They are also called the efferent neurons as they function after the interneurons. Interestingly, certain motor neurons are responsible for controlling voluntary actions, like walking, while other motor neurons control involuntary actions, like the movement of food from the stomach into the small intestines. Efferent neurons can therefore be divided into two groups, the somatic division for voluntary actions and the autonomic division for involuntary actions. Some stimuli are processed by integrators in different parts of the nervous system. Imagine you are thirsty and see a glass of water. Information is sent from the optical sensory neurons to the interneurons in the brain. The brain activates the somatic division of the efferent neurons leading to the skeletal muscles in your arm. The response is your arm muscles contract and you bring the glass to your mouth for a drink. But, what if instead, something unexpected happened to the glass? If the glass got knocked over towards us, our reaction is faster and different. This time a reflex response is activated. The same sensory neurons from the eye send a signal to interneurons in the spinal cord. Again the somatic division of efferent neurons take over and stimulate the skeletal muscles in our arm to catch the glass. Before we know what has happened we have responded. Electrical Signaling The nervous system is able to respond to change faster than any other system in the body. Neurons are the functional unit of the nervous system, but other cells provide important supportive roles. In order to understand how neurons are able to send signals practice good responsibility skills as you explore the cells and cell structures of the nervous system. We will be using details about neuron structure when describing electrical signals in neurons. There are two main locations along a neuron that are important to the transmission of information. As we have seen before, the axon terminal releases chemical neurotransmitter signals across the synapse to the dendrites downstream to a postsynaptic neuron. The distance that neurotransmitters travel across a synapse is small, typically about 0.02 μm wide, so information can be passed from neuron to neuron very quickly. Signalling within a neuron, on the other hand, is an electrical signal called an action potential. Just like for neurotransmission, action potentials involve changes along the neuron membrane. An action potential travels down a neuron always in the same direction, from dendrite to axon terminals. For this reason it is easy to think of neurons like batteries lined up positive end to negative end in an electric circuit. The incredible speed of an action potential is accomplished by changes in homeostasis at the Nodes of Ranvier along an axon. Normally, when resting, sodium-potassium pumps at the Nodes of Ranvier establish an electrochemical gradient. When stimulated, two other transport proteins change the balance in sodium and potassium ions. Explore how cellular transport is involved in electrical signaling with a neuron. How do ions move through different membrane proteins for a resting neuron or a stimulated neuron? Click on the “stimulate neuron” tab and observe the changes in the membrane. Try zooming into the membrane to see the movement closer. How do the electrochemical gradient and charge of the interior of the neuron change? Neurological Disorders Neurons are delicate cells. Some of them are almost half the length of our body, stretching from the base of our spine to the tip of our toes. Most of that distance is covered by the long axon. Damage to neurons can have serious consequences, including feeling pain, numbness, or loss of sensation. In other cases, if a person loses a limb, finger or toe to amputation they can sometimes feel it as if it were still there. Neurobiologists study neurons in order to help patients. The nervous system allows for sophisticated differentiation between types and strengths of signals. This is remarkable accomplishment given that neurons have only two states: stimulated or resting. We describe this as an all-or-none response. Once a stimulus is strong enough, it can cause the depolarization of the neuron as it opens its sodium channels followed by its repolarization as it opens its potassium channels. Sensory neurons are distributed differently throughout the body. For example, if the number of touch receptors in our body were given an equal space in the brain then the map of the body would look distorted. Our fingertips have many more touch receptor than our shoulders. This is why we can feel the texture of a wool sweater better with our fingers than with our shoulders. In addition, the ability of a neuron to reach its threshold can change. There are 10 major neurotransmitters that can be broadly categorized into either excitatory or inhibiting neurotransmitters. As you look at this video identify how ion concentrations are changed because of different neurotransmitters. Activity 2: Homeostasis 2 Chemicals that Regulate Hormones are chemical messengers in your body. Look back to your graphic organizer from Unit 1, Activity 3 on Proteins, to see how chemical signals can be either hydrophilic protein hormones or hydrophobic steroid hormones. They are produced by glands located throughout the body. Unlike neurotransmitters that move signals across a synapse in the nervous system, we saw that hormones move through the blood to specific target cells. These target cells have a receptor that matches the shape of the correct hormone. Hydrophilic protein hormones have receptors on their cell membranes that send a second messenger in the cytoplasm to cause a response. Steroid hormones can pass right through the cell membrane to react with receptors inside the cell. Often these receptors, when bound to their hormone, act as transcription factors to turn on gene expression. You can revisit these differences in this video from Sinauer Associates. Glands The concept of homeostasis has been recurring throughout this Unit. Homeostasis is important at the cellular level and is controlled by the semi-permeable cell membrane. On a population level, homeostasis is controlled by the interactions of individuals with biotic and abiotic factors. On an organism level homeostasis is controlled by several important systems. We have already examined the importance of the nervous system. Three other systems come into play here as well: the reproductive system, the excretory system and the endocrine system. For most people, the glands of the endocrine system are difficult to identify and locate in the body. Practice good Self-Regulation skills and without using any other sources of information see how many glands you can correctly identify. It’s important to know more than just where glands are located and which hormones they produce. The following video provides a good overview of the importance of the endocrine system and how it fits into homeostasis. Growth of the Body Unlike the nervous system, the endocrine system responds more slowly to a stimulus. In fact, between hydrophobic and hydrophilic hormones, it’s the hydrophobic ones that take the longest time to respond because they diffuse slowly across membranes. The slowness of endocrine signaling is therefore a good fit for changes in the body leading to growth. Growth in humans occurs in three stages: infancy, childhood, and puberty. Many hormones are important in how we grow. They are produced by two endocrine glands, the pituitary gland and thyroid, as well as the hypothalamus in the brain. In the previous video we saw that the hypothalamus acts to coordinate responses between the endocrine and nervous systems. Here, the hypothalamus coordinates metabolic activity. The stimulus could be a decrease in body temperature or it could be a drop in thyroid hormone levels in the blood. Another stimulus could be increased nutrition as we grow bigger and develop in the lead up to puberty. In all cases, hormones are secreted. Hormones associated with the thyroid gland help regulate metabolism. One of these hormones is growth hormone, GH, which stimulates cells in our body to undergo mitosis. There are other thyroid hormones associated with growth and metabolism. Explore the following image and pay attention to different feedback mechanisms. Puberty is the last of three stages in the growth of humans, after infancy and childhood. The timing of puberty onset is still an area of scientific investigation. We do know that control over sexual maturity and production of gametes is controlled by the hypothalamus. It is generally accepted that, in general, female puberty occurs earlier than in males. Some research suggests that increased metabolic activity leads to a stimulation of the GnRH-secreting neurons. Other research indicate that with hormones produced by the gonads, stress and seasonal changes all play a role. Transcription of dozens of genes in the hypothalamus changes at the onset of puberty. New genes are turned on which allow the hypothalamus to behave differently than during childhood. Now adolescents, like adults, are able to produce mature sperm, spermatogenesis, and egg cells, oogenesis, for the purpose of reproduction. Just like for metabolism regulation, control over the reproductive system involves the hypothalamus and pituitary glands. Both processes use negative feedback. The target cells for pituitary hormones have different receptors depending on their biological role. For metabolism homeostasis, cells in the thyroid have cell surface receptors to TSH. For the reproductive systems, Sertoli cells in the testes and follicle cells in the ovaries have cytoplasmic receptors to FSH, follicle stimulating hormone. Production of mature gametes involves other hormones, such as luteinizing hormone, LH, as well as estrogen (sometimes also called estradiol or oestrogen) and testosterone depending on sex Blood Homeostasis In Grade 11 we saw how the circulatory system carries nutrients and wastes around the body. Organs like the lungs, small intestines and kidneys are t

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