Biology 1 Module 1 Guided Notes PDF
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This document is a set of guided notes for a Biology module. Topics include organic macromolecules, including carbohydrates, lipids, proteins, and nucleic acids. It also includes descriptions of monomers and polymers, and the molecular structure of various compounds.
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MODULE 1 Guided Notes Note: Do not submit the guided notes as your assignment. Here is a video of one of our FLVS Biology teachers going over all of the concepts in Module 1. Quick Links: Click the topics below and it will take you straight to that section of notes without needing to s...
MODULE 1 Guided Notes Note: Do not submit the guided notes as your assignment. Here is a video of one of our FLVS Biology teachers going over all of the concepts in Module 1. Quick Links: Click the topics below and it will take you straight to that section of notes without needing to scroll. This is very useful in DBAs! Don’t erase the highlighted segment titles! The links will not work if you do this.These links are found at the bottom of each segment to help with quick navigation. 1.01 Exploring Life 1.02A Chemistry of Life Honors 1.02 Chemistry of Life 1.03 Earth’s Early Atmosphere 01.02 Biology Notebook: Chemistry of Life Page 1: Introduction to Chemistry of Life Identify the four main types of organic macromolecules. Carbohydrates, lipids, nucleic acids, and proteins. What do all these macromolecules have in common? They all provide energy and functioning for the human body in our foods for the structure of living organisms and their cells. Key Terms: Jot down terms and definitions that are new to you. You will see them used in the lesson. Page 2: Biological Macromolecules What is a monomer? A monomer is a molecule that can react together with other monomer molecules to form a larger polymer chain or three-dimensional network12345. Monomers are the building blocks of polymers and can be either natural or synthetic in origin. What is a polymer? A polymer is any of a class of natural or synthetic substances composed of very large molecules, called macromolecules, which are multiples of simpler chemical units called monomers. Polymers make up many of the materials in living organisms and are the basis of many minerals and man-made materials. List the four macromolecules and describe the function(s) of each? Name Function(s) 1 Carbohydrates. Provide the cells with energy. 2 Lipids. Store Energy. 3 Proteins. Are building blocks, transports other substances, storage. 4 Nucleic Acids. Carries genetic information. Page 3: Carbohydrates (sugars) Define the following terms & provide 2 examples: Name 2 examples Image Some many types of Monosaccharide monosaccharides are glucose molecules, galactose Define: A molecules, and fructose monosaccharide—the prefix molecules. mono means “one”—is the smallest type of carbohydrate molecule. There are many types of monosaccharide molecules, the two most common being glucose and fructose. Monosaccharides, particularly glucose, are important energy sources for cells. In addition to providing energy, the carbon atoms in glucose can be used by the cells to build other important molecules, like fatty acids and amino acids. If the monosaccharides are not immediately used by the cells, they can be stored in larger carbohydrate molecules to be used later. Disaccharide Sucrose is a disaccharide that you probably use every day. It is made up Define: Disaccharides are carbohydrate molecules made of one fructose molecule up of two monosaccharide and one glucose molecules, bonded together. molecule, bonded Monosaccharides and together. Lactose, the disaccharides are classified as major sugar in milk, is simple carbohydrates. Most simple carbohydrates have a made of one glucose sweet taste, and they are molecule and one collectively referred to as galactose molecule, "sugars" in biology. Table bonded together. Maltose sugar, called sucrose, is a disaccharide that you probably is a disaccharide use every day. It is made up of produced during the one fructose molecule and one digestion of starch. It is glucose molecule, bonded made of two glucose together. Lactose, the major sugar in milk, is made of one molecules. glucose molecule and one galactose molecule, bonded together. These polysaccharides are each Polysaccharide polymers, made up of the same monomer: glucose. Define:Polysaccharides are Starch is a polysaccharide formed by plants as a way to store the large carbohydrate polymers made amounts of glucose produced during up of hundreds to thousands of photosynthesis. Animals are able to monosaccharide units, bonded break down starch into individual together. The polysaccharides glucose molecules, which makes starch an important food source. that are produced and consumed by living organisms, Cellulose, a polysaccharide made up such as starch, cellulose, and of glucose, is a very strong material glycogen, are all made up of the that serves as the primary structural monomer glucose. Even though component of plants. Most animals are not able to break cellulose down they are all made up of the into glucose. However, cellulose in same monomer, their the food that we eat is important properties are different because because it serves as dietary fiber of the differences in how the that regulates digestion. glucose molecules are arranged Glycogen is the polysaccharide that in the different animals and fungi use to store excess polysaccharides. glucose molecules from their food. It serves as an energy reserve that can be broken down into individual glucose molecules when they are needed. Your athletic endurance is related to the amount of glycogen you have stored away, but even a significant supply of glycogen in an average human can be used up in a day if it is not replenished by carbohydrates from food. Chitin is another structural polysaccharide made up of glucose molecules. However, it is different than cellulose because it has amino groups (NH2) bonded to the glucose. It is found in the exoskeletons of arthropods, such as insects, spiders, lobsters, and crabs. These protective exoskeletons, or anything else made of chitin, cannot be digested by animals. —But how are all of these polysaccharides??? All of these substances—starch, cellulose, glycogen, and chitin—are polysaccharides because they are all made up of long chains of glucose molecules linked together. Think of glucose as tiny building blocks. When many glucose molecules join together, they form a long chain, much like how a train is made up of many cars linked together. Depending on how these glucose molecules are arranged and what other molecules might be attached to them, the resulting polysaccharide can have different properties and functions: Starch: Glucose chains in starch are arranged in a way that makes them easy for animals to digest and use for energy. Cellulose: The glucose chains in cellulose are arranged to make them strong and hard to break down, which helps plants stay rigid and upright. Glycogen: The glucose chains in glycogen are branched, making it easy to quickly release glucose when animals need energy. Chitin: This polysaccharide has glucose molecules with an added amino group, making it very strong and tough, ideal for protective shells in insects and crustaceans. So, all these polysaccharides are just different forms of long chains of glucose, 🌿🐾🦀 tailored for specific roles in plants and animals. What are the functions of carbohydrates? To provide energy for the cells of a living organism. What is the name of the monomer, or single unit, of a carbohydrate? (Look in the table above) The monomer, or single unit, of a carbohydrate is called a monosaccharide. These simple sugars include glucose, fructose, and galactose, which are the building blocks for more complex carbohydrates like starches and fibers. Describe the molecular structure of a carbohydrate (shape, atoms/elements, etc). Molecular structure: The shape would be classified as a hexagon what does the shape as it has 6 sides basically. But it does look look like? like a trapezoid. Molecular structure: The molecular structure, is Carbon, what atoms does it Hydrogen, and Oxygen which looks like— contain? What is the chemcial or maolecular Glucose formular for carbohydates please??? The general chemical formula for carbohydrates is Cn(H2O)n\text{C}_n(\text{H}_2\text{O})_ n. This formula indicates that for every carbon atom, there are two hydrogen atoms and one oxygen atom. The “n” represents the number of carbon atoms in the carbohydrate molecule. For example, here are the formulas for some common carbohydrates: Glucose: C6H12O6\text{C}_6\text{H}_{12}\te xt{O}_6 Fructose: C6H12O6\text{C}_6\text{H}_{12}\te xt{O}_6 Ribose: C5H10O5\text{C}_5\text{H}_{10}\te xt{O}_5 These formulas reflect the ratio of carbon, hydrogen, and oxygen atoms in each type of carbohydrate. Example: The Structure of Glucose Let's review the structure of carbohydrates, using a glucose molecule. You can see that the carbon molecules are the base for the structure. The "C" represents carbon, the "O" represents oxygen, and the "H" represents hydrogen. Let's break it down! The chemical formula for glucose is C6H12O6. The carbons are numbered 1–6. OH and H molecules form bonds with the linked carbons. Describe the function of each carbohydrate, or polysaccharide, below: Starch-Starch is a polysaccharide formed by plants as a way to store the large amounts of glucose produced during photosynthesis. Animals are able to break down starch into individual glucose molecules, which makes starch an important food source. Cellulose-Cellulose, a polysaccharide made up of glucose, is a very strong material that serves as the primary structural component of plants. Most animals are not able to break cellulose down into glucose. However, cellulose in the food that we eat is important because it serves as dietary fiber that regulates digestion. Glycogen-Glycogen is the polysaccharide that animals and fungi use to store excess glucose molecules from their food. It serves as an energy reserve that can be broken down into individual glucose molecules when they are needed. Your athletic endurance is related to the amount of glycogen you have stored away, but even a significant supply of glycogen in an average human can be used up in a day if it is not replenished by carbohydrates from food. Chitin-Glycogen is the polysaccharide that animals and fungi use to store excess glucose molecules from their food. It serves as an energy reserve that can be broken down into individual glucose molecules when they are needed. Your athletic endurance is related to the amount of glycogen you have stored away, but even a significant supply of glycogen in an average human can be used up in a day if it is not replenished by carbohydrates from food. Page 4: Lipids ** This is the only macromolecule group that does NOT have repeating structural units, or monomers. What are the three main categories of lipids? The three main categories of lipids are fats, phospholipids, and steroids. What are the function(s) of lipids, or fats? The functions of lipids are to store energy in the human body. Describe the function and molecular structure of lipids (fats). Include shapes, atoms/elements, etc. Function Fats are stored in the body in fat deposits, which serve as stored energy for the organism. Fat deposits under the skin can also provide insulation for an animal, while fat surrounding vital organs provides protection and cushion for the organs. Example(s) Triglyceride (blood fat) Molecular structure: THe molecular structure of fats, are Molecular structure of a triglyceride (fat) what does the shape macromolecules made up of much smaller look like? molecules. The reason why fats are also called, triglycerides, is because the fat macromolecule is made up of one glycerol molecule, and three fatty acid molecules. The fatty acid molecules may vary in the number of atoms, usually 16 to 18 carbons, and they may have single or double bonds between the carbon atoms. Molecular structure: It contains one glycerol molecule, and then what atoms does it three fatty acid molecules. THese molecules contain? I am listing here are all of the much smaller molecules that make up the molecular structure, but remember in whole, all fats are made up of carbon, hydrogen, and oxygen macromolecules. Which provides more kilojoules of energy, fats or carbohydrates? Fats because a fat can provide up to 38 kilojoules of energy, while a carbohydrate or protein only provides 17 kilojoules of energy basically. Describe the differences between saturated and unsaturated fatty acids and give examples. Saturated Ex: Saturated fats have no double bonds in their chemical molecular structures. While unsaturated fats do. Saturated fats are said to less healthy than unsaturated fats too. And—Examples of this are: Butter, lard, coconut oil, and animal fats. Health Impacts: High intake of saturated fats is associated with increased levels of LDL cholesterol, which can lead to heart disease. Solid at room temperature Unsaturated Ex: Unsaturated fats have a double bond in its chemical molecular structures, and it can either have one double bond, or can have multiple in its molecular structure too. Unsaturated fats are known to be healthier than saturated fats, and examples are this are:Olive oil, canola oil, sunflower oil, and fish oil. Health Impacts: Unsaturated fats are generally considered healthier than saturated fats. They can help reduce LDL cholesterol levels and are beneficial for heart health. Liquid at room temperature How is the structure of phospholipids different from a fat? Phospholipids are similar in structure to fat molecules. Instead of three fatty acids found in a fat molecule, phospholipids have two fatty acids and one phosphate group bonded to the glycerol molecule. Having a phosphate group instead of the third fatty acid gives phospholipids a hydrophilic end and a hydrophobic end to the molecule. SO basically, while fats have three fatty acids and a glycerol molecule, phospholipids have TWO fatty acids and one phosphate group bonded to the one glycerol molecule. **Phospholipids make up the majority of the cell membrane! Molecular structure of a phospholipid: Portion of a Cell Membrane Define hydrophobic. -Lacking affinity for water; tending to not mix well with water. Which part of the phospholipid is The tail of the molecules. For example, as shown hydrophobic? in the picture above, the parts of the phospholipid are those of saturated and unsaturated fats. Define hydrophilic. -Having a strong affinity for water; tending to mix well with water. Which part of the phospholipid is The part of the phospholipid that is hydrophilic is hydrophilic? the head of the molecules, which as shown in the picture above again, those molecules are made up of the phosphate molecules and the glycerol molecules. Look at the images and definitions above. How do the 2 terms (hydrophobic & hydrophilic) change the relationship that phospholipids would have to water flowing through the cell membrane? In the Cell Membrane: Phospholipids form a bilayer, with the hydrophilic heads facing the water on each side of the membrane, and the hydrophobic tails tucked inside, away from water. This arrangement creates a selectively permeable barrier that regulates what enters and leaves the cell. Water and Small Nonpolar Molecules: Can pass through the membrane relatively easily due to their small size and lack of strong charge interactions. Large Polar Molecules and Ions: Generally cannot pass through the hydrophobic interior of the membrane and require specific transport proteins to assist their movement. Describe the function and molecular structure of a steroid. Give an example of a steroid. Function -Many steroids are hormones that control a number of the body's metabolic processes. Cholesterol is the most abundant steroid and is the starting material for most other types of steroids. Cholesterol is found throughout your body and it is important for synthesizing other Molecular structure of a steroid steroids, such as male and female hormones. Example(s) -Cholesterol, Vitamin D, Cortisol, and Testosterone. Molecular structure: what does the shape look like? Molecular structure: -Steroids are another category of what atoms does it lipids. The macromolecules in this contain? category all share a similar structure of four linked rings of carbon atoms. **You’ll notice that the shape of a steroid looks somewhat similar to a carbohydrate, but the rings in a steroid are FUSED. (they look like they are touching each other) Page 5: Proteins What function(s) do proteins have in the body? (They have the most diverse set of functions) The word protein comes from the Greek word proteios, meaning "first place." This indicates how important they are to living organisms. Proteins make up more than 50 percent of the dry weight of cells, and they are important to almost every function of a cell. They are used for structure, transporting other substances, storage, signaling from one part of an organism to another, movement, and defense against foreign substances. Proteins can denature. What causes a protein to denature, and would it still be able to function? Proteins can only function properly under specific conditions, such as a small range of temperature and pH. Changes in these conditions can break the chemical attractions within the protein and change the molecule's shape. When this happens, the protein is said to be "denatured" because it is unable to serve its function. How is the structure of proteins related to the function? Proteins are large biological macromolecules that are made up of smaller molecules, called amino acids. There are 20 different amino acids that all share the same basic structure. Proteins are made up of 50 or more amino acids bonded together. A difference of only one amino acid in the protein chain can cause a big difference in the protein's function within a cell. The number and arrangement of amino acids in the chain determines the properties and functions of the protein. The table below lists some proteins and their functions. Notice the difference in the number of amino acids in the various proteins, as well as the variety in the functions of these proteins. What gives a protein its unique properties? The number and arrangement of amino acids in the chain determines the properties and functions of the protein. Choose three protein examples and describe their functions. Protein Example Function 1. Insulin Hormone for sugar metabolism-51 amino acids. 2. Growth Hormone Used in antiaging treatment-191 amino acids. 3. Gamma Globulin Part of immune system in blood-1320 amino acids. What is the name of the monomer, or single building block, of a protein? An amino acid. Describe the molecular structure of an amino acid. Molecular structure: The amino group is made up of two what does the shape hydrogen atoms, each bonded with a look like? single covalent bond to a nitrogen atom. The nitrogen atom of the amino group is attached to the central carbon atom of the amino acid by a single covalent bond. Molecular structure of an amino acid Molecular structure: what atoms does it contain? What part of the amino acid makes each one unique? (determines the function) What part of the amino acid makes each one unique? (determines the function) The part of an amino acid that makes each one unique and determines its function is the R-group or side chain. Each amino acid has a central carbon atom (called the alpha carbon) bonded to a hydrogen atom, an amino group (NH2), a carboxyl group (COOH), and a distinctive R-group. R-group (Side Chain) Variety: The R-group varies among different amino acids and gives each amino acid its unique properties. Functions: Depending on the nature of the R-group, amino acids can be nonpolar, polar, acidic, or basic, which influences how they interact with each other and with other molecules. Interactions: These interactions play a crucial role in the folding and functioning of proteins, affecting the protein's structure, stability, and interactions with other biomolecules. —Side Chain—The side chain is the only part of the molecular structure that varies between the 20 different amino acids that can make up a protein. The side chain may contain carbon, hydrogen, oxygen, or other atoms, and it is always attached to the central carbon atom of the amino acid by a single covalent bond. Types of Proteins and Their Functions Proteins can only properly function under specific conditions, such as a small range of temperature and pH. Changes in these conditions can break the chemical attractions within the protein and change the molecule's shape. When this happens, the protein is said to be "denatured" because it is unable to serve its function. The following table provides some examples of the various functions of proteins: Proteins Functions Antibodies Specialized proteins that help defend organisms from foreign invaders. Contractile Proteins responsible for the movement of muscles. Examples include actin Proteins and myosin. Hormonal Messenger proteins that help coordinate bodily activities. Examples include Proteins insulin and oxytocin. Transport Carrier proteins that move molecules from one place to another around the Proteins body. Examples include cytochromes and hemoglobin. Structural Fibrous and stringy proteins that provide support or protective coverings, like Proteins hair, feathers, horns, etc. Examples include collagen and elastin. Enzymes Specialized proteins that speed up reactions by decreasing the energy needed for the reaction to occur. Examples include lactase and pepsin. Page 6: Enzymes Define enzymes. -Enzymes are special proteins that increase the rate of a reaction by decreasing the amount of energy needed to get a reaction started. Enzymes are biological catalysts, molecules that increase the speed of a reaction without being used up in the reaction. For example, a wrench is a tool that loosens or tightens bolts. Just as the shape of the wrench determines the types of bolts it can tighten, the shape of an enzyme determines what reaction it can speed up within a cell. Also, a wrench is not changed or destroyed after its use, just as an enzyme remains intact after its use in a reaction. Which macromolecule group do enzymes belong to? Proteins. Enzymes are catalysts. What is the function of a catalyst? Enzymes are catalysts. What is the function of a catalyst? A catalyst is a substance that speeds up the rate of a chemical reaction without being consumed or altered in the process. It works by lowering the activation energy required for the reaction to proceed, making it easier for reactants to transform into products. Key Functions of a Catalyst: Increase Reaction Rate: Catalysts make reactions occur more quickly. Lower Activation Energy: They reduce the energy needed to start a reaction. Remain Unchanged: Catalysts are not used up or permanently changed by the reaction, so they can be used repeatedly. The graph below shows a chemical reaction occurring with and without an enzyme. Using the graph, describe what happens to a chemical reaction with and without an enzyme. Without an Enzyme: Higher Activation Energy: The amount of energy required to start the reaction (activation energy) is higher. This means it takes more time and effort for reactants to be converted into products. Slower Reaction Rate: Because it takes more energy for the reaction to proceed, the overall rate of the reaction is slower. As you can see in the graph, without enzyme, the amount of activation energy increases. When an enzyme is present, the activation energy is less/lowered. **The function of the enzyme depends on its shape. The active site on the enzyme has a certain shape and the substrate that it works upon has the same shape. There are many enzymes with different shapes for their active sites. You can think of it like a lock and key. Are enzymes reusable when they are in their optimal conditions? Yes/No Practice: Enzymes work best in their optimal conditions. To identify an enzyme’s optimal condition when analyzing a graph, look at the peak of the enzyme’s activity and follow that line straight down, as shown below with Enzyme A. What would the optimal pH be for Enzyme B in this graph? (type your answer in the box below) 7. Enzymes are also very sensitive to certain environmental conditions. Since they are proteins, they can become denatured. What changes on an enzyme when it becomes denatured? Will it continue to function? If temperature or pH is altered one way or another, the enzyme is denatured and no longer able to speed up the reactions. Another thing that can interfere with an enzyme's ability to speed up a reaction is an enzyme inhibitor. Enzyme inhibitors are substances that bind to an enzyme and change its shape or block its ability to interact with the chemical reaction. Click on the “Environmental Impacts on Enzymes” tab. Enzymes are very sensitive and have optimal conditions that they work well in. There are certain factors that affect the way an enzyme functions. In the chart below, describe how each of the following factors affect an enzyme’s activity. A few of them have been filled in for you. Be sure to mention whether it would denature, slow down, or speed up the enzyme’s activity. Hot temperatures High temperatures can denature enzymes, meaning the enzyme's structure is permanently altered, and it loses its functionality. This stops the enzyme from working altogether. Warm Warm temps can speed up an enzyme’s temperatures activity (Ex: low grade fevers), but we don’t want them getting too hot! Cold temperatures Cold temps slow down an enzyme’s activity. This can be reversed if the enzyme is warmed back up to its optimal temperature. Change in pH Enzymes have an optimal pH range. Deviation from this range can reduce enzyme activity. Extreme pH levels can denature the enzyme, altering its structure and hindering its function. Enzyme Inhibitors Inhibitors can slow down or stop enzyme activity by binding to the enzyme and preventing it from interacting with its substrate. These can be competitive (competing with the substrate) or non-competitive. Concentration of If the amount of enzyme or substrate enzymes and increases, the activity will be faster. If substrates the amount decreases, the activity will be slower. Enzymes ( catalyze ) biological processes by lowering the ( activation ) energy needed for chemical reactions to occur. Without the enzyme, the amount of activation energy (rises ). When an enzyme is present, the activation energy is ( lowered). Page 7: Nucleic Acids What is the function of nucleic acids? The fourth category of biological macromolecules is nucleic acids, which carry the genetic information needed to build organisms. There are two major types of nucleic acids: deoxyribonucleic acids (DNA) and ribonucleic acids (RNA). What are the two main types of nucleic acids? 1. Deoxyribonucleic acids. 2. Ribonucleic acids. RNA. DNA. Describe the structure and function of DNA. Where is DNA found? DNA contains an organism's genetic information and is usually found within a cell's nucleus. The RNA molecules are also very important because they transport the genetic coding from the DNA to other parts of the cell where proteins are built. A DNA molecule is actually made up of two nucleotide chains that spiral around an imaginary axis. This shape is called a double helix. A DNA molecule is very long and is made up of hundreds of thousands of genes. Describe the structure and function of RNA. RNA (Ribonucleic Acid) is a crucial molecule involved in various biological roles, particularly in coding, decoding, regulation, and expression of genes. Here’s a breakdown of its structure and function: Structure of RNA: Single-Stranded: Unlike DNA, which is double-stranded, RNA is typically single-stranded. Nucleotides: RNA is composed of nucleotides, which are the building blocks. Each nucleotide consists of: ○ A ribose sugar (which has an extra oxygen atom compared to the deoxyribose in DNA). ○ A phosphate group. ○ One of four nitrogenous bases: adenine (A), uracil (U), cytosine (C), and guanine (G). Note that RNA has uracil (U) instead of thymine (T), which is found in DNA. DNA serves as the master copy of an organism's genes. RNA copies sections of the DNA molecule and then carries the copies outside the nucleus. The genetic instructions provided by these copies direct the construction of protein molecules. What is the name of the monomer, or single building block, of a nucleic acid? Nucleotide-A monomer of nucleic acids; made up of a five: carbon sugar, a phosphate group, and a nitrogenous base Describe the monomer of a nucleic acid in the table below. Molecular structure: what does the shape look like? Molecular structure: what atoms does it contain? A nucleic acid is a chain of nucleotides bonded together. Each nucleotide is made up of a nitrogenous base, a sugar, and a phosphate group. Molecular structure What are the three main components of a nucleotide? The three main components of a nucleotide is a nitrogenous base, a sugar, and a phosphate group. Why are DNA and RNA important? DNA and RNA are very important because they allow cells to reproduce their structures from one generation to the next. Compare & contrast DNA & RNA: Write DNA, RNA, or BOTH in the box below each characteristic. Double Stranded Contain Cytosine & Guanine Found only in the nucleus DNA BOTH. DNA. Contains Deoxyribose Contains Thymine Made of nucleotides DNA. DNA. BOTH Contains Uracil Single Stranded Contains Ribose RNA. RNA RNA. Macromolecules at a Glance Test your memory! Can you fill in all the boxes in the table below? Carbohydrates Lipids Proteins Nucleic Acids Fatty Acids. Amino Acids. Nucleic Monomer Monosaccharid Acids. (base unit) e Structure & Properties To give energy To store Are building To carry, and Function(s) to the cells of a energy. blocks, carry across transports living other genetic organism. substances, information. storage. Basically just transportation of other substances in a living organism, and storage of energy in the living organism. Examples Practice questions: Highlight the correct answer. The building blocks of a carbohydrate are: A. Fatty acids B. Nucleotides C. Monosaccharides D. Amino acids Lipids are very diverse as it relates to their function. Which of the following is NOT a function of a lipid? A. Insulation B. Structural support C. Provide energy D. Control metabolic functions **Use the quick Links below for fast navigation. 1.01 Exploring Life 1.02A Chemistry of Life Honors 1.02 Chemistry of Life 1.03 Earth’s Early Atmosphere READ! You will only complete 1.02A if you are an HONORS student. If you are taking Standard Biology, you will go directly to the 1.03 notes. Standard students may wish to delete this Honors section to keep their notes more organized. 01.02A Biology Notebook: Chemistry of Life Honors ONLY Page 1: Macromolecules What holds macromolecules together? Chemical Bonds hold together macromolecules. Why are macromolecules important to living things? Macromolecules help provide energy and living functions and structure to any living organism. Key Terms: Jot down terms and definitions that are new to you. You will see them used in the lesson. Page 2: Carbon Based Molecules What are organic compounds? Organic compounds are things called carbon-based molecules. Carbon-based molecules are what all living organisms are made up of, so that is why it is called organic compounds. Define valence electrons. Valence electrons are those located in the outermost occupied energy level in an atom. These are the electrons that participate in chemical bonding between atoms. Like in a carbon molecule, there are four valence electrons in the outermost energy level of the molecule, which has the ability to form up to four covalent bonds with other atoms. For example, This can be as four single bonds, two single bonds and a double bond, or one single bond and one triple bond. The combination of bonds determines the chemical and physical properties of the molecule created. What unique ability does carbon have? Cabron has the unique ability to form bonds and structures, and chains, with any other molecule or element. It has the very unique ability to form any bond or structure and chain with any other molecule or element, and even with other carbon-based molecules. Life is based on carbon’s ability to form diverse molecular structures. Describe dehydration synthesis. Dehydration synthesis is when two molecules, or two monomers come together to make a polymer, but it is when these molecules are formed BY the removal of water. The term dehydration synthesis describes any process where two substances bond together by the removal of water. This is the way that many polymers are built. A hydrogen atom (H) is removed from one monosaccharide, and oxygen and hydrogen atoms (OH) are removed from another monosaccharide, allowing the two molecules to bond together. The hydrogen and oxygen atoms that were removed during the reaction are able to bond together to form a water molecule (H2O). Define hydrolysis. Now hydrolysis is the complete opposite basically. Hydrolysis is the chemical reaction that breaks down polymers into the smaller monomer units. During this reaction, a water molecule is split into OH and H, which are added back to the monomers as the bond between the monomers is broken. Four different types of polysaccharide molecules that are produced and consumed by living organisms are starch, glycogen, cellulose, and chitin. They are all polymers made up of hundreds to thousands of glucose molecules, bonded together, but the difference in their structures gives them different properties and functions. Describe the structure and function of starch. Starch molecules are long straight chains of glucose molecules, where all of the glucose molecules are turned the same direction. Some types of starch do contain some branching in their glucose chains. Starch is the principal polysaccharide used by plants to store glucose, to be used later as an energy source. Plants often store starch in seeds or other specialized organs. Common sources of starch in our diets include rice, beans, wheat, corn, and potatoes. When humans consume starch, an enzyme found in saliva and in the intestines breaks down the starch molecule into individual glucose molecules. This allows the glucose to be absorbed into the bloodstream and distributed to areas where it is needed for energy. Describe the structure and function of glycogen. Glycogen is the polysaccharide molecule used to store glucose in animals. Glycogen is a branched chain of glucose molecules. The glucose molecules in glycogen are all facing the same direction. The branches in glycogen molecules tend to be shorter and more frequent than any branching that may occur in some starch molecules. Humans and other animals consume starch as a primary energy source for everyday functions. If some of the glucose molecules from the broken down starch need to be stored for later use, they are stored in the polymer glycogen. The excess glucose is bonded together to form the branching glycogen molecules, which the humans and animals store primarily in the liver and muscle tissue to be broken down when energy is needed. Describe the structure and function of cellulose. Cellulose is a rigid polysaccharide found in plants. It is made up of long chains of glucose molecules, bonded together in an alternating manner, where every other glucose is turned in an opposite direction. The way the glucose molecules are arranged in cellulose allows hydrogen bonds to form between the cellulose molecules. These series of hydrogen bonds that form between the closely packed cellulose molecules provide a rigid and stable structure, used to give strength to plant cell walls. Cellulose is responsible for the rigidity and strength in leaves, stems, bark, and other plant structures. Cellulose, also known as plant fiber, cannot be digested by human beings and most animals. It just passes through the digestive tract without being absorbed into the body. Despite the fact that it cannot be used as an energy source in most animals, cellulose fiber is an important part of our diet because it helps exercise the digestive track and keep it clean and healthy. Describe the structure and function of chitin. Chitin is a rigid polysaccharide, similar to cellulose in its alternating arrangements of glucose molecules. It differs from cellulose by having amino groups (NH2) bonded to its glucose molecules. Because of its strength, it is used to form the exoskeleton of all arthropods: insects, spiders, lobsters, and crabs. These protective exoskeletons, or anything else made of chitin, cannot be digested by animals. Page 3: Lipids Describe the structure and function of fatty acids. A fatty acid is a long chain of carbon and hydrogen atoms, with a carboxylic acid group on one end of the molecule. The carbon chain is usually between 12 and 18 carbon atoms long, and it may contain single or double bonds between the carbon atoms. A chain with only single bonds between the carbon atoms is called “saturated,” and a chain that contains some double bonds is called “unsaturated.” Saturated fatty acid chains are straight, which allows them to pack tightly together. Because of this, saturated fats, like the fat found in meat, require a higher temperature to melt. This means they tend to be solid at room temperature. Unsaturated fatty acid chains are “kinked” because they bend where the double or triple bonds are locate in the carbon chain. Unsaturated fats are usually liquid at room temperature and are often called oils. Your body makes its own fat from taking in excess calories. Some fats are found in foods from plants and animals. Fat is essential to your health because it supports a variety of important functions. For example, some important vitamins must dissolve in fat in order to nourish your body. However, some fats are better than others. Saturated fats play a role in cardiovascular disease and other health problems. This is why saturated fats, found in foods from animals, should be eaten sparingly. Describe the structure and function of glycerol. A glycerol molecule has the formula C3H8O3. Dehydration synthesis occurs in order to attach fatty acid molecules to the glycerol molecule, removing a hydrogen atom from the glycerol molecule and oxygen and hydrogen atoms from the fatty acid to form a water molecule. This process leaves an available location for a covalent bond to form between the glycerol and fatty acid. Why are steroids important to life? Provide an example of a steroid. Steroid hormones are important to living things because they play a role in essential biological processes, such as: immune response regulating metabolism Reproduction Cholesterol is an important steroid in our bodies because it is used to make most of the other steroids that we need. Our bodies build cholesterol molecules in the liver, and we also acquire it from the food we eat. It is possible to have too much cholesterol in our bodies, which can be unhealthy, but a certain amount of cholesterol is important for our bodies to properly function. Describe the relationship between cholesterol and testosterone. Hormones such as testosterone and estrogen can be made from cholesterol. Notice that there are some similarities between the structures of these steroid molecules, but complex chemical reactions are involved in order to break and form the chemical bonds to change cholesterol into these other molecules. Describe the structure of a phospholipid. Phospholipids have two fatty acid molecules and one phosphate group bonded to the glycerol molecule. This structure gives phospholipids a hydrophobic end and a hydrophilic end to the molecule. How do hydrophilic and hydrophobic ends affect the structure and function of phospholipids? Having hydrophobic and hydrophilic ends to the molecule allow phospholipids to serve as a major component of cell membranes. The phospholipids are arranged in a double layer within the membranes, which allows the hydrophilic ends of the molecules to come in contact with the water inside and outside the cell. Describe the structure of the cell membrane. A cell’s membrane is made up of two layers of phospholipids. The hydrophobic fatty acid ends of the molecules face toward the center of the membrane. The phosphate groups on the other ends of the phospholipid molecules are hydrophilic, so they can interact well with the water inside and outside of the cell. Page 4: Proteins What are some functions of proteins? Proteins are used for structural support, movement, signaling from one part of an organism to another, transporting other substances, increasing the rate of chemical reactions, and defense against foreign substances. They are the most structurally sophisticated of the macromolecules. Each protein has a different combination of amino acids, which results in a unique three-dimensional shape. The shape of a protein is important for its function. How many different amino acids do cells use to build proteins? Cells build their proteins from 20 different amino acids. There are other amino acids that have important functions within cells, but they are not used to build proteins. Amino acids are organic molecules made up of an amino group, a carboxyl group, a hydrogen atom, and a side chain, bonded to the central carbon atom. The side chain is the part of the molecule that is different for each amino acid, and its physical and chemical properties determine the unique characteristics of a particular amino acid. What are the four main components of an amino acid? 1)Amino Group. 2)A Carboxyl Group. 3) A Hydrogen Atom. 4) And a Side Chain. What is a polypeptide bond and how does it form? When two amino acids form a bond between the carboxyl group of one and the amino group of another, this bond is called a peptide bond. This bond is formed by dehydration synthesis, and the reaction involves the help of an enzyme. Describe the shape of a protein molecule. Why is shape so important? A protein molecule is made up of one or more chains of amino acids twisted and folded in a unique three-dimensional shape. Many proteins form a roughly spherical shape, while some are long and fibrous in shape. In addition to structure, proteins serve other important functions within a cell. Many of these functions depend on the protein’s ability to recognize and bind to another molecule. Examples include: enzymes bind to reactants to speed up chemical reactions antibodies bind to foreign substances that are invading the body proteins in cell membranes allow certain molecules to pass through receptor proteins bind to specific signal chemicals, sending information to your brain Receptor proteins are important for sending information from various cells in our body to our brains, where that information is processed. For example, cells called olfactory receptor neurons allow us to smell. Olfactory is a word that describes something related to the sense of smell. The cell membranes that surround these olfactory receptor neurons contain odor receptor proteins with a variety of shapes. Scent molecules have shapes that fit specific odor receptor proteins, like two puzzle pieces fit together. When a scent molecule comes together with a protein, that protein sends a signal to the brain. Many scents that we smell are actually produced by a combination of several molecules activating several different receptor proteins. Page 5: Molecular Formula What are chemical formulas? Today we use a lot of abbreviated language. Texting and instant messaging are quick ways to communicate that use as few letters and numbers as possible to get your message across. There is a shorthand method for communicating information about chemical compounds. Chemical names can be very long. Fortunately, we have an abbreviated way to communicate them using symbols and numbers. This method uses chemical symbols and numbers to tell you which elements are in a compound and how much of each element is present. Chemical formulas have two parts: the symbol of each element in a molecule of the substance a number indicating how many atoms of each element are in each molecule of the substance We will start with a simple example. The chemical formula for the oxygen gas we breathe is O2. There is only one element in oxygen gas: oxygen. O is the symbol for the element oxygen, and the subscript 2 means that each molecule of oxygen contains two atoms of oxygen. The atoms of oxygen are covalently bonded together by sharing pairs of electrons. List the two parts of a chemical formula. 1)The abbreviation of the element/molecule used in the chemical formula. 2) And the number behind each of the molecules in the chemical formula. This number can be known as and called the subscript, and show how many atoms of each molecule are in the chemical formula. What is a subscript in a chemical formula? N/A. Describe each of the prefixes listed below: Prefix Meaning Example di- Two. Sulfur dioxide (SO2) tri- Three. Nitrogen trifluoride (NF3) tetra- Four. Carbon tetrachloride (CCl4) penta- Five. Phosphorus pentachloride (PCl5) hexa- Six. Sulfur hexafluoride (SF6) Page 6: Lesson Review What does glucose and fructose combined form? Sucrose. Practice Question: Highlight the correct answer The different properties and functions of carbohydrates, and other biological molecules, is due to what? A. Their structures B. Where they are found C. They are inorganic molecules D. Their bonds _______________________END OF HONORS 1.02A________________________ **Use the quick Links below for fast navigation. 1.01 Exploring Life 1.02A Chemistry of Life Honors 1.02 Chemistry of Life 1.03 Earth’s Early Atmosphere 01.03 Biology Notebook: Earth’s Early Atmosphere Page 1: Origin of Life on Earth What makes Earth an ideal home for its diverse inhabitants? It is not too close, nor too far in distance to the Sun, unlike other planets in our solar system. It has an atmosphere made up of important elements and molecules, like carbon-based molecules for life, such as animals, humans, and plants, to thrive and survive in. Key Terms: Jot down terms and definitions that are new to you. You will see them used in the lesson. Okay, Yes. Page 2: Early Earth Organize the characteristics of early Earth in the table below: Temperature? (hot, cold, mild) Hot. Protective atmosphere? (yes or no) No Protective Atmosphere. Presence of water? (yes or no) Yes. Presence of oxygen? (yes or no) No. Atmospheric gases (list) The atmosphere was primarily made up of carbon dioxide, water vapor, and nitrogen. There may also have been small amounts of carbon monoxide, hydrogen sulfide, and hydrogen cyanide. Compare and contrast early Earth and modern Earth. Modern Earth has oxygen which helped create new compounds with organic molecules, or carbon-based molecules, while Early Earth did not have oxygen then. Early Earth had no protective layer, while Modern Earth does. And Early Earth was filled with very hot temperatures due to an influx of many volcanoes on Earth then, which Modern Earth does not have to that extent now. This being the case in Early Earth then, made Earth inhabitable for humans or any form of life either, as humans and all animals and creatures of the Earth, need oxygen to survive, and also normal temperatures to survive. What are organic molecules? Organic Molecules are just another word for Carbon-based molecules, and were existent in Early Earth’s Atmosphere, as it is now in Modern Earth’s Atmosphere. Why are scientists interested in the origin of organic molecules? Because organic molecules are very important and necessary for life here on Earth too. What hypothesis did Oparin & Haldane propose for the origin of the first organic molecules? In the 1920s, A. I. Oparin, a Russian scientist, and J.B.S. Haldane, an English scientist, independently proposed ideas that the conditions of early Earth favored chemical reactions that were able to build small organic molecules from inorganic molecules in the atmosphere. The limited amount of oxygen in that early atmosphere, as well as the large amounts of energy provided by UV radiation and lightning, were thought to allow these reactions to occur spontaneously. They argued that the reason we do not observe these reactions occurring today is the atmosphere now has a greater amount of oxygen gas. Oxygen interferes with the reactions that would form carbon-based organic molecules. Theories suggest that some of the first organic molecules formed on Earth may have been amino acids and nucleotides. Amino acids are the small organic molecules that bond together to form proteins. Nucleotides, another type of small organic molecule, bond together to form RNA and DNA molecules. The spontaneous formation of these small organic molecules from nonorganic molecules can no longer happen in today's oxygen-rich atmosphere. There was a high amount of energy on early Earth. What 2 factors caused this? Uv Radiation, and lightning were two big causes to the high amounts of Energy on Early Earth. What are two examples of organic molecules that scientists think first formed? Amino acids, and nucleotides. Why can’t the reactions that occurred on early earth happen on modern Earth? Because the oxygen in our atmosphere in Modern Earth today, prevents the reactions that occurred in Early Earth’s Atmosphere. Page 3: Chemical Experiments What hypothesis did Miller and Urey want to test? Their hypothesis went over that organic molecules were created in a way, or formed, due to many smaller inorganic molecules that was present in early earth’s atmosphere which they tried to use to replicate the atmosphere in early earth, to see if organic molecules could be formed from many other inorganic molecules plus large amounts of energy from UV radiation, and volcanoes on early earth’s environment. What did the experiment produce? Their experiment produced a variety of amino acids and other small organic molecules. The gas mixture used to represent the early atmosphere contained water (H2O), hydrogen (H2), methane (CH4), and ammonia (NH3). What did they add to represent Earth’s early atmosphere? They added the elements/molecules, H20, Hydrogen, methane (CH4), and ammonia (NH3). Look at the image below. What was formed at the end of their experiment? 21 amino acids, and many other organic molecules were present at the end of the experiment after they replicated early earth’s atmosphere, and the chemical reactions that may have formed between all of the inorganic molecules in early earth’s atmosphere, and the intense and large amounts of energy from UV radiation, and lightning, and many other energy sources. Click the “Sources of Energy” tab. Name 3 energy sources that scientists say may have caused these reactions to occur. UV Radiation from the Sun. Lightning that comes from Earth, and early Earth’s atmosphere. And the deep-Sea Vents that may have provided the energy and chemical molecules needed to form the first organic compounds. Page 4: Chemical Evolution Read the “Organic Molecules” tab. If the first organic molecules did not form on early Earth, where did other hypotheses suggest that they may have come from? That they came to Earth from meteorites that hit and landed on Earth, which then allowed organic molecules to enter into Earth’s atmosphere. Read the “Building Larger Organic Compounds” tab. How did large organic molecules form without the presence of enzymes? In living cells, the formation of the large organic macromolecules from smaller organic molecules, such as forming proteins from amino acids or forming RNA from nucleotides, requires the help of specialized enzymes. So how did these large organic molecules form without the presence of these enzymes? Scientists have observed that chemical bonds sometimes form between small organic compounds on hot surfaces. Scientists speculate that ocean water containing small organic molecules, like those formed in the Miller-Urey experiment, splashed onto hot sand, clay, or rock. As the water evaporated on the hot surface, the small organic compounds could have bonded together. Although they have not been able to build large protein molecules in this way, scientists have been able to form smaller chains of amino acids using this method. Read the “Early Genetic Material” tab. What do all living organisms contain? All living organisms contain genetic information, stored in DNA and RNA molecules, which directs the functions of cells. Explain the RNA world hypothesis. (Be sure to explain the significance of RNA) That some of the first large organic molecules to form and self-replicate were RNA molecules, with DNA molecules forming much later. This is called the RNA world hypothesis. Define catalyst. A substance that increases the rate of reaction without undergoing any permanent chemical change Explain what helps RNA catalyze. This means that RNA helps to speed up reactions. One important reaction that RNA helps to catalyze is the building of new RNA molecules. Before this discovery was made, the long-held view was that only proteins could serve as biological catalysts. If RNA is able to self-catalyze, this means that early RNA molecules may have been able to self-replicate without the help of other molecules. If early RNA molecules were able to copy themselves to build new RNA molecules, this helps to explain why all organisms share the same genetic code. All organisms on Earth have a Universal Genetic Code. What does that mean? The Universal Genetic Code is a set of rules that dictate how the sequences of nucleotides in DNA and RNA are translated into the amino acid sequences of proteins. Essentially, it's the blueprint for building and maintaining every organism. The remarkable thing about the Universal Genetic Code is its consistency across almost all forms of life on Earth. The same codons encode the same amino acids in bacteria, plants, animals, and humans. This suggests a common evolutionary origin and allows for the incredible diversity of life we see today, all built from the same fundamental biological language. Fascinating, right? 🌱🔬 Page 5: Early Cells Describe the earliest cells. Prokaryotic Cells. We know from fossil evidence that the first true cells were flourishing and covered Earth's surface at least 3.5 billion years ago. These early single-celled organisms were prokaryotes, a small simple type of cell that lacks a true nucleus. These cells lived and evolved on Earth all alone for 2 billion years. Did the first prokaryotic cells need oxygen on early Earth? Would they be considered aerobic or anaerobic? No, they did not need oxygen on Early Earth, and they would be considered anaerobic. How did the first prokaryotic cells obtain energy? They were heterotrophs, so they fed off of other living organisms to get their energy. These cells were heterotrophs that had to obtain their energy by taking in nutrients as food. Scientists speculate that their food was the rich assortment of organic molecules thought to be present in the ocean water at that time. Define heterotroph. (click on the word in your lesson to see the definition) Organisms that must eat or consume other organisms, plants, animals, or both, to get their energy. What did the early cells use as a food source? They would have most likely used rich assorted organic molecules, thought to be present at the time on Early Earth, in the Ocean Waters. List the four types of cells found today that scientists believe are similar to the early cells on Earth and one interesting fact about each. The endosymbiosis theory explains that modern-day eukaryotic cells have evolved from two or more prokaryotic cells. Some single-celled organisms living today may be close descendants of the earliest cells on Earth. They have characteristics that allow them to survive and thrive under severe conditions, some of which may have been present on early Earth. Cells Interesting Fact 1. Methanogens. Single celled organisms that produce methane (CH4) in a form of anaerobic respiration. They are common in wetlands, marine sediment, and in the guts of many animals. 2. Thermophiles. Single-celled organisms that live at extremely high temperatures, between 45 and 80 degrees Celsius (113 and 176 degrees Fahrenheit). They can be found in hot springs and deep-sea vents. Scientists believe thermophilic bacteria may have been some of the first cells on Earth. 3. Halophiles. Organisms that thrive in environments with very high concentrations of salt. Many conduct photosynthesis. They can be found in places with salt concentrations five times greater than that of the ocean. 4. Cyanobacteria. Photosynthetic prokaryotes that live in the water. They are the most abundant bacteria on the planet and release large amounts of oxygen into the atmosphere. Even though these bacteria cells are very small, they often grow together in large colonies that can be seen with the naked eye. Cyanobacteria can be found in almost every conceivable environment, from oceans to fresh water to moist soil. These photosynthetic cells are essential to ocean ecosystems, serving as the autotrophs( Autotrophs are organisms that can produce their own food. ) at the base of many marine food chains. What does fossil evidence show us about the earliest and most abundant autotrophic cells? Fossil evidence shows that the most abundant autotrophic cells were those of modern-day descendents of cyanobacteria, and they are even to be considered one of the largest and most important cells existent in Earth today. And from Early Earth too. What are cyanobacteria and why are they important? Cyanobacteria are photosynthetic prokaryotes that live in water, and that release the most oxygen into Earth’s Atmosphere today. And they are important just because of this. They provide an oxygen rich environment for all of the diversity of life around us. From human beings, to all of the animals and creatures of the Earth, and all of the plants on Earth too. As cyanobacteria and other autotrophs increased, how did the atmosphere change? The atmosphere began to produce and be made up of more oxygen molecules in the Atmosphere, and as this happened many of the original anaerobic cells were getting killed off, scientists theorized and concluded. And there were some anaerobic cells though that may have survived through the oxygen molecules entering and being produced in Earth’s new Atmosphere. What became the dominant life forms on the planet as the oxygen became more abundant? The aerobic autotrophs and heterotrophs became the dominant life forms on the planet and evolved into all of the diversity of life now visible on Earth. The cyanobacteria cells. Page 6: Formation of Microspheres What is a microsphere? A microspheres are tiny bubbles filled with large groups of organic molecules, able to maintain an internal environment different than their surroundings Microspheres are not cells, but they do have similar characteristics. Identify the characteristics of microspheres. These bundles of molecules are able to maintain an internal environment different from the surroundings outside the bubble. They also have a simple way of storing and releasing energy. How do microspheres grow, and what happens when it reaches an unstable size? These bundles of molecules expand by absorbing additional molecules until they reach an unstable size, and then they split into smaller microspheres. This division is not true reproduction or cell division, but it may be a precursor (a predecessor ) to it. How does the hypothesis of microspheres build on the RNA world hypothesis and the universal genetic code? If RNA molecules could self-replicate, it would mean that whenever a microsphere split, the early genetic coding in the RNA would pass to the newly formed microspheres. This could be a predecessor to how cells pass on their genetic information today and may help explain why all organisms share a universal genetic code. Evolution of true cells was made possible when genetic information could be passed from one microsphere to another. What fossils have scientists found that date back to 3.5 billion years? They have found microscopic bacterial cells in rocks that are more than 3.5 billion years old How long ago did photosynthetic bacterial cells become common? By 2.2 billion years ago, did they become common. These cells used energy from sunlight to produce food, giving off oxygen gas in the process. As oxygen accumulated in the atmosphere, the ozone layer also began to form. Over time, the oxygen levels rose until they reached the levels present today. As the conditions of the atmosphere changed, different types of organisms developed to live in the now oxygen-rich environment. Practice question: Highlight the correct answer If there was not an increase in cyanobacteria in early Earth, what would have happened to Earth’s early atmosphere? A. The amount of oxygen would have increased, causing an increase in aerobic autotrophs and heterotrophs B. The amount of oxygen would have increased, causing a decrease in aerobic autotrophs and heterotrophs. C. The amount of oxygen would have decreased, causing an increase in aerobic autotrophs and heterotrophs. D. The amount of oxygen would have decreased, causing a decrease in aerobic autotrophs and heterotrophs. Which best describes the atmosphere of the early Earth? A. Little or no oxygen, mostly carbon dioxide, water vapor, and nitrogen B. Little or no carbon dioxide, mostly oxygen, water vapor, and nitrogen C. Little or no water vapor, mostly oxygen and carbon dioxide, with some nitrogen D. Large amounts of hydrogen cyanide, low amounts of carbon dioxide and oxygen **Use the quick Links below for fast navigation. 1.01 Exploring Life 1.02A Chemistry of Life Honors 1.02 Chemistry of Life 1.03 Earth’s Early Atmosphere Once you have finished all assignments in Module 1, it’s time to complete your 1.04 DBA (discussion based assessment) with your teacher. The DBA is open-note, but your lesson cannot be open. You will receive your exam password after completing the DBA. Make your appointment!