Chemistry 301 Introduction to Biochemistry

Study Guide :: UNIT 1

Cells, Water, and Buffers

Overview

Biochemistry is the study of the chemical processes that characterize “life.” Generally, it involves a study of biological molecules and the molecular reactions they undergo.

This course is provides a bridge between fundamental chemistry (elementary particles and chemical laws) and biology. It will also give you a sense of biochemistry as an ongoing field of research, by introducing you to the biochemical research literature and biochemical techniques.

In Unit 1, we begin the bridging process. The unit is divided into four lessons:

Note: Unless otherwise indicated, all page numbers in this study guide for this course refer to the course textbook, Biochemistry Free and Easy Version 3.0, by Dr. Kevin Ahern & Dr. Indira Rajagopal, Oregon State University.)

Learning Objectives

After completing this unit, you should be able to:

1. Define “biochemistry.”
2. Explain how the chemical properties of water make it the ideal biological solvent.
3. Describe the organization of a eukaryotic (nucleus‑containing) cell, and compare it to the organization of a prokaryotic (non‑nucleated) cell.
4. Name the major classes of biomolecules, and identify the atoms most commonly found in each class.
5. Define “metabolic pathway.”
6. Explain what is meant by “the biochemical literature,” and discuss why it is important for this (and other) biochemistry courses.

Glossary

A good definition identifies the thing described, and says something about where it is found and how it works. Each of the following definitions is incomplete. As you work through this and later units, you should develop a complete definition for the terms in each glossary.

Lesson 1: Introduction to Biochemistry and Biochemical Research Literature

Overview/Objectives

After completing this lesson, you should be able to:

1. Define “biochemistry”.
2. List the 6 elements that make up 99% of living cells.
3. List the classes of biomolecules.
4. Identify some applications of biochemistry.
5. Demonstrate an understanding of the format of a research article and how to read one.

Readings and Activities

1. In the textbook’s Chapter 1, Cells, Water, and Buffers, read the introduction (pages 11–13). This short reading introduces the field of biochemistry and provides an overview of how to use the open, interactive textbook.
2. Do a Google search of the word “Biochemistry”.
3. Biochemistry on Wikipedia provides a nice overview of the subject and some of its major areas of focus. Read the introductory and history sections of this page, and then scroll down to see the four main classes of biomolecules.

Commentary

Biochemistry is the study of the building blocks, or molecules, of life and how these interact in the processes that occur in living organisms. Biochemists are dedicated to understanding the structure and function of these molecules. This Commentary provides additional information about the field of biochemistry and biochemical research.

The consistent structure of nature’s major organic building blocks allows us to find similarities in the biochemical make‑up of all living creatures. These building blocks, termed “biomolecules,” are divided into four classes:

• proteins (and their building blocks, amino acids)
• carbohydrates or polysaccharides (and their building blocks, sugars)
• lipids (and their building blocks, fatty acids)
• nucleic acids (and their building blocks, nucleotides and ribonucleotides).

The building blocks of biomolecules (the amino acids, monosaccharides, fatty acids, and nucleotides and ribonucleotides), and the reactions biomolecules undergo, are virtually the same whether viruses, plants, or cows are being discussed. The great diversity of life (viruses don’t look like cows, after all) comes from the way the building blocks are put together.

This course emphasizes the similarity of biomolecules in diverse species. It also introduces a wide range of detailed biochemical reactions. It is easy to get lost in all the detail. Keep in mind that this course is a bridge between chemistry and biology. Chemistry is the study of molecules and reactions; biochemistry is the study of the ways in which the molecules and reactions of life interconnect. Biochemistry also concerns itself with how reactions can continue to function efficiently. The major difference between biochemistry and the chemistry you may have studied before is that biochemistry is about controlled, interconnected reactions. When all the biomolecules and biochemical reactions are in a “steady state” (i.e., a balanced supply of reactants and a constant output of products), we are in the world of biology. Life itself is about biochemical reactions, growth, and species perpetuation.

Biochemistry is a vibrant science. Biochemists study all aspects of the material presented in this course; hence, some of the “biochemical facts” you learn here will be modified when researchers use more sensitive instruments, discover new subclasses of biomolecules, and generally gain better insight into biochemical processes. This statement is particularly true in the fields of signal transduction (i.e., how external chemicals, such as hormones, control cellular metabolism).

It is important that you, as a biochemistry student, learn, not just “the facts,” but also how you can interpret and analyze the results of biochemical research. It is not always easy to read a research article. In most cases, the research article will be provided for you; however, it is important that you also know how to search efficiently through the mass of published biochemical research to find articles of interest.

Reading a Research Article

Most scientific articles have the same form. They include

• a descriptive title
• the names and addresses of the authors
• a 100–200 word summary of the article, known as an “abstract”
• a “literature search” section, usually included in the article’s introduction, that indicates why the problem is worth studying and what previous work has been done on it
• a description of the methods, instruments, animals, and chemicals used
• the results of the research
• a discussion of the significance of the results
• a list of articles cited.

Reading a research article is not like reading a novel. Research articles usually explore specific aspects of a particular field of study; for example, whether present theories are being supported or contradicted, or if the authors’ new biomolecule is similar to or different from others in its class.

It seems obvious to start by reading the abstract, but because the abstract condenses the important features of the article, it may at first be difficult to understand. It is a good idea to scan the abstract, to see if it can be easily understood. If not, try reading the last paragraph of the literature search and the last paragraph of the article. Often, authors will use the end of the literature search to connect previously published work with the current work. Then, they use the very last paragraph of the article to sum up and discuss the overall significance of the work. After reading these two paragraphs, go back to the abstract to see if it makes more sense. Next, examine the graphs and tables. Now you should have a good idea of what the authors are trying to say, and you are prepared to read through the article from the beginning.

The Research Literature as a Whole

Biochemists keep up with new theories and current discoveries by reading the biochemical research literature and annual reviews. Because so much new research is published each year, biochemists, like other scientists, are in danger of drowning in the literature. Most researchers do not start by reading the research journals, any more than they read whole articles. Rather, they use an abstracting service. Abstracting services work by selecting key words from research articles. Thanks to computers, a researcher can choose a set of words or phrases covering their interests. The computer will then produce a list of articles by matching key words in the articles with words or phrases fed in by the researcher. The researcher (or biochemistry student) then selects the articles of interest, and retrieves them from the library. The Athabasca University Library provides students with access to several retrieval networks. One of the most useful online services is PubMed, available through the Databases section of the Athabasca University Library home page. You can also use Google Scholar to search for research articles that are relevant to your topic of interest.

Study Questions

1. Which six elements make up 99% of the mass of living cells?
2. What are the four elements most commonly found in biomolecules?
3. List and describe the four main classes of biomolecules.
4. How would you test whether a population of microorganisms demonstrates life? Assume that you do not have the equipment you would need to monitor growth (e.g., a microscope, a spectrophotometer).

If you wish to discuss any of these questions or need assistance with the material, please contact your Academic Expert (AE) by emailing the Student Success Centre at fst_success@athabascau.ca..

Lesson 2: Cells: The Bio of Biochemistry

Overview/Objectives

After completing this lesson, you should be able to:

1. Demonstrate an understanding of the composition of cells.
2. Describe the organization of a eukaryotic (nucleus‑containing) cell.
3. List the structural differences between eukaryotic and prokaryotic cells.

Readings and Activities

1. Read “Cells: The Bio of Biochemistry” (pages 13–14 in the textbook).

2. For information on eukaryotic cells see Eukaryote on Wikipedia; for information on prokaryotic cells see Prokaryote on Wikipedia.

   Make a careful study of the diagrams and photographs, and pay attention to the names of the various structures within the prokaryotic cell and the eukaryotic cell. You can also consult other online images to visualize cell structure and organization. Read and understand how prokaryotic and eukaryotic cells differ in terms of the nucleus, internal structures, reproduction, cytoskeleton, and DNA organization.

Commentary

Chemistry of the Cell

Most of the biomolecules are found, and most of the reactions involving them take place, inside a cell. This lesson describes a typical eukaryotic cell, including the chemical composition of the cell, and the functions of cellular structures.

The cell evolved from separate molecules and from small assemblies of molecules. Therefore, we might expect the chemical elements that make up the cell to be similar in abundance to those of the Earth’s crust. This is not the case: of the four most common elements in the Earth’s crust (O, Al, Si, and Fe), two (Si and Al) are not even found in living matter. It seems that the atoms making up living matter are there because of their chemical fit or their similar atomic radii, rather than because they reflect the material from which the cell evolved. The list below indicates the relative abundance of the major elements in a typical cell.

As this table shows, the elements hydrogen (H), oxygen (O), carbon (C), and nitrogen (N) add up to 99.4% of a typical cell. Note that the elements in the second section of the table make up less than 1% of the cell. The elements in the third section, called “trace elements,” are found mostly within proteins. In general, the less abundant major elements and the trace elements are ionic or charged species, while H, O, C, and N are likely to be non‑charged species in organic compounds. Therefore, we can think of the cell as an aqueous solution of organic molecules and miniscule amounts of inorganic ions. We will examine the properties of water in Lesson 3.

Biology of the Cell

Cells can have a variety of shapes and functions, but all eukaryotic cells have common internal features. A brief description of the contents of a eukaryotic cell follows:

The nucleus is the site of RNA production. Newly produced (and short lived) RNA passes out of the nucleus and attaches to ribosomes in the cytoplasm, or to ER membranes. Amino acids in the cytoplasm are linked together on the ribosomes to make proteins. The newly produced proteins can be used within the cell, incorporated into membranes, or secreted into the extracellular space.

Sugars and fats are partially digested in the cytoplasm, and then are transported into the mitochondria, where they are converted into ATP. ATP is the fuel molecule that provides the energy for protein production and other cellular activities. Cells can also synthesize lipids, nucleotides, and ribonucleotides. All biochemical syntheses are accomplished in the cytoplasm or on a membrane surface.

Literally thousands of synthesis (anabolic) and degradation (catabolic) reactions occur in cells. The study of how these reactions are organized and regulated forms one of the most intense areas of biochemical research. Hormones are chemical signals, produced by specialized cells that trigger or suppress biochemical reactions in eukaryotic cells. Another class of biomolecules, called growth factors, are also important in cell regulation.

Study Questions

1. How does the composition of the earth’s crust and living cells differ?
2. What is the function of the following organelles?
   • Golgi apparatus
   • lysosome
   • ribosomes
   • mitochondria
   • cytoskeleton
3. Where are sugars and fats digested in the cell?
4. List the differences between prokaryotic and eukaryotic cells in terms of the following:
   • nucleus
   • internal structures
   • cytoskeleton
   • DNA organization
   • Reproduction

If you wish to discuss any of these questions or need assistance with the material, please contact your Academic Expert (AE) by emailing the Student Success Centre at fst_success@athabascau.ca.

Lesson 3: Water

Overview/Objectives

After completing this lesson, you should be able to:

1. Explain how the chemical properties of water have led to its being described as the “universal solvent.”
2. Describe hydrogen bonds (H‑bonds).
3. Describe the association of amphiphilic molecules in aqueous solution.

Readings and Activities

1. Read “Water, Water Everywhere” (pages 14–15 in the textbook).

2. After you read this, you may wish to view the introductory video lecture,  01 Biochemistry Introductory Lecture for Kevin Ahern’s BB 450/550.

   (A link to this is also provided on page 14 of the textbook.)

Commentary

As the textbook states, approximately 70% of the human body is water. Therefore, it is appropriate to begin the study of biochemistry by thinking about water.

Water as a solvent

H₂O is a polar molecule that interacts strongly with other H₂O molecules through hydrogen bonds (H‑bonds). An H‑bond is the weak attraction between a polar oxygen atom in one molecule and a polar hydrogen atom in a second molecule. An H‑bond (20 KJ/mol) is about 20 times weaker than a covalent bond (400 KJ/mol). Nevertheless, H‑bonds are a significant force, because only about 10% of the total H‑bonds in bulk water are broken when H₂O goes from the solid to the liquid phase. At 37°C, the structure of water can be thought of as a shifting mosaic, with H‑bonds continually breaking and reforming. The fluidity of water is a result of the speed with which this breaking and reforming occurs: it takes only 10⁻¹¹ seconds.

This property is significant for biochemistry, because water molecules can also H‑bond to biomolecules. In fact, it is the H‑bonds between bulk water and the outer surface of proteins that keep these enormous, largely organic molecules in solution. The design of “anti‑freeze proteins,” found in the blood of cold‑water fish, is particularly clever. The charged functional groups on the surface of these proteins are arranged in such a way that they break up the ice‑like mosaic structure of attached water molecules in the immediate vicinity of the protein.

Water is characterized by a high boiling point (compared with, say, NH₃ or CH₄), high surface tension, and high heat of vaporization. Therefore water forms a stable matrix for biomolecules. The body (or a given cell) can be thought of as a continuous aqueous phase, interrupted—or compartmentalized—by barriers (membranes).

Water as a reactant

The “concentration” of water in the body is ~ 55 Molar. The concentration of biomolecules in the body ranges from 10⁻³ to 10⁻¹² Molar. Therefore, by the laws of mass action alone, water is a significant participant in biochemical reactions. This point will be expanded in future units; for now, an example of water as a reactant in biochemical reactions is given here:

This image shows hydrolysis of the peptide bond in proteins.

Study Questions

1. Using the concept of H‑bonding, explain how small items that are denser than water (e.g., a fine needle or a water bug) can remain on the surface instead of sinking.
2. By considering an alternative way of doing things, we understand better how the natural situation works. Suppose that the solvent of life was ammonia rather than water. Consider the properties of water mentioned above (e.g., H‑bonding and high heat of vaporization). How different are the properties of ammonia and water? Do you think ammonia would support biochemical reactions? Why is the heat of vaporization important?

Lesson 4: pH and Buffers

Overview/Objectives

After completing this lesson, you should be able to:

1. explain how its chemical properties have led to water being described as the “universal solvent.”
2. describe hydrogen bonds (H‑bonds).
3. describe the association of amphiphilic molecules in aqueous solution.

Please note that, for Lesson 4, the textbook content needs no enhancement; we have therefore not included a Commentary section here.

Readings and Activities

1. Read “Buffers Keep the Cellular Environment Stable” (pages 15–17 in the textbook).

2. After you read this, you may wish to view the video lecture on Buffers, #02 Biochemistry Buffers Lecture for Kevin Ahern’s BB 450/550.

   (A link to this is also provided on page 17 of the textbook.)

3. Read “Henderson‑Hasselbalch” (pages 17–21).

Study Questions

1. Why is pH important for molecules, in particular proteins?
2. Define the terms “acid” and “base.”
3. Explain the properties of weak acids and weak bases.
4. What is a buffer and why are buffers important?
5. Explain pK_a and give an example to illustrate what this value means in terms of acids.

If you wish to discuss any of these questions or need assistance with the material, please contact your Academic Expert (AE) by emailing the Student Success Centre at  fst_success@athabascau.ca.

Answers to Unit 1 Study Questions

Lesson 1 Introduction to Biochemistry and Biochemical Research Literature

1. The six elements that make up 99% of the mass of living cells are carbon, hydrogen, nitrogen, oxygen, calcium, and phosphorus.
2. The four elements found most commonly in biomolecules are C, H, N, and O. Of these four, three are small atoms that are close together in the periodic table. Because they are close, they should share similar chemical properties. C, N, and O are approximately the same size. In addition, these three elements position their bonded partners in a tetrahedral array. Because these elements have the same approximate size and bonding geometry, biomolecules should “stack” well together.
3. The four main classes of biomolecules and their building blocks are:
   • proteins: are made up of amino acids; have many functions, e.g., enzymes or structural (muscle).
   • carbohydrates: also known as polysaccharides or sugars; are made up of monosaccharides or simple sugars; function in energy use and storage.
   • lipids: are made up of fatty acids; make up membranes, and function in energy use.
   • nucleic acids: made up of nucleotides; are the main component of genetic information.
4. In this simple experiment, you can assume that the microorganisms probably need water and a supply of nutrients (i.e., reactants) to thrive. Place one small sample of the microbial population in a clean dry beaker, a second sample in a water‑filled beaker, and a third sample in a water‑filled beaker to which a pinch of sugar and another of salt have been added. Wrap a blanket around the beakers and put a thermometer in each. Wait. Increasing turbidity in the second or third beakers, or increasing temperature in any of the beakers, might be interpreted as “life.” Turbidity = multiplication; increasing temperature = activity of biochemical reactions. This is not the only possible answer. The critical points are to observe growth or multiplication, and to deduce metabolic activity.

Lesson 2 Cells: The Bio of Biochemistry

1. The earth’s crust is mostly composed of O, Al, Si, and Fe. Living cells are mostly composed of H, C, O, and N. Two elements found in the earth’s crust, Si and Al, are not found in living matter.
2. Golgi apparatus is involved in protein assembly and secretion. Lysosomes are responsible for digestion. Ribosomes synthesize proteins. The mitochondria synthesize ATP. The cytoskeleton provides support and structure to the cell.
3. Sugars and fats are partially digested in the cytoplasm. They are then transported into the mitochondria, where they are converted into ATP.
4. The differences between prokaryotic and eukaryotic cells in terms of the following:
   • nucleus: present only in eukaryotes
   • internal structures: only eukaryotes have organelles and an internal membrane system.
   • cytoskeleton: eukaryotes have a cytoskeleton, but prokaryotes do not although they have some cytoskeletal proteins.
   • DNA: eukaryotic DNA is linear and packaged with histones; prokaryotic DNA is circular and negatively supercoiled and is not associated with histones.
   • reproduction: eukaryotes perform mitosis and meiosis, but prokaryotes only divide by binary fission.

Lesson 3 Water

1. Water is a mosaic structure in which ~ 90% of the H‑bonds are intact at any given moment. Therefore, water can be thought of as a semi‑solid as well as a liquid. An object that is relatively small, and whose surface area is relatively large for its mass, rests on the surface of water as if it were on a solid. “Surface tension” is the term used to describe this semi‑solid property of water: the forces holding water molecules together at the surface are greater than the forces holding internal water molecules together.
2. Consider the last part of the question first: heat of vaporization reflects both the mass and the amount of hydrogen bonding in a liquid. For similar masses (ammonia = 17 daltons, water = 18 daltons) a lower heat of vaporization means less H‑bonding. NH₃ has a lower heat of vaporization than water, and therefore H‑bonds less well to itself and to other polar molecules. Because NH₃ is a solvent for polar molecules, it can support biochemical‑type reactions, but not as well as water can. A lower heat of vaporization also means ammonia will evaporate more readily than water. We can conclude, then, that water is a superior biochemical solvent, but that an ammonia‑based biochemistry is possible.

Lesson 4 pH and Buffers

1. pH is important for molecules, proteins in particular, because changing charges on biological molecules due to pH changes can affect how these molecules function.
2. An acid is a substance with protons that can dissociate when dissolved in water. A base is a substance that can absorb protons when dissolved in water.
3. Weak acids do not lose protons as readily (H+) and weak bases do not absorb protons readily (OH−) when dissolved in water.
4. A buffer is a weak acid. Buffers are important because they resist changes in pH by releasing protons to compensate for those “used up” or that have dissociated in reacting with hydroxyl ions (OH). Buffers provide or absorb protons as needed. They help to keep the H+ concentration, or pH, relatively constant.

5. The stronger the acid the more protons will dissociate from it and the higher the dissociation constant (K_a) will be. The higher the K_a, the lower the pK_a value and so the stronger the acid.

   pK_a = −Log K_a, just as pH = −Log [H+]

   Formic acid has a pK_a of 3.75. Acetic acid has a pK_a of 4.76. Therefore formic acid is a stronger acid than acetic acid.

If you wish to discuss any of these questions or need assistance with the material, please contact your Academic Expert (AE) by emailing the Student Success Centre at fst_success@athabascau.ca.