MLS 064 Biochemistry Module 2 - PDF

# MLS 064: Biochemistry ## Module #2 Student Activity Sheet **Name** **Section** **Schedule** **Class number** **Date** ## Lesson title: Relationship of Cell Biology and Biochemistry ### (Water and pH) **Learning Targets:** At the end of the module, students will be able to: 1. Describe properti...

# MLS 064: Biochemistry ## Module #2 Student Activity Sheet **Name** **Section** **Schedule** **Class number** **Date** ## Lesson title: Relationship of Cell Biology and Biochemistry ### (Water and pH) **Learning Targets:** At the end of the module, students will be able to: 1. Describe properties of water 2. Understand how pH affects the body and how pH is maintained 3. Define biochemical reactions 4. Identify the parts and functions of the cells. 5. Understand how pH and buffer works inside the body. **Materials:** * Book, Pen and Notebook **References:** * Ubalde, Biochemistry for Allied Health Sciences: Edric Publishing, 2019 **A. LESSON PREVIEW/REVIEW** The instructor will be starting the class by recalling the previous activity that was discussed which talked about the basic of organic chemistry, characteristics of water and pH. The instructor will ask the following questions: * What is Biochemistry? * Why is studying biochemistry important in medical laboratory science profession? **B. MAIN LESSON** ### Role of Carbon in the Study of Life Long ago, scientists believed that all carbon compounds were the result of biological processes, which meant organic chemistry was synonymous with biochemistry under the Vital Force Theory. However, it was discredited when in the mid-1800s it was discovered that urea could be synthesized from inorganic materials and showed that there were other paths to the production of carbon compounds. ### Why is carbon important? * Carbon atoms are capable of forming stable bonds to other carbon atoms. The process of one type of atom bonding to identical atoms is catenation. Many other elements can catenate, but carbon is the most effective at it. * Carbon is capable of forming stable bonds to a number of other elements. These include the biochemically important elements hydrogen, nitrogen, oxygen and sulfur. The latter three elements form the foundation of most if the functional groups (reactive groups of a molecule) necessary for life. Bonds between carbon and hydrogen are usually unreactive under biochemical conditions; thus, hydrogen often serves as an "inert" substituent. ### Carbon bonds Carbon is capable of forming four bonds. In bonding to itself and other elements, carbon uses a variety of types of hybridization - when it bonds to another carbon molecule, for example, these may have four single bonds, a double and two single bonds, two double bonds, or a triple and a single bond. Double bonds to oxygen atoms are particularly important in many biochemical. ### Chemical bonds Covalent bonds are important intramolecular forces (forces within the same molecule) in biochemistry. Intermolecular forces (forces between chemical species) are also extremely important. Among other things, intermolecular forces are important to hydrophilic and hydrophobic interactions. ### Intermolecular forces All intermolecular forces are van der Waals forces that is they are not true bonds in the sense of sharing or transferring electrons, but are weaker attractive forces. These forces include dipole-dipole forces, hydrogen bonding and ionic interactions. * **Dipole-dipole forces**: Dipole-dipole forces exist between Polar Regions of different molecules. The presence of a dipole means that the molecule has a partially positive end and a partially negative end. Biological systems utilize a special type of dipole-dipole force known as hydrogen bonding. * **Hydrogen bonding**: Hydrogen bonding, as the name implies, involves hydrogen. The hydrogen atom must be bonded to either an oxygen atom or a nitrogen atom. Hydrogen bonding is significantly stronger than a normal dipole-dipole force. Hydrogen bonding may be either intramolecular or intermolecular. * **lonic interactions**: In biological systems, ionic interactions may serve as intermolecular or intramolecular forces. In some cases, these may involve metal cations, such as Na, or anions, such as Cl. Oppositely charged ions attract each other strongly. ### Water-related interactions The predominant factor leading to hydrophobic (water-hating) interactions is the presence of portions of a molecule containing only carbon and hydrogen. Hydrocarbon regions are nonpolar and are attracted to other nonpolar regions by London dispersion forces. In general, the presence of any atom other than carbon and hydrogen makes a region polar. Oxygen and nitrogen are the most effective elements in biochemistry for making a region of a molecule polar. ### Functional Groups Most carbon compounds have one or more reactive sites composed of a specific grouping of atoms in their structure. It is at these sites that chemical reactions occur. These specific grouping of atoms that react are called functional groups. These functional groups contain atoms other than carbon and hydrogen and/or double or triple bonds and define the reactivity of the organic molecule. * **Hydrocarbons**: Alkanes are hydrocarbons- compounds containing only carbon and hydrogen with no traditional functional groups. For this reason, they are not very reactive. Alkenes and alkynes are also hydrocarbons. They contain a carbon-carbon double and tripled bond, respectively. * **Groups with oxygen and sulfur**: Many functional groups contain oxygen, including alcohols, ethers, aldehyde and ketones, which appear in carbohydrates. In carbohydrates, many ether groups are known as glycoside linkages. In addition, carboxylic acids and esters are important functional groups that appear as fatty acids and in fats and oils. Sulfur, the element immediately below oxygen on the periodic table, may replace oxygen in both alcohols and ethers to give thiols (mercaptans) and thioethers. * **Groups containing nitrogen**: Amines and amides are two important functional groups containing nitrogen. Amines are present in amino acids and alkaloids. Amides are present in proteins where they are known as peptide bonds. * **Groups containing phosphorus**: Phosphorus is also an important element in biological systems and is normally present as part of a phosphate group. Phosphate groups come from phosphoric acid, $H_2PO_4$. The phosphate groups may be alone, part of a diphosphate, part of a triphosphate or part of a phosphate ester. ### Reactions of functional groups As you study the different biochemical molecules and their functions within the living organism, you see that the way a certain molecule reacts is primarily determined by the functional groups in the molecule's structure. Do not forget to take a moment to revisit your organic chemistry books. * **Alcohols** * Alcohols are subject to oxidation. Mild oxidation of a primary alcohol (where the -OH is attached to an end carbon) produces an aldehyde, which may undergo further oxidation to a carboxylic acid. In similar conditions, a secondary alcohol (-OH is attached to a carbon bonded to two other carbons) will yield a ketone, and a tertiary alcohol (-OH attached to a carbon bonded to three other carbons) will not react. * The presence of the OH leads people mistakenly to assume that alcohols are bases. Remember that under biological conditions, alcohol are neutral compounds, though, phenols, are weak acids. * **Aldehydes and ketones** * Aldehydes easily undergo oxidation to carboxylic acids, but ketones do not undergo mild oxidation. With difficulty, it is possible to reduce aldehydes and ketones back to the appropriate alcohols. * **Carboxylic acids** * Carboxylic acids, along with phosphoric acid, are the most important biological acids. Carboxylic acids react with bases such as the amines to produce salts. The salts contain an ammonium ion from the amine and a carboxylate ion from the acid. * **Thiols and amines** * Under mild oxidation, two thiols join to form a disulfide. Mild reducing conditions, catalyzed by enzymes, reverse this process. Such formation of disulfide linkages is important in the chemistry of many proteins, such as insulin. * Amines are the most important biological bases. As bases, they can react with acids. * **Phosphoric acid** * Phosphoric acid, may behave like a carboxylic acid and form esters. The esters will have an organic group, R, replacing one, two or three of the hydrogen atoms. The resultant compounds are monoesters, diesters and triesters. The hydrogen atoms remaining in the mono- and diesters are acidic. ### Functional groups and pH Many of the biological functions of substances are pH dependent. For his reason, it is important to know which functional groups are acidic, basic or neutral. Neutral functional groups behave the same no matter what the pH is. The table below lists the functional groups and whether or not they are acidic, neutral or basic. The weaker a substance in terms of pH, the less likely it will be affected by its solution pH. | Acid-Base Properties of Biologically Important Functional groups | |---|---| | **Acids** | Monophosphate esters and diphosphate esters | | | Carboxylic acids (weak) | | | Phenols (weak) | | | Thiols (very weak) | | | Amine salts (very weak) | | **Bases** | Amine (weak) | | | Carboxylate ions (very weak) | | **Neutral** | Alcohols | Carboxylic esters | | | Ethers | Triphosphate esters | | | Thioethers | Disulfides | | | Amides | Ketones | | | Aldehydes | ### Acids, Bases and Buffers * Many biochemical compounds, ranging from small molecules to large polymers are capable of releasing or accepting protons at physiologic pH, and consequently, may carry a charge. * Most biochemical reactions are classified according to the functional groups that react and examples include esterifications, hydroxylations, carboxylations and decarboxylations. * The pH of a solution is the negative log of its hydrogen ion concentration: $pH= -log [H^+]$ ### A. Water * Water is the solvent of life. It dissociates: $H_2O \rightleftharpoons H^+ + OH^-$ with an equilibrium constant of: $K= [H^+][OH^-]/[H_2O]$ * Because the extent of dissociation is not appreciable, $H_2O$ remains constant at 55.5 M, and the ion product of $H_2O$ is: $K= [H^+][OH^-]= 1 \times 10^{-14}$ * The pH of a solution is the negative log of its hydrogen ion concentration [$H^+$]: $pH= -log [H^+]$ * For pure water, $[H^+]= [OH^-]= 1 \times 10^{-7}$ * Therefore, the pH of pure water is 7. ### B. Acids and bases * Acids are compounds that donate protons and bases are compounds that accept protons. * Acids dissociate. * **Strong acids**, such as hydrochloric acid (HCL), dissociate completely. * **Weak acids**, such as acetic acid, dissociate only to a limited extent: $HA \rightleftharpoons H^+ + A^-$ Where HA is the acid and A is its conjugate base. * The dissociation constant for a weak acid is: $K= [H^+][A^-]/[HA]$ * The Henderson-Hasselbach equation was derived from the equation for the dissociation constant: $pH= pK + log_o [A^-][HA]$ Where pH is the negative logo of K, the dissociation constant. * The major acids produced by the body include phosphoric acid, sulfuric acid, lactic acid and the ketone bodies, acetoacetic acid and ẞ-hydroxybutyric acid. $CO_2$ is also produced, which combines $H_2O$ to form carbonic acid in a reaction catalyzed by carbonic anhydrase (first reaction): $CO_2 + H_2O \rightleftharpoons HCO_3H + HCO_3^-$ ### C. Buffers * Buffers consist of solutions of acid-base conjugate pairs, such as acetic acid and acetate. * Near its pK, a buffer maintains the pH of a solution, resisting changes due to addition of acids or bases. For a weak acid, the pk is often designated as pK.. * At the pK., [A-] and [HA] are equal, and the buffer has its maximal capacity. * Buffering mechanisms in the body: * The normal pH range of arterial blood is 7.35 to 7.45. * The major buffers of blood are bicarbonate (HCO/H₂CO) and hemoglobin. These buffers act in conjunction with mechanisms in the kidneys for excreting protons and mechanisms in the lungs for exhaling CO₂ to maintain the pH within the normal range. ### Living Cells All living organisms contain cells. There are two types of cells: prokaryotes and eukaryotes. Prokaryotic cells are the simplest types of cells. Many one-celled organisms are prokaryotes. The simplest way to distinguish these two types is that a prokaryotic cell contains no well-defined nucleus, whereas the opposite is true for a eukaryotic cell. In this activity, we are going to focus with the eukaryotic cell. The table below shows the chief distinguishing characteristics of prokaryotes and eukaryotes. | **CHIEF DISTINGUISHING CHARACTERISTICS**| **PROKARYOTES** | **EUKARYOTES** | |:---|---|---| |1. | Their genetic material (DNA) is not enclosed within a membrane. | Has true nuclear membrane, which bind/enclose the nucleus and DNA.| |2. | They lack other membrane-bound organelles.| Contain membrane-bound organelles | |3. | Their DNA is not associated with histone proteins, which are special chromosomal proteins, found in eukaryotes).| Closely associated with histones| |4. | Their cell walls usually contain the complex polysaccharide peptidoglycan.| NO peptidoglycan. | |5. | They usually divide by binary fission (during this process the DNA is copied and the cell splits into two cells).| Divide by mitosis. They have mitotic apparatus.| |6.| Transcription (mRNA synthesis) and translation (protein synthesis) occur simultaneously in the cytoplasm.| Transcription: nucleus mRNA is translocated into the cytoplasm into the cytoplasm to be translated by ribosomes.| ### Eukaryotic cell The most characteristic feature of eukaryotic cell, the nucleus, consists of a nucleoplasm surrounded by a double nuclear membrane pierced by nuclear pores. The role of the nucleus is three-fold: * Storage and protection of the genome. * Regulation of gene expression. * Creation of ribosomes. ### Membrane of Eukaryotic cell * Membranes are lipid structures that separate the contents of the compartment they surround from its environment. * Plasma membranes separate the cell from its environment. * Organelles have membranes that separate the internal compartment of the organelle from the cytoplasm. * **The plasma membrane:** * Consists of a lipid bilayer containing embedded and peripheral proteins * The major component of membranes is lipids. * The lipids in the plasma membrane are in the form of phospholipids, which contain a polar head group attached to two hydrophobic fatty acid tails; the head group faces the aqueous environment, the fatty acid tails the interior of the bilayer. * The embedded proteins in the plasma membrane function as either channels or transporters for the movement of compounds across the membrane, as receptors for the binding of hormones and neurotransmitters, or as structural proteins. * lonic agents can remove the peripheral membrane proteins from the membrane; these can provide mechanical support to the membrane through the inner membrane skeleton or the cortical skeleton. An example of this is spectrin in the red blood cell membrane. * The plasma membrane glycocalyx consists of short chains of carbohydrates attached to proteins and lipids that extend in the aqueous media and both protects the cell from digestion and restricts the uptake of hydrophobic molecules. ### Transport of molecules across the plasma membrane * **Simple diffusion** is utilized for gases and lipid-soluble substances (such as steroid hormones). In simple diffusion, there is a net movement from a region of high concentration to a region of low concentration, and neither energy nor a carrier protein is required for diffusion. For uncharged molecules, the same concentration of the molecule will eventually be reached on both sides of the membrane. * **Facilitative diffusion** requires that the transported molecule bind to a specific carrier or transport protein in the membrane. Energy is not required, and the compound equilibrates in concentration on both sides of the membrane. * **Gated channels** are transmembrane proteins that form a pore for ions that is either opened or closed in response to a stimulus. * **Voltage-gated channels** respond to a change in voltage across the membrane. * **Ligand-gated channels** respond to the binding of a ligand to the protein. * **Phosphorylation-gated channels** respond to a covalent change (phosphorylation) on the protein. The cystic fibrosis transmembrane conductance regulator protein (CFTR) is a chloride channel that provides an example of a ligand-gated channel regulated through phosphorylation. * **Active transport** requires energy and transporter proteins. * **Vesicular transport across the plasma membrane** * **Endocytosis** refers to condition when the vesicle forms around the fluid containing dispersed molecules. * **Pinocytosis** * **Phagocytosis** * **Exocytosis** refers to the vesicular transport out of the cell. Other organelle of the eukaryotes and their functions are listed in the table below. |Organelle | Structure/Function | |---|---| |Cell membrane | The cell membrane keeps the cell together by containing the organelles within it. Cell membranes are selectively permeable, allowing materials to move both into and outside of the cell.| |Centrosomes | Active and passive transport systems; receptors and signal processing systems (synthesis of various second messengers etc)| |Cytoplasm | The centrosomes contain the centrioles, which are responsible for cell division. Cytoplasm is a jelly-like substance that is sometimes described as the "cell matrix." It holds the organelles in place within the cell.| |Golgi apparatus | Site for glycolysis and most of gluconeogenesis, pentose-phosphate shunt and fatty acid biosynthesis. The Golgi apparatus of a cell is usually connected to an endoplasmic reticulum (ER) because it stores and then transports the proteins produced in the ER. | |Glycogen granules | Further modification of membrane and transport proteins. Enzymes of glycogen synthesis and breakdown including branching and debranching. | |Lysosomes| Lysosomes are tiny sacs filled with enzymes that enable the cell to utilize its nutrients. Lysosomes also destroy the cell after it has died, though there are some circumstances (diseases/conditions) in which lysosomes begin to "break-down” living cells. Hydrolytic (digestive) enzymes localization. | |Microvilli | Microvilli are finger-like projections on the outer surface of the cell. Their function is to increase the surface area of the cell. | |Mitochondria | Mitochondria are the powerhouse of the cell. These are the energy producers within the cell. The quantity of mitochondria within cells varies with the types of cell. Generally, the more energy a cell needs, the more mitochondria it contains. Mitochondria have the capacity to multiply as well (increase energy requirement).| |Nuclear membrane | The nuclear membrane separates the nucleus and the nucleolus from the rest of the contents of the cell. | |Nuclear pore | Nuclear pores permit substances (such as nutrients, waste and cellular information) to pass both into and out of the nucleus. | |Nucleolus | The nucleolus is responsible for the cell organelles (e.g lysosomes, ribosomes, etc)| ### CELL DIVISION Because cells are always exposed to stresses such as physical and chemical stresses, cells become damaged, diseased or worn out but they remain in normal numbers as they have the capacity to reproduce by cellular division. The two types of cell division are the somatic cell division and the reproductive division (meiosis). In this activity, we are going to focus in somatic cell division. In somatic division, a cell undergoes a nuclear division called mitosis and a cytoplasmic division called cytokinesis to produce two identical daughter cells. Each daughter cell has the same number and kind of chromosomes as the original cell. The following table describes the stages of mitosis: | Interphase | The cell is engaged in metabolic activity and performing its prepare for mitosis. Chromosomes are not clearly discerned in the nucleus, although a dark spot called the nucleolus may be visible. The cell may contain a pair of centrioles both of which are organizational sites for microtubules. | |---|---| | | * First gap phase (G1) growth and normal metabolic roles * Synthesis phase (S) DNA replication * Second gap phase (G2) growth and preparation for mitosis | | Prophase | Chromatin in the nucleus begins to condense and becomes visible in the light microscope as chromosomes. The nucleolus disappears. Centrioles begin moving to opposite ends of the cell and fibers extend from the centromeres. Some fibers cross the cell to form the mitotic spindle. | | Metaphase | Spindle fibers align the chromosomes along the middle of the cell nucleus. This line is referred to as the metaphase plate. This organization helps to ensure that in the next phase, when the chromosomes are separated, each new nucleus will receive one copy of each chromosome. | | Anaphase | The paired chromosomes separate at the kinetochores and move to the opposite sides of the cell. Motion results from a combination of kinetochore movement along the spindle microtubules and through the physical interaction of polar microtubules.| | Telophase | Chromatids arrive at opposite poles of cell and new membrane form around the daughter nuclei. The chromosomes disperse and are no longer visible under the light microscope. The spindle fibers disperse and cytokinesis or the partitioning of the cell may begin during this stage. | | Cytokinesis| In animal cells, cytokinesis results when a fiber ring composed of a protein called actin around the center of the cell contracts pinching the cell into two daughter cells, each with one nucleus. | ### CHECK FOR UNDERSTANDING #### Multiple Choice 1. Movement of water from an area of higher to an area of lower water concentration through selectively permeable membrane. * **a.** Osmosis * **b.** Diffusion * **c.** Pinocytosis * **d.** Exocytosis 2. Vesicular transport is the * **a.** Transport of substance either into or out of the cell by means of small, spherical membranous sac * **b.** Vesicular movement involving endocytosis on one side of a cell and subsequent exocytosis on the opposite of the cell * **c.** Both a and b * **d.** None of the above 3. Type of endocytosis that involves the nonselective uptake of tiny droplets of extracellular fluid * **a.** Phagocytosis * **b.** Receptor-mediated endocytosis * **c.** Pinocytosis * **d.** None of the above 4. The basic structural unit of the plasma membrane is the * **a.** Lipid bilayer * **b.** Integral protein * **c.** Cholesterol * **d.** Peripheral protein 5. Integral proteins can function in the cell membrane in all the following ways except: * **a.** As a channel * **b.** As a transporter * **c.** As a receptor * **d.** As an exocytosis vesicle 6. Part of the cell that is described to be networks of protein filaments that extend throughout the cytoplasm, providing cellular shape and organizations: * **a.** Cilia * **b.** Peroxisomes * **c.** Centrioles * **d.** Cytoskeleton 7. Functions for ATP production * **a.** Golgi complex * **b.** Centrosome * **c.** Mitochondria * **d.** Lysosomes 8. The following factors influence the diffusion rate of substances through a plasma membrane except? * **a.** Concentration of gradient * **b.** Temperature * **c.** Surface area * **d.** Size of diffusing substance * **e.** All of the above 9. Which of the following statements regarding the nucleus are true? 1. Nucleoli within the nucleus are the sites of ribosome synthesis. 2. Most of the cell's hereditary units, called genes, are located within the nucleus. 3. Proteins synthesis occurs within the nucleus. 4. In non-dividing cells, DNA is found in the nucleus in the form of chromatin. * **a.** 1, 2, 3, 4 * **b.** 1, 2, 3 * **c.** 1, 2, 4 * **d.** 1, 3, 4 10. Stage when chromatin fibers condense and shorten to form chromosomes * **a.** Metaphase * **b.** Prophase * **c.** Telophase * **d.** Anaphase 11. Which one of the following types of bonds is covalent? * **a.** Hydrophobic * **b.** Hydrogen * **c.** Disulfide * **d.** Electrostatic **Answer: c** Disulfide bonds are an example of covalent bonds. 12. What is the pH of a solution containing 0.2 M acetic acid (pKa=4.7) and 0.1 M sodium acetate? * **a.** 5.4 * **b.** 6.7 * **c.** 4.4 * **d.** 3.7 13. A weak acid HA, has a pKa of 5.0. If 1.0 mol of this acid and 0.1 mol of NaOH were dissolved in one liter of water, what would the final pH be? * **a.** 4.00 * **b.** 4.05 * **c.** 5.00 * **d.** 5.05 14. All of the following are true regarding vital force theory except: * **a.** Organic compound are formed and synthesized only within living species (plants and animals). * **b.** Emphasizes on a special force or a living force or presence of life as basic requirement for formation of organic compounds. * **c.** Urea can be synthesized from simple inorganic compounds. * **d.** None of the above. * **e.** All of the above are true. 15. A patient seen in the ER has ingested antifreeze in a suicide attempt. Other than bicarbonate, which one of the following is the major buffer of acids to help maintain the pH in the blood within the range compatible with life? * **a.** Hemoglobin * **b.** Acetoacetate * **c.** Phosphate * **d.** Collagen ### RATIONALIZATION ACTIVITY (THIS WILL BE DONE DURING THE FACE-TO-FACE INTERACTION) The instructor will now rationalize the answers to the students. You can now ask questions and debate among yourselves. Write the correct answer and correct/additional ratio in the space provided. 1. **ANSWER:** **RATIO:** 2. **ANSWER:** **RATIO:** 3. **ANSWER:** **RATIO:** 4. **ANSWER:** **RATIO:** 5. **ANSWER:** **RATIO:**