4-2 Protein Synthesis

The endoplasmic reticulum (EN-doh-PLAZ-mik ri-TIK-yuh-luhm), abbre- viated ER, is a system of membranous tubes and sacs, called cisternae (sis-TUHR-nee). The ER functions primarily as an intracellu- lar highway, a path along which molecules move from one part of the cell to another. The amount of ER inside a cell fluctuates, depending on the cell’s activity. There are two types of ER: rough and smooth. The two types of ER are thought to be continuous. Rough Endoplasmic Reticulum The rough endoplasmic reticulum is a system of interconnected, flattened sacs covered with ribosomes, as shown in Figure 4-15. The rough ER produces phospholipids and proteins. Certain types of proteins are made on the rough ER’s ribosomes. These proteins are later exported from the cell or inserted into one of the cell’s own membranes. For example, ribosomes on the rough ER make digestive enzymes, which accumulate inside the endoplasmic retic- ulum. Little sacs or vesicles then pinch off from the ends of the rough ER and store the digestive enzymes until they are released from the cell. Rough ER is most abundant in cells that produce large amounts of protein for export, such as cells in digestive glands and antibody-producing cells. Smooth Endoplasmic Reticulum The smooth ER lacks ribosomes and thus has a smooth appear- ance. Most cells contain very little smooth ER. Smooth ER builds lipids such as cholesterol. In the ovaries and testes, smooth ER produces the steroid hormones estrogen and testosterone. In skeletal and heart muscle cells, smooth ER releases calcium, which stimulates contraction. Smooth ER is also abundant in liver and kidney cells, where it helps detoxify drugs and poisons. Long-term abuse of alcohol and other drugs causes these cells to produce more smooth ER. Increased amounts of smooth ER in liver cells is one of the factors that can lead to drug tolerance. As Figure 4-15 shows, rough ER and smooth ER form an interconnected network. Copyright © by Holt, Rinehart and Winston. All rights reserved. reticulum from the Latin rete, meaning “net”; reticulum means “little net” Word Roots and Origins The endoplasmic reticulum (ER) serves as a site of synthesis for proteins, lipids, and other materials. The dark lines in the photo represent the membranes of the ER, and the narrow lighter areas between the dark lines show the channels and spaces (cisternae) inside the ER. FIGURE 4-15 Smooth ER Ribosomes Rough ER Cisternae 82 CHAPTER 4 GOLGI APPARATUS The Golgi apparatus, shown in Figure 4-16, is another system of flattened, membranous sacs. The sacs nearest the nucleus receive vesicles from the ER containing newly made proteins or lipids. Vesicles travel from one part of the Golgi apparatus to the next and transport substances as they go. The stacked membranes modify the vesicle contents as they move along. The proteins get “address labels” that direct them to various other parts of the cell. During this modification, the Golgi apparatus can add carbohydrate labels to proteins or alter new lipids in various ways. VESICLES Cells contain several types of vesicles, which perform various roles. Vesicles are small, spherically shaped sacs that are surrounded by a single membrane and that are classified by their contents. Vesicles often migrate to and merge with the plasma membrane. As they do, they release their contents to the outside of the cell. Lysosomes Lysosomes (LIE-suh-SOHMZ) are vesicles that bud from the Golgi appa- ratus and that contain digestive enzymes. These enzymes can break down large molecules, such as proteins, nucleic acids, car- bohydrates, and phospholipids. In the liver, lysosomes break down glycogen in order to release glucose into the bloodstream. Certain white blood cells use lysosomes to break down bacteria. Within a cell, lysosomes digest worn-out organelles in a process called autophagy (aw-TAHF-uh-jee). Lysosomes are also responsible for breaking down cells when it is time for the cells to die. The digestion of damaged or extra cells by the enzymes of their own lysosomes is called autolysis (aw-TAHL-uh-sis). Lysosomes play a very important role in maintaining an organism’s health by destroying cells that are no longer functioning properly. Copyright © by Holt, Rinehart and Winston. All rights reserved. The Golgi apparatus modifies many cellular products and prepares them for export. FIGURE 4-16 CELL STRUCTURE AND FUNCTION 83 Peroxisomes Peroxisomes are similar to lysosomes but contain different enzymes and are not produced by the Golgi apparatus. Peroxisomes are abundant in liver and kidney cells, where they neutralize free radicals (oxygen ions that can damage cells) and detoxify alcohol and other drugs. Peroxisomes are named for the hydrogen peroxide, H2O2, they produce when breaking down alco- hol and killing bacteria. Peroxisomes also break down fatty acids, which the mitochondria can then use as an energy source. Other Vesicles Specialized peroxisomes, called glyoxysomes, can be found in the seeds of some plants. They break down stored fats to provide energy for the developing plant embryo. Some cells engulf material by surrounding it with plasma membrane. The resulting pocket buds off to become a vesicle inside the cell. This vesicle is called an endosome. Lysosomes fuse with endosomes and digest the engulfed material. Food vacuoles are vesicles that store nutrients for a cell. Contractile vacuoles are vesicles that can contract and dispose of excess water inside a cell. Protein Synthesis One of the major functions of a cell is the production of protein. The path some proteins take from synthesis to export can be seen in Figure 4-17. In step , proteins are assembled by ribosomes on the rough ER. Then, in step , vesicles transport proteins to the Golgi apparatus. In step , the Golgi modifies proteins and pack- ages them in new vesicles. In step , vesicles release proteins that have destinations outside the cell. In step , vesicles containing enzymes remain inside the cell as lysosomes, peroxisomes, endo- somes, or other types of vesicles. 5 4 3 2 1 Copyright © by Holt, Rinehart and Winston. All rights reserved. Proteins are assembled by ribosomes on the rough ER. Vesicles carry proteins from the rough ER to the Golgi apparatus. Proteins are modified in the Golgi apparatus and enter new vesicles. Some vesicles release their proteins outside the cell. Other vesicles remain in the cell and become lysosomes and other vesicles. Nucleus

What is a Plant Cell? Plant cells are eukaryotic cells that vary in several fundamental factors from other eukaryotic organisms. Both plant and animal cells contain a nucleus along with similar organelles. One of the distinctive aspects of a plant cell is the presence of a cell wall outside the cell membrane. Plant Cell Structure Just like different organs within the body, plant cell structure includes various components known as cell organelles that perform different functions to sustain itself. These organelles include: Cell Wall It is a rigid layer which is composed of polysaccharides cellulose, pectin and hemicellulose. It is located outside the cell membrane. It also comprises glycoproteins and polymers such as lignin, cutin, or suberin. The primary function of the cell wall is to protect and provide structural support to the cell. The plant cell wall is also involved in protecting the cell against mechanical stress and providing form and structure to the cell. It also filters the molecules passing in and out of it. The formation of the cell wall is guided by microtubules. It consists of three layers, namely, primary, secondary and the middle lamella. The primary cell wall is formed by cellulose laid down by enzymes. Cell membrane It is the semi-permeable membrane that is present within the cell wall. It is composed of a thin layer of protein and fat. The cell membrane plays an important role in regulating the entry and exit of specific substances within the cell. For instance, cell membrane keeps toxins from entering inside, while nutrients and essential minerals are transported across. Nucleus The nucleus is a membrane-bound structure that is present only in eukaryotic cells. The vital function of a nucleus is to store DNA or hereditary information required for cell division, metabolism and growth. 1. Nucleolus: It manufactures cells’ protein-producing structures and ribosomes. 2. Nucleopore: Nuclear membrane is perforated with holes called nucleopore that allow proteins and nucleic acids to pass through. Plastids They are membrane-bound organelles that have their own DNA. They are necessary to store starch and to carry out the process of photosynthesis. It is also used in the synthesis of many molecules, which form the building blocks of the cell. Some of the vital types of plastids and their functions are stated below: Leucoplasts They are found in the non-photosynthetic tissue of plants. They are used for the storage of protein, lipid and starch. Chromoplasts They are heterogeneous, colored plastid which is responsible for pigment synthesis and for storage in photosynthetic eukaryotic organisms. Chromoplasts have red-, orange- and yellow-colored pigments which provide color to all ripe fruits and flowers. Central Vacuole It occupies around 30% of the cell’s volume in a mature plant cell. Tonoplast is a membrane that surrounds the central vacuole. The vital function of the central vacuole apart from storage is to sustain turgor pressure against the cell wall. The central vacuole consists of cell sap. It is a mixture of salts, enzymes and other substances. Golgi Apparatus They are found in all eukaryotic cells, which are involved in distributing synthesized macromolecules to various parts of the cell. Ribosomes They are the smallest membrane-bound organelles which comprise RNA and protein. They are the sites for protein synthesis, hence, also referred to as the protein factories of the cell. Mitochondria They are the double-membraned organelles found in the cytoplasm of all eukaryotic cells. They provide energy by breaking down carbohydrate and sugar molecules, hence they are also referred to as the “Powerhouse of the cell.” Lysosome Lysosomes are called suicidal bags as they hold digestive enzymes in an enclosed membrane. They perform the function of cellular waste disposal by digesting worn-out organelles, food particles and foreign bodies in the cell. In plants, the role of lysosomes is undertaken by the vacuoles. Chloroplasts It is an elongated organelle enclosed by phospholipid membrane. The chloroplast is shaped like a disc and the stroma is the fluid within the chloroplast that comprises a circular DNA. Each chloroplast contains a green colored pigment called chlorophyll required for the process of photosynthesis. The chlorophyll absorbs light energy from the sun and uses it to transform carbon dioxide and water into glucose. Structure of Chloroplast Chloroplasts are found in all higher plants. It is oval or biconvex, found within the mesophyll of the plant cell. The size of the chloroplast usually varies between 4-6 µm in diameter and 1-3 µm in thickness. They are double-membrane organelle with the presence of outer, inner and intermembrane space. There are two distinct regions present inside a chloroplast known as the grana and stroma. • Grana are made up of stacks of disc-shaped structures known as thylakoids or lamellae. The granum of the chloroplast consists of chlorophyll pigments and are the functional units of chloroplasts. • Stroma is the homogenous matrix which contains grana and is similar to the cytoplasm in cells in which all the organelles are embedded. Stroma also contains various enzymes, DNA, ribosomes, and other substances. Stroma lamellae function by connecting the stacks of thylakoid sacs or grana. The chloroplast structure consists of the following parts: Membrane Envelope It comprises inner and outer lipid bilayer membranes. The inner membrane separates the stroma from the intermembrane space. Intermembrane Space The space between inner and outer membranes. Thylakoid System (Lamellae) The system is suspended in the stroma. It is a collection of membranous sacs called thylakoids or lamellae. The green colored pigments called chlorophyll are found in the thylakoid membranes. It is the sight for the process of light-dependent reactions of the photosynthesis process. The thylakoids are arranged in stacks known as grana and each granum contains around 10-20 thylakoids. Stroma It is a colorless, alkaline, aqueous, protein-rich fluid present within the inner membrane of the chloroplast present surrounding the grana. Grana Stack of lamellae in plastids is known as grana. These are the sites of conversion of light energy into chemical energy. Chlorophyll It is a green photosynthetic pigment that helps in the process of photosynthesis. Functions of Chloroplast Following are the important chloroplast functions: • The most important function of the chloroplast is to synthesize food by the process of photosynthesis. • Absorbs light energy and converts it into chemical energy. • Chloroplast has a structure called chlorophyll which functions by trapping the solar energy and is used for the synthesis of food in all green plants. • Produces NADPH and molecular oxygen (O 2 ) by photolysis of water. • Produces ATP – Adenosine triphosphate by the process of photosynthesis. • The carbon dioxide (CO2) obtained from the air is used to generate carbon and sugar during the Calvin Cycle or dark reaction of photosynthesis. Mitochondria “Mitochondria are membrane-bound organelles present in the cytoplasm of all eukaryotic cells, that produce adenosine triphosphate (ATP), the main energy molecule used by the cell.” What are Mitochondria? Popularly known as the “Powerhouse of the cell,” mitochondria (singular: mitochondrion) are a double membrane-bound organelle found in most eukaryotic organisms. They are found inside the cytoplasm and essentially function as the cell’s “digestive system.” They play a major role in breaking down nutrients and generating energy-rich molecules for the cell. Many of the biochemical reactions involved in cellular respiration take place within the mitochondria. The term ‘mitochondrion’ is derived from the Greek words “mitos” and “chondrion” which means “thread” and “granules-like”, respectively. It was first described by a German pathologist named Richard Altmann in the year 1890. Structure of Mitochondria • The mitochondrion is a double-membraned, rod-shaped structure found in both plant and animal cell. • Its size ranges from 0.5 to 1.0 micrometers in diameter. • The structure comprises an outer membrane, an inner membrane, and a gel-like material called the matrix. • The outer membrane and the inner membrane are made of proteins and phospholipid layers separated by the intermembrane space. • The outer membrane covers the surface of the mitochondrion and has a large number of special proteins known as porins. Cristae The inner membrane of mitochondria is rather complex in structure. It has many folds that form a layered structure called cristae, and this helps in increasing the surface area inside the organelle. The cristae and the proteins of the inner membrane aid in the production of ATP molecules. The inner mitochondrial membrane is strictly permeable only to oxygen and ATP molecules. A number of chemical reactions take place within the inner membrane of mitochondria. Mitochondrial Matrix The mitochondrial matrix is a viscous fluid that contains a mixture of enzymes and proteins. It also comprises ribosomes, inorganic ions, mitochondrial DNA, nucleotide cofactors, and organic molecules. The enzymes present in the matrix play an important role in the synthesis of ATP molecules. Functions of Mitochondria The most important function of mitochondria is to produce energy through the process of oxidative phosphorylation. It is also involved in the following process: 1. Regulates the metabolic activity of the cell 2. Promotes the growth of new cells and cell multiplication 3. Helps in detoxifying ammonia in the liver cells 4. Plays an important role in apoptosis or programmed cell death 5. Responsible for building certain parts of the blood and various hormones like testosterone and estrogen 6. Helps in maintaining an adequate concentration of calcium ions within the compartments of the cell 7. It is also involved in various cellular activities like cellular differentiation, cell signaling, cell senescence, controlling the cell cycle and in cell growth. Disorders Associated with Mitochondria Any irregularity in the way mitochondria function can directly affect human health, but often, it is difficult to identify because symptoms differ from person to person. Disorders of the mitochondria can be quite severe; in some cases, they can even cause an organ to fail.

Ions Ions are charged substances that have formed through the gain or loss of electrons. Cations form from the loss of electrons and have a positive charge while anions form through the gain of electrons and have a negative charge. Cation Formation Cations are the positive ions formed by the loss of one or more electrons. The most commonly formed cations of the representative elements are those that involve the loss of all of the valence electrons. Consider the alkali metal sodium (Na) . It has one valence electron in the n=3 energy level. Upon losing that electron, the sodiu ion now has an octet of electrons from the second energy level and a charge of 1+ . The electron arrangement of the sodium ion is now the same as that of the noble gas neon. Consider a similar process with magnesium and aluminum. In this case, the magnesium atom loses its two valence electrons in order to achieve the same arrangement as the noble gas neon and a charge of 2+ . The aluminum atom loses its three valence electrons to have the same electron arrangement as neon and a charge of 3+ . For representative elements under typical conditions, three electrons is usually the maximum number that will be los. Representative elements will not lose electrons beyond their valence because they would have to "break" the octet of the previous energy level which provides stability to the ion. Anions Anions are the negative ions formed from the gain of one or more electrons. When nonmetal atoms gain elections, they often do so until their outermost principal energy level achieves an octet. For fluorine, which has an electron arrangement of (2, 7), it only needs to gain one electron to have the same electron arrangement as neon. Forming an octet (eight electrons in the outer shell) provides stability to the atom. Fluorine will gain one electron and have a charge of 1− . The electron arrangement of the fluoride ion (2, 8) will also change to reflect the gain of an electron. Oxygen has an electron arrangement of (2, 6) and needs to gain two electrons to fill the n=2 energy level and achieve an octet of electrons in the outermost shell. The oxide ion will have a charge of 2− as a result of gaining two electrons. Under typical conditions, three electrons is the maximum that will be gained in the formation of anions. Subatomic Particles in an Ion Since ions form from the gain or loss of electrons, we can also look at the number of subatomic particles (protons, neutrons, and electrons) found in an ion. Remember that the number of protons determines the identity of the element and will not change in a chemical process. Example 2.5.1 How many protons, neutrons, and electrons in a single oxide (O2−) ion? Solution Oxygen has the atomic number 8 so both the atom and the ion will have 8 protons. The average atomic mass of oxygen is 16. Therefore, there will be 8 neutrons (atomic mass−atomic number=neutrons) . A neutral oxygen atom would have 8 electrons. However, the anion has gained two electrons so O2− has 10 electrons. We can also use information about the subatomic particles to determine the identity of an ion. Example 2.5.2 An ion with a 2+ charge has 18 electrons. Determine the identity of the ion. Solution If an ion has a 2+ charge then it must have lost electrons to form the cation. If the ion has 18 electrons and the atom lost 2 to form the ion, then the neutral atom contained 20 electrons. Since it was neutral, it must also have had 20 protons. Therefore the element is calcium. Polyatomic Ions A polyatomic ion is an ion composed of two or more atoms that have a charge as a group (poly = many). The ammonium ion (see figure below) consists of one nitrogen atom and four hydrogen atoms. Together, they comprise a single ion with a 1+ charge and a formula of NH+4 . The hydroxide ion (see figure below) contains one hydrogen atom and one oxygen atom with an overall charge of 1− . The carbonate ion (see figure below) consists of one carbon atom and three oxygen atoms and carries an overall charge of 2− . The formula of the carbonate ion is CO2−3 . The atoms of a polyatomic ion are tightly bonded together and so the entire ion behaves as a single unit. The figures below show several examples. Soult Screenshot 2-2-1.png Figure 2.5.1 : The ammonium ion (NH+4) is a nitrogen atom (blue) bonded to four hydrogen atoms (white). Soult Screenshot 2-2-2.png Figure 2.5.2 : The hydroxide ion (OH−) is an oxygen atom (red) bonded to a hydrogen atom. Soult Screenshot 2-2-3.png Figure 2.5.3 : The carbonate ion (CO2−3) is a carbon atom (black) bonded to three oxygen atoms. The table below lists a number of polyatomic ions by name and by structure. The heading for each column indicates the charge on the polyatomic ions in that group. Note that the vast majority of the ions listed are anions - there are very few polyatomic cations. 1− 2− 3− 1+ Table 2.5.1 : Common Polyatomic Ions acetate, CH3COO− carbonate, CO2−3 arsenate, AsO3−3 ammonium, NH+4 bromate, BrO−3 chromate, CrO2−4 phosphite, PO3−3 chlorate, ClO−3 dichromate, Cr2O2−7 phosphate, PO3−4 chlorite, ClO−2 hydrogen phosphate, HPO2−4 cyanide, CN− oxalate, C2O2−4 dihydrogen phosphate, H2PO−4 peroxide, O2−2 hydrogen carbonate, HCO−3 silicate, SiO2−3 hydrogen sulfate, HSO−4 sulfate, SO2−4 hydrogen sulfide, HS− sulfite, SO2−3 hydroxide, OH− hypochlorite, ClO− nitrate, NO−3 nitrite, NO−2 perchlorate, ClO−4 permanganate, MnO−4 The vast majority of polyatomic ions are anions, many of which end in -ate or -ite. Notice that in some cases such as nitrate (NO−3) and nitrite (NO−2) , there are multiple anions that consist of the same two elements. In these cases, the difference between the ions is the number of oxygen atoms present, while the overall charge is the same. As a class, these are called oxyanions. When there are two oxyanions for a particular element, the one with the greater number of oxygen atoms gets the -ate suffix, while the one with the fewer number of oxygen atoms gets the -ite suffix. The four oxyanions of chlorine are shown below, which also includes the use of the prefixes hypo- and per-. ClO− , hypochlorite ClO−2 , chlorite ClO−3 , chlorate ClO−4 , perchlorate Not your usual ion Soult Screenshot 2-2-4.png "Drink you milk. It's good for your bones." We're told this from early childhood, and with good reason. Milk contains a good supply of calcium, part of the structure of bone. However, there are two other ionic components of hydroxyapatite, the mineral component. Phosphate ion and hydroxide ion make up the remainder of the inorganic material in bone. News You Can Use Bone is a very complex structure. It is composed of protein (mainly collagen), hydroxyapatite (a calcium-phosphate-hydroxide mixture), some other minerals, and contains 10 - 20% water. The calcium/phosphate ratios are not stoichiometric, but vary somewhat from one portion of bone to the next. Bones are very strong but will break under enough stress. Regular exercise and proper nutrition help to increase bone strength. Watch a video about bone structure at http://www.youtube.com/watch?v=d9owEvYdouk Nitrate is an anion with a complex bonding structure. Major sources for this ion in drinking water are runoff from fertilizer, septic tank leakage, sewage, and natural deposits. High concentrations of nitrates represent a significant health hazard, especially to infants. The nitrate in the body is converted to nitrite, which then binds to hemoglobin. This binding decreases the ability of hemoglobin to transport oxygen, thus depriving the cells of the O2 needed for proper functioning. Cyanide production is widespread throughout nature. Forest fires will produce significant amounts of cyanide. Many plants contain cyanide, and it is produced by a number of bacteria, algae, and fungi. Cyanide is used industrially in metal finishing, iron and steel mills, and in organic synthesis processes. This material is also an important component for the refining of precious metals. Formation of a complex between cyanide and gold allows extraction of this metal from a mixture.

LESSON 4. Cellular Respiration • Define cellular respiration • Identify the stages of clan respiration You have just learned how the energy from the sun is captured, processed, and stored in the form of glucose. Cellular respiration, another important life process, is the means by which cells release the stored energy in glucose to make adenosine triphosphate (ATP). The primary goal of this life process is to convert stored energy into usable form, such as ATP, for the cells to carry out their functions. Cellular respiration involves several chemical reactions. The reactions can be summed up in the following equation: C6 H12 O6 + 602 ----- 6 CO₂ +6H₂O + ATP Glucose oxygen carbon dioxide water energy Aerobic respiration reactions, or cellular respiration that takes place in the presence of oxygen, can be grouped into three stages glycolysis, Krebs cycle, and electron transport chain (ETC). Stage 1: Glycolysis Glycolysis is the process that breaks down one molecule of 6-C glucose into 3-C pyruvates or pyruvic acids. It also releases four molecules of ATP. This process occurs in the cytoplasm of the cell. The following is the step-by-step process of glycolysis. Take note that several enzymes are involved in this process. 1. The first step of glycolysis requires energy. It can only proceed when the two ATP molecules donate energy to the glucose by transferring a phosphate group with the help of an enzyme, producing glucose 6-phosphate 2. Then, a specific enzyme promotes the rearrangement of the atoms, producing the fructose 6-phosphate. 3. The action of the enzyme in step 2 promotes the transfer of a phosphate group from another ATP molecule, forming fructose 1,6-bisphosphate. 4. The resulting fructose 1,6-bisphosphate molecules, with the help of another enzyme, splits into two molecules, each with three carbon backbones. These two sugars are dihydroxyacetone phosphate and glyceraldehyde 3-phosphate. 5. Another important enzyme then rapidly interconverts the molecules of dihydro-xyacetone phosphate and glyceraldehyde 3-phosphate. This produces two molecules of glyceraldehyde 3-phosphate or 3-phosphoglyceraldehyde (PGAL) 6. The succeeding step involves another enzyme-mediated action. The hydrogen (H) from PGAL is transferred to the oxidizing agent, nicotinamide adenine dinucleotide (NAD), which forms NADH. A phosphate (P) is also added from the cytosol of the cell to oxidize the two molecules of PGAL, forming two 1.3-bisphosphoglycerate. 7. A phosphate (P) from 1,3-biphosphoglycerate is transferred to ADP to form ATP. This happens for each of the two 1,3-bisphosphoglycerate. resulting to a yield of two ATP and two 3-phosphoglycerate molecules. 8. A phosphate is transferred from 3-phosphoglycerate molecules from the third carbon to the second carbon, forming 2-phosphoglycerate molecules A hydrogen atom and a hydroxyl ((OH) group is released, which then combines to form water (H2O). The removal of H2O from 2-phosphoglycerate results in the formation of 2- phosphoglycerate molecules. 9. A hydrogen atom and a hydroxyl ((OH) group is released, which then combines to form water (H2O). The removal of H2O from 2-phosphoglycerate results in the formation of two phosphoenolpyruvic acid (PEP) 10. Phosphate (P) from PEP is transferred to ADP (and forms ATP) and the final product, pyruvic acid. This reaction yields two molecules of pyruvic acid and two ATP molecules In summary, a single glucose molecule that undergoes the process of glycolysis produces two molecules of pyruvic acid, four molecules of ATP, two molecules of NADEL and two molecules of H.O. However, only two molecules of ATP are counted as net products since two molecules of ATP are spent throughout the process. Stage II: Krebs Cycle The Krebs cycle, named after its proponent Sir Hans Adolf Krebs, is a cyclical series of enzyme-controlled reactions. This stage of cellular respiration occurs in the matrix of the mitochondria. It is sometimes. called the citric acid cycle (CAC) since it produces citric acid. Citric acid contains three carboxyl (COOH) groups; hence, it is also called the tricarboxylic acid cycle (TCA). This requires the pyruvic acids produced during glycolysis. The main function of this cycle is to produce high-energy-yielding molecules, namely, NADH and flavin adenine dinucleotide (FADH) that will later on be used in the electron transport chain reaction. Figure 6-7. Summary of glycolysis and corresponding products in each reaction presented (See Appendix F on page 285 for an enlarged and complete version of the image.) An initial process is needed for the Krebs cycle to begin. As a pyruvate molecule from glycolysis enters the mitochondrion, it undergoes an important preliminary ate to form acetyl-CoA reaction. Coenzyme-A (COA) combines with pyruvate help of an enzymatic complex. This conversion also produces CO, and NADH. The Krebs cycle is summarized as follows. Take note that several enzymes are involved in this process. 1. The Krebs cycle technically begins when the acetyl-CoA combines with oxaloacetic acid (OAA), a 4-C molecule, to produce citric acid, a 6-C molecule. 2. With the aid of an enzyme, the citric acid now goes through a series of reactions that releases energy. Water molecule is removed from the citric acid and is returned in a different location. The-OH group is repositioned, forming the molecule isocitrate. 3. Isocitrate is then oxidized, forming the a-ketoglutarate, a 5-C molecule. The byproducts of this reaction are NADH and CO, 4 The a-ketoglutarate loses its CO, and a coenzyme-A is added in its place. The decarboxylation occurs with the help of NAD, which then becomes NADH. The resulting molecule is called succinyl-CoA. 5. Succinyl-CoA is converted into succinate. Also in this reaction, a molecule of guanosine triphosphate (GTP) is synthesized. The GTP molecule has similar structure and energy properties to that of ATP and is used by cells the same way. The free phosphate group attacks the succinyl-CoA molecule, which detaches the COA. Then, phosphate is attached to GDP to come up with GTP, similar to the process that occur in ATP synthesis (from ADP to ATP). 6. Two hydrogens are removed from succinate, A molecule of flavin adenine dinucleotide (FAD), a coenzyme similar to NAD, is reduced to FADH, as it takes the hydrogens from the succinate. This reaction produces the fumarate. 7. Fumarate is then converted into malate as the addition of a water molecule is catalyzed. The final reaction is the regeneration of oxaloacetate. The resulting byproduct of this regeneration is NADH Recall that two pyruvate molecules were produced during glycolysis, causing the Krebs cycle to turn twice. Each tuts produces three molecules of NADH, single ATH one FADIH, and the by-product CO, which is exhaled. Stage III: Electron Transport Chain The electron transport chain (ETC) is a series of photon pumps on the inner membrane of the mitochondrion. Electron transport is the last stage of the cellular respiration. In this stage, the energy from NADH and FADH, from the Krebs cycle is transferred to ADP to produce ATP. This process is generally known as oxidative phosphorylation. This energy coupling mechanism in the cell was revealed by the work of Peter stored energy in the form of proton (1) gradient to phosphorylate (add phosphate) ADP and produce ATP. The pumping of hydrogen sons across the inner membrane creates higher concentration ions in the inner membrane than on the outside of the membrane. This chemiosmotic gradient causes the ions to flow back across the membrane where the concentration of ions is lower. ATP synthase lined in the matrix serve as a channel protein, helping the ions to move across the membrane. The chemiosmotic gradient powers the phosphorylation of ADP to ATP, which also occurs in the ATP synthase. After passing through the ETC, the oxygen, being the final hydrogen acceptor, combines with two electrons and two protons, forming a water molecule. Water is a by-product of cellular respiration and is excreted. MINI TEST 6-3 1. Which energy-releasing pathway yields the most ATF in each glucose molecule? 2. Briefly describe the two stages of aerobic respiration that follow glycolysis: (a) Krebs cycle (b) Electron transport chain Anaerobic Respiration Most cells carry out arrobic respiration when oxygen is present. Aerobic respiration is an efficient process that yields a lot of ATP. However, many organisms thrive in mud, marshes, animal gut, canned goods, sewage treatment pond, and deep oceans where oxygen is scarce. Organisms that can live without oxygen are called anaerobes. Cellular respiration that proceeds without the presence of oxygen is called anaerobic respiration. In the event that the oxygen supply becomes low, aerobic cells also perform fermentation and lactic acid fermentation anaerobic pathways. There are two common anaerobic pathways in these cells, alcoholic fermentation and lactic acid fermentation. In alcoholic fermentation, ethyl alcohol and carbon dioxide are produced by some cells using the pyruvate from glycolysis. Each pyruvate molecule is rearranged into acetaldehyde and carbon dioxide, which is eventually released. NADII gives up electrons to acetaldehyde to form ethanol Fermentation is widely used in the industry. Yeast, a fungus used in making bread. can undergo anaerobic respiration. Bakers aux sugar, flour, water, and yeast to form the bread dough. The dough rises due to the carbon dioxide and alcohol released by the yeast cells trapped in air bubbles. Beer and wine manufacturers, we yeast to ferment the sugars in wheat and grape juice, forming alcoholic beverages such as beer and wine. In some cells, glycolysis produces two pyruvates, two NADH molecules, and two ATP molecules. Pyruvate itself becomes the final acceptor of the electrons from the NADH that produces the final product: lactate. Oftentimes, this product is called lactic acid. Human skeletal muscles can carry out fermentation when the blood cannot supply the cells with adequate oxygen during strenuous activities. When lactic acid builds up in the muscles, fatigue, burning sensation, and cramps result. Lactic acid will continue to build up until there is adequate supply of oxygen. Lactic acid is then converted back into pyruvate in the liver. Muscles also restore normal functions. Have you ever wondered why milk or cream turns sour after some time? Bacterial cells that undergo fermentation are responsible in producing lactate that turns the milk sour. These bacteria are used in manufacturing yogurt and sour milk products. Fermentation pathways do not breakdown and utilize the glucose completely. ATP is no longer produced beyond the process of glycolysis. Thus, energy produced is just enough for some single-celled organisms, or the energy can only be used by multicellular organisms for a short period.

PHOTOSYNTHESIS LIGHT DEPENDENT REACTION 1. Photosystem II (PSII) – Light Absorption & Water Splitting • Light energy (photons) excites electrons in chlorophyll molecules. • These high-energy electrons leave PSII and are passed into the electron transport chain (ETC). • Meanwhile, water molecules are split (photolysis) into: o O₂ (released as a by-product into the atmosphere) o H⁺ ions (protons, which build up inside the thylakoid) o Electrons (e⁻), which replace the ones lost by PSII. 2. Electron Transport Chain (ETC) • Excited electrons move through protein carriers embedded in the thylakoid membrane. • As they move, their energy pumps H⁺ ions into the thylakoid space, creating a proton gradient (high H⁺ inside, low outside). 3. ATP Production (ATP Synthase) • The buildup of H⁺ ions acts like a “waterfall” of potential energy. • These protons flow back across the membrane through ATP synthase, a protein complex that acts like a turbine. • This flow drives the conversion of ADP + Pi → ATP, which provides energy for the Calvin cycle. 4. Photosystem I (PSI) • Electrons arriving from the ETC enter PSI. • Sunlight excites them again, boosting them to a higher energy level. 5. NADPH Production • The energized electrons are transferred to NADP⁺. • Along with a proton (H⁺), this forms NADPH, another energy carrier. • NADPH is then delivered to the Calvin cycle to help build glucose. End Products of Light-Dependent Reactions: • ATP (energy source for Calvin cycle) • NADPH (reducing power for glucose synthesis) • O₂ (released into the atmosphere as waste) Light-Independent Reactions (Calvin Cycle) • These reactions do not directly require sunlight. • They occur in the stroma of the chloroplast (the fluid-filled space surrounding the thylakoids). • The inputs are ATP and NADPH (from light-dependent reactions) and CO₂ (from the atmosphere). • The outputs are glucose (C₆H₁₂O₆) and other carbohydrates. Think of the Calvin cycle as a factory that uses the energy and “raw materials” made in Stage I (ATP & NADPH) to build sugars. The 3 Main Steps of the Calvin Cycle 1. Carbon Fixation • CO₂ from the atmosphere enters the chloroplast and diffuses into the stroma. • Each CO₂ molecule attaches to a 5-carbon sugar called RuBP (ribulose-1,5-bisphosphate). • This reaction is catalyzed by the enzyme RuBisCO (Ribulose-1,5-bisphosphate carboxylase/oxygenase — the most abundant enzyme on Earth!). • The result is a short-lived 6-carbon compound, which immediately splits into two 3-carbon molecules called 3-PGA (3-phosphoglycerate). Summary: CO₂ + RuBP → 2 × 3-PGA 2. Reduction Phase • The 3-PGA molecules are “energized” and converted into G3P (glyceraldehyde-3-phosphate), a more energy-rich 3-carbon sugar. • This transformation requires: o ATP (provides energy) o NADPH (provides high-energy electrons and hydrogen atoms). • Some of the G3P molecules will eventually be combined to form glucose and other sugars. Summary: 3-PGA + ATP + NADPH → G3P 3. Regeneration of RuBP • Not all G3P molecules leave the cycle. Most of them are used to regenerate RuBP so the cycle can continue. • This regeneration also requires ATP. • For every 3 turns of the cycle, 5 G3P molecules are recycled to regenerate 3 molecules of RuBP. Summary: G3P + ATP → RuBP The Full Cycle Balance • To make one G3P molecule that can exit the cycle (and later form glucose), the cycle must run 3 times, fixing 3 molecules of CO₂. • To make one glucose molecule (C₆H₁₂O₆), the cycle must run 6 times (since glucose needs 6 carbon atoms). Inputs (for 1 glucose): • 6 CO₂ • 18 ATP • 12 NADPH Outputs: • 1 glucose (C₆H₁₂O₆) • 18 ADP + 18 Pi • 12 NADP⁺ Day vs Night Clarification • The Calvin Cycle is called light-independent, but that doesn’t mean it only happens at night. • It usually happens during the day because it depends on ATP and NADPH, which are only produced in light-dependent reactions (when sunlight is available). Simplified Analogy • Carbon fixation = The factory brings in CO₂ as raw material. • Reduction = Workers use energy (ATP & NADPH) to shape the raw material into useful products (G3P). • Regeneration = Some products are recycled to keep the factory running (RuBP is re-formed). • Output = After enough cycles, the factory produces glucose, the “food” of the plant.

The cytoskeleton is a network of thin tubes and filaments that crisscrosses the cytosol. The tubes and filaments give shape to the cell from the inside in the same way that tent poles support the shape of a tent. The cytoskeleton also acts as a system of internal tracks, shown in Figure 4-18, on which items move around inside the cell. The cytoskeleton’s functions are based on several struc- tural elements. Three of these are microtubules, microfilaments, and intermediate filaments, shown and described in Table 4-2. Microtubules Microtubules are hollow tubes made of a protein called tubulin. Each tubulin molecule consists of two slightly different subunits. Microtubules radiate outward from a central point called the centrosome near the nucleus. Microtubules hold organelles in place, maintain a cell’s shape, and act as tracks that guide organelles and molecules as they move within the cell. Microfilaments Finer than microtubules, microfilaments are long threads of the beadlike protein actin and are linked end to end and wrapped around each other like two strands of a rope. Microfilaments con- tribute to cell movement, including the crawling of white blood cells and the contraction of muscle cells. Intermediate Filaments Intermediate filaments are rods that anchor the nucleus and some other organelles to their places in the cell. They maintain the inter- nal shape of the nucleus. Hair-follicle cells produce large quantities of intermediate filament proteins. These proteins make up most of the hair shaft. 84 CHAPTER 4 TABLE 4-2 The Structure of the Cytoskeleton Property Microtubules Microfilaments Intermediate filaments Structure hollow tubes made of two strands of intertwined protein fibers coiled into coiled protein protein cables Protein subunits tubulin, with two subunits: å actin one of several types of and ∫ tubulin fibrous proteins Main function maintenance of cell shape; cell maintenance and changing of maintenance of cell shape; motility (in cilia and flagella); cell shape; muscle contraction; anchor nucleus and other chromosome movement; movement of cytoplasm; cell organelles; maintenance of organelle movement motility; cell division shape of nucleus Shape Microtubules provide a path for organelles and molecules as they move throughout the cell. FIGURE 4-18 Microtubules Nucleus Endoplasmic reticulum Mitochondrion Ribosomes Copyright © by Holt, Rinehart and Winston. All rights reserved. Copyright © by Holt, Rinehart and Winston. All rights reserved. CELL STRUCTURE AND FUNCTION 85 1. Explain how the fluid mosaic model describes the plasma membrane. 2. List three cellular functions that occur in the nucleus. 3. Describe the organelles that are found in a eukaryotic cell. 4. Identify two characteristics that make mitochon- dria different from other organelles. 5. Contrast three types of cytoskeletal fibers. CRITICAL THINKING 6. Relating Concepts If a cell has a high energy requirement, would you expect the cell to have many mitochondria or few mitochondria? Why? 7. Analyzing Information How do scientists think that mitochondria originated? Why? 8. Analyzing Statements It is not completely accurate to say that organelles are floating freely in the cytosol. Why not? SECTION 3 REVIEW During cell division, centrioles organize microtubules that pull the chromosomes (orange) apart. The centrioles are at the center of rays of microtubules, which have been stained green with a fluorescent dye. FIGURE 4-20 Cilia and Flagella Cilia (SIL-ee-uh) and flagella (fluh-JEL-uh) are hairlike structures that extend from the surface of the cell, where they assist in movement. Cilia are short and are present in large numbers on certain cells, whereas flagella are longer and are far less numerous on the cells where they occur. Cilia and flagella have a membrane on their outer surface and an internal structure of nine pairs of micro- tubules around two central tubules, as Figure 4-19 shows. Cilia on cells in the inner ear vibrate and help detect sound. Cilia cover the surfaces of many protists and “row” the protists through water like thousands of oars. On other protists, cilia sweep water and food particles into a mouthlike opening. Many kinds of protists use flagella to propel themselves, as do human sperm cells. Centrioles Centrioles consist of two short cylinders of microtubules at right angles to each other and are situated in the cytoplasm near the nuclear envelope. Centrioles occur in animal cells, where they organize the microtubules of the cytoskeleton during cell division, as shown in Figure 4-20. Plant cells lack centrioles. Basal bodies have the same structure that centrioles do. Basal bodies are found at the base of cilia and flagella and appear to organize the devel- opment of cilia and flagella.

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