ELSC 05 - Bioenergetics PDF

Bioenergetics Earth and Life Science Bioenergetics Is a field of biochemistry that discusses how energy flows through living organisms. Includes processes such as photosynthesis and cell respiration. The Cell as the Basic Unit of Life The Cell as the Basic Unit of Life Cells can eithe...

Bioenergetics Earth and Life Science Bioenergetics Is a field of biochemistry that discusses how energy flows through living organisms. Includes processes such as photosynthesis and cell respiration. The Cell as the Basic Unit of Life The Cell as the Basic Unit of Life Cells can either be prokaryotic (unicellular) or eukaryotic (multicellular). The Cell as the Basic Unit of Life Cells make up all living organisms, although its structure differ from one another. The Cell as the Basic Unit of Life The Cell as the Basic Unit of Life The study of cells is not possible… …without the assistance of microscopes. Discovery of Cells In 1665, Robert Hooke coined the term “cell” to describe the small, honey-comb like structures that he was able to view on a cork bottle. Discovery of Cells In 1668, Anton van Leeuwenhoek constructed the first simple microscope. Discovery of Cells Using the first simple microscope, we were able to study bacteria, protozoa, spermatozoa, and red blood cells. Discovery of Cells In 1838, Matthias Schleiden proposed that all plants are made up of cells. Discovery of Cells In 1839, Theodor Schwann proposed that all animals are also made up of cells. Discovery of Cells Together, they studied a lot of animal and plant tissues and proposed the Cell Theory in 1839. Discovery of Cells Cell Theory states that “all living organisms are made up of cells, which are the basic structural unit of life.” Discovery of Cells In 1858, Rudolf Virchow modified the Cell Theory stating that “all cells can only come from pre- existing cells.” Discovery of Cells The three tenets of the Cell Theory are: 1. All living organisms are made up of cells. 2. Cell is the most basic unit of life. 3. All cells arise from pre-existing cells. Discovery of Cells In 1861, Max Schultze found that cells were not empty but is filled with protoplasm (currently known as cytoplasm). Discovery of Cells During the 1950s, scientists were able to classify cells into prokaryotic and eukaryotic cells. Discovery of Cells Biologists made some additions to the cell theory, which now include: 1. All known living things are made up of one or more cells. 2. All living cells arise from pre-existing cells by division. 3. The cell is the fundamental unit of structure and function in all living organisms. Discovery of Cells 4. The activity of an organism depends on the total activity of independent cells. 5. Energy flow (metabolism and biochemistry) occurs within cells. 6. Cells contain DNA which is found specifically in the chromosome and RNA found in the cell nucleus and cytoplasm. 7. All cells are basically the same in chemical composition in organisms of similar species. Structure of the Cell Structure of the Cell Both prokaryotic and eukaryotic cells have a plasma membrane, the outermost surface of the cell and cytoplasm, the aqueous content of the cell where its components can be found. Structure of the Cell The plasma membrane is a semi- permeable membrane present in all cells. It is composed of carbohydrates, proteins, phospholipids, and cholesterol. Structure of the Cell Lipids are fats, such as oils, that are insoluble to water. Structure of the Cell Two important regions of a lipid are essential to the lipid bilayer. The polar head (hydrophilic region) and non-polar tail (hydrophobic region). Structure of the Cell Hydrophilic region (hydro – water, philia – love), is attracted to water conditions, while the hydrophobic region (phobia – fear) is repelled. Structure of the Cell The most abundant types of lipids found in the plasma membrane are phospholipids. It have two nonpolar fatty acid chain groups and a tail. The tail is composed of a string of carbons and hydrogens. Structure of the Cell The lipids organize themselves spontaneously wherein they expose their hydrophilic region and hide their hydrophobic region. Structure of the Cell Due to its semi-permeable structure, only gas and water can pass through the lipid bilayer. Other molecules could only pass through with the assistance of other structures. Structure of the Cell The cytoplasm is a jelly-like, semi-fluid matrix found between the cell membrane and nuclear membrane. Structure of the Cell It contains the living (organelles) and non- living components (ergastic substances and cytoskeletal elements) of a cell. Without the organelles, the cytoplasm is called cytosol. Structure of the Cell It provides structural support for the cell, as it usually comprises 50% of the cell and is also where protein synthesis occurs. Structure of the Cell The cytoskeleton is another cell component which gives the cell its structure and allows the cell to adapt. Cells can reorganize their cytoskeletal components to change shape. Structure of the Cell It has tracks which allow the organelles to move around the cell. The cytoskeleton is also involved in intercellular communication, as it can also move entire cells in multicellular organisms. Structure of the Cell The cytoskeleton is composed of three (3) protein filaments; intermediate filaments, microtubules, and actin filaments (or microfilaments). Structure of the Cell The intermediate filaments are rope- like and fibrous. They have a diameter of approximately 10 nm. Structure of the Cell The microtubules are long, cylindrical structures composed of tubulin. They are organized around a centrosome. These filaments provide tracks upon which organelles can move inside the cells. Structure of the Cell The actin filaments or microfilaments are double-stranded, thin, and flexible structures. It is also the most abundant protein in eukaryotic cells. Structure of the Cell The nucleus is one of the largest organelles inside a cell. It comprises about 10% of the cell volume and is usually found at the center of eukaryotic cells. Structure of the Cell It is the storage space for DNA and is composed of two layers which form an envelope around the cell and only allows selected molecules to enter and leave the cell. Structure of the Cell The DNA found in the nucleus are packed in chromosomes. The nucleus comes into a direct contact with the endoplasmic reticulum and is the site of DNA and RNA synthesis. Structure of the Cell The mitochondria is a specialized double- membrane structure. It is known as the powerhouse of the cell as it generates ATP. Structure of the Cell The outer membrane of the mitochondria is smooth, while the inner membrane produces finger-like infoldings called cristae. Structure of the Cell The inside of the mitochondria is filled with the homogenous, granular mitochondrial matrix. This matrix has mitochondrial DNA, RNA, lipids, proteins, enzymes, and 70S ribosomes. Structure of the Cell The endoplasmic reticulum is a network of tubular structures found in the cytoplasm and is bound by a membrane. Structure of the Cell Its functions include; helping in intracellular transportation, providing mechanical support for the cytoplasmic matrix… Structure of the Cell Ribosomes are granular, non- membraneous structures inside the cells present in the cytoplasm, mitochondria, chloroplast and endoplasmic reticulum. Structure of the Cell Eukaryotes have 80S ribosomes in the cytoplasm and 70S ribosomes in the plastids and mitochondria. Structure of the Cell 70S ribosomes are smaller in size, primarily found in the cytoplasm of prokaryotes, and are involved in protein synthesis in bacteria and archaea. Structure of the Cell 80S ribosomes are larger and more complex, located in the cytoplasm of eukaryotic cells, and participate in the synthesis of a wide range of proteins. Structure of the Cell Centrosomes form spindles during cell division. They are surrounded by a denser type of cytosol called the centrosphere. Centrosomes have two cylindrical structures called centrioles at the center. Structure of the Cell The Golgi complex are a group of curved, flattened, plate-like cisternae. The cisternae produce a network of tubules from its outer limits which also end in vesicles. Structure of the Cell It is also known as the packaging center of the cell as they package protein, carbohydrates, etc. in their vesicles. Structure of the Cell It also produces enzymes called lysosomes, which break down excess or worn-out cell parts and can also be used to destroy invading microorganisms. Structure of the Cell Plastids are found in plant cells and euglenoids, an organism exhibiting both plant and animal properties. Structure of the Cell Vacuoles are single- membrane bound sacs that are present in the cytoplasm. Plant cells have large vacuoles and animal cells have small vacuoles. Structure of the Cell The tonoplast is term for the vacuoles’ membrane which is filled with cell sap, a liquid filled with sugars, salts, pigments, and enzymes. Structure of the Cell There are four types of vacuoles: 1.Sap vacuoles, which can be found on plant and animal cells. 2.Contractile vacuoles, which can be found on protistan and algal cells in freshwater environments. Structure of the Cell 3.Food vacuoles, which can be found on single-celled protists, several lower animals, and phagocytes of higher animals. 4.Gas vacuoles, which can be found on prokaryotes or single-celled organisms. Photosynthesis Photosynthesis The process wherein plants use solar energy to convert water (H2O) and carbon dioxide (CO2) into sugars and other organic compounds, while releasing oxygen (O2) as a byproduct. Photosynthesis Organisms that are able to make their own food are called autotrophs. “auto” means self, “troph” means feeding. Plants use light energy to produce food, they are called photoautotrophs. “photo” means light. Photosynthesis Chloroplasts are located within the mesophyll, the interior tissue of the leaf. A mesophyll cell has about 30 to 40 chloroplasts. Photosynthesis A leaf’s green color comes from chlorophyll, a pigment in the chloroplasts that plays a central role in photosynthesis. Photosynthesis Inside the chloroplast you can find: Stroma, the fluid that fills the chloroplasts. Thylakoids, an interconnected system of membranous sacs. Photosynthesis Thylakoid membrane, where the chlorophyll molecules are located and houses the “machinery” that converts light energy into chemical energy. Photosynthesis It is an anabolic pathway. Carbon dioxide and water are consumed to produce glucose and oxygen. Photosynthesis Light-dependent reactions, wherein the light reactions absorb solar energy which is converted to chemical energy. These reactions produce no sugar, as it is only produced in the… Photosynthesis Calvin cycle, also known as light- independent reactions, the second stage of photosynthesis. Photosynthesis In light dependent reactions, light energy is absorbed by chlorophyll and converted into stored chemical energy, in the form of the electron carrier molecule NADPH and the energy currency molecule ATP. Photosynthesis NADPH stands for Nicotinamide Adenine Dinucleotide Phosphate. ATP stands for Adenosine Triphosphate. Photosynthesis Light is absorbed by one of the many pigments in photosystem II (PSII), then energy is passed inward from pigment to pigment until it reaches the reaction center. There, energy is transferred to P680, boosting an electron to a high energy level. The high energy electron is passed to an acceptor molecule and replaced with an electron from water. This releases the O2 we breathe. Photosynthesis The high-energy electron travels down an electron transport chain, losing energy as it goes. Some of the released energy drives pumping of H+ ions from the stroma into the thylakoid interior, building a gradient. As H+ ions flow down their gradient and into the stroma, they pass through ATP synthase, driving ATP production in a process known as chemiosmosis. Photosynthesis The electron arrives at photosystem I (PSI) and joins the P700 special pair of chlorophylls in the reaction center. When light energy is absorbed by pigments and passed inward to the reaction center, the electron in P700 is boosted to a very high energy level and transferred to an acceptor molecule. Photosynthesis The high-energy electron travels down a short second leg of the electron transport chain. At the end of the chain, the electron is passed to NADP+ to make NADPH. Photosynthesis A CO2 molecule combines with a five-carbon acceptor molecule, ribulose-1,5- bisphosphate (RuBP). This step makes a six-carbon compound that splits into two molecules of a three- carbon compound, 3- phosphoglyceric acid (3- PGA). This reaction is catalyzed by the enzyme RuBP carboxylase / oxygenase, or rubisco. Photosynthesis ATP and NADPH are used to convert the 3-PGA molecules into molecules of a three-carbon sugar, glyceraldehyde-3- phosphate (G3P). This stage gets its name because NADPH donates electrons to, or reduces, a three-carbon intermediate to make G3P. Photosynthesis Some G3P molecules go to make glucose, while others must be recycled to regenerate the RuBP acceptor. Regeneration requires ATP and involves a complex network of reactions. Cellular Respiration Cellular Respiration It is the process of using O2 as organic molecules, being broken down as CO2 and H2O, and the cell captures the energy released in ATP. Cellular Respiration Metabolic pathway is a series of chemical reactions in a cell that build and breakdown molecules for cellular processes. Each reaction step is facilitated, or catalyzed, by a protein called an enzyme. Cellular Respiration Cellular Respiration Enzyme reactions have 3 major parts: Substrate – reactant in a chemical reaction is called a substrate when acted upon by an enzyme. Enzyme – proteins that speed up reactions. Cellular Respiration Active Site – the part of an enzyme to which substrates bind and where a reaction is catalyzed. Cellular Respiration The enzyme-substrate interaction suggests that the enzyme and the substrate possess specific complementary geometric shapes that fit exactly into one another. This is called enzyme lock-and-key theory. Cellular Respiration According to the type of reactions that the enzymes catalyze, enzymes are classified into several categories: Oxidoreductases are involved in oxidation and reduction. Transferases transfer functional groups. Hydrolases transfer water. Lyases add or remove the elements of water, ammonia, carbon dioxide to or from double bonds. Isomerases catalyzes rearrangements of atoms within a molecule. Ligases join two molecules. Cellular Respiration Carbohydrates contain a lot of chemical bonds which means they have a lot of chemical energy. Cellular Respiration It is a catabolic pathway. Oxygen along with organic compounds is consumed as a reactant. Cellular Respiration Cellular respiration involves three stages: 1. Glycolysis 2. Krebs’ Cycle 3. Electron Transport Chain Cellular Respiration Glycolysis came from the words “glyko” means sweet, “lysis” means splitting. It occurs in the cytosol, is anaerobic, and is an exergonic process. Cellular Respiration It can be broken down into two phases: energy- requiring phase and energy-releasing phase. Cellular Respiration In the energy-requiring phase, the starting molecule of glucose gets rearranged, and two phosphate groups are attached to it. The phosphate groups make the modified sugar, now called fructose-1,6-bisphosphate, unstable, allowing it to split in half and form two phosphate-bearing three- carbon sugars. Cellular Respiration Because the phosphates used in these steps come from ATP, two ATP molecules get used up. Cellular Respiration In the energy-releasing phase, each three- carbon sugar is converted into another three-carbon molecule, pyruvate, through a series of reactions. In these reactions, two ATP molecules and one NADH molecule are made. Cellular Respiration Because this phase takes place twice, once for each of the two three-carbon sugars, it makes four ATP and two NADH overall. Cellular Respiration Because this phase takes place twice, once for each of the two three-carbon sugars, it makes four ATP and two NADH overall. Cellular Respiration In pyruvate oxidation, the junction between glycolysis and Krebs’ cycle, a carboxyl group is snipped off of pyruvate and released as a molecule of carbon dioxide, leaving behind a two-carbon molecule. Cellular Respiration The two-carbon molecule from step 1 is oxidized, and the electrons lost in the oxidation are picked up by NAD+ to form NADH. Cellular Respiration The oxidized two- carbon molecule is attached to Coenzyme A (CoA), an organic molecule derived from vitamin B5, to form acetyl CoA. Cellular Respiration Krebs’ cycle also known as citric acid cycle, is named after Hans Krebs, occurs in the mitochondria and is aerobic. Cellular Respiration In the first step of the Krebs’ cycle, acetyl CoA joins with a four- carbon molecule, oxaloacetate, releasing the CoA group and forming a six-carbon molecule called citrate. Cellular Respiration The second step is a two-step process, it involves the removal then the addition of a water molecule. The result is the conversion of citrate into isocitrate, its isomer. Cellular Respiration The third step involves the oxidation of isocitrate which results in a five-carbon molecule, α- ketoglutarate. During this step NAD+ is reduced to form NADH, carbon dioxide is also released as a result of the oxidation. Cellular Respiration The fourth step is like the third step, but it involves oxidation of α- ketoglutarate. The remaining four-carbon molecule picks up Coenzyme A, forming the unstable compound succinyl CoA. Cellular Respiration The fifth step involves the replacement of the CoA in succinyl CoA with a phosphate group, which is then transferred to ADP to make ATP, while in some cells GDP (guanosine diphosphate) is used to make GTP. Cellular Respiration The four-carbon molecule produced in this step is called succinate. Cellular Respiration The sixth step involves the oxidation of succinate, producing another four- carbon molecule called fumarate. In this reaction, two hydrogen atoms with their electrons are transferred to FAD, producing FADH2. Cellular Respiration The seventh step involves the addition of water to fumarate, converting it to malate, another four- carbon molecule. Cellular Respiration The eighth step involves the regeneration of oxaloacetate via the oxidation of malate. Another molecule of NAD+ is reduced to NADH in the process. Cellular Respiration The electron transport chain is a series of proteins and organic molecules found in the inner membrane of the mitochondria. Cellular Respiration NADH and FADH2 from other steps of cellular respiration transfer their electrons to molecules near the beginning of the transport chain. In the process, they turn back into NAD+ and FAD, which can be reused in other steps of cellular respiration. Cellular Respiration As electrons are passed down the chain, they move from a higher to a lower energy level, releasing energy. Some of the energy is used to pump H+ ions, moving them out of the matrix and into the intermembrane space. This pumping establishes an electrochemical gradient. Cellular Respiration At the end of the electron transport chain, electrons are transferred to molecular oxygen, which splits in half and takes up H+ to form water. Cellular Respiration As H+ ions flow down their gradient and back into the matrix, they pass through an enzyme called ATP synthase, which harnesses the flow of protons to synthesize ATP.