LEC_Week 2-3 (Cells-Intro to Biochem) 2024-2025 PDF

KOLEHIYO NG LUNGSOD NG DASMARIÑAS Course Module Biochemistry Prepared by: Christopher A. Malay  Institute of Science Integrated Sciences Unit MODULE 1 Preliminary Lessons in Biochemistry Image source: https://bit.ly/3SAmGZ...

KOLEHIYO NG LUNGSOD NG DASMARIÑAS Course Module Biochemistry Prepared by: Christopher A. Malay  Institute of Science Integrated Sciences Unit MODULE 1 Preliminary Lessons in Biochemistry Image source: https://bit.ly/3SAmGZ6 Shown is an empty fat cell or adipocytes. Fats cells are one of the largest cells in the human body. Fats serves as insulator and precursors of many biochemical activities in the body. Just like living organisms, our body, aside from adipocytes are made of cells functioning and catering to several biochemical processes. Biochemistry  Institute of Science Integrated Sciences Unit Learning Outcomes 1. Explain the role of cell and cellular organelles in the development of various products that are necessary to sustain life processes in the human body. 2. Discuss the different functions of cellular organelles in a cell. 3. Relate the chemical structures of biomolecular structures in its physiological role inside the cell. 4. Explain the different cellular activities that is related to the biomolecules. 5. Compare the different types of cells and its functions with focus on human system. 6. Review basic concepts of organic chemistry. 7. Discuss and differentiate the functional groups and structures of the common classes of organic molecules. 8. Draw and name an organic compound using IUPAC criteria, then describe the physical features of each class of organic compounds. Biochemistry  Institute of Science Integrated Sciences Unit OUTLINE OF TOPICS 1. Cell structure and function 2. Introduction to Biochemistry LESSON PROPER Development of the lesson: Motivation. 1. At the start of the lesson ask the students about their prior knowledge about the cells. 2. Correct some misconceptions about cells i.e. cells are all small TOPIC 1: The Cell – Structures and Functions Cell is the basic functional unit of life. Every living organism is made up of cell. Each cell has its own function. When cells aggregate and perform a similar function it forms tissues. Similar tissues create an organ. Similar organs with related role make an organ system. And several organ systems make an organism. However, not all organisms are made up of several cells. Some living organisms, function as one cell unit. Most cells are minute or too small to be seen. Hence, called microscopic. Although, some like the chicken egg is macroscopic. Special instrument can help visualize microscopic cells. This instrument is called microscope. From the unicellular or one-celled organisms like bacteria, yeasts, and algae to multicellular entities like skin, cheek scraping, and blood cells are the fundamental functioning unit of life. General features of cell It is a common knowledge that all living things are made up of cells. However, this notion should not be taken in a general perspective. Even though all living things are made up of cells, cells may still vary in size, shape, habit, and function. Cellular diversity in terms of size means that most cells are microscopic, and few are not. In fact, some cells ranged from 0.2 micrometers (µm) to the 2 meter long. Most plant cells range from 10 to 50 µm in diameter and are visible under the microscope while animal cell like the nerve cell could reach up to a meter in length. Aside from cell size, cellular volume also varies. As cell grows, its volume and surface area also increase. The bigger the cell the bigger its capacity to hold substances inside it. Biochemistry  Institute of Science Integrated Sciences Unit Prokaryotic cells and Eukaryotic cells Living organisms belong to either one of the three major domains of life. These domains are the Archaea, the Bacteria, and the Eukarya. Collectively, Archaea and Bacteria are often termed as prokaryotic organisms. Even though Archaea and Bacteria are generally single cell organisms, there are distinct differences between them. Bacteria (bacterium- singular) are often associated with diseases of human, animal, and even plants. There is truth to this claim however not all bacteria can cause diseases. In fact, one group of bacteria, the actinomycetes, produces the antibiotic streptomycin and nocardicin. Some bacteria form symbiotic relationships with other organisms like the bacteria in the gut (digestive system) and roots of plants. Bacteria is also widely used by man in fermentation like in yoghurt, wine, beer production, and even in some bread. Bacteria are essential in the recycling of organic material. They aid in the decomposition and breakdown of dead organic matter. Figure 1. Diversity of cells: a) animal cells, b) plant cells, c) bacterial cells (Source: https://s3-us-west- 2.amazonaws.com/courses-images/wp-tent/uploads/sites/3206/2018/05/03174526/Figure_04_00_00.jpg). Archaea are unicellular organisms like Bacteria. However, the range of environment that they live in makes them unique and different from Bacteria. Such environments include acid pools, the Dead Sea, thermal vents and even the deepest parts of the ocean or ocean floor. Some species can tolerate intense heat (hyperthermophiles), below zero temperature (psychrophiles), very salty medium (halophiles), acidic environment (acidophiles) and even m tolerate the presence of toxic methane compounds (methanogens). Eukaryotes (eu- true, karyon-nut) includes all animals, plants, fungi, and protists. Eukaryotes may be unicellular (one-celled) or multicellular (many celled) organisms. Members of the domain Eukarya have true nucleus. The next table summarizes the main differences between a prokaryote and eukaryotes. Biochemistry  Institute of Science Integrated Sciences Unit Figure 2. Major domains of living things (Source: https://cdn.britannica.com/09/108909-050- 681E996E/tree-life-three-domain-system.jpg Table 1. Differences between Prokaryotes and Eukaryotes Criteria Prokaryotes Eukaryotes Relative size 1-5 µm 10-100 µm - Circular, not enclosed, and DNA scattered in the cytoplasm Linear and enclosed in the nucleus Number of chromosomes Single chromosomes called plasmid Several Ribosome size Small large Cytoskeleton Absent Present No true nucleus, no membrane Contains nucleus and membrane Organelles bound organelles bound organelles Some are unicellular (yeasts and Cell arrangement Unicellular amoeba) others are multicellular (plants and animals) Presence of Present Present cilia/flagella Reproduction Asexual through binary fission Both asexual and sexual Biochemistry  Institute of Science Integrated Sciences Unit Cell Structure The cell wall and cytoplasm The cytoplasm (cyto = cell) is the gel-like substance enclosed within the membrane of the cell (cell membrane). Cytoplasm is mainly water (85%), protein (10-15%), lipids (2-4%), nucleic acids, sugars, and inorganic salts. About 80-90% of the entire cell is the cytoplasm. Included in the cytoplasm are the organelles except for nucleus. On the other hand, cytosol is the liquid part of the cytoplasm without the organelles in it. Figure 5 shows the typical feature of a cell’s cytoplasm Cytoplasm plays an important role by supporting and help organelles suspend inside in the cells. A common mistake among student studying cell is that cell is never plane or two-dimensional but rather three-dimensional. Imagine a jelly with suspended fruits where the jelly is the cytoplasm while the fruits are the organelles. Aside from this, cytoplasm also caters numerous cellular activities like energy production, protein synthesis, respiration or glycolysis, and cell division (mitosis and meiosis). Lastly, cytoplasm facilitates the transport of materials like hormones, proteins, and wasters in and out the cell. Figure 3. Typical cell and its cytoplasm and nucleus (Source:https://www.genome.gov/sites/default/files/tg/en/illustration/cytoplasm.jpg The control center of the cell: Nucleus The word nucleus came from the Latin word nuc meaning little nut. Nucleus is a membrane-bound organelle that contains the genetic information of the cell. This genetic information is the key to most cell’s action and decision. Nucleus is the predominant structure in the cell. In fact, in most cases, it is the easiest to stain. Because it contains the genetic material of the cell, nucleus is regarded as the control center. Generally, nucleus (nuclei-plural) is spherical, but some nuclei appear to be flat, ellipsoid, or irregular depending on the type of cell. However, not all cells have nucleus. A good example of unnucleated cell is the red blood cell (erythrocytes) of humans. Biochemistry  Institute of Science Integrated Sciences Unit Figure 4. Structure of a nucleus (Source: https://biologydictionary.net/wp- content/uploads/2017/07/Nucleus.jpg) The nucleus is covered by a membrane known as the nuclear membrane. The presence of nuclear membrane is one of the distinguishing characteristics of a eukaryotic cell from prokaryotic cell. The nuclear membrane is a double layer of phospholipid that protects the material inside the nucleus. In the nuclear membrane are the nuclear pores. Nuclear pores are openings in the nuclear membrane where substances enter or leave the nucleus. These substances may include RNA, and proteins. The nuclear membrane continuous outside the nucleus and into the endoplasmic reticulum. Nucleus made up of several materials like DNA (9-12%), histones (15%), combination of enzymes, neutral proteins, and acid proteins (65%), RNA (5%), and lipids (3%). production, cell division, and differentiation. It also controls the production of enzymes involved in cellular metabolism. It stores protein and genetic materials like DNA and RNA. And facilitates the transcription of RNA required for protein making. Nucleoplasm or karyoplasm or nucleus sap, is composed of several materials that include enzymes, organic salts, and other organic molecules. Nucleoplasm maintains the shape of the nucleus while protecting the material (nucleolus and chromosomes) inside the nucleus. Nucleolus (nucleoli- singular) is the small structure inside the nucleus. It occupies almost a quarter of the nucleus. This dense and non-membraned structure breaks up during cell division. Nucleolus is the site of transcription and ribosome production in eukaryotes. Depending on the organism, the nucleus could have as four nucleoli. Biochemistry  Institute of Science Integrated Sciences Unit Chromosomes (chroma- color, soma- body) are the condensed DNA inside the nucleus. Chromosomes are tightly packed inside the nucleus. This allows the cell to store a large amount of genetic material, through DNA, without occupying so much space. If chromosomes will be unwound and stretch into a single DNA thread, a single cell would have 2 meters of DNA strand. Organelles of the endomembrane system The endomembrane system (endo- within) is a collection of structures that is concern with the transport of materials within the cell. These membranous structures change, package, and ship materials like lipids and proteins. Endomembrane system includes the nuclear envelope, lysosomes, endoplasmic reticulum, and Golgi apparatus. Endoplasmic reticulum or ER is a system of channels that is connected to the nuclear envelope. It should be remembered that nuclear membrane is the membrane that covers the nucleus. Both the ER and nuclear membrane is composed of lipid bilayer material. The ER acts as passageway for transporting, synthesizing, and storing materials in the cell. Due to its zigzagging feature, surface area in ER is large enough to accommodate several materials and other cellular functions. There are two types of ER: Rough endoplasmic reticulum (RER)- a continuous channel of flattened sacs. As the name suggest, has bumpy ribosomes attached to its surface- hence rough. Because of its numerous ribosomes, RER functions in the synthesis of proteins. It also helps in the modification of protein that will be released by the cell. Some proteins will be modified to enzymes. Cells that secrete large number of enzymes like the liver cell possesses lots of RER. Smooth endoplasmic reticulum (SER) is like the RER but with fewer ribosomes attached on to it. Its main roles are the synthesis of materials inside the cells. These materials include lipids, carbohydrates, detoxification of medicine and toxic substances like poison metabolic byproducts and storage. SER also aids in the absorption of calcium ions within the cell particularly in the muscle cells. Golgi apparatus also known as Golgi complex or Golgi body are also membrane-bound organelles composed of a series of flattened and stacked sacks (cisternae). Golgi are found within the cytoplasm. It aids in the transport, modification, and packaging of protein and lipids via vesicle (vesicular transport). Vesicles are minute structures that are enclosed by lipid bilayer, and it is transported to other cells through cell signaling. Plant cells contains hundreds of Golgi apparatus. Biochemistry  Institute of Science Integrated Sciences Unit Lysosomes are membrane-bound organelle that acts as the garbage disposal system of cells. Lysosomes contains digestive enzymes break down worn-out cell parts and organelles. It also destroys foreign materials like viruses and bacteria in the cell. Scientist have revealed that severely worn-out cells, beyond repair, undergo a ‘self-destruct process called apoptosis. This program cell death is facilitated by lysosomes. Even though lysosomes are very acidic in nature, its membrane bound layer protects the cells from possible spill out. Figure 5. Endomembrane channels showing connection from nucleus to endoplasmic reticulum (Source: https://cdn1.byjus.com/wp-content/uploads/2019/01/Endomembrane-System.png) Organelles for energy production and waste management Ribosome was mentioned in the endomembrane system. It is found within the cytoplasm or attached to the rough endoplasmic reticulum (RER). Ribosome is considered as site of protein synthesis. Molecular analysis reveals that a ribosome has two subunits: the small subunit (30S) and the large subunit (40S). Ribosomes are essential to life because it translates information coded by cell nucleus and this will determine the protein that the cell will produce. This protein will eventually be modified to become another protein or enzyme and will be delivered to other organelles or other cells. Ribosomes are numerous and can be as many as 10 million especially in mammalian cells. Biochemistry  Institute of Science Integrated Sciences Unit Figure 6. 3D structure of ribosome (Source: https://microbenotes.com/wp- content/uploads/2019/01/Ribosomes-Structure-and-Functions.jpg) Peroxisomes are small, membrane-enclosed organelles that resembles mitochondria. Peroxisomes are involved in energy and metabolic reactions inside the cell. In fact, peroxisomes contain around 50 different enzymes in that are involved in several biochemical processes in the cell. Peroxisomes initiates oxidation reaction that produces hydrogen peroxide. Due to the toxic property of hydrogen peroxide to cell, peroxisomes also produce catalase. Catalase decomposes hydrogen peroxide to water and oxygen. Oxidation, or use of oxygen for chemical reactions, allows cell to produce energy from organic compounds such as uric acid, amino acids, and fatty acids. Mitochondria (mitochondrion, singular), often regarded as the powerhouse of the cell, generate most of the chemical energy for the cell. This energy is stored in a small molecule call adenosine triphosphate (ATP). Amazingly, mitochondria have its own DNA and RNA. Hence called mDNA and RNA. In fact, our mitochondria are more of a maternal structure because during the fertilization process only the nucleus is donated by the sperm and the rest of the organelles came from the mother. Different cells have different amounts of mitochondria. Cells needing more energy usually contains more mitochondria. For example, our leg muscles contain more mitochondria than our muscles in the lower back (lumbar multifidus). This is the same reason why fish meat varies in color especially near the tail. Biochemistry  Institute of Science Integrated Sciences Unit Chloroplasts are only found in plants and photosynthetic bacteria and protists. chloroplast is responsible for photosynthesis, the food-making process of photosynthetic organisms. In terms of size, chloroplasts are much larger and more complex compared to mitochondria. Both mitochondria and chloroplast generate ATP or the energy unit of cells. However, only chloroplasts can convert CO 2 to carbohydrates and oxygen. Figure 7. Structural differences between mitochondria and chloroplast (Source: https://biologyeducare.com/wp-content/uploads/2019/06/Mitochondria-Chloroplast-1.jpg) Structure, support, and mobilization Cytoskeleton may be imagined as the steel frames of a house. Cytoskeleton helps cells maintain its shape and structural integrity. Aside from this structural support, cytoskeleton is also critical for cell’s movement, reproduction, and transportation of substances within the cell. There are three components of cytoskeleton. They are: 1. Microtubule- rigid hollow rods around 25 nm in diameter. Microtubule undergoes continues assembly and disassembly. Microtubule helps cell maintain its and aids cell movements, transport of organelles, and the separation of chromosomes during cell division. 2. Microfilament- also known as actin filaments. Microfilaments are helical in orientation with 6-8 nm in between. It is primarily structural in function. Even though they are the smallest components of the cytoskeleton, they are important in cytokinesis, amoeboid movement, and cell motility. 3. Intermediate filaments – around 10 nm in diameter. Unlike the microtubule and microfilaments, intermediate filaments that are only involve in cells’ structural support. Intermediate filaments provide mechanical strength to cells and tissues. Biochemistry  Institute of Science Integrated Sciences Unit Figure 8. Cytoskeleton and its components (Source: https://blog.abclonal.com/hs- fs/hubfs/Cytoskeleton.png?width=468&name=Cytoskeleton.png) Centrioles are cylindrical structures made up of microtubules. They are found near the nucleus. Centrioles aids in cell division by assisting the separation of chromosomes. Also, centrioles are involved in the development of cilia and flagella. Centrioles are found in animal and lower plant cells like moss and liverworts. Almost related to centrioles, centrosome is the combination of centrioles surrounded by a protein matrix. Centrosomes appear before cell division and direct the movements of microtubules and other cytoskeletal structures and proteins during cell division. Centrosomes facilitates changes in cells’ shape during cell division. Cilia and Flagella are projections from the cell. Both are made up of microtubules. They are design to aid motility for cells. Flagella is a longer than cilia, but both are made up of the same protein components. The cells of the bronchus of our respiratory system have cilia to move mucus and other materials to and from while the sperm cell is the only known animal cell with flagella. Figure 9. Structure of centrioles in relation to flagella and cilia (Source: https://microbenotes.com/wp- content/uploads/2018/11/Cilia-and-Flagella-Structure-and-Functions.jpg) Biochemistry  Institute of Science Integrated Sciences Unit Cell Types (Eukaryotes) Eukaryotic cells are diverse. Animal, plant, fungal and protist cells are unique on their own. For simplicity, this module will make comparison of animal and plant cells. In general, animal cells and plant cells share similar components. Both cells have nucleus, cytoplasm, mitochondria, and cell membrane. However, plant cells have a vacuole, chloroplast, and a cell wall while animals do not. Below is a more detailed differences in animal and plant cells. Figure 10. Typical structure of eukaryotic (left) and prokaryotic (right) cells (Source: https://cdn.technologynetworks.com/tn/images/body/image-3-smaller1625492532736.jpg) Chemical Composition Cell Water, inorganic ions, and organic molecules make up cells. At least 70% of cells are water. As such, interactions between water and other cell components are crucial to understanding biological chemistry. Water molecules can interact with positively or negatively charged ions as well as other polar molecules and form hydrogen bonds with them due to their polar nature. These interactions make polar molecules and ions easily soluble in water (hydrophilic). Nonpolar molecules, on the other hand, are poorly soluble in an aqueous environment because they cannot interact with water (hydrophobic). As a result, nonpolar molecules usually associate closely with one another to reduce their contact with water. As will be covered later in this chapter, interactions between polar and nonpolar molecules and water are essential for the development of biological structures like cell membranes. Biochemistry  Institute of Science Integrated Sciences Unit About one percent or less of the mass of the cell is made up of the inorganic ions like sodium (Na+), potassium (K+), magnesium (Mg2+), calcium (Ca2+), phosphate (HPO42-), chloride (Cl-), and bicarbonate (HCO3). These ions serve crucial functions in cell function because they are engaged in several facets of cell metabolism. On the other hand, the distinctive components of cells are organic molecules like lipids, proteins, carbohydrates, and nucleic acids. These molecules are often called macromolecules because of their structure which is made up of hundreds or thousands of low-molecular-weight precursors. These precursors are either amino acid, nucleotides, and simple sugars. Most cells' dry weight is made up of 80– 90% of these macromolecules. The other important component of cells is lipids. In addition to macromolecular precursors, the remaining portion of the cell mass is made up of a variety of tiny organic compounds. Hence, the four main types of organic molecules' forms and functions can be used to explain the fundamental chemistry of cells. Figure 11. Structure of plasma membrane (Source: https://cdn.britannica.com/74/53074-004- 9F65D813/lipid-bilayer-proteins-surfaces-phospholipids-thickness-cholesterol.jpg) - Why are cells generally small? Essential - Do all cells have the same parts? Why? Question Biochemistry  Institute of Science Integrated Sciences Unit Useful - Supplemental online videos o o Types of cells https://youtu.be/192M4oDLTdc?t=197 Biology: Cell Structure I Nucleus Medical Media Links o o https://youtu.be/URUJD5NEXC8 Prokaryotic vs. Eukaryotic Cells (Updated) https://youtu.be/Pxujitlv8wc Specialized Cells: Significance and Examples https://youtu.be/wNe6RuK0FfA o How Cells Become Specialized https://youtu.be/t3g26p9Mh_k TOPIC 2: Introduction to Biochemistry Biochemistry the chemistry of life. Moreso, it is the molecular level study of life. It also concerns the chemistry of living organisms and its biological processes that involves organic compounds. Other disciplines like cell biology, genetics, immunology, microbiology, pharmacology, and physiology are all included in biochemistry. The basics of biochemistry start with carbon, hydrocarbons, and functional groups. Review Concepts: Organic Chemistry Scientists in the 18th and early 19th century examined chemicals derived from plants and animals and gave them the name "organic." Inorganic substances are those that have been isolated from nonliving systems like rocks and ores, the atmosphere, and the oceans. For a long time, scientists believed that only living systems could produce organic chemicals because they possessed a vital force that was unique to living systems. In 1828, when German scientist Friedrich Wöhler produced urea from inorganic raw materials. He combined ammonium chloride (NH4Cl) and silver cyanate (AgOCN), hoping to produce ammonium cyanate (NH4OCN). The equation that follows describes what he anticipated. AgOCN + NH4Cl → AgCl + NH4OCN Wöhler discovered that the substance was urea (NH2CONH2), an easily separated well-known organic substance from urine. This outcome sparked a series of studies in which numerous organic molecules were created from inorganic raw components. After chemists discovered that they could create many organic molecules in the lab, the vital force theory that only living organisms can give rise to organic compounds progressively disappeared. Biochemistry  Institute of Science Integrated Sciences Unit Now we define Organic chemistry is the study of carbon compounds. Organic compounds are compounds composed primarily of a carbon skeleton. All living things are composed of organic compounds. Organic chemistry is available to man in terms of the following: Part of the food: vitamins, fats, proteins, and carbohydrates Medicine/drugs: aspirin, Tylenol, decongestants, sedatives, and insulin. Common products: alcohol, caffeine, nicotine Products for sale: plastics, nylon, rayon, and polyester Neurotransmitters: dopamine, serotonin, and adrenaline Genetics: RNA and DNA Carbon What makes Carbon Special? Why is Carbon so different from all the other elements on the periodic table? The answer derives from the ability of Carbon atoms to bond together to form long chains and rings. Carbon can form single, double, triple bonds with other atoms, H, O, N, S. Carbon has several allotropes, or different forms in which it can exist. These allotropes include graphite and diamond, which have very different properties. Despite carbon’s ability to make bonds and its presence in many compounds, it is highly unreactive under normal conditions. Carbon exists in 3 main isotopes: 12C, 13C, 14C. 14C is radioactive and used in dating carbon-containing samples (radiometric dating). Carbon can form immensely diverse compounds, from simple to complex including a structure called hydrocarbon Hydrocarbon Hydrocarbons are molecules that only include carbon and hydrogen. They are by far the most prevalent constituents of crude oil, processed petroleum hydrocarbons like gasoline, diesel, kerosene, fuel oil, and lubricating oil. Hydrocarbons are either aliphatic or aromatic. Hydrocarbons with larger molar mass have a higher boiling point likewise the bigger the compound the higher boiling point eg Methane – MW: 16 g/mol, -161.5oC vs Butane- MW 58 g/mol, -0.5oC Table 2. Comparison of aliphatic and aromatic hydrocarbons Aliphatic Aromatic hydrocarbons Open-chain molecules with a linear or branching Aromatic hydrocarbons (also known as structure a arenes) frequently (but not always) have Aliphatic hydrocarbons come in three different distinguishing scents (odors). varieties. Aromatic hydrocarbons are cyclic, planar o Alkanes only have one covalent bond. compounds that resemble benzene in o Alkenes are hydrocarbons with at least one C-C electronic configuration and chemical double bond behavior. o Alkynes are hydrocarbons with a C-C triple bond Biochemistry  Institute of Science Integrated Sciences Unit Alkanes are also known as saturated hydrocarbons because they contain the most H atoms while the rest are considered unsaturated. Figure 12. Structures of aliphatic and aromatic hydrocarbons (Source: https://coredifferences.com/wp- content/uploads/2020/04/Difference-between-Aromatic-and-Aliphatic-Compounds.png) Functional groups Functional groups are the structural characteristics that allow substances to be grouped into families. Every molecule that contains a particular functional group generally exhibits the same chemical behavior. For instance, contrast menthene, a far more intricate chemical present in peppermint oil, with ethylene, a plant hormone that promotes fruit ripening. Because both compounds have a functional group composed of two carbon atoms in a double bond, they react with bromine in the same way, producing products that have each had a Br atom added. In general, no matter how big or complicated an organic molecule is, its functional groups dictate its chemistry. Biochemistry  Institute of Science Integrated Sciences Unit Figure 13. Ethylene and menthene's interactions with bromine (McMurry, 2011). Table 3. Important Functional Groups Functional group Description Alkanes Without any other functional groups, single-bonded organic compounds only contain carbon and hydrogen atoms. Alkenes Compounds containing at least one double bond connecting a carbon atom to another. Olefins is a different name for alkenes. Due to the double bond, alkenes are more reactive than alkanes. Alkynes Hydrocarbons with triple bonds between carbon atoms. When it comes to molecules with one triple bond, their usual formula is CnH2n-2 (and no rings). Alkynes undergo many of the same reactions as alkenes, but because the triple bond contains two p-bonds, they can react twice. Alcohols An organic substance that has an aliphatic carbon atom with a hydroxyl (OH) functional group. As OH serves as all alcohols' functional group and generally described as ROH, where R is an alkyl group. Phenols Organic substances made composed of a carbon atom in a benzene ring and a hydroxyl (—OH) group. Because they cannot go through the same oxidation events that alcohols do, their chemical behavior is substantially different from that of alcohols. Aldehydes Any of a class of organic compounds where an atom of carbon has three single bonds: one with hydrogen, one with oxygen, and one with another atom or group of atoms Biochemistry  Institute of Science Integrated Sciences Unit Ketones Any member of the category of organic compounds known as ketones has a carbonyl group, which is made up of a carbon atom covalently linked to an oxygen atom. The final two bonds (R) are to hydrocarbon radicals or other carbon atoms. Carboxylic acids Contains the functional group carboxyl. RCOOH is an acronym for a carboxylic acid's general formula. The carboxyl group's carbon atom can be joined to either a hydrogen atom or a carbon chain. esters Have a carbonyl + connecting oxygen function with two linked alkyl or aromatic groups. Esters are utilized as ingredients in perfumes, essential oils, food flavorings, cosmetics, and other products that have a pleasant aroma. They are often used as organic solvents. ethers An organic chemical group that has an oxygen sandwiched between two alkyl groups. They have the formula R-O-R', where the alkyl groups represent the Rs. These substances are utilized industrially, in dyes, fragrances, oils, and waxes. Alkoxyalkanes are a term for ethers. Amines Amines are organic substances that have a lone pair of nitrogen atoms in them. In essence, they are produced by replacing one or more hydrogen atoms in ammonia (NH3) with an alkyl or aryl group, giving them the names alkylamines and arylamines, respectively. Amides The nitrogen atom of the amide functional group is joined to the carbonyl carbon. Simple amides are referred to as carboxylic acid derivatives. Acyl halide Acid halides are organic compounds created from carboxylic acids by substituting a halide group for a hydroxyl group. Naming organic compounds Naming organic compounds follow the International Union of Pure and Applied Chemistry (IUPAC) rules. The complete process of naming organic compounds can be found in http://www.chem.uiuc.edu/GenChemReferences/nomenclature_rules.html Biochemistry  Institute of Science Integrated Sciences Unit Figure 14. Common functional groups and their generic structure. (Source: https://i0.wp.com/www.compoundchem.com/wp-content/uploads/2014/09/Benzene-Derivatives-in- Organic-Chemistry.png?ssl=1). Biochemistry and its discipline Biochemistry is the chemistry of life. It is the study of life at the molecular level. Biochemistry is the study of the chemistry of living things and life processes. It includes organic molecules and their chemical reactions. This field encompass other disciplines like cell biology, genetics, immunology, microbiology, pharmacology, and physiology. Around the turn of the 20th century, researchers united the fields of chemistry, biology, and physiology to study the chemistry of living systems, giving rise to the distinct field of biochemistry. By this subject, we were able to gain a fundamental grasp of how life works and operates, such as information transfer, digestion, absorption, cell growth and death, etc. We are able to comprehend the crucial concerns in nutrition, health, and medicine thanks to biochemistry. using biological components to do valuable technical tasks, such as using enzymes in the pharmaceutical industry to create complicated medications. Biochemistry  Institute of Science Integrated Sciences Unit What Is Biochemistry Used For? The study of biological processes that take place in cells and organisms is done through the study of biochemistry. For several reasons, biochemistry can be utilized to: 1. Investigate the characteristics of biological substances - a biochemist may research the properties of keratin in hair to create a shampoo that improves softness or curliness. 2. Employ biomolecules in many ways - food biochemist might add a specific lipid to food, for instance. 3. Discover novel biomolecule - biochemists can design artificial molecules such as artificial sweeteners or polymer 4. Generating new technology – can be an important tool in gene therapy and creation of biological machinery. Useful Supplemental online videos and learning materials a. Basic Introduction to Organic Chemistry - Links https://www.youtube.com/watch?v=B_ketdzJtY8 b. Organic Chemistry Nomenclature IUPAC Practice Review - Naming Alkanes, Alcohols, Alkenes & Alkynes- https://youtu.be/O8wKk6wkcEs c. Naming hydrocarbons (answer included)- https://library.vcc.ca/learningcentre/pdf/vcclc/Chem0871- NamingOrganicCompoundsPractice.pdf KEY POINTS Cells vary in shape and size. Some cells are microscopic while others are macroscopic There are 3 main domains of life: Eukarya, Bacteria, and Archaea. Eukaryotes are groups of cells with membrane bound organelles and true nuclei. Prokaryotes, collective term for Bacteria and Archaea, have no true nucleus and membrane bound organelles. The major parts of the cell are the cell membrane, cytoplasm, nucleus, endoplasmic reticulum, Golgi bodies, ribosomes, chloroplast, lysosomes, peroxisomes, and cytoskeleton. Some cells, like plant cells, contain more than the usual cell organelles. Cells are made up of both organic and inorganic materials. Biochemistry  Institute of Science Integrated Sciences Unit Macromolecules like carbohydrates, proteins, lipids, and nucleic acids form the fundamental chemical structure of cells. Organic chemistry is the study of carbon compounds, and all living things are composed of organic compounds. Organic chemistry is part of man’s life from food to medicine to products used in daily activities. Carbon is an essential atom that is the central material for most organic compounds. With hydrogen, they form hydrocarbons a fundamentally important molecule. Functional groups are atoms or group of atoms inside a molecule that share chemical characteristics when they appear in different compounds. ASSESSMENT After reading and learning the lesson in the module, students can: A. Based on the discussion, create a table enumerating five important organelles/cellular components and their functions in maintaining self-regulating process. Submit this activity in a short bond paper. Absolutely no erasures or alterations. Provide appropriate citation. Each row will be given a maximum of 5 points. 5 pts – Answers show quality of information, cites specific examples and discussion. 3 pts – Answers show only trivial information, lacks specific examples and discussion. 1 pt – Answers were poorly prepared. B. Group work. Make a table of containing the following information. Finish this short groupwork activity in a short bond paper. Always add your references in APA 7th edition. Functional group Brief description of the functional group Simplified structure of the functional group Biomedical function or properties of the functional group REFERENCES 1. Blanco, A., & Blanco, G. (2017). Medical Biochemistry. In Medical Biochemistry. https://doi.org/10.1038/199943a0 2. Burrows, A. (2017). Chemistry3 : introducing inorganic, organic, and physical chemistry / Andrew Burrows, John Holman, Andrew Parsons, Gwen Pilling, Gareth Price. (pp. 1–1433). Biochemistry  Institute of Science Integrated Sciences Unit 3. Cooper, G. M. (2000). Intermediate Filaments. https://www.ncbi.nlm.nih.gov/books/NBK9834/ 4. CPCH. (n.d.). Structures of Some Common Functional Groups Name Structure* Name ending Example Alkene C C-ene. 5. Eukaryotic Cell vs Prokaryotic Cell - Difference and Comparison | Diffen. (n.d.). Retrieved July 16, 2020, from https://www.diffen.com/difference/Eukaryotic_Cell_vs_Prokaryotic_Cell 6. Golgi apparatus | Definition, Function, Location, & Facts | Britannica. (n.d.). Retrieved July 12, 2020, from https://www.britannica.com/science/Golgi-apparatus 7. Lysosome. (n.d.). Retrieved July 12, 2020, from https://www.genome.gov/genetics- glossary/Lysosome 8. McMurry, J. (2011). Fundamentals of Organic Chemistry (7th ed.). Cengage Learning. 9. The Cytoplasm and Cellular Organelles – Anatomy and Physiology. (n.d.). Retrieved July 12, 2020, from https://opentextbc.ca/anatomyandphysiology/chapter/3-2-the-cytoplasm-and- cellular-organelles/ 10. The Molecular Composition of Cells - The Cell - NCBI Bookshelf. (n.d.). Retrieved February 19, 2023, from https://www.ncbi.nlm.nih.gov/books/NBK9879/ 11. Umadevi, D., Sastry, G. N., & Gamez, J. A. (2014). Saturated vs. unsaturated hydrocarbon interactions with carbon nanostructures. https://doi.org/10.3389/fchem.2014.00075 Biochemistry