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CHEM 313 Chapter 1 Notes

by: ishoemak

CHEM 313 Chapter 1 Notes CHEM

Cal Poly
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These notes cover the first chapter of the textbook and the first day of lecture.
Survey of Biochemistry and Biotechnology
Dr. Anya Goodman
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This 6 page Class Notes was uploaded by ishoemak on Sunday April 3, 2016. The Class Notes belongs to CHEM at California Polytechnic State University San Luis Obispo taught by Dr. Anya Goodman in Spring 2016. Since its upload, it has received 99 views.


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Date Created: 04/03/16
California Polytechnic St ate University, San Luis Obispo; CHEM 313; Goodman; Spring 2016 CHEM 313-11 Survey of Biochemistry Chapter 1 Notes Highlight = Important Principle Highlight = Important Concept Highlight = Key Term Ch. 1 Biochemistry and the Unity of Life Intro - Biochemistry is the study of life at the molecular le vel. - The goal of biochemistry is to understand what it takes to be alive on the molecular level and then extend that understand that understanding to the organismal level. - Unity of Biochemistry : All organisms are very similar at the molecular level 1.1 Living Systems Require a Limited Variety of Atoms and Molecules - Oxygen, Hydrogen, and Carbon make up 98% of all atoms in an organism . - Oxygen and Hydrogen owe their popularity to the fact that water is required for all life and makes up 65% of a cell’s mass . - Carbon atoms makes very strong bonds with other Carbon atom s - This results in large molecules with strong construction and a large amount of energy released when C-C bonds are broken in combustion reactions. - Carbon Dioxide (CO ) 2s a gas byproduct of combustion reactions and is soluble in water allowing Carbon to stay in circulation in the body. - Nitrogen, Phosphorous, and Sulfur are three other elements that play vital roles in organisms. 1.2 There Are Four Major Classes of Biomolecules Proteins are Highly Versatile Biomolecules - Proteins are unbranched polymers consisting of a combination of the 20 different amino acids connected by peptide bonds. Protein Amino Acid Peptide Bond - Protein polymers are folded into 3D structures that determine the protein’s function. - Functions of proteins: - Serving as signaling molecules - Serving as receptors for signaling molecules - Aiding in structure - Allowing for transport - Providing defense against external dangers - Acting as catalysts (protein catalysts are called enzymes) Ian Shoemaker Spring 2016 California Polytechnic St ate University, San Luis Obispo; CHEM 313; Goodman; Spring 2016 Nucleic Acids Are the Information Molecules of the Cell - Nucleic acids are linear molecules consist ing of nucleotides connected by phosphodiester linkages. Nucleic Acid Nucleotide - A nucleotide is made up of a five-carbon sugar (ribose or deoxyribose) connected to one 2- of five heterocyclic ring structures called bases and at least one phosphoryl group ( PO 3 ). Nucleotide Base 2- PO 3 Phosphoryl Group Five-Carbon - There are two types of nucleic acids: Sugar - Ribonucleic acid (RNA) - Deoxyribonucleic acid (DNA) - When a nucleotide is made with ribose as its five -carbon sugar it is called a ribonucleotide and is used in RNA - When a nucleotide is made with deoxyribose as its five -carbon sugar it is called a deoxyribonucleotide and is used in DNA - There are five bases three of which are used by RNA and DNA and two that are each used exclusively by one nucleic acid or the other Used in RNA Used in DNA - The bases are sorted into two categories: Pyridines and Pyrimidines - Pyrimidines: single-ringed bases (Thymine, Cytosine, and Uracil) - Purines: double-ringed bases (Guanine and Adenine) - In the DNA double helix, A bonds to T and C bonds to G (in RNA U bonds to A) - Functions of nucleic acids - Storage and transfer of information - Ribosomes function in structure and catalysis - Short RNA molecules function in regulation Ian Shoemaker Spring 2016 California Polytechnic St ate University, San Luis Obispo; CHEM 313; Goodman; Spring 2016 Lipids Are a Storage Form of Fuel and Serve as a Barrier - Lipids are not polymers and, therefore, do not have subunits . - Lipids are unique in that one of their parts is hydrophilic and the other part is hydrophobic. - This dual nature allows cells to have membranes that chemically separate it from the environment and even have internal compartments that are chemically independent. Lipid Head Hydrophilic Extracellular matrix Phospholipid Hydrophobic bilayer Lipid Tail Cytoplasm - The lipid tails interact with other lipid tails while the lipid head interact with the aqueous solutions. This results in the formation of a bilayer with a hydrophilic surface and a hydrophobic inside. - The hydrocarbon chains that make up lipid tails can undergo combustion to release large amounts of cellular energy. - Functions of Lipids: - Energy Storage - Signaling - Membrane Composition Carbohydrates Are Fuels and Informational Molecules - Carbohydrates are linear or branched molecules made up of monosaccharides connected by glycosidic linkages. Glucose polymer (Glycogen, Starch, Cellulose) Glucose - The most common monosaccharide (simple sugar) is glucose which is stored in plants as the polymer starch and in animals as the polymer glycogen. - Functions of carbohydrates: - Energy storage - Plant and Bacteria cell wall structure - Carbohydrate heteropolymers function in signaling Ian Shoemaker Spring 2016 California Polytechnic St ate University, San Luis Obispo; CHEM 313; Goodman; Spring 2016 1.3 The Central Dogma Describes the Basic Principles of Biological Information Transfer - The Central Dogma: the scheme describing information processing at the level of gene expression Replication DNA RNA Protein - The genome is the heritable information in cells and consists of DNA - The information in DNA is packaged into units called genes - A gene is a section of DNA that has a specific order of nucleotides - The way that DNA is packaged and how tightly it is packaged is also heritable and is called epigenetics. - Phenotypes and traits are determined by the genes units in DNA - When a cell duplicates itself, its DNA undergoes replication with the help of a group of enzymes collectively called DNA polymerase to produce to identical genomes in the two new daughter cells. - In order to get the information out of genes, DNA must undergo transcription. With the help of RNA polymerase DNA is converted into mRNA. - It is important to remember that all cells in the body have the same genome and that it is the selective process of gene expression that defines the nature of a cell or tissue. - In order to translate the genetic information into a functional form mRNA must undergo translation with the help of ribosomes to be converted into polypeptide chains of amino acids. - These chains of amino acids are then folded into the proteins that do all the work in the cells of the body. 1.4 Membranes Define the Cell and Carry Out Cellular Functions Biochemical Functions A re Sequestered in Cellular Compartments - There are certain requirements that must be satisfied before something is considered to be alive: - The capacity to grow and replicate - The capacity to metabolize - The capacity to ‘communicate’ with the environment - Cells are the most basic units of life because they are the simplest things that can perform all of these functions - There are things that can do some but not all of these things on their own and are therefore not considered alive. - All cells have a membrane called a lipid bilayer that separates the inside of the cell from the external environment (plasma membrane) and have an internal environment that is chemically different from the external environment and is conducive to biochemical processes (cytoplasm). - There are two types of c ells: - Eukaryotic: Cells that have membrane -enclosed compartments called organelles Ian Shoemaker Spring 2016 California Polytechnic St ate University, San Luis Obispo; CHEM 313; Goodman; Spring 2016 - Prokaryotic: Cells that lack the membrane -enclosed compartments called organelles - Prokaryotic cells are surrounded by two membranes separated by the periplasmic space. The Plasma Membrane - The plasma membrane is impermeable to most substances and therefore must be made selectively semi-permeable to allow for the flow of molecules and information into and out of the cell. - Membrane proteins embedded in the membrane allow for this selective permeability by facilitating the transport of molecules and transducing information across the membrane. The Plant Cell Wall - In plants, the plasma membrane is surrounded by a cell wall made up of strands of polysaccharides of glucose called cellulose. The cell walls functions in protection and structure. The Cytoplasm - The cytoplasm is the inner substance of all cells where multiple biochemical processes take place. - In eukaryotes there are three types of protein fibers that make up the highly organized network of structural filaments called the cytoskeleton - Actin filaments - Intermediate filaments - Microtubules - These protein fibers support the structure of the cell, help localize biochemical processes, and help shuttle molecules around the cell Biochemical Functions Are Sequestered in Cellular Compartments - Eukaryotic cells contain intracellular, membrane -bound compartments called organelles. The Nucleus - The largest organelle and the location of the genome. - The nucleus has a double membrane that has pores to allow molecules in and out. - The nucleus is the site of transcription. The Mitochondrion - The mitochondrion has one membrane that separates the cytoplasm from its intermembrane space and another that is highly folded an d contains the mitochondrion ’s matrix. - 90% of the energy used by the cell is produced in mitochondria through the combustion of fuel molecules into CO , 2 O,2and ATP. The Chloroplast - Chloroplasts are double-membrane-bound organelles only found in plants and are the sites of photosynthesis in plant cells. Some Organelles Process and Sort Proteins and Exchange Material with the Environment The Endoplasmic Reticulum - The endoplasmic reticulum (ER) is a series of membrane-bound sacs where various biochemical reactions occur. - The smooth ER (SER) plays a large role in the processing of chemicals that originated outside the cell. Ian Shoemaker Spring 2016 California Polytechnic St ate University, San Luis Obispo; CHEM 313; Goodman; Spring 2016 - The rough ER (RER) is ‘rough’ due to the ribosomes attached to its cytoplasmic side. Ribosomes that are free in the cytoplasm synthesize proteins that are to be used inside the cell while ribosomes bound the RER synthesize proteins that will be inserte d into the plasma membrane or secreted from the cell. - During translation of mRNA, the forming protein is transported into the lumen of the RER where it is folded by proteins called chaperones. These folded proteins are then moved to areas of the RER that lack ribosomes that will eventually bud off as transport vesicles. The Golgi Complex - The Golgi complex is a series of stacked membranes where the transport vesicles fuse and release their proteins. The proteins are further processed and sorted in the Golgi complex. Secretory Granules - Secretory granules, or zymogen granules, are the result of vesicles budding off of the Golgi complex. The granule is directed toward the plasma membrane wh ere it waits for a signal to fuse with the membrane and secrete its protein contents into the extracellular environment. This process is called exocytosis. The Endosome - Endocytosis is the process in which the plasma membrane buds inward containing some molecule from the extracellular environment. These buds are called endosomes and they transport small amounts of biochemical into the cell. - When large amounts of material are transported into this cell the process is called phagocytosis. Lysosomes - A lysosome is an organelle that contains a wide variety of digestive enzymes. - Lysosomes form in a manner similar to that of secretory granules; however, lysosomes fuse with endosomes and digest whatever the endosome was carr ying. The lysosome then releases the digested material in the form of useful molecules. - Lysosomes can also digest damaged intracellular organelles. Plant Vacuoles - Vacuoles are unique to plant cells and can take up as much as 80% of the cell ’s volume. - Vacuoles store water, ions, and nu trients for the cell and use proteins to transport molecules across their membranes. REMEMBER: 1. Work to understand organismal and cellular processes at the molecular level 2. Use the concepts of energy, equilibrium, kinetics, and binding specificity to describe the structure and behavior of molecules 3. Molecular structure is determined by covalent bonds and weak interactions between a toms and determines the function of the molecule 4. Genes and the environment interact to determine the traits and phenotypes of an organism 5. The life processes of an organism are regulated in order to maintain homeostasis Ian Shoemaker Spring 2016


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