Al-Farahidi University College of Pharmacy Biochemistry 2023-2024 Lecture Notes PDF

Al-Farahidi University College of Pharmacy 3rd grade Biochemistry 2023-2024 By Assistant Lecturer Nabigh Al-Sharifi Lecture : 1 Assistant lecturer:Nabigh Al-Sharifi Reference texts: ⚫ Harpers Biochemistry. 29th Illustrated edition ⚫ Biochemistry...

Al-Farahidi University College of Pharmacy 3rd grade Biochemistry 2023-2024 By Assistant Lecturer Nabigh Al-Sharifi Lecture : 1 Assistant lecturer:Nabigh Al-Sharifi Reference texts: ⚫ Harpers Biochemistry. 29th Illustrated edition ⚫ Biochemistry Lippincott’s Illustrated Reviews. 6th edition Introduction to Biochemistry Overview: ⚫ What we mean by Biochemistry? ⚫ What is the aim of Biochemistry? ⚫ What dose the Biochemistry discuss? ⚫ General review of biochemistry.  Biochemistry = Chemistry of life ⚫ Biochemistry can be defined as the science concerned with the chemical basis of life. ⚫ Since cells are the structural units of living systems. Thus, biochemistry can also be described as the science concerned with the chemical constituents of living cells and with the reactions they undergo. ⚫ Because life depends on biochemical reactions, biochemistry has become the basic language of all biologic sciences.  The Aim of Biochemistry ⚫ The major aim of biochemistry is the complete understanding, at the molecular level, of all of the chemical processes associated with living cells. ⚫ To achieve this objective, biochemists have sought to isolate the numerous molecules found in cells, determine their structures, and analyze how they function. What dose the Biochemistry discuss? ⚫ Biochemistry discusses: ⚫ Structure and function of cellular components 🞄 Proteins 🞄 Carbohydrates 🞄 Lipids 🞄 Nucleic acids and other biomolecules ⚫ Metabolism and Regulation ⚫ Gene expression and modulation Biochemistry in Health and Disease  Perhaps All Disease Has a Biochemical Basis. ⚫ Knowledge of the biochemical molecules shown in the top part of the diagram has clarified our understanding of the diseases shown in the bottom half—and conversely, analyses of the diseases shown below have cast light on many areas of biochemistry Examples of the two-way street connecting biochemistry and medicine  Starting materials: Elements of life ⚫ Around 25 of the 94 naturally occurring chemical elements are essential to various kinds of biological life. ⚫ Just six elements (carbon, hydrogen, nitrogen, oxygen, sulfur, & phosphorus ) make up almost 99% of the mass of a human cells. ⚫ Life on earth depends on the chemical element carbon, which is present in every living thing. Biochemistry is concerned with the entire spectrum of life forms, from relatively simple viruses and bacteria to complex human beings..  Organization of Life ⚫ Elements ⚫ Simple organic compounds (monomers) ⚫ Macromolecules (polymers) ⚫ Supramolecular structures ⚫ Organelles ⚫ Cells ⚫ Tissues ⚫ Organisms  Elements of Life Most abundant, essential for all organisms: C, N, O, P, S, H Less abundant, essential for all organisms : Na, Mg, K, Ca, Cl Trace levels, essential for all organism: Mn, Fe, Co, Cu, Zn Trace levels, essential for some organisms:V, Cr, Mo, B,Al, Ga, Sn, Si,As, Se, I.  Biomolecules of life ⚫ There are 4 classes of biomolecules to be studied in this biochemistry course: 1. Proteins 2. Carbohydrates 3. Lipids 4. Nucleic acids  Many Important Biomolecules are Polymers Biopolymers are macromolecules created by joining many smaller organic molecules called (monomers) by a reaction named Condensation reactions (H2O is removed in the process). Each monomer in the polymer chain is a Residue.  Monomers and Polymers Macromolecule Monomer Carbohydrates Monosaccharide Lipids Not always polymers; Hydrocarbon chains Proteins Amino acids Nucleic acids Nucleotides  1. Carbohydrates  Carbohydrate s monomer glucose Carbohydrates are made from monomers called monosaccharides. Some of these monosaccharides include polymer cellulose glucose (C6H12O6), fructose (C6H12O6), and deoxyribose (C5H10O4) supramolecular cell wall structure Glucose disaccharide polysaccharide carbohydrate  Carbohydrate s ⚫ Carbohydrates are the main source of energy for living organisms and are made of carbon, hydrogen, and oxygen. ⚫ Chlorophyll in plants absorbs light energy from the sun. This energy is used in the process of photosynthesis, which allows green plants to take in carbon dioxide and release oxygen and allows for the production of carbohydrates. ⚫ Plants transform carbon dioxide (CO 2 ) from the air, water (H 2 O) from the ground, and energy from the sun into oxygen (O 2 ) and carbohydrates.  Carbohydrate s ⚫ Humans and other animals obtain carbohydrates by eating foods that contain them. ⚫ In order to use the energy contained in the carbohydrates, humans must metabolize , or break down, the structure of the molecule in a process that is opposite that of photosynthesis. ⚫ It starts with the carbohydrate and oxygen and produces carbon dioxide, water, and energy. The body utilizes the energy and water and rids itself of the carbon dioxide.  Carbohydrates Functions ⚫ Carbohydrates serve as energy source. ⚫ Ribose and deoxyribose sugars form part of of RNA and DNA. ⚫ Polysaccharides are structural elements in the cell. ⚫ Carbohydrates are linked to many proteins and lipids, forming different molecular classes are the proteoglycans, the glycoproteins and the glycolipids.  2. Proteins  2. Proteins Proteins are large biomolecules, monomer amino acid or macromolecules, consisting of one or more long chains of amino acid residues. polymer protein subunit Proteins perform a vast array of functions within organisms, supramolecular Enzyme complex including catalyzing metabolic structure reactions, DNA replication, responding to stimuli, and transporting molecules from one location to another. Amino acid D ipeptide Protein subunit Protein  Protei ns ⚫ Proteinsare the most complex and varied class of molecules ; they are large polymer composed of carbon, nitrogen, oxygen and hydrogen. ⚫ Upon hydrolysis proteins produce monomeric units called amino acids. Amino acids have amino group NH2- on alpha carbon atom located next to the carboxylic group.  Protei ns Proteins are composed of 20 common amino acids Each amino acid contains: (1) Carboxylate group (-COO¯) (2) Amino group (-NH2) (3) Hydrogen atom (- H) (4) Side chain (R) unique to each amino acid  Structure of an amino acid and a dipeptide (a) Amino group (blue), carboxylate group (red) (b) Dipeptides are connected by peptide bonds 3. Lipids  3- Lipids lipids comprise a group of naturally monomer fatty acid occurring molecules that include fats, waxes, sterols, fat-soluble vitamins (such as vitamins A, D, E, and K), triglycerides, polymer phospholipid phospholipids, cholesterol and others. The main biological functions of lipids supramolecular membrane include storing energy, signaling, and acting structure as structural components of cell membranes. Supramolecular Fatty acid Phospholipids structure  Lipids Lipids are rich in carbon and hydrogen, but contain little oxygen Lipids are not soluble in water Fatty acids are the simplest lipids: long chain hydrocarbons, with a carboxylate group at one end Fatty acids are often components of glycerophospholipids  Model of a Membrane lipid Phospholipids composed from a Hydrophilic (water-loving) head interacts with H2O and a Hydrophobic (water-fearing) tail A biological memberane usually composed from a lipid bilayer with associated proteins 4.Nucleic Acids  4. Nucleic Acids A nucleic acid is a large macromolecule or polymer composed of chain of monomeric monomer nucleotide nucleotides. These molecules carry the genetic information polymer DNA or form structures within the cells. Nucleic acids, present as DNA (deoxyribonucleic acid) and RNA (ribonucleic supramolecular chromatin acid). structure Nucleic acids are among the most important biological macromolecules, they are found in abundance in all living things, where they function in encoding, transmitting and expressing genetic information. Nucleotide D N A strand supramolecular structure  GENE EXPRESSION DNA GENE EXPRESSION PROTEIN  Protein Synthesis  Note: Monomers form polymers through condensations Polymers are broken down through hydrolysis.  Anabolic ⚫ Building block ⚫ Macromolecule ◦ Simple sugar ◦ Polysaccharide ◦ Amino acid ◦ Protein (peptide) ◦ Nucleotide ◦ RNA or D N A ◦ Fatty acid ◦ Lipid Catabolic Functional Groups in Biochemistry  Biomolecu les ⚫ Just like cells are building blocks of tissues, biomolecules are building blocks of cells. ⚫ Animal and plant cells contain approximately 10,000 kinds of biomolecules. ⚫ Water constitutes 50-95% of cells content by weight. ⚫ Ions like Na+, K+ and Ca2+ may account for another 1%. ⚫ Almost all other kinds of biomolecules are organic (C, H, N, O, P, S). ⚫ Organic compounds are compounds composed primarily of a Carbon skeleton.  Carbon ⚫ Carbon is more abundant in living organisms than it is in the rest of the universe. ⚫ 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 immensely diverse compounds, from simple to complex. Methane with 1 D N A with tens of Billions Carbon atom of Carbon atoms Biomolecules are compounds of carbon with a variety of functional groups Functional groups in biochemistry Functional groups - specific parts of molecules involved in biochemical reactions Functional Groups Functional groups Functional groups Functional groups Example : Functional groups in Acetyl- coenzyme A  Examples of Cells Amoeba Proteus Plant Stem Bacteria Red Blood Cell Nerve Cell  Cells May be Prokaryotic or Eukaryotic ⚫ Prokaryotes (Greek: pro-before; karyon-  nucleus) include various bacteria ◦ lack a nucleus or membrane-bound structures called organelles ⚫ Eukaryotes (Greek: eu-true; karyon-nucleus) include most other cells (plants, fungi, & animals) ◦ have a nucleus and membrane-bound organelles Eukaryotic Cell Cell Organelles Review of Eukaryotic Cells Review of Eukaryotic Cells Structural hierarchy in the molecular organization of cells