Lec 1 and 2 Final Biochemistry Principles PDF

Course Code: Bio 323 Course Name: Principles of Biochemistry Prof. Walaa Hozayen Dr/ Amal Khedr Dr/ Basma Sayed  Bio 323 Principles of Biochemistry NO. of hours: 2 Total: 100 Final exam 50 Mid-term 20 Student activity...

Course Code: Bio 323 Course Name: Principles of Biochemistry Prof. Walaa Hozayen Dr/ Amal Khedr Dr/ Basma Sayed  Bio 323 Principles of Biochemistry NO. of hours: 2 Total: 100 Final exam 50 Mid-term 20 Student activity 20 Oral exam 10  Overall aims of course  Provide students with information needed to understand the essential topics of biochemistry including the structure of micro and macromolecules.  Provide students with the basic concepts of the classification of micro and macromolecules of carbohydrates, lipids, proteins, nucleotides, nucleic acids & vitamins.  Apply the processes of scientific research and experimental design to the diversity of biomolecules in living cells.  Describe how biomolecules control every aspect of the cell functions.  Provide the students with the skills of self-learning and work in groups.  Metabolism Plant Enzymology Biochemistry Molecular Genetics Biochemistry Biology Animal Biochemistry Immunology Cell Biology Three areas to study Structural and Functional Biochemistry: Chemical structures and 3D arrangements of molecules. Informational Biochemistry: Language for storing biological data and for transmitting that data in cells and organisms. Bioenergetics: The flow of energy in living organisms and how it is transferred from one process to another.  Principles of Biochemistry Cells (basic structural units of living organisms) are highly organized and constant source of energy that is required to maintain the ordered state. Living organism contains thousands of chemical RXs. All organisms use CHO, proteins, lipids & nucleic acids. Instructions for growth, reproduction & development for organism is encoded in their DNA.  What are types of the cells? Cells are broadly categorized into two types: Prokaryotic cells: – Which lack a nucleus but have a nucleoid region ‘DNA‘ is found in the form of bundles called nucleoids. – are single-celled organisms. Eukaryotic cells: – Which possess a nucleus. – eukaryotes can be either single-celled or multicellular. Prokaryotic Cell Eukaryotic Cell  Comparison between prokaryotic and eukaryotic cells  Eukaryote Cells: More Complexity Eukaryotic Cell  Comparison between prokaryotic and eukaryotic cells Animal Cell  The cell is the fundamental unit of life Cells are composed of small molecules (water), macromolecules and organelles macromolecules fold into complex 3D structure. Macromolecules can be classified into 4 different categories: carbohydrates, proteins, lipids and nucleic acids. Each type possesses distinct chemical properties that suit it for the functions it serves in the cell.  Characteristics of Cells All cells share four common components: 1) A plasma membrane, an outer covering that separates the cell’s interior from its surrounding environment. 2) Cytoplasm, consisting of a jelly-like region within the cell in which other cellular components are found. 3) DNA, the genetic material of the cell. 4) Ribosomes, particles that synthesize proteins. Cell Organelles and their Functions Cell Membrane The plasma membrane is one type of cell membrane, provides protection for a cell. It also provides a fixed environment inside the cell.  Nucleus 1. The nucleus is the most vital organelle within the cell. 2. It contains the genetic material, the DNA, which is liable for controlling and directing all the activities of the cell. Nuclear membrane Nucleolus The nucleolus is the site of ribosome synthesis. It is involved in controlling cellular activities and cellular reproduction.  Chromosomes Chromosomes play an important role in determining the sex of an individual. Each human cells contain 23 pairs of chromosomes  Endoplasmic reticulum The endoplasmic reticulum can either be smooth or rough, and in general its function is to biosynthesis, processing & transport for protein and lipid.  Golgi Bodies Also known as a Golgi apparatus Named after its discoverer, Camillo Golgi, The factory in which proteins received from ER are further processed and sorted for transport for using inside & outside from the cell.  Ribosome Ribosomes are found 'free' in the cytoplasm or bound to the endoplasmic reticulum (ER) to form rough ER. Responsible for synthesizing proteins by translating the genetic code transcribed in mRNA into an amino acid sequence.  Mitochondria A mitochondrion is a round to oval-shaped organelle found in the cells of almost all eukaryotic organisms. It produces energy, known as ATP.  Lysosomes The lysosomes are the animal cell's “garbage disposal or digestive system of cell” because it contains an array of enzymes capable of breaking down all types of biological polymers: proteins, nucleic acids, carbohydrates and lipids. Vacuole It consists of a bubble of fluid surrounded by a membrane. A vacuole, like a closet‫ دوالب‬in a house, can store whatever a cell needs at the time. Finally: Summarize the functions of cell organelles  What are the cell types in human? Based on where they are found and their function, human cells can be divided into 1- Stem cells 2- Bone cells, 3- Blood cells 4- Muscle cells, 5- Fat cells 6- Skin cells, 7- Nerve cells 8- Epithelial cells, 9- Sex cells 10- Cancer cells. What are the major functions of the cell  Structure and Support The cell wall and the cell membrane are the main components that function to provide support and structure to the organism. Transp ort The waste produced by the chemical processes is eliminated from the cells, Small & The larger molecules diffuse across the cell membrane through active transport where the cells require a lot of energy to transport the substances.  Energy Production Cells require energy to carry out various chemical processes. This energy is produced by the cells through a process called photosynthesis in plants and respiration in animals. Growth In complex organisms such as humans, the tissues grow by simple multiplication of cells. Hence, cells are responsible for the growth of the organism. The entire thing takes place via a process of mitosis.  There are two types of cell division: mitosis and meiosis Mitosis is termed as a sexual reproduction where the parent cell divides to form daughter cells. Meiosis causes the daughter cells to be genetically different from the parent cells. Differences between Mitosis & Meiosis  Do normal cells live forever? The normal cells in our bodies get old and die. For example, white blood cells only live for about 13 days, whereas red blood cells live for about 120 days. Liver cells, on the other hand, can live up to 18 months. Cells in the brain will stay alive throughout a person's life.  Cell death is a normal process in multicellular organisms, playing an important role in homeostasis.  There are two types of cell death: necrosis (or accidental cell death), and apoptosis, a form of programmed cell death (PCD) characterized by specific morphological changes.  Apoptosis is responsible for the removal of damaged or unnecessary cells throughout the lifecycle, including normal cell turnover,  Apoptosis is a natural and essential process required for growth as well as maintenance of a healthy state. Cell apoptosis occurs in a gentle, controlled manner without causing damage to neighboring cells. What is Homeostasis? 2 important cellular processes must balance each other perfectly Apoptosis is the mechanism by which old or damaged cells normally self-destruct. Proliferation refers to the growth and reproduction of cells. Lec 2  Biological Molecules = Biomolecules Biomolecules are essential molecules for all living organisms. Have unique characteristics and properties that show how they contribute to the structure and function of the cells.  Biomolecules consist mainly of 6 elements: Carbon Hydrogen Oxygen Nitrogen Sulphur Phosphorus Biomolecules are very large molecules of many atoms that are covalently bound together. Four Classes of Biomolecules  Water is the solvent of life and contributes to more than 60% of the weight. This is followed by protein (mostly in muscle) and lipid (mostly in adipose tissue). The carbohydrate content is rather low which is in the form of glycogen. The biomolecules is made of smaller components called monomers.  Monomers and Polymers of Biomolecules. Biological Monomer Polymer Molecules Carbohydrate Monosaccharides Polysaccharides Proteins Amino Acids Polypeptide Lipids Fatty Acids, Lipid Glycerol Nucleic Acids Nucleotide Nucleic Acids Another definition of Biomolecules: Biomolecules: any molecule that is involved in the metabolic processes of living organisms. What Are Metabolic Processes? Is the sum of chemical reactions that occur throughout the body within each cell and that provide the body with energy.  These reactions are controlled by the presence of enzymes which act as catalysts. Metabolic pathways can be described as a series of chemical reactions that: Start with a substrate Finish with an end product  Metabolic processes = metabolism.  Metabolism is a balancing action involving two kinds of activities that go on at the same time: Building up body tissues and energy consumed (called anabolism) Breaking down body tissues and energy produced to get more fuel for body functions (called catabolism)  Types of Metabolic Reactions 1- Anabolic reactions build complex molecules from simpler subunits (for organic monomers, this involves condensation polymerization). 2- Catabolic reactions break down complex molecules into smaller components (for organic polymers, this involves hydrolysis reactions into monomers)  Anabolism Catabolism This is building process This is a breaking down process Small molecules combine Large molecules break into together to form larger smaller molecules molecules Energy required for the Release energy when bonds formation of chemical bonds are broken (Exergonic) (Endergonic) Involves creation of bonds by Involves breaking of bonds reduction or condensation by oxidation or hydrolysis reactions reactions Anabolic Reaction Catabolic Reaction Cellular Respiration: Harvesting Chemical Energy  To use ATP for energy, the cell cleaves the chemical bond between phosphate groups. This bond, called a phosphodiester bond, holds a lot of energy.  Why is it so important? There are basically three reasons why ATP is so, important in biology: 1. It’s the molecule the body uses directly as energy. 2. It’s easy to recycle, so a cell can use a single molecule again and again. It’s often called the “energy currency” of metabolism and cells. ATP acts as an energy link between the catabolism and anabolism in the biological system. How Do Cells Keep Metabolic Reactions in Balance?  Cells employ various mechanisms to regulate their metabolism. Three primary methods through which cells control metabolic processes include: – Managing substrate availability, – Modulating enzyme concentration, – Regulating enzyme activity.  Elements Simplest form of a substance. Cannot broken down into more simpler form. 98-99% of the body is composed of 6 major elements C, H, O, N, S, P. Other than C, H, O, N, P, S are also common, Metal ions (e.g., K+, Na+, Ca++, Mg++, Zn++, Fe++) play important roles in metabolism.  Compounds A substance composed of 2 or more elements that are chemically bonded together. Can be classified into inorganic or organic compounds. Functional Groups determine chemical properties of compounds.  Major Types of Chemical bonds in Biomolecules Ester Bond Disulphide Bond Peptide Bond Glycosidic Bond Ester Bond Disulfide Bond ‘ Peptide Bond Glycosidic Bond  Major Types of Chemical reactions occur in the cell Group transfer Oxidation- reduction Rearrangem ent Cleava ge Condensati on Group transfer Oxidation- reduction Rearrangem ent Cleava ge Condensati on