Cells & Macromolecules, Biology A, University of Crete, 2024-2025 PDF

BIOLOGY A Life at the Cellular and Molecular level Course Coordinator: Marina Vidaki, PhD Ass Prof Cellular Molecular Biology School of Medicine University of Crete [email protected] BIOLOGY A: what to expect Outline of the universal...

BIOLOGY A Life at the Cellular and Molecular level Course Coordinator: Marina Vidaki, PhD Ass Prof Cellular Molecular Biology School of Medicine University of Crete [email protected] BIOLOGY A: what to expect Outline of the universal features common to all cells: v Basic Chemical Compounds and Macromolecules (Proteins, Nucleic Acids, Lipids, Carbohydrates) DNA replication-recombination-repair, Transcription, Translation v Basic Structures and Organelles (Membranes, Nucleus, Mitochondria, Cytoskeleton, Extracellular Matrix) v Basic Functions (Intracellular Transport, Communication, Motility, Cell Cycle) v Connection to human health and disease BIOLOGY A: what to expect The program https://elearn.uoc.gr/course/view.php?id=4313#section-0 Time Date Course Lecturer 9-11am Mon 25/11/2024 Cells & macromolecules M. Vidaki 11-1pm Tue 26/11/2024 Protein structure & function M. Vidaki 11-1pm Wed 27/11/2024 Chromosome & DNA structure A. Tatarakis 9-11am Thu 28/11/2024 DNA replication A. Tatarakis 9-11am Mon 2/12/2024 DNA repair/recombination A. Tatarakis 11-1pm Tue 3/12/2024 Transcription A. Tatarakis 11-1pm Wed 4/12/2024 Translation A. Tatarakis 11-1pm Thu 5/12/2024 Gene regulation A. Tatarakis 9-11am Mon 9/12/2024 Genome Evolution A. Tatarakis 11-1pm Tue 10/12/2024 Midterm test/ Assignments M. Vidaki 11-1pm Wed 11/12/2024 Cytoskeleton I E. Petsalaki 9-11am Mon 16/12/2024 Cytoskeleton II E. Petsalaki 11-1pm Tue 17/12/2024 Cell communication & signaling I M. Vidaki 11-1pm Wed 18/12/2024 Cell communication & signaling II M. Vidaki 11-1pm Wed 8/1/2025 Cell Cycle E. Petsalaki 11-1pm Thu 9/1/2025 Cell death E. Petsalaki 11-1pm Fri 10/1/2025 Membrane Structure & Functions D. Karagogeos 9-11am Mon 13/1/2025 Membrane Transport D. Karagogeos 11-1pm Tue 14/1/2025 Intracellular compartments D. Karagogeos 11-1pm Wed 15/1/2025 Organelles D. Karagogeos 11-1pm Thu 16/1/2025 Extracellular Matrix D. Karagogeos 11-1pm Fri 17/1/2025 Assignment presentations M. Vidaki 9-11am Mon 20/1/2025 Assignment presentations M. Vidaki 11-1pm Tue 21/1/2025 Assignment presentations M. Vidaki 9-11am Wed 22/1/2025 Assignment presentations M. Vidaki 11-1pm Thu 23/1/2025 Assignment presentations M. Vidaki  Biology A Cells & Macromolecules Marina Vidaki [email protected] School of Medicine University of Crete 4 LIVING THINGS… Curious, intricately organized chemical factories: They take in matter from their surroundings and use these raw materials to generate copies of themselves Extremely DIVERSE Common feature: LIFE LIVING THINGS… Life… LIVING THINGS… Highly organized structure and functions Homeostatic mechanisms Reproduction Growth and development Metabolism Response to stimuli Adjustment to environment Life… LIVING THINGS… Highly organized structure and functions Homeostatic mechanisms Reproduction Growth and development Metabolism Response to stimuli Adjustment to environment Life… All Living things are made of CELLS: small, membrane-enclosed units filled with a concentrated aqueous solution of chemicals and endowed with the extraordinary ability to create copies of themselves by growing and then dividing in two Cells: the fundamental units of life Highly organized structure and functions Homeostatic mechanisms Reproduction Growth and development Metabolism Response to stimuli Adjustment to environment Life… All Living things are made of CELLS “The key to every biological problem must finally be sought in the cell; for every living organism is, or at some time has been, a cell.” E. B. Wilson (Cell Biologist, 1856 –1939) CELL BIOLOGY — the study of the structure, function, and behaviour of cells Deeper understanding of cells and their evolution, can tackle the grand historical questions with respect to life : its mysterious origins its stunning diversity its invasion of every conceivable habitat its malfunction (disease, death) CELL BIOLOGY — the study of the structure, function, and behaviour of cells Understanding function will lead to the elucidation of malfunction CELLS QUICK RECAP of the BASICS CELLS CELLS: Procaryotic CELLS: Eucaryotic Cells: variety and constancy Remarkable variety in individual particulars Remarkable constancy in fundamental mechanisms Cells: variety and constancy Despite the variability in morphology and function, eucaryotic cells share remarkable internal similarities in structures, organelles, chemistry and molecular codes Eucaryotic cell chemistry and molecular codes The main chemical elements found in cells 99% of the total number of atoms present in the human body 0,9% of the total number of atoms present in the human body Required in trace amounts in humans Unclear whether they are essential in humans Major chemical bonds in cells The atoms of the elements can be linked with covalent bonds (common electron contribution) to form molecules: Covalent bonds are 100 times stronger than thermal energy They are resistant to breakdown by thermal movements They are broken down only through specific reactions controlled by special catalysts (enzymes) Major chemical bonds in cells atoms The atoms of the elements can be linked with non-covalent bonds (transfer of electrons from one atom to another) Electron transfer to form molecules: Much weaker bonds (1/20 the strength of a covalent bond) Important in multiple biological processes, where molecules need to be quickly Positively charged Negatively charged ion ion assembled and disassembled Non-covalent Bond Types of non-covalent bonds in cells HYDROGEN BONDS - formed between a slightly positive hydrogen atom and a slightly negative atom, usually oxygen or nitrogen. In cells, these bonds are primarily formed between water molecules, DNA bases, and certain functional groups in proteins - Very weak bonds - Easily broken down by random thermal movements in cells (short lifetime) - Hydrophilic molecules can form hydrogen bonds and dissolve easily in water - Hydrophobic molecules do not have polarity and do not form hydrogen bonds. Non-water soluble Types of non-covalent bonds in cells Electrostatic attraction - A bond is formed between ions of different charge (e.g. NaCl) VAN DER WAALS forces - Transient attraction between charged atoms in close proximity - Non-specific interactions Hydrophobic interactions - Nonspecific interactions caused by non- polar groups of atoms in an aquatic environment - They participate in the structure of cell membranes consisting mainly of lipid molecules Organic Molecules a few categories of molecules, give rise to all the extraordinary richness of form and behavior shown by cells and living things: most of them are based on carbon Single bond Double bond covalent C–C bonds can form chains and rings and hence generate large and complex Triple bond molecules with no obvious upper limit to their size CELL Building Blocks 1. Organic Molecules 4 main families of organic molecules in cells: 2. Biomolecules Molecules found in cells, essential for biological processes CELL Building Blocks 3. Macromolecules Macromolecules are polymers, derived by monomers (subunits) bound together by covalent bonds Lipids Molecules that contain hydrocarbons not soluble in water as they are non-polar, but are thus soluble in non-polar solvents such as chloroform. They are not strictly categorized as Macromolecules, because they are not considered polymers. Examples of lipids include fats, oils, waxes, certain vitamins (such as A, D, E and K), hormones and most of the cell membrane that is not made up of protein Lipids Triglycerides (Triacylglycerols) 1 Glycerol + 3 Fatty acids In cells, fatty acids are stored in the form of triglycerides Lipids Triglycerides (Triacylglycerols) 1 Glycerol + 3 Fatty acids Saturated Fatty acids (no double covalent bonds between C atoms) Unsaturated Fatty acids (1 or more double covalent bonds between C atoms) Lipids Triglycerides (Triacylglycerols) 1 Glycerol + 3 Fatty acids Saturated Fatty acids (no double covalent bonds between C atoms) Unsaturated Fatty acids (1 or more double covalent bonds between C atoms) Saturation affects conformation and behaviour Lipids Compound Include fatty acids, alcohol, and chemical groups, for example, phosphorus and nitrogen Lipids Compound Include fatty acids, alcohol, and chemical groups, for example, phosphorus and nitrogen Lipoproteins Lipids Compound Include fatty acids, alcohol, and chemical groups, for example, phosphorus and nitrogen Mostly membrane lipids (polarity) Glycolipids Phopsholipids Lipids Compound Include fatty acids, alcohol, and chemical groups, for example, phosphorus and nitrogen Mostly membrane lipids (polarity) Glycolipids Phopsholipids Lipids Derived When both simple and compound lipids combine and undergo the process of hydrolysis, the produced chemical is known as the derived lipids. Derived lipids include cholesterol, carotenes, steroids and prostaglandins etc. Lipids Derived When both simple and compound lipids combine and undergo the process of hydrolysis, the produced chemical is known as the derived lipids. Derived lipids include cholesterol, carotenes, steroids and prostaglandins etc. Lipids Lipids Molecules that contain hydrocarbons not soluble in water as they are non-polar, but are thus soluble in non-polar solvents such as chloroform. FUNCTIONS They serve as fuel molecules. 1 gm of fat provides 9 kcal of energy. Phospholipids and triglycerides are important to structure, composition and permeability of cell wall and cell membrane. Lipoproteins help in transporting lipids in blood. Skin waxes act as defense mechanism in avoiding thermal and physical shock. Fats present in food help to carry fat soluble vitamins so that they are efficiently absorbed. Fats serve as vitamins, emulsifiers and flavour and aroma compounds. Polysaccharides Monomers: Monosaccharides carbohydrate molecules that cannot be broken down by hydrolysis into simpler (smaller) carbohydrate molecules (simple sugars) Polysaccharides Monomers: Monosaccharides carbohydrate molecules that cannot be broken down by hydrolysis into simpler (smaller) carbohydrate molecules (simple sugars) Through condensation and the formation of glycosidic bonds, monosaccharides form disaccharides condensation hydrolysis Polysaccharides Disaccharides Polysaccharides Nucleic Acids Monomers: Nucleotides Nucleic Acids Monomers: Nucleotides Nucleic Acids Polynucleotides (Nucleic Acids): Polymers of nucleotides linked by phosphodiester bonds (covalent bond) Nucleic Acids DNA is formed by two polynucleotide strands with anti-parallel orientation A B C D Nucleic Acids RNA is a single polynucleotide strand Nucleic Acids Nucleotides are not just the monomers for nucleic acids Additional functions in cells include: 1. Energy carriers 2. Part of large complex molecules like coenzymes 3. Signaling molecules Proteins Monomers: amino acids Proteins Proteins Proteins Proteins Refers to the association of multiple individual protein chains into a single protein with multiple subunits The subunits may be identical or different When different they tend to have different functions Not all proteins have quaternary structure Very stable structures Variety of non-covalent bonds between chains 2 major types of quaternary structure: FIBROUS (e.g.keratins, etc) GLOBULAR (e.g. insulin, haemogobin, most enzymes, etc) CELL Building Blocks Cells: variety and constancy Despite the variability in morphology and function, eucaryotic cells share remarkable internal similarities in structures, organelles, chemistry and molecular codes Eucaryotic cell structures and organelles NUCLEUS: storage of genetic material Eucaryotic cell structures and organelles MITOCHONDRIA: Energy producing factories Mitochondria take up oxygen and harness energy from the oxidation of food molecules, to produce most of the ATP that powers the cell’s activities Similar in size to small bacteria Own genome in the form of a circular DNA molecule, Own ribosomes that differ from those elsewhere in the eukaryotic cell Own transfer RNAs Eucaryotic cell structures and organelles MITOCHONDRIA: Energy producing factories 1.5 billion years old Free-living oxygen-metabolizing (aerobic) bacteria that were engulfed by an ancestral cell that could otherwise make no such use of oxygen (that is, was anaerobic) Escaping digestion, these bacteria evolved in symbiosis with the engulfing cell, receiving shelter and nourishment in return for the power generation they performed for their hosts. Eucaryotic cell structures and organelles ENDOPLASMIC RETICULUM: protein and lipid synthesis Eucaryotic cell structures and organelles Golgi Apparatus: protein and lipid modification, vescicle packaging Eucaryotic cell structures and organelles VESCICLES: material transport, degradation Eucaryotic cell structures and organelles CYTOSKELETON: shape, endurance, motility, division CELL Recap All living organisms are composed of cells Cells are extremely variable in morphology and functions All cells have very well conserved chemistry/molecular basis All cells have very well conserved structures All cells share vey well conserved processes All cells have the same ultimate goal of survival, growth and proliferation Understanding all of the above will advance our understanding of human health and disease “The key to every biological problem must finally be sought in the cell; for every living organism is, or at some time has been, a cell.” E. B. Wilson (Cell Biologist, 1856 –1939)  Biology A Cells & Macromolecules Marina Vidaki [email protected] School of Medicine University of Crete 63