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Science, Chemistry, and Cells Dr. Praveen Babu Life Science for Engineers BIO 213  What is Life? Biology is the scientific study of life The cell is the basic unit of life & every organism consists of one or more cells Despite tremendous diversity, coding i...

Science, Chemistry, and Cells Dr. Praveen Babu Life Science for Engineers BIO 213  What is Life? Biology is the scientific study of life The cell is the basic unit of life & every organism consists of one or more cells Despite tremendous diversity, coding instructions of all living organisms are written in nucleic acids We can define life by listing its basic components, but still more is necessary Scientists have settled on five qualities that, in combination, constitute life  What is Life? Biology is the scientific study of life The cell is the basic unit of life & every organism consists of one or more cells Despite tremendous diversity, coding instructions of all living organisms are written in nucleic acids We can define life by listing its basic components, but still more is necessary Scientists have settled on five qualities that, in combination, constitute life Can we create life synthetically?  What is Life? Biology is the scientific study of life The cell is the basic unit of life & every organism consists of one or more cells Despite tremendous diversity, coding instructions of all living organisms are written in nucleic acids We can define life by listing its basic components, but still more is necessary Scientists have settled on five qualities that, in combination, constitute life Can we create life synthetically?  Human Genome Project cost ~$3 billion Celera sequences human genome for $300 million  D. radiodurans can withstand up to 5kGy 1 Gray = 1 Joule γ radiation absorbed per kilogram  What is Life? Biology is the scientific study of life The cell is the basic unit of life & every organism consists of one or more cells Despite tremendous diversity, coding instructions of all living organisms are written in nucleic acids We can define life by listing its basic components, but still more is necessary Scientists have settled on five qualities that, in combination, constitute life Can we create life synthetically? Yes.  What is Life? Scientists have settled on five qualities that, in combination, constitute life  What is Life? Scientists have settled on five qualities that, in combination, constitute life 1. Life is organized into a tremendous hierarchical pattern Life is Organized ATOM The smallest chemical unit of a type of pure substance (element). Example: Carbon atom Life is Organized MOLECULE A group of joined atoms Example: DNA Life is Organized ORGANELLE A membrane- bounded structure that has a specific function within a cell. Example: Chloroplast Life is Organized CELL The fundamental unit of life. Example: Leaf cell Life is Organized TISSUE A collection of specialized cells that function in a coordinated fashion. Example: Epidermis of lea Life is Organized ORGAN A structure consisting of tissues organized to interact and carry out specific functions. Example: Leaf  Life is Organized ORGAN SYSTEM Organs connected physically or chemically that function together. Example: Aboveground part of a plant Life is Organized ORGANISM A single living individual. Example: One acacia tree Life is Organized ORGANISM A single living individual. Example: One acacia tree Life is Organized POPULATION A group of the same species of organism living in the same place and time. Example: Multiple acacia trees Life is Organized COMMUNITY All populations that occupy the same region. Example: All populations in a savanna Life is Organized ECOSYSTEM The living and nonliving components of an area. Example: The savanna  Life is Organized BIOSPHERE The global ecosystem; the parts of the planet and its atmosphere where life is possible.  Life is Organized Emergent properties (new Sheet of complex Endothelial endothelial functions) arise at cell cells each level of biological organization The capillary has properties that its components alone Capillary Multiple Agent Simulation System in Virtual Environment lack “And going back to that famous case of the first battle that Endothelial we did where we had agents running away... Emergent Red blood -- StephencellRegelous cell (From vfxBlog interview) properties result  What is Life? Scientists have settled on five qualities that, in combination, constitute life 1. Life is organized into a tremendous hierarchical pattern 2. Life requires energy  Life Requires Energy Energy from sunlight Producers extract energy and nutrients from the nonliving environment.  Life Requires Energy Heat Consumers obtain energy and nutrients by eating other organisms. Energy from sunlight  Life Requires Energy Heat Energy from sunlight Heat Heat Decomposers: consumers that obtain nutrients from dead organisms and organic wastes.  Life Requires EnergyHeat Energy from Note: sunlight Heat is lost Heat Heat every time energy is transferred. Heat  What is Life? Scientists have settled on five qualities that, in combination, constitute life 1. Life is organized into a tremendous hierarchical pattern 2. Life requires energy 3. Life maintains internal consistency Cells or organisms maintain an equilibrium state through homeostasis  What is Life? Scientists have settled on five qualities that, in combination, constitute life 1. Life is organized into a tremendous hierarchical pattern 2. Life requires energy 3. Life maintains internal consistency Cells or organisms maintain an equilibrium state through homeostasis 4. Life reproduces, grows and develops Some organisms reproduce asexually, others reproduce sexually and combine characteristics  What is Life? Scientists have settled on five qualities that, in combination, constitute life 1. Life is organized into a tremendous hierarchical pattern 2. Life requires energy 3. Life maintains internal consistency Cells or organisms maintain an equilibrium state through homeostasis 4. Life reproduces, grows and develops Some organisms reproduce asexually, others reproduce sexually and combine characteristics  What is Life? Scientists have settled on five qualities that, in combination, constitute life 1. Life is organized into a tremendous hierarchical pattern 2. Life requires energy 3. Life maintains internal consistency Cells or organisms maintain an equilibrium state through homeostasis 4. Life reproduces, grows and develops 5. Live evolves: In biology, adaptation occurs through mutation & natural selection; in engineering, you make a mock up and troubleshoot What is Life? What is Life?  Taxonomy: Classifying Life Now we can catalog and classify life using taxonomy (the naming & classification of organisms) Living organisms are classified into one of three domains and then further classified from there  Taxonomy: Classifying Life Now we can catalog and classify life using taxonomy (the naming & classification of organisms) Living organisms are classified into one of three domains and then further classified from there  The Chemistry of Life What have we learned from the scientific study of life? Like all matter, organisms are composed of elements, BUT not all elements are in living matter… Only about 25 elements are essential to life Bulk elements make up the vast majority of every living cell; trace elements are sparse  The Chemistry of Life What have we learned from the scientific study of life? Like all matter, organisms are composed of elements, BUT not all elements are in living matter… Like all matter, living matter contains atoms of these essential elements chemically bonded to one another Each molecule or compound formed is not alive, but they are utilized to maintain the life of an organism  The Chemistry of Life What have we learned from the scientific study of life? Like all matter, organisms are composed of elements, BUT not all elements are in living matter… Like all matter, living matter contains atoms of these essential elements chemically bonded to one another Water is essential to life! Water has extraordinary properties because it’s polar and can H-bond Water is cohesive  The Chemistry of Life Water is essential to life! Water has extraordinary properties because it’s polar and can H-bond Water is cohesive Water is a solvent  The Chemistry of Life Water is essential to life! Water has extraordinary properties because it’s polar and can H-bond Water is cohesive Water is a solvent Water regulates temperature allowing for homeostasis  The Chemistry of Life Water is essential to life! Water has extraordinary properties because it’s polar and can H-bond Water is cohesive Water is a solvent Water regulates temperature allowing for homeostasis Water expands as it freezes Water participates in life’s chemical reactions  The Organic Chemistry of Life In addition to water, carbon-based organic molecules are essential to life They are often polymers of monomeric subunits Nucleic acid polymer Monom er Carbohydrate polymer Monom Monom er er Protein polymer  The Organic Chemistry of Life In addition to water, carbon-based organic molecules are essential to life They are often polymers of monomeric subunits  The Organic Chemistry of Life In addition to water, carbon-based organic molecules are essential to life They are often polymers of monomeric subunits Living organisms utilize polymers to make more complex macromolecules with specialized functions Carbohydrates: energy storage, structure Lipids: membranes, energy storage, signaling Proteins: structure, locomotion, transport, storage, catalysis and many more functions Nucleic acids: information storage and transmission  Carbohydrates Carbohydrates are sugars; simple sugars like monosaccharides are joined to form disaccharides…  Carbohydrates Complexity grows from there giving polysaccharides  Lipids All lipids are hydrophobic and do not dissolve in water Lipids are also known as fats But some are used in building membranes and chemical signaling like cholesterol and testosterone  Proteins Proteins are complex and highly versatile Membrane proteins, hemoglobin, keratin, polymerases, antibodies, enzymes, etc. etc.  Proteins A protein is a chain of amino acids linked together by peptide bonds to form one or more polypeptides We can make some of the 20 naturally occurring amino acids from scratch, but we get half—the essential amino acids—from the proteins we eat Protein shape is critical for function!  Proteins A protein is a chain of amino acids linked together by peptide bonds to form one or more polypeptides We can make some of the 20 naturally occurring amino acids from scratch, but we get half—the essential amino acids—from the proteins we eat Protein shape is critical for function! Proteins Proteins  Proteins Proteins are vulnerable to heat, pH, salts, etc. that can denature them and render them nonfunctional  Nucleic Acids Nucleotide monomers make up long nucleic acid polymers like deoxyribonucleic acid (DNA) or ribonucleic acid (RNA) DNA is the data storage molecule in cells and encodes the “blueprints of life” RNA serves multiple roles in the utilization of the genetic information stored in DNA  Cells are the Units of Life Cell theory: (1) organisms are made up of 1+ cell(s), (2) the cell is the fundamental unit of life, and (3) cells come from preexisting cells Cells are small  Cells are the Units of Life Cells all have certain features in common: DNA & RNA Ribosomes Proteins Cytosol/cytoplasm Cell Membrane Membranes are central to life They make it possible to and maintain the exchange of nutrients into and out of the cell Also control the ratio of surface area to volume Different Cells for Different Domains Used to only be prokaryotic (“before” nucleus) and eukaryotic (“true” nucleus) cells However, prokaryotes were divided into domains bacteria and archaea Bacteria are the most abundant and diverse organisms on Earth  Domain Bacteria Critical as decomposers & producers, yet structurally simple Nucleoid: cell’s circular DNA molecule congregates Most have a rigid cell wall for protection, structural rigidity (e.g., to prevent lysis if too much water is absorbed), and shape Some have means of motion like those that have a flagellum  Domain Archaea Archaean cells resemble bacterial cells in many ways Nucleoid: cell’s circular DNA molecule congregates Most have a rigid cell wall for protection, structural rigidity (e.g., to prevent lysis if too much water is absorbed), and shape Some have means of motion like those that have a flagellum However, archaea contain biochemicals that are different than bacteria or eukaryotes Ribosomes are more similar to eukaryotes Considered to be closest relative to eukaryotes  Domain Eukarya Domain eukarya is very diverse (e.g., animals, yeasts, mushrooms & other fungi, plants, and protists) All are larger than bacteria & archaea and all share many cellular features Most important difference is the presence of a membrane-bound nucleus and organelles  Domain Eukarya An animal cell  Domain Eukarya A plant cell Note: Cell wall Chloroplasts  The Eukaryotic Cell Domain eukarya is very diverse (e.g., animals, yeasts, mushrooms & other fungi, plants, and protists) All are larger than bacteria & archaea and all share many cellular features: A cell membrane separates each cell from its surroundings  The Eukaryotic Cell Membranes are composed of a phospholipid bilayer and proteins that provide selective permeability  The Eukaryotic Cell Some prescribe to the fluid mosaic model Transport proteins, Enzymes, Recognition proteins, Adhesion proteins, and Receptor proteins… …all float freely within the plane of the membrane  Eukaryotic Organelles Organelles have specialized functions and carry out the work of the cell Many form a coordinated endomembrane system (e.g., nuclear envelope, ER, Golgi apparatus, lysosomes, vacuoles, & cell membrane) “Connected” by vesicle transport System enables cells to produce, package, distribute and release complex mixtures of biochemicals  Eukaryotic Organelles Nucleus is the site of gene expression mRNA exits nuclear envelope through nuclear pores Nucleolus also provides ribosomes through pores System enables cells to produce, package, distribute and release complex mixtures of biochemicals  Eukaryotic Organelles Secreted proteins are synthesized at the rough endoplasmic reticulum (Soluble proteins in free ribosomes) Lipids are made in the smooth ER System enables cells to produce, package, distribute and release complex mixtures of biochemicals  Eukaryotic Organelles System enables cells to produce, package, distribute and release complex mixtures of biochemicals  Eukaryotic Organelles Proteins from the ER pass through the Golgi apparatus Complete folding and mature Enzymes in Golgi also add sugars to proteins/lipids Golgi sorts and packages materials System enables cells to produce, package, distribute and release complex mixtures of biochemicals  Eukaryotic Organelles System enables cells to produce, package, distribute and release complex mixtures of biochemicals  Eukaryotic Organelles Besides producing molecules, eukaryotic cells break them down in specialized membranous compartments Lysosomes, vacuoles, and peroxisomes are cellular digestion centers Lysosomes: contain break-down enzymes made in the RER and directed by the Golgi  Eukaryotic Organelles Besides producing molecules, eukaryotic cells break them down in specialized membranous compartments Lysosomes, vacuoles, and peroxisomes are cellular digestion centers Lysosomes: contain break-down enzymes made in the RER and directed by the Golgi Vacuoles: “lysosome” of the plant cell; also fills with water to apply turgor pressure to the cell wall and keep the plant cell rigid  Eukaryotic Organelles Besides producing molecules, eukaryotic cells break them down in specialized membranous compartments Lysosomes, vacuoles, and peroxisomes are cellular digestion centers Lysosomes: contain break-down enzymes made in the RER and directed by the Golgi Vacuoles: “lysosome” of the plant cell; also fills with water to apply turgor pressure to the cell wall and keep the plant cell rigid Peroxisomes: contain several types of enzymes to dispose of toxic substances; originate in ER (not Golgi) and contain different enzymes  Eukaryotic Organelles Some organelles are the site of energy transduction or production in a cell Photosynthesis occurs in chloroplasts in plant cells  Eukaryotic Organelles Some organelles are the site of energy transduction or production in a cell Photosynthesis occurs in chloroplasts in plant cells Double membrane system Mitochondria extract energy from nutrients gives tremendous surface area on which to conduct chemical reactions Like chloroplasts, mito- chondria have their own DNA Inherited maternally  supports Eukaryotic Cells Eukaryotic cells contain a cytoskeleton, an intricate network of protein “tracks” and tubules Actin fibers or micro- filaments provide strength for cells to survive stretching or compression Intermediate filaments function is a similar way and help some bind cells together Microtubules have many functions  Adhere & Communicate Plant cells have plasmodesmata: channels connecting adjacent cells for intercellular exchange of nutrients, etc.  Adhere & Communicate Animal cells may use an extracellular matrix to hold cells close to one another or junctions to connect cells Tight junctions fuse cells together (e.g., blood-brain barrier) Adhering junctions connect adjacent cells like “spot welds” by utilizing intermediate filaments Gap junctions act as protein channels that link the cytoplasm of adjacent cells; allows many cells to act in unison (like heart muscle)