BIOL2146 Module 1: 10 CURRENT BIG IDEAS IN MOLECULAR LIFE

Molecular evolution evolution of living organisms requires changes to DNA that produce heritable genetic variation and diverse phenotypes. Essential molecular structures and cellular processes are conserved through evolution. Self assembly biological systems self-assembly: process in which molecules spontaneously fold and aggregate to form ordered structures. Aggregation often involves non-covalent interactions between molecules with complementary surfaces. Compartmentalisation fluid membranes define the systems (cells and organelles) that make life possible. They allow molecules and functions to be compartmentalised and regulated. Information and communication - a distinguishing property of living systems is the ability to collect and transmit, interpret and respond, store and replicate information. Regulation - biological systems are dynamic. Complex networks of processes regulated behave coherently and achieve physiological goals efficiently. Catalysis most biological reactions require catalysis by enzymes to increase rates by reducing the activation energy of the reaction. Enzymes provide targets for kinetic control. Energy and organisation biological systems maintain a steady state (homeostasis) at a position away from equilibrium by the import of energy (i.e. they obey the second law of thermodynamics). Complexity of molecular structure biological systems are functionally complex and diverse. This requires complexity in the structures of biological macromolecules, An input of energy is needed for their synthesis from simple starting materials. Complementarity of molecular structures - cellular processes require a high degree of specificity of molecular interactions. This is achieved through selective binding of complementary surfaces. The aqueous environment of the cell the unique behaviour of water as a liquid and a solvent is a major determinant of structure and function in living systems.

FUNDAMENTAL UNIT OF ALL LIFE: Unicellular: consisting of a single cell Protozoans: certain algae and spores. Multicellular: having or consisting of many cells Prokaryote: single-celled organisms without a distinct nucleus or specialized organelles. Eukaryote: organism consisting of cells/s in which genetic material (DNA chromosomes) is contained within a distinct nucleus. Excludes eubacteria and archaebacteria. Derived from single ancestor.

3 main branches/domains: Bacteria Archaea Eukaryotes

CELL THEORY: Theodor Schwann and Matthias Schleiden. Cells building blocks of living tissue Postulates: All living organisms are composed of one or more nucleated cells Cells are the minimum functional units of living organisms Cells arise only from pre-existing cells by a process of division. All living cells arise from pre-existing cells August Weissman 1880: that cells living today can trace their ancestry back to ancient times Therefore, there must be a common ancestral cell. MODERN TENENTS OF CELL THEORY: 1. All known living things are made up of cells. 2. Tell is structural and functional unit of all living things 3. All cells come from pre-existing cells by division spontaneous generation does not occur 4. Cells contain hereditary information passed from cell to cell during cell division 5. All cells are basically the same in chemical composition 6. All energy flow (metabolism and biochemistry) of life occurs within cells Most cells between 1 and 100 m in diameter Bacteria: 1 - 10 m Eukaryotic cells: 10 -100 m Vary in size and shape As size increase volume grows proportionally more than surface area.

MICROSCOPES:
Light microscopes: examine cells and components Electron microscope: fine structure.

1665 - Robert Hooke: Home-made light microscope. Thin slice of cork, honeycomb compartments First to use term cell Late 1670s Anton van Leeuwenhoek: Dutch amateur microscopist. Described bacteria. Protozoa, blood, sperm 1833 Robert Brown: Microscopic structure of reproductive organs of plants Nucleus a constant feature Nuclei fundamental unit of all living organisms. 1839 Theodor Schwann: German biologist Animal cell resemble cellular tissue of plants Amphibian cartilage Cellular nature of animal tissue STUDY CELL: Light microscopy depends on: Magnification and resolution Magnification: ratio of the size of the image and size of object Resolution: ability to distinguish detail. Ability to distinguish detail resolving power (RP) depends on: Wavelength of light () of light to illuminate Numerical aperture (NA): how much light enters. Higher NA greater resolution and brightness

Ability to see fine detail Minimum distance distinguish 2 points separately Cells closely packed and separated by extracellular matrix. Scanning power: 4x Low power: 10x High power: 40x Oil immersion: 100x

LIGHT MICROSCOPE: Wavelength: 400-740nm Structure less than of a wavelength long not visible Resolve objects down to 200nm Resolving power depends on wavelength of light and lens quality Maximum magnification: 2000x Enhancing contrast Most organelles too small to be observed. Fixed/preserved, embedded, sections and stained before viewing

1. Bright light focused onto specimen by lens in condenser 2. Specimen prepared to allow light to pass 3. Appropriate lens used (objective and eyepiece)

CONFOCAL FLUORESCENT MICRSCOPY: 3D Lasers focus through pinholes then to specimen Emitted light focused on second pinhole Light from unclear area largely excluded Laser scan throughout image, building 3D image Fluorescent labeled cell components Able to view large macromolecular complex: 80-90 proteins and RNA molecules (ribosomes)

FLUORESENCE MICROSCOPY See fluorescently labeled cell components in finer detail. Optical set-up of fluorescence microscope Particular wavelength illuminate specimen Allow light of only certain wavelength to pass through objective lens. 2 sets of filters 1. Filter specific wavelength 2. Passes wavelength emitted when dye fluoresces. - Examine ribosomes (2o nanometers)

Intact tissue fixed and sectioned prior microscopy 1-10 Tissue may be closely packed or separated by extracellular matrix. Dense material protein fibers embedded in polysaccharide gel. 520 m in diameter

ELECTRON MICROSCOPE (EM) Highest magnification and best resolution Beam of electron through/on specimen -

Wavelength 0.1-0.2 nm 10000x resolving power 0.2 nm resolution Make larger molecules visible individually Unable to look at living, wet cells. No microscope can visualize the individual atoms that make up biological molecules X-ray crystallography used to determine precise 3D structure of protein molecules

TRANSMISSION ELECTRON MICROSCOPE: Specialize in thin sections of tissue Sections must be cut thinner Must be fixed, embedded, sectioned, stained. Fixed: preserved by pickling in reactive chemical solution Embedded: in solid wax/resin Contrast introduced by staining with electron-dense heavy metals absorb or scatter electrons

SCANNING ELECTRON MICROSCOPE: Scatter electrons off surface of samples Examine surface details of cell/structures

PROKARYOTIC CELL:
Most diverse and numerous cells on Earth Join to form clusters, chains, organized multicellular structures Bacterium and prokaryote used interchangeably. Divided into 2 domains: Eubacteria Archaea Pro: before, Karyon: kernel Relatively simple bacteria Aerobic: using oxygen to oxidize food molecules Anaerobic: killed by slightest exposure to oxygen. DNA genetic in region in nucleoid No membrane separates DNA from cell Metabolically diverse Plasma membrane-bound cytoplasm 3 basic cell shapes Cocci: spherical Bacilli: rod-shaped Spirochaetes: spirally twisted Prokaryote cell walls: External to plasma membrane Peptidoglycan: substance forming cell walls of many bacteria Carbohydrate matrix peptide cross linked Tough, protective coat/cell wall surrounding plasma membrane Prokaryotes DO NOT have membrane enclosed nucleus Prokaryotes DO NOT have internal membrane system Can duplicate within 20 minutes Any organic, carbon-containing material can be used as food by prokaryotes Can live off inorganic substances - CO2, N2

EUKARYOTIC CELLS:
Single-celled: amoebae and yeast Multicellular. Plants, animals and fungi Much larger than prokaryotic cells. Theory: predator that fed by capturing other cells.

Organelles: internal compartmentalization of function May have originated as predators Flexible cell membranes allows phagocytosis Extensive internal membranes Sexual reproduction Nucleus: information stored in cell Genes (DNA + chromosomes): 1000x more than prokaryotes Enclosed within 2 concentric membranes (nuclear envelope) Mitochondria: generate usable energy from food to power cell Enclosed in 2 separate membranes inner membrane form folds Generators of chemical energy Harness energy from oxidation of food molecules sugar adenosine triphosphate (ATP) ATP: basic chemical fuel for cell activity Consume oxygen and release carbon dioxide

Cellular respiration: breathing on cellular level consume oxygen and release carbon dioxide Originated from bacteria that were engulfed by ancestral pre-eukaryotic cell. Symbiotic relationship help one another survive and reproduce. Contain own DNA reproduce by dividing.

Chloroplast: capture energy from sunlight Large, green organelles Only in plants and fungi More complex than mitochondria Internal stacks of membranes contain chlorophyll. Photosynthesis trap energy from sun in chlorophyll molecules release oxygen (molecular by-product) and produce ATP. Oxidize sugars in mitochondria Energy directly from sunlight Contain own DNA; reproduce dividing in 2, evolved from bacteria photosynthetic bacteria engulfed by early eukaryotic cell. Internal membranes: Inner intracellular compartments with different functions Involve cells ability to import raw materials and export substances and waste products. Cytosol: Concentrated aqueous gel of large and small molecules Part of cytoplasm not contained within intracellular membranes. Not including nucleus Large, small molecules water-based gel texture. Site of chemical reactions fundamental to cells existence. Breakdown of nutrients Cytoplasm: Very motile (protoplasm within cell excluding nucleus) constant movement Motor proteins: move organelles and protein throughout cytoplasm Endoplasmic reticulum (ER): irregular maze of interconnected spaces enclosed by membrane Site where most cell-membrane components (materials for export) made. Specialize in secretion of proteins. Golgi apparatus/complex: Modifies and packages molecules made in the ER Transported to another cell compartment or excreted. Lysosomes: Small, irregular Intracellular digestion occurs. Release nutrients from ingested food particles Break down unwanted molecules Recycle or excrete Peroxisomes: Small, membrane-enclosed vesicles Safe environment for reactions Hydrogen peroxide used to inactivate toxic molecules

Cytoskeleton: Direct cell movements System of protein filaments anchored to plasma membrane or adjacent to nucleus. 3 types of filaments: ACTIN FILAMENTS: MICROTUBULES: INTERMEDIATE FILAMENTS: Abundant in all eukaryotic cells Thickest filament Intermediate thickness between Especially in muscle cell muscle Minute hollow tubes actin and microtubules. contraction Pull duplicated chromosomes in Strengthen cell opposite directions. When combined with protein form girders, ropes, motors mechanical strength, control shape, drive/guide movements In plant, animal, bacteria. ORGANELLES: Nucleus Golgi complex/apparatus Peroxisomes Cytoskeleton -

Ribosomes Lysosomes Mitochondria Extracellular matrix

Endoplasmic reticulum Vacuoles Chloroplast

Chromosomes visible prior to cell division Lysosomes: digestion and recycling Peroxisomes: specialized reactions Vesicles: transport

Essential Cell Biology: GENES Genetic information (genes) carried in DNA molecules Information written in same chemical code same building blocks Genetic information replicated when organism reproduces DNA polymer chain made from same set of 4 monomers nucleotides Transcribed to RNA. Translated to polymer protein. DNA to RNA to protein central dogma. Appearance and behaviour of cell dictated largely by protein molecule: Structural support

Chemical catalyst Molecular motorsetc. Proteins built from amino acid Linked in different sequence different 3D shape (conformation) Cell reproduce and divide daughter cell Instructions corrupted by mutations that change DNA Mutations in offspring: Less able to survive and reproduce - eliminates Better able to survive and reproduce - favors Genetically different but equally viable tolerates Pattern of descent complicated by sexual reproduction 2 cells of same species fuse Evolution: the process by which living species become gradually modified and adapted to their environment in more sophisticated ways. Inherit genetic instruction from same common ancestor. Genome: The total genetic information carried by all the chromosomes of a cell or organism. Entire sequence of nucleotides in an organisms DNA. Provide genetic program that instructs cell behaviour. Direct growth and development Differentiated cell types generated during embryonic development from single fertilized egg cell. Activity depend on environment and history