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BIOL2146 Module 1:

10 CURRENT BIG IDEAS IN MOLECULAR LIFEMolecular evolution evolution of living organisms requires changes to DNA that produce heritable geneticvariation 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 toform 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 activationenergy of the reaction.Enzymes provide targets for kinetic control.

Energy and organisation biological systems maintain a steady state (homeostasis) at a position away fromequilibrium 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 requirescomplexity 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 molecularinteractions. 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 majordeterminant 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.

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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 things3. All cells come from pre-existing cells by division spontaneous generation does not occur4. Cells contain hereditary information passed from cell to cell during cell division5. All cells are basically the same in chemical composition6. 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.

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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, sperm1833 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

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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, sectionsand stained before viewing

1. Bright light focused onto specimen by lens incondenser2. Specimen prepared to allow light to pass3. 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 RNAmolecules (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 filters1. Filter specific wavelength2. Passes wavelength emitted when dye

fluoresces.

- Examine ribosomes (2o nanometers)

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- Intact tissue fixed and sectioned priormicroscopy

- 1-10 Tissue may be closely packed orseparated by extracellular matrix.

Dense material protein fibersembedded in polysaccharide

gel. 5 20 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.

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 ELECTRONMICROSCOPE: - Scatter electrons off surface

of samples- Examine surface details of

cell/structures

No microscope can visualize the individual atoms that make up biological moleculesX-ray crystallography used to determine precise 3D structure of protein molecules

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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

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Cytoskeleton:- Direct cell movements- System of protein filaments anchored to plasma membrane or adjacent to nucleus.- 3 types of filaments: -

ACTIN FILAMENTS: Abundant in all eukaryotic cellsEspecially in muscle cell musclecontraction

MICROTUBULES:Thickest filamentMinute hollow tubesPull duplicated chromosomes inopposite directions.

INTERMEDIATE FILAMENTS: Intermediate thickness betweenactin and microtubules.Strengthen cell

- When combined with protein form girders, ropes, motors mechanical strength, control shape,drive/guide movements

- In plant, animal, bacteria.

ORGANELLES:Nucleus Ribosomes Endoplasmic reticulumGolgi complex/apparatus Lysosomes VacuolesPeroxisomes Mitochondria ChloroplastCytoskeleton Extracellular matrix

- 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

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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