Lecture 2 - Macromolecules, Cell Theory, Microscopy PDF

III. The molecules of life (see the “purple pages”) I. Course introduction II. What is biology / Life III. Molecules of life (from the “purple pages” in the text) IV. Cell theory V. Microscopy VI. Prokaryotes vs. eukaryotes VII.Cellular organization /organelles 1 The mo...

III. The molecules of life (see the “purple pages”) I. Course introduction II. What is biology / Life III. Molecules of life (from the “purple pages” in the text) IV. Cell theory V. Microscopy VI. Prokaryotes vs. eukaryotes VII.Cellular organization /organelles 1 The molecules of life (as we know it!) ▪ Water ▪ Macromolecules 2 Water ▪ H20 is the solvent of life ▪ Dissolves more molecules than any other solvent ▪ A polar molecule (i.e. opposite charges on either end) ▪ dissolves other polar molecules ▪ dissolves charged molecules 3 The molecules of life – macromolecules ▪ Carbohydrates ▪ Lipids ▪ Proteins ▪ Nucleic acids 4 The molecules of life – macromolecules ▪ Carbohydrates – polymers of sugars ▪ Lipids – not polymers ▪ Proteins – polymers of amino acids ▪ Nucleic acids – polymers of nucleotides 5 Polymers ▪ Chains composed of molecules called monomers ▪ Polymerize and depolymerize source 6 Polymerization/depolymerization reactions involve loss or addition of water. ▪ Therefore they can also be described as: dehydration synthesis (polymerization) hydrolysis (depolymerization) dehydration synthesis hydrolysis H2O H2O 7 source Polymerization/depolymerization reactions involve loss or addition of water. ▪ Addition or loss of water happens at the bonds between monomers Polymerization (dehydration synthesis) Depolymerization (hydrolysis) 8 Enzymes make/hydrolyze polymers ▪ Enzymes catalyze the synthesis / hydrolysis of polymers ▪ Polymerases ▪ Hydrolases ▪ *Nice trick: -ase = enzyme 9 Enzyme example: polymerization of DNA (a nucleic acid) by DNA polymerase More later in the course, just an example for now. 10 Most biopolymers are not just simple chains of monomers ▪ The chains usually twist and fold up 11 Most bio-polymers are not just straight chains of monomers ▪ The chains arrange into varied levels of higher-order structure ▪ Examples: DNA double helix protein folding example: a protein 12 Higher-order polymer structure example: proteins 1°structure - amino acid chain 2°structure – ex) α-helix, β-sheet 3°structure - folding 13 Higher-order polymer structure example: proteins 1°structure - amino acid chain 2°structure – ex) α-helix, β-sheet 3°structure - folding 4°structure – assembling with other proteins into a complex 14 Polymer example: proteins Q. What determines a protein’s structure? A. The properties and order of the amino acids. 15 Amino acids ▪ Contain Nitrogen, mildly acidic ▪ R = sidechain ▪ Sidechain properties define the chemistry of proteins N—C —C N—C —C N—C —C N—C —C R C C C (side C C C C chain) C C O O 16 Primary protein structure ▪ Amino acids are linked by covalent bonds called peptide bonds ▪ Proteins also known as polypeptides 17 Amino acid structure and properties ▪ Earthlings use 20 different AA’s R 18 Secondary protein structure ▪ Hydrogen bonds between nearby amino acids cause the polypeptide to twist (alpha helix) or form sheets (beta sheets) 19 Tertiary protein structure ▪ Chemistry between sidechains causes higher-order folding 20 Quaternary protein structure ▪ Individual proteins interact to form complexes ▪ Again, determined by their structure and chemistry 21 Fun fact slide: chains of glucose (a sugar) Small difference in glucose bonds creates huge differences in the properties of these carbohydrates 22 https://mysciencesquad.weebly.com/ib-hl-23a1--s1-cellulose--starch-v-glycogen.html IV. Cell theory I. Course introduction II. What is biology / Life III. Molecules of life IV. Cell theory V. Microscopy VI. Prokaryotes vs. eukaryotes VII.Cellular organization /organelles 23 Cell Theory 1. All organisms are composed of one or more cells. 2. The cell is the basic structural and functional unit of all living organisms. 3. Cells arise only from the division of pre-existing cells. 24 First observations of cells using microscopes – 1600’s ▪ Robert Hooke looked at cork cells ▪ Anton Van Leeuwenhoek made a better microscope and saw “many very little animacules, very prettily a-moving” cork (from the bark of cork oak tree) 25 Cellular scales 1000 µm = 1 mm ▪ Cells are generally pretty small human hair for reference (width ~150 µm = 0.15 mm) Typical mammalian somatic cell ~10 µm frog egg cell ~1000µm (1mm) human egg cell ~100 µm 26 Cell size scales and visibility ▪ unaided human eye ▪ light microscope ▪ electron microscope Why do cells tend to be so small? 27 Why cells tend to be small ▪ surface area must be sufficient to allow exchange of stuff between the cell and its surroundings ▪ Larger volumes require more surface area to achieve this ▪ Larger volumes need more structural support 28 Trade-off between cell surface area and volume ▪ The problem is that as volume increases, the surface area does not increase proportionately. volume surface area cell size 29 But what if the cell really requires a large surface area? microvilli on intestinal epithelial cells ▪ develop convoluted / branchy surface morphologies brain cells https://biolength.com/microvilli-and-rule-in-absorption/ leaf epidermal cells https://en.wikipedia.org/wiki/Neuron#/media/File:GFPneuron.png Dr. A, unpublished 30 What if the cell needs a large volume? ▪ Use cell walls ▪ example: xylem vessels from wood human hair for reference 31 V. Microscopy I. Course introduction II. What is biology / Life III. Molecules of life IV. Cell theory V. Microscopy VI. Prokaryotes vs. eukaryotes VII.Cellular organization /organelles 32 Resolution, magnification, and contrast ▪ Resolution - the ability of a microscope to distinguish two objects as being separate ▪ Higher magnification increases resolution ▪ Higher contrast gives more detail, but can’t increase resolution 33 Resolution, magnification, and contrast - illustrated low mag high mag low contrast high contrast 34 Microscopy types A. Light Microscopy 1) reflected light 2) transmitted light 3) fluorescence B. Electron Microscopy 1) transmission 2) scanning 35 Reflected light ▪ stereo microscope (a.k.a. dissecting microscope) ▪ lighting from top ▪ can see bigger size cells 36 Transmitted light ▪ Stereoscopes (some can also use light from bottom) ▪ compound microscopes 37 Variations on transmitted light compound ▪ brightfield (like the ones you use in lab) ▪ darkfield ▪ phase-contrast ▪ Differential Interference Contrast (DIC, a.k.a. Nomarski) contrast-enhancing methods Exploit the light-scattering (refractive) properties of specimens Variations in specimen thickness and density influence how light passes through it 38 Brightfield ▪ brightfield (like the ones you use in lab) ▪ staining often required to see more detail cross-section of a stem 39 Contrast enhancing methods - dark field ▪ Illuminates sample at an angle so light does not hit the objective lens directly ▪ Only light that is scattered upwards by the sample reaches the objective lens bright field dark field 40 Contrast enhancing methods – phase contrast ▪ This method creates slight phase shifts in the illuminating light, which manifest as higher detailed images bright field phase contrast 41 Contrast enhancing methods – DIC ▪ Similar concept to phase-contrast ▪ Gives a pseudo-3D appearance bright field DIC 42