Biology Quick Notes PDF

Life September 4, 2024 3:46 PM 7 Characteristics Of Life Display order - Arranged highly ordered manner, cell being fundamental unit exhibits all properties of life Reproduce - All forms of life acquire energy from the environment, use it to maintain high...

Life September 4, 2024 3:46 PM 7 Characteristics Of Life Display order - Arranged highly ordered manner, cell being fundamental unit exhibits all properties of life Reproduce - All forms of life acquire energy from the environment, use it to maintain highly ordered state Utilize energy - All organisms have ability to make more of there own kind Respond to stimuli - All organisms can make adjustments to their structure, function and behaviour in response to changes to external environment Exhibit Homeostasis - All organisms are able to regulate internal environment such that conditions remain constant Grow and develop - All organisms increase there size or number of cells Evolve - Organisms change over course of generations to become better adapted to there environment Life Exhibits Emergent Properties emergent properties: characteristics or behaviors that arise from the interactions of simpler components within a system, which are not predictable from the properties of the individual components themselves. Individual atoms become increasingly organized into larger, more complex structures essentially on their own. atoms --> molecules --> cells --> tissues --> organs --> organisms --> ecosystems. Quick Notes Page 1 Cell Theory September 9, 2024 1:02 PM Cell Theory - All organisms are composed of one ore more cells - The cell is the basic structural and functional unit of all life - Cells only come from pre existing cells History 1600's Robert Hooke- Looked at cork cells through microscope 1600's Anton Van Leuwenhoek- made better microscope, saw many very little animalcules moving Cell Scales Mammalian Somatic cell=10 um Human egg cell=100um Frog egg cell=1000um Why so small? - Surface area must be sufficient to allow exchange of stuff between the cell and its surroundings - Large volume requires more surface area - Larger volume needs more structural support What if cell requires large surface area? - Develop convoluted/branchy surface morphologies What if cell needs large volume? - Use cell walls Quick Notes Page 2 Molecules Of Life September 9, 2024 1:02 PM Water: H20 is the solvent of life Dissolves more molecules than any other solvent A polar molecule Dissolves other polar molecules Dissolves other charged molecules Molecules Of Life Carbs: Polymers of sugars Lipids: Not polymers Proteins: polymers of amino acids Nucleic Acids: Polymers of nucleotides Polymers: - Chains composed of monomers - Polymerize (dehydration synthesis) and depolymerize (hydrolysis) Addition or loss of water between bonds What determines a proteins structure? The PROPERTIES and ORDER of the amino acids Amino Acids - Contains nitrogen - R=sidechain - Sidechain properties define chemistry of proteins - Linked by covalent bonds called peptide bonds - Proteins are also called polypeptides Quick Notes Page 3 Microscopy September 9, 2024 12:58 PM Microscopy 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 Types Light Microscopy: 1. reflected light See bigger sized cells Lighting from top Dissecting microscope 2. Transmitted light Stereoscope Compound microscopes 3. Fluorescence - Electron absorbs a photon gets higher energy state - Excited electron returns to ground state, releasing photon of LONGER wavelength Why use fluorescence in bio? - Intrinsic fluorescence from specimen - Fluorescent dyes - Fluorescent proteins - Allows visualization of specific structures - High resolution images in microscopy Confocal fluorescence microscopes: INCREASES contrast by capturing thinner image Electron Microscopy: - High resolution then light since electrons have much shorter wavelength then visible light - No colours seen since its not light - Requires dead specimens - Specimens are stained with heavy metals so electrons cannot pass through Two types: 1. Transmission Electron Microscopy (TEM) - Very thin sections are cut using microtome - Images appear as black and white - Light regions are wear the electrons pass through - Dark regions are wear electrons did not pass through 2. Scanning Electron Microscopy (SEM) - No sectioning needed, just coat sample with heavy metal (usually gold) - 3d contours of the surface are visualized by scanning an electron beam on specimen - Typically used at a much lower magnification then TEM Contrasting Enhancing Methods: Dark field: illuminates sample at angle so light does not hit objective lens directly Phase contrast - Illuminates light for higher detail Quick Notes Page 4  - Illuminates light for higher detail DIC - Similar to phase contrast, pseudo 3d appearance Quick Notes Page 5 Prokaryotes vs Eukaryotes September 9, 2024 1:03 PM Differences between the two Prokaryotes: Bacteria, Archaea - Uni cellular - Small - No membrane bound organelles - Nucleoid - Single circular chromosome Eukaryotes: Animals, Plants, Fungi, Protists - Uni or Multi cellular - Small to Large - Membrane bound organelles - Nucleus - Linear DNA in chromosomes DNA (deoxyribonucleic acid) >Transcription>RNA ( ribonucleic acid)>Translation>Protein Organization of DNA Prokaryote- DNA found in nucleoid, single circular chromosome Eukaryote- DNA housed in nucleus, one or more linear chromosomes Phospholipid bilayer: - Hydrophilic head - Hydrophobic tail Cytoplasm: - Consists of cytosol and organelles - Cytosol is an aqueous liquid ○ Mostly water ○ Full of macromolecules and smaller molecules ○ Metabolic activities ○ Signal transduction Ribosomes: - Highly organized machine consisting of proteins and rRNA - More of an enzyme than an organelle - Reads the sequence of mRNA's to coordinate their translation into proteins - Prokaryotic ribosomes are a bit smaller, but do same thing Cytoskeleton: - Filamentous polymers that participate in many processes such as: ○ Cell division ○ Cell shape ○ Intracellular transport - Prokaryotes have simpler, ancient version of eukaryotic cytoskeleton Quick Notes Page 6 Organelles/Cell Organization September 11, 2024 12:33 PM Nucleus: - Nuclear pores ○ Determines what goes in and out of nucleus - Nuclear envelope ○ Double membrane surrounding nucleus - Chromatin ○ DNA + associated proteins - Nucleolus ○ Site of ribosomal subunit - Nucleoplasm ○ "cytoplasm" of the nucleus Some cells, as they mature lose their nucleus, they are anucleate Some cells, Protista Endomembrane: - Nuclear envelope ○ Extension of the ER - Endoplasmic reticulum ○ Allows transfer of substances between the two ○ Rough ER- protein translation, folding and modification (studded with ribosomes, flattened cisternae) ○ Smooth ER- lipid synthesis, detoxification (no ribosomes, tubular cisternae) ○ ER lumen=inside the er - Golgi ○ Cisternae ○ Cis-face, trans-face ○ Receives vesicles from the ER and other locations ○ Adds the final "touch ups" to proteins (addition of small molecules like sugars and lipids) ○ Like a post office, sorts, labels, and packages items for delivery to different parts of the cells - Vesicles ○ Transport stuff between endomembrane compartments(synthesis, breakdown, storage, other metabolic activities) ○ Then fuse with membrane to release contents - Lysosomes ○ "Stomach of the cell", acidic, breaks things down ○ Its enzymes only function at acidic pH, so great example of compartmentalization ○ Hydrolyses both internal and external stuff ○ Not present in plant cells - Vacuoles ○ Present in plant and fungi ○ Storage of nutrients ○ Digest waste products ○ Turgor pressure of cell enlargement ○ Pigmentation - Plasma membrane ○ Surround cell ○ Control in and out Endocytosis- contents entering Quick Notes Page 7  Endocytosis- contents entering Ex. Covid-19 Exocytosis- contents leave Move from ER-> Golgi->Plasma membrane Ex. Neurotransmitters Compartmentalization of metabolic activities creates specialized conditions for specific processes, Ex. Lysosomes are acidic because their enzymes only work in acidic conditions Changing their membrane surface areas influences the degree of these metabolic activities Ex. Increasing amount of smooth ER for increased lipid synthesis The different endomembrane compartments are highly interdependent because they exchange contents Ex. Movement of proteins from ER to Golgi like an assembly line Semi-autonomous (do not send or receive vesicles) - Mitochondria ○ Sugars to ATP ○ Source of all Cellular Respiration ○ Has two membranes , inner one has folds called Cristae ○ Matrix is "cytoplasm" - Chloroplasts ○ CO2 to Sugars ○ Photosynthesis ○ Two boundary membranes + internal thylakoid membrane ○ Stroma is the "cytoplasm" ○ Photosynthesis reactions occur in thylakoids and stroma ○ Stacks of thylakoids are called grana - Both use electrochemical reactions to make energy - Both have internal membranes with extensive folding to increase surface area of the energy protection Cytoskeleton - Functions ○ Cell shape ○ Cell polarity ○ Cell division ○ Cell movement and migration ○ Intracellular transport and cytoplasmic organization - Filamentous protein polymers ○ Microtubules ▪ Cell shape and movement ▪ Cell division ▪ Polymers of tubulin ▪ Made of 13 protofilaments ▪ Have + and - ends, which gives them and inherent polarity ▪ Switch between growing (polymerization) and shortening (depolymerization) ▪ Most growth/shortening occurs at the + ends ○ Intermediate filaments ▪ Structure, support, adhesion ▪ Ex. Collagen, keratin, nuclear lamins ▪ Plants and fungi do not have intermediate filaments because they have cell wall ▪ Do not have polarity and dynamics like the microtubules, and microfilaments ▪ Can be both inside and outside of the cell ○ Microfilaments ▪ Cell shape and migration Quick Notes Page 8  ▪ Cell shape and migration ▪ Cell division (mostly during cytokinesis) ▪ Organelle movement and cytoplasmic streaming (in plants*) ▪ Components of contractile elements in muscle fibers ▪ Polymers of Actin ▪ Two protofilaments form a helix ▪ Also have + and - ends, which gives them inherent polarity ▪ Also grow by polymerization and shorten by depolymerization ▪ Also grow/shorten at the + ends - Movement of things/organization ○ Motor proteins ▪ Walk along cytoskeletal filaments carrying vesicles and other organelles ▪ Motor families □ Myosins □ Kinesins □ Dyneins ▪ Bind to filament on one end and cargo to other ▪ Energy for "walking" comes from ATP ▪ No motors for intermediate filaments ▪ No known motors in prokaryotes ○ Centrosomes ▪ Tether microtubules at their bases ▪ Creates cell polarity ▪ Found in □ Mitotic spindle, ends □ Base of cilia and flagella ▪ Consists of two centrioles surround by dense matrix of proteins ○ Cilia and Flagella ▪ Cilia- Short hairs, move fluids over cell, or move as little legs ▪ Flagella- Long whip like tail for movement ▪ Both surrounded by plasma membrane ▪ Both use same structural microtubules to bend ▪ Dyneins motors move in tubes inside of the flagellum/cilia, off and on in other sides of the tail to create the tails movement ▪ Prokaryotic flagellum- Totally different mechanism, rotating disc at base of tail Extra cellular matrix/Cell walls - Functions ○ Support ○ Adhesion ○ Protection ○ Gateway for in/out - Secreted from cells - Animals extra cellular matrix ○ Mostly proteins + glycoproteins(proteins with sugar attached) ○ Widely variable ○ Roles ▪ Adhesion ▪ Support ▪ Shape/migration ▪ Cell division ○ Lots of intermediate filaments such as collagens ○ Forms mass of skin, bones, tendons ○ Animal cell junctions ▪ Hold cells together Quick Notes Page 9  ▪ Hold cells together ▪ Allows selective intercellular movement of stuff ▪ Seals neighboring cells to prevent passage - Cells Walls - Plant, Fungi, Bacteria ○ Plants cell wall ▪ Made of mostly Cellulose ▪ Support cell shape ▪ Holds cell together ▪ Protection ▪ Intercellular communication ○ Fungi - mostly Chitin ○ Bacteria cell wall ▪ Mostly Peptidoglycans ▪ Coated with polysaccharides called a Capsule ▪ Capsule can also form a gooey "slime layer" to help in surface adhesion and biofilm formation ○ Turgor pressure ▪ Cells have pressure to keep their shape ▪ Bacteria=14psi ▪ Plants=145psi ▪ Fungi=1,450psi ○ Structure ▪ Pectin rich middle lamella joins adjacent cells ▪ Plasmodesmata allow intercellular transport and communication - Quick Notes Page 10 Membrane September 20, 2024 12:31 PM Structure and Composition - Plasma membrane: ○ Outer and inner leaflets differ in composition (lipids, proteins, carbs) ○ In other words, the cells outer surface is way different than the inner surface ○ Referred to as membrane asymmetry ○ Phospholipid bilayers ▪ Hydrophilic head (likes water) ▪ Hydrophobic tails (avoids water) □ Has a saturated fatty acid □ Has an unsaturated fatty acid □ Saturated tails = straight, Viscous Membrane fluidity - Lipid membranes are fluid - Factors influencing membrane fluidity (less fluidity = viscous) ○ Temperature ▪ Heat makes membranes more fluid, so don’t need as much enzyme hotter the cell ▪ Desaturase levels determined by measuring mRNA for desaturase ▪ Higher temp = more fluidity ○ Structure and composition of phospholipids ▪ Unsaturated tails = kinked (double bonds cause lipid tail to kink), more fluid ▪ Saturated = less fluidity ▪ Longer fatty acid tail = less fluidity ▪ Desaturase enzyme ○ Cholesterol levels ▪ Helps maintain proper membrane fluidity in response to temperature changes ▪ Cholesterol acts as a "fluidity buffer" - Why fluid? ○ Proper function ○ Adaptability ○ Homeostasis ○ Examples ▪ During exocytosis, after vesical membrane is incorporated into plasma membrane, things need to spread out since that membrane region is different composition ▪ During cell division, needs to be flexible and able to be remodelled Membrane Proteins - Functions ○ Transporters ○ Enzymes ○ Signal transduction ○ Cell surface attachment/recognition - Locations ○ Integral membrane proteins ○ Peripheral proteins - Can be identified based on their amino acid sequences ○ Stretches of non-polar amino acids indicate transmembrane domains ○ Non-polar = hydrophobic, like the inside of the membrane bilayer Movement across membrane - Very important to be able to control who comes in and out of the cell - Passive transport- NO energy required, with concentration gradient=easy, no energy Imbalance->equilibrium, moves water ○ Diffusion ▪ Things move from HIGH -->LOW concentration, with the concentration gradient, it naturally wants to flow that way so it does not require energy ○ Facilitated diffusion ▪ Membrane proteins form channels to facilitate diffusion of stuff across the membrane ▪ Channel proteins ▪ Gated channel proteins ▪ Carrier proteins - Active transport- Energy IS REQUIRED, against concentration gradient=hard, requires energy/ATP Equilibrium->Imbalance, moves molecules ○ Primary ▪ Uses ATP, to move molecules from equilibrium to imbalance ▪ Why would you want imbalance though? □ When more molecules are inside, it is stored energy, can be used for later Quick Notes Page 11  □ When more molecules are inside, it is stored energy, can be used for later ▪ Example □ Sodium-Potassium pump (example) Moves sodium ions (Na+) out of cell Moves potassium ions (K-) into the cell Uses ATP to do this Both ions are moved against there gradient so it requires energy ○ Secondary ▪ Uses electrochemical gradients ▪ Symport - transported molecule x driving ion same direction ▪ Antiport - transported ion x driving ion opposite direction ▪ Example □ Sodium-glucose cotransporter Moves sodium ions (Na+) into cell, down its concentration gradient Energy released from this, moves glucose into the cell, against its concentration gradient This is how your body gets glucose into the cell ○ Things move against there concentration gradient so it requires energy - Exo/Endocytosis ○ Endocytosis 1. Receptor - mediated □ Receptors link to specific molecules and then swallow it in 2. Bulk - phase □ Water molecules and solute molecules get swallowed 3. Phagocytosis □ Organisms just eats a vesicle/cell ○ Signal transduction ▪ Signal molecules binds to receptor ▪ Transduction occurs □ Signal is changed into form for eliciting the cellular response □ Typically involves a signalling cascade, a sequence of reactions t ○ Transduction by phosphorylation ▪ Kinase - an enzyme that phosphorylates other proteins things using ATP ▪ Protein Quick Notes Page 12 Osmosis September 25, 2024 12:43 PM Hypo=less Hyper=more Iso=same Passive transport: with concentration gradient=easy, no energy Imbalance->equilibrium Active transport: against concentration gradient=hard, requires energy/ATP Equilibrium->Imbalance Quick Notes Page 13 Cell Cycle October 2, 2024 12:31 PM Eukaryotic cell cycle: - Grow, replicate DNA, divide, repeat - Interphase ○ G1 - cell grows and prepares for S phase ○ S - synthesis of DNA. DNA is replicated to make a complete copy ○ G2 - cell grows and prepares for mitosis - Chromosomes replication ○ Replication of eukaryotic chromosomes creates two sister chromatids ○ Sister chromatids are held together by centromeres ○ Haploid vs Diploid Prokaryotic cell cycle: - Divide by binary fission - Single circular chromosome is pulled apart during replication - During cytokinesis, membrane constricts and new cell wall is formed between daughters - Very fast Quick Notes Page 14 Mitosis October 2, 2024 12:55 PM 1. Interphase ○ G1 - cell grows and prepares for S phase ○ S - synthesis of DNA. DNA is replicated to make a complete copy ○ G2 - cell grows and prepares for mitosis 2. Prophase ○ Chromosomes condense and become visible ○ Nuclear envelope begins to break down ○ Spindle starts to form 3. Prometaphase ○ Nuclear envelope breaks down ○ Chromosomes attach to microtubules and moved to midzone 4. Metaphase ○ Chromosomes attached to microtubules and align at the metaphase plate 5. Anaphase ○ Sister chromatids separate/pulled apart and move to opposite poles of the cell 6. Telophase ○ Chromosomes decondense ○ Nuclear envelope reforms around daughter nuclei ○ Spindle fibers disappear 7. Cytokinesis ○ The division of the cytoplasm, typically begins during late anaphase or telophase, resulting in two daughter cells Animal vs Plants Mitosis - Spindles ○ Plants have microtubules ○ Animals have spindles - Cytokinesis ○ Plants split by a cell plate ○ Animals a microfilaments contract to create a cleavage furrow Quick Notes Page 15 Meiosis October 4, 2024 12:51 PM Purpose: to create genetic variation Result: 4 genetically unique haploid gametes - Prophase DNA has condensed, nuclear envelope begins breakdown, centrosomes (animals) duplicated and migrating to poles - Prometaphase: nuclear envelope gone, MTs “search and capture” chromosomal kinetochores, move them toward spindle midzone, centrosomes migrating to create two poles - Metaphase: chromosomes are attached to MTs, aligned at metaphase plate, spindle is bipolar - Anaphase: chromosomes separate, pulled toward poles (as kinetochore fibers shorten), spindle elongates (as non-kinetochore MTs slide apart) - Telophase: nuclear division (karyokinesis) is complete, the spindle disassembles, chromosomes decondense, nuclear envelope reforms in each daughter cell - Cytokinesis: overlaps with telophase/late anaphase, ends when daughter cells completely separated (each having their own plasma membrane and cytoplasm) Genetic crossover - Crossover between homologous chromosomes lead to regions being swapped - Crossover sites are called CHIASMATA/CHIASMA - Synapsis = homologs pair up during meiosis - Held together by synaptonemal complex Meiosis Stages Overview Interphase 1 Prophase 1 Metaphase 1 Anaphase 1 Telophase 1 Prophase 2 Metaphase 2 Anaphase 2 Telophase 2 Quick Notes Page 16