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Bio 1000 Midterm notes.docx

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York University
BIOL 1000
Nicole Nivillac

Lecture 1 - Slide 1 o What things are needed in life to exist  Sunlight  Water  Food  Oxygen/Nitrogen - Slide 2 o What is light  Visible portion of the electromagnetic spectrum  It is described as a wave  Short Wave = high energy (blue)  Longer wave = lower energy (Red)  Photons are bundles of electromagnetic energy particles  Weightless  Rods/Cons cannot see 380 & 750nm.  C Reignhardtii  Uses light for energy and information  Eukaryotes have a sensor called eyespot o Gives the ability to sense light direction and intensity - Slide 3 o How does light interact with matter  Reflected off the object (color shown is the color reflected, not absorbed)  Transmitted through objects (Through chloroplast)  Absorbed by the object (Need to absorb to use energy)  Pigments absorb light  Most biologically relevant/useful - Slide 4 o Pigments  Determines what colour can be absorbed  Photons must be absorbed, and molecule that absorbs this is a pigment  Light energy must be absorbed by pigments for it to be used  All have a conjugated system  Alternating double/single bond o Delocalization of electrons allows pigments to absorb waves - Slide 5 o Light and Life  Photosynthesizing organisms can be any colour based on the pigment  Photoreceptors are pigment molecules bounded to a protein  When light is absorbed, the photoreceptor changes its shape o This change causes a change in the cell o Causes a series of events happening in the cell  Chlorophyll  Has 2 states o Before absorption electron is at 0 o After absorbing red light, it reaches state 1 o After absorbing blue light, it reaches state 2 (More energy absorbed)  1 photon = excitation of 1 electron o Action spectrum shows the plot of effectiveness of different wavelength - Slide 6 o Plants and light  Plants have phytochrome  Rhydopsin is made from opsin  Absorption of light causes retinal to change its shape  It is activated in the light  The eyespot indicates the light - Slide 7 o Phototaxis  When an organism moves in response to the light  Positive Phototaxis (They move towards the light)  Negative Phototaxis (They move away from the light) o Example of negative Phototaxis is Dugesia  Occurs when a signalling molecule activates a cell surface receptor o 2 stages  Molecules activates receptor in cell membrane nd  2 messenger transmits signal into cell resulting in movement  Phytocrine o Important for photomorphogenesis (activation of gene when exposed to light) o Located at the cystol of the cell - Slide 8 o The eye  Senses light and is important for vision  Simple eye  Ocellus o Has 100 photoreceptors o Covered by pigment cells on one side, which blocks light from opposite side  Compound Eye  Omniatidium o Each Omniatidium gets a piece of the image, creating a full mosaic image o Each has a lens (Cornea/Eye facet)  Crystalline Curve (Focuses light on the cell)  Light blocking pigment  Separates the Omniatidium  Single lens eyes o Enters through cornea  Goes to photoreceptors to pick up the light  The light is translated and image is created  The curvature of the eye allows for a better focus  The outer layer protects the eye  Examples of different eyes  Eyespot (Snail)  Eye cup (Dugesia)  Pinhole eye (Nautilus)  Primitive Lens (Box jellyfish) - Slide 9 o Blind spot  There is a portion in the back of the retina that doesn’t have photo receptors  It is also called the optic nerve  Suboptimal feature - Slide 10 o Light and circadian Rhythms  The circadian rhythm is controlled by the internal biological clock  Endogenous clock  The biological clock responds to light and darkness  It enables organisms to anticipate changes to their light environment  The suprachiasmatic nucleus of the brain receives light inputs from the eye through the optic nerve  Nucleus is located in the hypothalamus  This light at the optic nerve is used to set the biological clock  Do not respond to change in light environment  Melatonin has a role in controlling out sleep cycle  Melatonin production occurs during the night  Inhibited during the day - Slide 11 o Organisms that are functionally blind  Photoreceptors are still present  The photoreceptors sense the light direction and intensity  Melatonin stays at a constant rate if photoreceptors cannot indicate light - Slide 12 o Camouflage  Works when an animal fails to distinguish another from the background  Survival trait to avoid predators  Peppered moth  The more distinguishable moth was the easier pray  Natural selection can occur when all the distinguishable moths are killed  All attributable to perception  Pattern and behaviour play a role in camouflage - Slide 13 o Using colours as signals  Scent/Sound/Colour are other means of signalling  Many use colors to hide/attract/warn  The signal must be received for it to work. - Slide 14 o Flower colour and pollination  Relationship between plants and animal pollinators  Co-Evolution o Simultaneous evolution 2 or more populations that interact o Each is a strong selective force to the other  Pollination involves the movement of pollen from the anther to the stigma o Anther for males o Stigma for females  Characteristics of flower make them more attractive to specific pollinators - Slide 15 o Light in aquatic habitats  Long wavelengths are created  Below 30m = blue wavelengths  Below 150m = absence of light  Fish in deep water have darker bodies  Fish in shallow water are brighter  Water absorbs wavelengths more effectively - Slide 16 o Bioluminescence  Use of chemical energy to make light  Used to attract a mate/camouflage/attract prey/communicate  Chemical energy as ATP excites an electron, and when the electron returns to the ground state, it omits energy as a photon of light  Common in organisms that re found in the deep oceans  Organisms that use Bioluminescence must have light sensing organs - Slide 17 o Dark side of light  Light can damage molecules  Can cause a dimer (mutation in the proteins – 2 nucleotides become covalently linked) o Change in the DNA o Prevents replication o Damages gene expression  Plants are vulnerable to the mutation  But they have repair mechanisms to prevent the mutations - Slide 18 o Melanin  Pigment that absorbs UV Wave radiation  At 350nm, there is a stronger energy for the melanin to absorb  People in constant sun have more melanin to protect them  Albino people are those without melanin - Slide 19 o Vitamin D  Sun gives off UV rays that is absorbed to produce Vitamin D  It helps with Calcium uptake  Rickets occurs due to a low amount of Vitamin D  High melanin = Low vitamin D  Animals in the dark can make Vitamin D - Slide 20 o Light Pollution  Fluorescent light can increase blood pressure  Slight light presence can disrupt melatonin production during your sleep Lecture 2 – Evolution/Selection/Species - Slide 1 o Levels of ecological Scale  Biosphere (sum of ecosystem)  ecosystem (Community of living organisms and non-living things)  Communities (combination of 2 or more different populations in the same geographical area)  Population (all organisms in the same group that can interbreed in the same geographical area  Organism (Capable of reducing/growing/developing/respond to stimuli) - Slide 2 o Biodiversity  The degree of variations of life forms  Greater the biodiversity, the healthier the climate  One organism can live but rest dying is unhealthy  Difficult to know number of small species  Numbers of larger things allow for better estimation because they are visible  Incorrect biodiversity counts occur due to perception  The organism can also camouflage making it hard - Slide 3 o Species  Group of organisms that can interbreed/produce offspring’s  Have DNA similarities with others - Slide 4 o Modes of nutrition  Heterotrophs (Carbon by consuming other organisms)  Autotrophs (Synthesize carbon by using CO 2  Photoautotrophs (use light for photosynthesis)  Chemoautotrophs (Get energy from oxidation of molecules)  Photoheterotrophs (Light and organic molecules as energy)  Autotrophs obtain energy by oxidizing inorganic substances  Phototrophs obtain energy from light  Bacteria have great biodiversity - Slide 5 o Philogenic tree  The closest the link between the 2 species, the more commonly related they are  Shows the common ancestor between 2 species - Slide 6 o E. Coli  Present in cold/hot climates  Has DNA present in the nucleoid and plasmid  The nucleoid is the differentiating factor  Prokaryotic cells  Reproduce through binary fission - Slide 7 o Archaea  Single celled  Have introns & exons  Found in extreme areas  Similar to prokaryotes  Has no organelles o Eukarya  Reproduces sexually  Numerous amount of cells - Slide 8 o Unity and diversity of Life  There are commonalities in different organisms  This is an indication of evolution - Slide 9 o Concepts of biology  2 concepts  Cell Theory  Theory of Evolution - Slide 10 o Hypothesis in Science  A hypothesis is specific to the question  Can be testable/foldable  Turn the data you receive into a hypothesis  Match a prediction to the hypothesis  Test the hypothesis  Needs to be able to reproduce the same data - Slide 11 o Theory  Has to be accepted as a true phenomena  Has evidence backing it up  Aids in creating other hypotheses - Slide 12 o Theory of Evolution by Natural Selection  Characteristics of population change over time (pattern)  Individuals with heritable traits produce more offspring’s that those without the traits (mechanism) - Slide 13 o Selection  Force or phenomenon that affects the survival/reproduction of organisms  The one that can escape can pass on their trait  Have to survive to pass on the trait  Key factors are selective force (Pressure/Lethal force) and capacity for growth o Artificial Selection  Select an heritable trait and breed them based on the trait - Slide 14 o Resistant Variety  It can occur when you take antibiotics  When it becomes resistant, the bacteria will multiply and the new bacteria becomes resistant  Leading to a possible population being resistant - Slide 15 o Evolution  Change in the heritable traits overtime  Important in our lives through multiple ways  Evidence based and must be accepted  Observable and testable  Rates are used in labs because they have similar features to humans - Slide 16 o Theory of Evolution  Variation in heritable traits needs to be present  Competition needs to occurs for resources  Organisms need to produce offspring’s to pass on traits  Organisms with beneficial traits will survive  Resources need to remain constant - Slide 17 o Anoxygenic  Photosynthesis without oxygen  Provides sulfur  Oxygenic  Photosynthetic bacteria is present and O2is produced - Slide 18 o Cell Theory  All organisms are made up of cells (Pattern)  Come from pre-existing calls (Mechanism)  Cells is the smallest property of life  If a cell is broken, the property is gone  Eggs is the largest/expensive cell - Slide 19 o Prokaryotes/Eukaryotes  Prokaryotes lack a nucleus  Found in bacteria.  Plasma membrane separates outside from cytoplasm o Contains cytosol (Protein to form electron transport chain)  DNA is found in the nucleoid  Shapes  Cocci, Bacilli, Spirilla, Square  O2methods  Aerobic respiration (Other method includes fermentation) o If O2is not enough, the pyruvate stays in the cytosol after glycolysis o Energy is extracted from food molecules (O2is final electron acceptor)  Lactate fermentation (Pyruvate to lactate, in muscle cells)  Alcohol fermentation (Pyruvate is oxidize to make C2 and ethyl as NADH to convert to NAD +  Both have  DNA  Transcription/Translation machinery  Electron transport chain o cyanobacteria  Cyanobacteria is the first to produce2O by photosynthesis  First to produce CO2and release O2  Oxidizes water  releases electrons & protons  getting O 2 - Slide 20 o DNA/RNA  DNA  has a double stranded/helix appearance  DNA is copies onto molecules of RNA  RNA  is composed from nucleotide bases  RNA directs production of protein molecule  Has uracil instead of thymine  tRNA transcribes the RNA into proteins - Slide 21 o Nucleotides  Composed of nitrogenous base  Pentose sugar  Phosphate group  5’ and 3’ ends  Determines how they will attach together  Bases added at the 3’ end - Slide 22 o Linking nucleotides  Done through phosphodiaster bonds  Sugar phosphate outside  Nitrogenous phosphate inside - Slide 23 o Anti-Parallel Arrangement  Opposites are needed to facilitate replication  Complementary base pairing  Adenine-Thymine (Double bond)  Guanine-Cytosine (Triple bond) - Slide 24 o Information flow  Cells require development of a system to store information/protein  Pathway (DNARNAProtein)  Goes to mRNA then transcribes into proteins - Slide 25 o Protein Structure  Primary (Straight sequence)  Secondary (Folding) – bonds are formed between amino acids  Tertiary (Long range folding) – more bonds are created  Qautenary (Different protein associate)  Drugs attack tertiary/Qautenary - Slide 25 o Oxidation-reduction reactions (Redox)  Chemical reactions where electrons are transferred  Metabolism allows a cell to extract energy and use it to their benefit  Either to grow, reproduce or for maintenance  Redox reactions need to be reduced and oxygized  Oxidation is losing electrons  Reduction is gaining electrons  - Slide 26 o Energy-Harnessing pathways  ATP links energy-releasing reactions to those that require energy  Generated by chemiosmosis  Electrons pass from an electron donor through a chain  ATP is entered in the cells as organic molecule  Hydrolyzed to ADP and inorganic phosphate  Eventually ATP becomes the primary substance connecting energy-releasing and energy requiring reactions in early cells - Slide 27 o Cell membrane  Lipid bilayer  Protects the cell/acts as a barrier for things to enter/leave - Slide 28 o Diversity of prokaryotes  Greatest metabolic diversity is prokaryotes  Simple in structure  Has non-membrane nucleus  Have cell wall  Made up of peptidoglycan o Give cell strength  Cytosol is the same as all cells Lecture 3 – Cells - Slide 1 o Prokaryotic Peptidoglycan characteristics  Gram Dye is used to distinguish characteristics  Gram-Positive o The prokaryote holds onto the dye o Is a single think, purple coloured peptidoglycan layer  Gram-Negative o Thin Peptidoglycan layer o Surrounded by the outer membrane o Magenta o Less sensitive to penicillin - Slide 2 o Capsule  Polysaccharide layer  Protects bacteria from extreme temperature/antibiotics/viruses - Slide 3 o Flagellum  Made up of series of protein  Hair like projections that Helps move the bacteria forwards  Move like a boat propeller in prokaryotes  Move like a whip in Eukaryotes - Slide 4 o Pilli  Look like hair coming out  Used for adherence (Cell connector)  Extend from cell wall outwards  Involved in the transfer of genetic material - Slide 5 o Bacterial Chromosome  Circular (No start/finish)  DNA packed into nucleoid of cell  Helps with transcription/translation  Plasmids also replicate independently  Not part of the DNA  Extra pieces the bacteria can acquire  Give them an added feature o Possible resistance to antibiotics  Chromosome is double stranded  Proteins help package the chromosome - Slide 6 o Prokaryotic Reproduction  Asexual reproduction results in rapid population growth  Binary Fission o Produces the exact copy of the parent o Makes it easy for the bacteria to grow  Rolling Circle replication o One of the strands are cut and transferred o This is done through villi o Each has a copy of the DNA o Exotoxins  Bacteria can produce exotoxins (Toxic proteins)  Can cause muscle paralysis  Endotoxins are part of gram-negative - Slide 7 o Archaea  Similar structure with eukaryotes  Have peptidoglycan walls (Cannot use gram staining)  Membrane has an ether linkage  Lipids are more resistant to disruption  They are extremophiles  rRNA is used to differentiate the 3 different branches - Slide 8 o Euryarchaeota  Found in extreme environments  Methanogens o Methane generators o Low o 2nvironments o 50% of all Archaea 2 o Use CO 2nd H to create methane  Halophiles o Salty environments o Need a minimum of 9% salt and max of 32% o Light is their energy source st o Oxidation is 1 source  Extreme thermophiles (75-90) o Extreme hot environments  Psychrophiles (-10 - -20) o Cold environments  Mesophiles o Cold/Marine environments o Orienarchaeota  Include extremophiles  Psychrophiles (-10 to -20)  Mesophilic (plankton)  Found in cheese, yogurt, beer, wine o Korarchaeota  Recognized in DNA samples  Hydrothermal environments  Oldest Archaeal linage - Slide 9 o Archaea  Peptidoglycan cell wall  Flagella is present but has a different structure o Organization of Archaea  DNA Packaging with histone proteins  Plasmids may be present - Slide 10 o Eukaryotic cells  Membrane bound nucleus  Liquid inside is cytosol  Liquid and organelle is cytoplasm  Plant has chloroplast/cell wall - Slide 11 o Endomembrane System  Things move inside it  Membranous sac divides cells into organelles  Made up of a phospholipid bilayer  Hydrophobic tail  Hydrophilic head  The membrane is related internally  Have common ancestors through evolution  Membranes are able to fuse portions of another organelle as their own - Slide 12 o Organelle  Needs a specialized feature  Have a membrane  Be inside the cytoplasm (surrounded by cytosol)  Only in eukaryotes - Slide 13 o Nucleus  Separates the hereditary material from the rest  Has a nuclear envelope  Pores allow for enter/exit of material  Laminae gives support  Nucleolus is white rRNA is transcribed  Regulates with DNA Gene expression - Slide 14 o What needs to get in and out of nucleus  Nutrients  Transcription factors for gene expression - Slide 15 o Nuclear membrane  Protects our DNA - Slide 16 o Prokaryotic Ribosomes  Bacteria (Protein synthesis)  Archaea (Different structure, protein synthesis is a combination of bacterial/eukaryotes) - Slide 17 o Organization of Eukaryotes  Histone packs DNA into the nucleus  Present in Archaea and Eukarya  Archaea have 4 histones (H3/H4)  Non-Histones regulate gene expression (How tight it will be)  Known as chromosomal protein  Present in bacteria  DNA & Protein = chromatin - Slide 18 o DNA Packaging  Histone and Non-histone protein  DNA wraps around a nucleosome (two molecules of H2A, H2B, H3, H4)  Form 8-protein nucleosomes  Linker connects the nucleosomes o 10 nanometers  H1 bindings causes nucleosomes to package in a solenoid o 30 Nanometers  Euchromatin  Loosely packed, active RNA transcription  Proteins are able to be produced  Heterochromatin (H1) – 30 nanometers of chromatin fibers  Densely packed  Packing DNA protects it but to be active it must unwind  No proteins are made due to no transcription taking place  Folds and packs to form chromosomes  Packs into a solenoid - Slide 19 o DNA Girase  Facilitates in the twisting process  Helps it twist even more - Slide 20 o Non-Histone proteins  Associated with DNA  Negative charged  Control gene expression  Change how packed DNA is for gene expression  Densely packed = not access to chromatin  Loosely = access to chromatin - Slide 21 o Endoplasmic Reticulum  Rough ER  Has ribosomes attached to it o Involved in protein folding o Synthesizes protein and releases it outside the cell o Goes to the lumen to become folded  Smooth ER  Plays a role in metabolism o Synthesizes lipids o Calcium metabolism o Steroid production - Slide 22 o Vesicle transport  Transports proteins and lipids to the Golgi Apparatus  Secretary vesicle transports proteins to plasma membrane - Slide 23 o Golgi Apparatus  Modifies proteins from ER  Adds things to further direct it  Glycosylation directs the proteins by adding sugar groups  Between rough ER and plasma membrane - Slide 24 o Vacuoles  Stores the nutrients  Eliminates the waste  Involved in growth  Transport materials in animal cells - Slide 25 o Lysosomes  Where the material is sent after the Golgi  Breaks stuff down  Acidic pH o 4.3-4.8  Has hydrolytic enzymes to digest enzymes  Involved in autophagy o Degrading polymers to monomers  Immune response o Macrophages engulf it and sent to lysosomes to be broken down o Ribosomes  Make proteins by putting amino acids together  Found in the rough ER  Need to be modified by Golgi complex, so the protein knows where to go  Can leave the cell through exocytosis - Slide 26 o Cell division  Organelles come from pre-existing organelles  Enlarge and make new copies  Daughter cells have a complete set of organelles - Slide 27 o Mitochondria/Chloroplast  Contain own DNA  Circular feature like bacteria  Multiply by binary fission like bacteria  Have transcription/translation machinery - Slide 28 o Endosymbiosis  Cell engulfs the other and created a symbiotic relationship  The become used to one another and cannot live without each other  Mitochondria from prokaryotes (due to aerobic respiration)  Chloroplast from cyanobacteria (Due to photosynthesis)  Mitochondria & Chloroplast rise in Atmospheric O2 o Evidence of Endosymbiosis (Mitochondria/Chloroplast come from prokaryotes)  Morphology (Shape of mitochondria/Chloroplast are same as prokaryotes)  Reproduction (All divide by binary fission)  Genetic Information (All have DNA that codes for proteins)  Transcription/Translation (All have machineries) - Slide 29 o Cytoskeleton  Not static  Constantly being rebuilt and broken down  Helps the cell to move  The movement is a push/pull  Give the cell its shape  Animal cell (Microtubule, Intermediate filaments, Microfilaments)  Plant cells (Microtubule, Microfilaments)  Microtubule (Rigid and hollow tube, 25 nm thick) o Composed of tubulin o Attached to centrosome for transport and mitosis  Intermediate Filament – 10nm thick o Only in animal cells o Rope like fibres o Composed of nuclear lamina and epithelial cells o Provides mechanical strength  Microfilaments (Actin) – 5 to 9nm thick o Flexible bundles under plasma membrane o Found in the microvilli and muscle  Has a dynamic feature  Has actin molecules that are important for movement  Moves in direction to the production of actin - Slide 30 o Motor Proteins  Help move things  Push/pull microfilaments/microtubules  One end attaches to motor protein, and the other end attaches to the microfilament/microtubule  Example is Kinesin o Carries organelles/vesicles o Brings things out of the cell o Requires ADP for ATP  Hydrolysis of ATP  Dyneins o Travels in the opposite direction of Kinesin o Brings things from the outside of the cell, to the inside o Involved with cilia and flagella movement o Energy dependent - Slide 31 o Flagella and Ciliary Patterns  Flagellin makes up Flagellum  9+2 complex (9 outside, and 2 inside)  9 Double microtubules surrounded by single microtubules  Subunit is microfilaments  Cilia clears things in the respiratory tracts - Slide 32 o Actin/Myosin  Help with muscle contraction  They are muscle protein - Slide 33 o Extracellular matrix  Gives specialized features to the other cells  Determines the specialization of the cell  Example is elastin o Used for stretch  Another is collagen o Used for structural support  Extracellular matrix is composed of sugar, water and proteins - Slide 34 o Eukaryotes vs. Prokaryotes  Eukaryotes are bigger  Size of the cell determined by surface area
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