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BIOL MIDTERM 1 CLASS NOTES 18 Sept. 2017 Introduction to Evolution, Selection and Species Artificial Selection (ex. broccoli) Why do we care about evolution? Linked to everything such as: Genetics, medicine, ecology, molecular biology, agriculture, behaviour, physiology Evolution is looked at in ref...

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BIOL 1000 MIDTERM 1 CLASS NOTES 18 Sept. 2017 Introduction to Evolution, Selection and Species Artificial Selection (ex. broccoli) Why do we care about evolution? — Linked to everything such as: Genetics, medicine, ecology, molecular biology, agriculture, behaviour, physiology — Evolution is looked at in reference to population in the ecological scale Population — same species, same geographical area & regularly interbreed Generation 1 —> (some evolutionary process) —> Generation 10 Evolution is Valid Because… — Evidence based — evidence from numerous branches of science — Biology, palaeontology, geology, geography, chemistry, physics & ecology — Question is, how did evolution take place (process/mechanism) — Observable and testable Dichromatic —> Trichromatic? (look back at ppt and finish) 1. Variation: Genetic variation in every population with heritable traits 2. Reproduction: Organisms produce more offspring than can survive due 3. Inheritance: Organisms pass genetic traits to offsprings Selection 1. Key: survive to pass on genes to next generation 2. Most successfully reproduce 3. Individuals survive or don't, populations evolve 4. Selection is directed by circumstances (environment) — and this changes, so does direction of selection Mutation as a Source of Genetic Variation (finish notes look at ppt) — UV damage to DNA, affects DNA replication, transcription, and cell division\ — Mutation in gametes have a bigger effect on the population Cell Theory — All organisms are made of one or more cells — Cell is the smallest unit that has properties of life — Cells arise only from the growth and division of preexisting cells

Characteristics of Life — Order (communication, transcription, osmosis) — Energy (photosynthesis, cell to cell communication) — Reproduction — Response (negative positive feedback, photosynthesis) — Homeostasis (balance, homeostasis, osmosis, memory transport — Growth and development (meiosis, mitosis, feedback, DNA replication) — Evolution and adaption (gene expression, replication) — Everything is linked Characteristics of Cells All Domains Share Bacteria, Archaea, Eukarya 1. 2. 3. 4.

Basic building blocks (chemical molecules used to make functional cell) Genetic Information flow (DNA—> RNA—> Proteins) Plasma membrane Use and need for energy (energy metabolism)

1. Basic building blocks are: amino acids, carbohydrates, lipids, & nucleotides Amino Acids — Each amino acid has a different side chain (R) — Side chain determines the chemical and physical characteristics of amino acids (ex. atomic and molecular interactions, and molecular structure) Carbohydrate — Amylose (plants), glycogen (liver), cellulose (plants), chitin (insects) Lipid — Types: phospholipids (plasma membrane), cholesterol (has a sterol ring structure, also found in plasma membrane), triglycerides (glycerol & 3 fatty acids, found in human body fat, and oil on skin) — Phospholipids contains a hydrophobic tail made of triglyceride, and a hydrophilic head (polar alcohol, phosphate group) Nucleotides — Make up structure of DNA and RNA 2. Pathway of Information Flow (common to all cells) DNA —> RNA is transcription (RNA polymerase) RNA — > Protein is translation (ribosomes)

Protein Structure Primary Protein Structure — Linear sequence, amino acids joined together by peptide bonds (free amino group to free carboxyl group) Secondary Protein Structure — Interactions between chains so formations of hydrogen bond between the backbone, dependent on how these hydrogen bonds form it will create a alpha helix ex. Spider silk (strength, stop stop with this structure) Tertiary Protein Structure — one peptide chain, interactions between the R-groups (hydrogen bonds, disulphide bonds, ionic bonds), and also can form binding sites, some proteins stop in this state Quaternary Protein Structure — 2 or more proteins (peptide chain) joined together *** Structure is important for function, amino acids make the proteins different sizes, structure & function Ex. Sickle Cell Anemia — inherited blood disorder, only one changed amino acid 3. Plasma membrane Cell Membrane — The phospholipid bilayer —acts as a separation between the outside and inside of a cell 4. Need for Energy (Energy Metabolism) — Breaking and making things to carry out functions of cell Modes of Nutrition: a) How carbon is obtained? — Heterotrophs: Obtain organic carbon by consuming other organisms — Autotrophs: Synthesize organic carbon molecular using inorganic carbon, CO2 Found life on our planet exist without carbon? — Possibly, with silicon b) How energy is obtained? — Phototrophs: Use light as a source of energy for photosynthesis — Chemotrophs: Use reduced chemicals rich in electrons as an energy source Why we need Energy: cellular respiration, active transport, movement, Calvin cycle, break molecules, make molecules, etc. 4 Classifications: 1) Chemoautotroph 2) Photoautotroph 3) Chemoautotroph 4) Photoheterotroph Bacteria can live almost in ay environment because of their diversity

Oxidation-Reduction Reactions — Redox reactions are chemical runs where there is a transfer of one or more electrons from one reactant (donor) to another (recipient) Metabolism: Biochemical reaction that allow a cell or organism to extract energy from its. Surroundings and use that energy to maintain itself, grow, and reproduce Energy-Harnessing Reaction Pathways — ATP became established as coupling agent that links energy-releasing reactions to those requiring energy

Differences of Bacteria, Archaea, Eukarya Bacteria & Archaea — Both have the greatest metabolic diversity of all organisms, use variety of substances as energy and carbon sources to synthesize almost all required organic molecules — Outnumber all other types of organisms — Live successfully almost anywhere — Vary in shape, size, cell structure, energy metabolism and habitat Structure and Function — Simple structure and small compared to eukaryotic cells —Appear in a variety of shapes Bacterial Cell Structure Common: Plasma membrane, DNA, ribosomes Unique: Cell wall, capsule, flagellar structure, pili, plasmids

Bacterial DNA: Bacterial Genomic DNA — Most bacteria have one circular piece of DNA — Contained in nucleoid — No nuclear membrane Bacterial Chromosome Replication — Closed, circular molecule of DNA packed into nucleoid region of cell — Replication begins from a single origin Bacteria Archaea — can have extra DNA called plasmids Plasmids — Extra-chromosomal small circular DNA molecules, often carry more than one copy — Carry nonessential genes but genes with beneficial functions (antibiotic resistance, metabolism, toxins, etc.) — Replicates independently of the chromosomal DNA

Vertical Gene Transfer: Transmission of genetic traits from generation to generation (parent to offspring-daughter) 3 Mechanisms of Horizontal Gene Transfer — DNA transfer between neighbouring cells (not parent to daughter cells) 1) Transformation — Recipient cell is picking up DNA from the environment (lysis of donor cell where DNA is released) 2) Transduction — Viral particle injected to cell (bacterial phage) in the donor cell and used to replicate their own cells, reincorporate viral phages into new cells 3) Conjugation — Cell remains intact & tra-gene causes two cells connect to and channel is formed and plasmids move through

Bacterial Cell Wall — Made of peptidoglycan — Provides strength, rigidity and protection Classify Bacteria According to Cell Wall Gram Positive Bacterial Cell Wall — Membrane with thick peptidoglycan — Carbohydrate backbone and peptide cross-bridge Gram Negative Bacterial Cell Wall — Thin layer of peptidoglycan — Lipopolysaccharide - lipoprotein - phospholipid outer membrane — Channel proteins embedded in outer membrane Prokaryotic Cell Wall How Do You Know? Gram Staining Take a slide, dunk in crystal violent (dark. Purple dye), add second component and dunk into iodine which forms complex with crystal violet and embeds itself in thick peptidoglycan layer in gram positive or in the outer layer for gram negative, then go through alcohol wash if gram positive the cells will remain purple or if gram negative then crystal iodine goes away and then cell appears colourless, then application of safranin (counterstain) pink stain and it will stain all cells but if gram positive it looks the same as purple or gram negative will look pink because dye goes to the thin peptidoglycan layer

Gram Negative — Lipid A (Endotoxin) is dangerous if the bacterial cell breaks which can make very sick (shock, fever, etc) 1. LPS – endotoxin (distinct from exotoxin – secret proteins by both Gram +/-) 2. Triggers of the pathogenesis of diarrhea, septic shock and multiple organ failure 3. Release when gram negative bacteria cell wall is ruptured Weakening Cell Wall Leads to Cell Rupture and Death — Antibiotics targeting peptidoglycan synthesis — Lysozyme: breaks the cell wall (found in saliva, mucus, etc. Bacterial Glycocalyx — Layer of polysaccharide surround cell wall — Protects from extreme temperatures, desiccation, antibiotics, viruses, and antibodies Types: Slime —Loosely associated Capsule — Watery Flagellum: Extends from cell wall— Made of rigid — Tail of flagellum is made of proteins that comes together and forms it Bacterial Pili — Extensions off the cell surface (hair-like structure) — Help cells attach and helps movement — Helps with adherence to other cells and in transfer of plasmids from one cell to another — Only function is to bring cells together Ex/ plaque in teeth is because of pili Ex/ Food poisoning bacteria forms lining because of pili Ex/ Contact Lens Archaea — three evolutionary branches of archaea have been found — difference based on rRNA sequence data — Three groups — Similar to both bacteria and eukaryotes Like bacteria because of circular DNA in single chromosome, in a nucleiod and in similar shapes to bacteria Like eukarya because similar “packaging” proteins (histones) — Many Archaea are extremophiles — live in extreme conditions Archaeal Cell Wall — Archaea lack peptidoglycan. They have a cell wall but cannot be classified in terms of how they react to Gram staining — They also have flagella which are similar to bacterial flagella and carry out the same function but have different components

Eukaryotic Cells 1) Distinct nucleus surrounding nuclear envelope 2) Membrane bound organelles — endomembrane system Endomembrane System — Collection of interrelated internal membranous sacs that divide cell into functional and structural compartments called organelles Membrane — Lipid Bilayer — Hydrophilic head, hydrophobic tail 4 criteria of an organelle: 1) membrane bound 2) specialized function 3) inside cell 4) found in eukaryotic cell The Endomembrane System — Same common membrane ancestor, hypothesis is that though evolution, many membranes derived from the same one — Nuclear membrane, ER (SER & RER), Golgi apparats, vesicles, lysosomes, and vacuoles The Nucleus — Physically separates our hereditary material from the rest of the cell — Double membrane (2 phospholipid bilayers), it is connected to the ER — Contains nuclear pores which are made of a series of proteins that come together to form the big structure — Liquid inside is nucleoplasm What Needs to Enter Nucleus? —Enzymes for replication, ions, What Needs to Leave Nucleus? —rRNA, proteins, mRNA Transcription Factor — binds to DNA, helps to start transcription — Specific proteins help move things in and out of nucleus Nuclear Import Signal — to move into cell, but if mutated then moves out — Proteins have import/export sequences Nucleolus — non-membrane bound inside the nucleus —Structure made of proteins and nucleic acids — rRNA (RIBOSOMAL RNA) is transcribed and assembled within the nucleolus

Nuclear Lamina —Mesh like structure that provides support made of protein filaments and reinforce the nucleus — Found inside the nucleus under the double membrane Chromatin — DNA plus associated proteins (histone and non-histone proteins) DNA Organization (Eukaryotes) Heterochromatin: Densely packed DNA —> Genes inactive and transcription not occurring Euchromatin: Loosely packed DNA —> Genes active and transcription occurring — Some regions will be euchromatin and other regions are heterochromatin Insulin Synthesis and Secretion — Insulin is a gene on chromosome, this gene turns into protein and in order to leave must be secreted, how is this hormone functional?? — Insulin first is a chain of amino acids, then in body some portions are removed and strands join together by disulphide bonds — How? The genes together must be active Eukaryotic DNA packing - Histones Histones: proteins that come together to make a bigger structure Nucleosome: Histone octamer (two molecules each of histones H2A, H2B, H3, H4) which DNA wraps around — Linker DNA connects adjacent nucleosomes — Binding of histone H1 causes nucleosomes to package into a coiled structure (solenoid or 30nm chromatin fibre) — Folds and packs to form thick, rodlike chromosomes during nuclear division Non-Histone Proteins — Dont interact with DNA — Proteins associated with DNA that are NOT histones — Involved in regulation of gene expression — Control gene accessibility loosening or tightening of association b/w DNA and the histones Free and Bound Ribosomes —Ribosomes in cytoplasm floating around then As protein is translated from mRNA through ribosomes the protein slowly leaves

Sept. 29, 2017 Microtubules — Made of subunits called tubulins and arrange themselves from alpha to beta ends — Form from the centrosome, Polymerization starts at nucleotide sites — rapid growth with GTP cap end, but when tis GTP is lost that is when depolymerization occurs — Motor proteins (kinesin) for microtubules are involved in moving vesicles, walk along the microtubules Kinesin — Kinesins goes from —ve end to +ve end, away from centre of cell towards plasma membrane — Regulated by ATP, needs an exchange of ADP for ATP, it is the hydrolysis of ATP — example of conformational change — two feet interacts with microtubule, so one foot with ATP is more attached and the one without moves Dyneins — similar movement to kinesis, but moves towards the centre of cell so +ve to —ve end — involved in flagella movement Flagella in Eukaryote — Associated with microtubules and dynes — Whip-like or oar-like movement — Used for locomotion Cilia in Eukaryotes — more than flagella — Associated with microtubules and dyneins — Found in trachea — Shorter than flagella, but similar movements to flagella — Move fluids over the cull surface — 9+2 complex — Spokes on microtubules restrict the dyne movement, eventually causing it to bend, going back and forth Bacterial vs Eukaryotic Flagella — Analogous structure, same function but different structure, not evolutionarily evolved

Actin Filaments — Lies below the plasma membrane — Important function: Muscle contraction — Needs a motor protein, this is myosin — works together for muscle contraction — Specifically on skeletal muscle — Sarcoplasmic Reticulum — contain calcium (important for muscle contraction), this is wrapped around all cells because they should all have calciums at the same time so muscle contracts altogether — Neurotransmitter released, into tubule releasing calcium which reacts with actin molecule and myosin cross bridge interacts and contracts — Myosin makes actin closer together (contraction) — Myosin bound to actin — to release myosin from actin bring in ATP which binds to ATP binding cleft, and weakens the binding — When myosin is released, it tilts myosin (conformational change) and in order to bind to actin again, then get rid of ATP — Hydrolyzed ATP with phosphate ticked off, bring back myosin bound to actin, which pulls the actin with it — Myosin moves along actin, when myosin tilts in tilts toward positive, bringing minuses together (no charge) Cell Movement — Actin fibres are responsible for cell crawling, depolymerizes and polymerizes in certain spots, if it wants to move forward it moves all actin to that side Summary • Kinesin – plus direction • Dynein – minus direction • Myosin – plus direction Intermediate Filaments — Under nucleus to provide structural support — hair, nails, skin cells, under nucleus — doesn't have motor proteins that move along intermediate filaments Cell Surface Specializations — Glycoproteins — Which cells to stimulate? Cell Junctions — attached cells together and communication between cells — reason why we humans are together

Anchoring Junctions — holds cell together, and some movement involved —heart muscle, skin (heart contracts, stretch skin) —made of proteins and through proteins is cytoskeletal component one called desmosomes (intermidiate filaments) and other type is adherent junctions with microfilaments portion of cytoskeleton Tight Junctions —No movement —some organs, like stomach, organ, bladder whatever inside will not come out —nothing passing through (no leaking) — Proteins stay where they need to be — help restrict movement of transport proteins Gap Junctions — tunnels connect cytoplasm of one cell to another — important for cell communication — Simultaneous heart contract, uterus when having a baby — singling molecules are small thus can move very quickly through channels Plants — Plasmodesmata — type of gap junction for plants How come eukaryotic cells be larger than bacterial cells? —surface are vs volume — when increase volume, it increases faster than surface ares — cells are all the same size of eukaryotes — bigger because of surface are to volume ratio — High surface area and less volume facilitates the transport of material (e.g. ions, nutrients, waste) across the cell membrane — Volume increase faster than SA — Eukaryotic are bigger because of the organelles — Compartmentalization is a big way eukaryotic cells increase size

Compensate for larger volume = increase your surface area ******—because it has the surface area to support it Neurons Overcome SA to V ratio by: — being thin — thin projections (dendrites and axons) — SA is high and cytoplasm is close to the membrane to optimize transport

— Cell, cytoplasm, cytosol, organelle, lumen — Terms to Know

Oct 2. 2017 Energy in Systems 1) Isolates System — No energy or matter exchange (e.g. Universe) 2) Closed System — Exchanges energy but not matter(e.g.Earth) 3) Open System — Exchange energy and matter(e.g. the cell) Energy — Capacity to cause change Potential Energy — amount of energy stored in a system (chemical bonds, arrangements of atoms) Kinetic Energy — Energy associated with motion (movement of electrons) Enthalpy (H) — internal energy First Law of Thermodynamics — Energy cannot be created or destroyed but only converted from one form to another (conservation of energy) Chemical Energy — Results from chemical reactions, energy (potential) is in the bonds of the molecules — When bonds break, energy is released, meaning it is being transferred to another form — Building bonds mean energy is stored Metabolism — Sum of all chemical reactions in the body Types: 1) Catabolic (exergonic reaction) — breakdown of complex molecules into simpler compounds, release of energy (ex. starch broken down into glucose) 2) Anabolic (endergonic reaction)— Using simples molecules to build more complex ones, use of energy (ex. Protein synthesis) — Catabolic pathways turn into useful forms of energy (used to drive anabolic pathways) and also lost as heat, or used for building blocks (ATP —> ADP +Pi) — when ATP is broken, hydrolysis reaction when the last phosphate group is removed, and this phosphate gets attached to other molecules (phosphorylation), this energy is now in ADP and the inorganic phosphate — Not all energy released by catabolic reactions is used for anabolic reactions Second Law of Thermodynamics — During every energy transfer some energy becomes unusable — As humans we are homeotherms, we use this heat to maintains internal temperature — important for functions (enzymes)

Entropy (S) — measure of energy dispersal — energy of system increases, meaning energy turns from being localized to dispersed 1. Increase in Volume (phase change) 2. Increase in Number (catabolic reaction) 3. Increase in Molecular Random Motion (heat release) — If enthalpy increases, ...