Biol 100 Notes.docx

Aug 31 Scientific Method “to do science is to search for repeated patterns, not simply to accumulate facts.” (R.H> Macarthur (1930 – 1988) “Scientific knowledge is a body of statements of varying degrees of certainty – some most unsure, some nearly sure, none absolutely certain” QUOTE LATER Ofte...

Aug 31 Scientific Method “to do science is to search for repeated patterns, not simply to accumulate facts.” (R.H> Macarthur (1930 – 1988) “Scientific knowledge is a body of statements of varying degrees of certainty – some most unsure, some nearly sure, none absolutely certain” QUOTE LATER Often described as “a system of thought that is based on reasoning, logic, and evidence” Used to figure out how things work; gain new knowledge/insight. Some philosophers of science suggests that there is no scientific method Philosophers of Science often describes two types of science: Induction-based (Generalizations based on past experiences) Example; cell theory Hypothesis-based (A tentative explanation for an observation; educated guest at an explanation; sometimes referred to as “conjecture”. Reasoning from more general statements Hypothetico-deductive method (Major focus on hypothesis testing in the Hypothetico-deductive) Places emphasis on outcomes consistent with the predictions, supports hypothesis, does not equal proof Scientific method is very good at disproving things and not proving things. It supports assumptions but not necessarily proves it September 1st 2023 BIOL-100 All experiment always need to have a control, without a control there is no way of telling the validity of the experiment Positive Controls: A known treatment that produces an effect similar/identical to what you predict your experimental treatment will produce. (Often part of experiments, but not always: Predominantly used in chemical analysis) Negative Control: Nothing Added (Mandatory for all experiments) “Scientist are better at disproving than proving) *Outcome is predictable if the hypotheses are correct* “Old ideas are rejected; new ideas are tested” Theories attempt to explain so much, they only become accepted if they are supported by a large body of evidence *Larger Sample Sizes Reinforce the validity of the experiment* The Experiment must be repeatable and results must be consistently reproducible by anyone, anywhere and any given time. Occam’s Razor If Several explanations are compatible with the evidence at hand. The simplest should be considered the most likely Atoms and Chemical Bonds Atoms are the basic building blocks of matter (Atoms are mostly empty space) Electrons are smaller than neutrons and protons The Mass Number = # of protons + number of neutrons Hydrogen bonds are weak; they are constantly breaking and re-forming Water Water is the solution of life There is no solvent that can dissolve everything Water will also dissolve small polar molecules (molecules that have partial charges), e.g. sugars: Non-Polar = Electronegativity less than 0.5 ( 0 < EN < 0.4) Polar = Electronegativity between 0.5 – 2.0 Ionic Bonds = Electronegativity larger than 2 Hydrophobic molecules are largely composed of non-polar bonds Fats are hydrophobic Important biological non-polar covalent bonds include: C – C / C – H September 8th 2023 Condensation produces water as the reaction requires the removal of water from the molcules to create a covalent bond between the two molecules. And hydrolysis uses water as a reactant to break a polymer back into a monomer. Example: In the synthesis of Maltose; condensation occurs as the water is the byproduct of the reaction In the breakdown of maltose into glucose the opposite happens. Water is used as a reactant to separate the maltose into two glucose molecules. Monosaccharides (One sugar) 3 fundamental molecules Oligosaccharides – Short chain of sugar monomers. Consists of 2 or more sugar monomers The shorter chain oligosaccharides are highly water solubility and decreases in solubility the more links and chains are made. September 11th Polymers such as starch and glycogen are composed of glucose subunit molecules linked together via alpha 1-4 bonds Cellulose is a glucose polymer composed of glucose subunits linked together with beta 1-4 bonds Amphipathic: Have both hydrophilic and hydrophobic parts on the molecule (Phospholipids) Saturated fats contain only single bonds between C-C, whereas unsaturated fats contain one or more double bonds Two kinds of Unsaturated Fatty acids: Monounsaturated and Polyunsaturated Saturated fats are solid at room temperature Unsaturated fats are liquid in room temperature, but will go solid if the temperature is low enough *anything positive is hydrophilic* The phospholipid bilayer is a fluid not a solid Proteins have a structural role such as: Proteins are part of the Cellular cytoskeleton Some Proteins have a catalytic role such as Enzymes (Aids in the reaction of the metabolic path + all enzymes are proteins, but not all enzymes are proteins) Active transport proteins Amino acids have different side chains (R groups) and that’s how they are discerned from each other. Quaternary v Tertiary protein structure Some amino acids can’t be produced by mammal, so it must be consumed/intake via diet. Primary -> Secondary (Contains peptide bonds to form pattern) -> Tertiary Structure -> Quaternary Structure (4th structure is three dimensional structure of a protein composed of 2 or more polypeptide subunits) All proteins exhibit structures 1-3 Sept 13 2023 A protein must maintain a “native” structure to maintain it’s function Some proteins may be able to reverse denaturation but not always. Nucleic Acids 2 types – RNA and DNA September 18 2023 Plants don’t have a extracellular matrix, it’s unique to animal cells(ECM is the relatively flimsy outer covering found on animals) The ECM functions: as a shock absorber for cells, and has very important roles in cell migration, signalling, tissue development, cell to cell adhesion and communication. (Flimsy compared to a true cell wall) Fluid Mosaic Model of Biological Membrances “Fabric” of the membrane is a phospholipid bilayer The Phospholipid Bilayer is a fluid Water is present on both sides Phospholipids can diffuse from one part of the membrane to another The Fluid Mosaic has three possible, but two common movements (refer to slide 4-5) Phospholipids are amphipathic (Contains hydrophilic and hydrophobic parts) Integral Protein membrane spanning Peripheral Protein typically outside the plasma membrane (Non-membrane spanning) Hydrogen is a very small polar molecule Anything will cross a membrane if given sufficient time O2, CO2, H20 movement across membrane (no energy required) is simple diffusion (H20 Osmosis) Diffusion Higher Concentration to lower concentration Active Transport is against a concentration gradient (requires energy) Lower to Higher gradient requires energy Diffusion of Solutes in a Solvent happens down in a concentration gradient (Higher to Lower) When there’s no more concentration gradient the solution is at equilibrium, but diffusion is still actively happening (net movement stops) Water diffuses (so do other solvents) Osmosis – the diffusion of water across a selectively (semi-permeable) permeable membrane Aquaporins – membrane-spanning channel proteins (water channels) Allows the fascilitation of water diffusion without having to interact with the hydrophobic portion of the membrane Water always moves from the lower solute to the higher solute concentration gradient Animal cells prefer an environment with equal environment and internal solution concentrations (isotonic) Diffusion of Solutes: Simple diffusion cannot happen for polar molecules or ions; so they must be transported across membranes via facilitated diffusion through transport or channel proteins Channel Proteins: allows specific or a small range of similar molecules to diffuse down a concentration gradient Transport Proteins (Carrier Proteins): has substrate binding sites with specificity There are no general transporters *Diffusion of solutes is always down a concentration gradient* Uniport: Transports a molecule down a concentration gradient Two Types of Transport Against a Concentration Gradient Active Transport – directly uses ATP Co-transport – indirectly uses ATP Active Transport – Performed by transport protein called ion pumps Lower Cation Concentration Higher Cation Concentrations • 1 H+ pumped out per ATP spent Co-Transport (Secondary Transport) Most anions and polar molecules are transported via secondary transports against a concentration gradient Uniporter – Transports one molecule in one direction Symporter – Transports two molecules in one direction Antiporter – Transports two molecules in two different directions