Biology Notes: Cells, Evolution, and Molecular Biology PDF

What does it mean to say that something is alive? -​ Cells -​ All organisms are made of membrane-bound cells -​ Replication -​ All organisms are capable of reproduction (copy them self) -​ Information -​ All organisms process hereditary information as well as informa...

What does it mean to say that something is alive? -​ Cells -​ All organisms are made of membrane-bound cells -​ Replication -​ All organisms are capable of reproduction (copy them self) -​ Information -​ All organisms process hereditary information as well as information absorbed from the environment -​ Energy -​ All organisms acquire and use energy -​ Evolution -​ Population of organisms are continually evolving The nature of Science -​ All experimental scientist ask question that can be answered by measuring things - collecting data Science involves -​ Formulating hypotheses -​ Finding evidence that supports or conflicts with those hypotheses Terminology Theory -​ Refers to explanation for broad patterns Hypothesis -​ A testable statement that explains something observed Experiment -​ Allows researchers to test the hypothesis Prediction -​ Measurable or observable result (if I do this something will happen) -​ Must be correct if hypothesis is valid Hypothesis testing - two-step process 1.​ State hypothesis as precisely as possible and list prediction it makes 2.​ Design observation or experiment study capable of testing those predictions Important Characteristics of Good Experiment Design -​ Critical to include a control group -​ Experiment conditions must be constant -​ Repeating test essential -​ Use large sample size Cells What is a Cell? The cells theory -​ Cell theory 1800s states that -​ All organisms are mades of cells -​ Cells spontaneously appear -​ All cells come from preexisting cells -​ Two flash (straight and swan) -​ Boiled broth -​ Implication of Cell Theory -​ All cells and all organisms are related by a common ancestry Evolution Evolution by natural selection -​ All species are related by common ancestry -​ Characteristics of species can be modified from generation to generation -​ Descent with modification;things very (process) -​ Changes every generation Evolution is a change in population characteris over time Natural selection explains/process how evolution occurs Population a group of individuals of the same species living in the same area at the same time (millions of years) Requirements for natural selection 1.​ Individuals vary in heritable characteristics (everyone one have variable traits) 2.​ In a particular environment, certain heritable traits help individuals survive better AND reproduce more the do than do other versions Evolutionary change -​ Beneficial heritable traits lead to increase production of offspring -​ Thies traits become more common in the population over time -​ Characteristics of the population changes -​ Natural selection acts on individuals -​ Evolutionary change occurs in populations Example - covid by natural selection Evolution relations between organisms and the tree of life -​ If all cells derive from other cells then all organism are related -​ A Phylogenetic tree Tree of life Eukaryotes - have nucleus Prokaryotes - no nucleus ​ Bacteria and archaea ​ —---------------------------- Molecule - 2 or more atoms held together by covalent bonds Atoms are the building blocks of molecules -​ Proton + -​ Electrons - -​ Neutrons (no change) Mass number - number of protons + neutrons (same number of protons and neutrons) Atomic number - number of protons Every atom is defined by the number of protons/atomic number it has Isotopes - Atomic mass - average mass of all the isotopes -​ Study Covalent bonds - two atoms share one or more pairs of electrons Why? - because the outer valence(outermost) shell wanted to contain 8 electrons Nonpolar covalent bonds -​ Electron are share equally halfway between the two atoms Polar covalent bonds -​ Electrons are shared unequally between more with one element then the other Electronegativity - how strong an atom pulls unequally shared electrons toward the nuclei in a bond ​ What is responsible for the electronegativity -​ Number of protons in the nucleus -​ Distance between nucleus and the valence shell Ionic bonds - a bond where the electron is completely transferred from one atom to another Getting a filled out shell by gaining or losing electrons -​ Cation formation - positively charged ion that lose of electron -​ Anion formation - negatively charged ion that gain of electron -​ Can share electrons to fill outer shell Carbon and hydrogen will share electrons equally Oxygen and hydrogen, Hydrogen likes the the electron mores (electronegativity) Hydrogen bonds - weak interaction between two molecules or different parts of the same molecule resulting from the attraction between a hydrogen atom with a partial positive charge and another atom negatively charged Single bond - one pair of electrons Double bond - two pairs of electrons Etc Atoms and Reactivity -​ The rule of 2–2 e- in s orbital -​ Up to 2 electron in first circle -​ The rule of 8–8 e- in the p orbital optimal -​ Up to 8 electron in 2 and 3rd circle Atoms prefer to have a filler outer shell (8) Electrons NOT always shared equally -​ Shifts the characteristics How many bonds can an atom have? -​ Based on the rule of 2 and the rule of 8 -​ H, C, O, N, P, Na, Cl Carbon and hydrogen share equally Carbon and oxygen don’t share equally WATER Properties of water and the early -​ Life is base are water -​ Water is an excellent solvent -​ Solute dissolved into solvent makes a solution  -​ Solute is what is dissolved in water Water is unique due to its structure -​ Small size -​ Bent shape -​ Highly polar covalent bonds -​ Overall polarity Water is polar -​ O - partial negative charge -​ H - partial positive charge Hydrogen bonds can also form between water molecules and polar solute Hydrophilic -​ Likes water -​ Ions and polar molecules stay in solution due to the reaction with water partial charges Hydrogen bonding -​ Makes it possible for almost any charged or polar molecules to dissolve in water Water can dissolve polar and charged molecules —----------------------------- Diagram of atoms Mass number = protons + neutrons Atomic number = protons Filled outer shell has 4 pairs of electrons 8 total electrons -​ Stable and un More protons is positive charge More electron is negative charge Valence electron that are reaction that can join a pair of electrons Ionic Bond - sharing electrons helps fill the outer shell for both atoms -​ Every covalent will have 2 electrons one donated from each atom Covalent bonds Hydrogen bonds Ion Formation and Ionic Bonding  -​ Atoms that lose electron are positively charged -​ Atoms the gain electrons are negatively charged Carbon and hydrogen will share electrons equally Oxygen and hydrogen, Hydrogen likes the the electron mores (electronegativity) Charged- lost or gain electrons Water is polar -​ Electrons are pulled towards oxygen Hydrogen bonds form between water molecules -​ Water hold onto each other to stay together Non- polar = hydrophobic Polar and charged = hydrophilic Examples -​ NaCl and water will dissolve -​ Sugar Carbon and Hydrogen = hydrophobic hydrophobic - polar -​ Charges -​ OH Water is a good solvent (dissolves in water) Hydrophobic molecules - Nonpolar molecules do not dissolve in water Cohesion, Adhesion and Surface tension -​ Water and Interactions with its surrounding -​ Adhesion attraction between unlike molecules -​ Cohesion: attraction between like molecules -​ Surface tension: cause by cohesion at surface Other properties of Water -​ Density: water is more dense as a liquid than a solid -​ Ice is less dense so it will rise -​ High Specific Heat - energy needed to reais temperature of the solutions -​ Takes a lot of heat to boil water -​ Hugh heat of Vaporization - energy needed to convert liquid to a gas The roles of water in acid-base chemical reactions -​ Water molecules dissociate into a hydrogen ion (H+)and hydroxide ion -​ Acid - adding acid increasing protons concentration -​ Bases - adding base decreasing proton concentration The impotence of Carbon -​ Carbon is the most versatile atom on Earth -​ Carbon has four valence electrons and will always form 4 covalent bond -​ The types of bonds can vary -​ Carbon structures varys Carbon and Macromolecules -​ Small molecular structure make bigger molecules structure Macromolecules of the Cell -​ Proteins -​ Amino acids -​ R groups -​ Charged -​ Non polar -​ Polar -​ Carbohydrates -​ Structure -​ Sugar variation -​ -​ Nucleic acids -​ Lipids Amino acid the building blocks of proteins -​ Non ionized form of amino acids 20 Amino Acid All 20 amino acids differ in r groups Types of amino acids -​ Non polar -​ Polar -​ Charged How do we get Protein from amino acids? -​ Polymer -​ Take individual units to a combined structure -​ Polymerizations Negative and positive charges cancel eachother out after the reaction occurs ​ ​ ​ ​ ​ Polymer is forming What do proteins look like? Primary -​ Order in which amino acids are listed -​ Polymer - chain of amino acids (look at pic bellow)  How to determine if an R group is nonpolar/polar or charged ? -​ Polar - Contains Oxygen -​ Non Polar - only Carbon and Hydrogen -​ Charged - has a charge Tertiary -​ 3 dimensional structure of a protein -​ Different proteins structures for different functions -​ Structure determines its functions Quaternary -​ protein complex with multiple proteins involved Order/sequence of amino acids determines the structure which that Structure determines function -​ Be able to recognize an amino acid -​ And nuticotide How do we get from amino acids to protein? -​ Polymerization -​ Individual units into a combined structure What do Proteins do? Proteins are crucial to most tasks required for cells to exist -​ Catalysis - enzymes speed up chemical reactions -​ Defence - antibodies and complement protein attack pathogens -​ Movement - motor and contractile proteins move the cell or molecules -​ Signaling - proteins convey signals between cells -​ Structure - structural transport proteins carry materials; membrane proteins control molecular movement into and out of the cells —------------------------ Cues Purpose of DNA/RNA -​ Transmission of information Phosphate: Characteristics -​ Negative charge -​ High energy structure -​ Example ATP -​ Hydrophilic (polar bonds) Sugar -​ Polarity (See OH groups) -​ Numbering systems -​ Compare to Ribose to Deoxyribose -​ Hydrophilic Base -​ Purines -​ 2 ring structure -​ Pyrimidines -​ 1 ring -​ Site of Sugar link -​ Possible H bonding sites -​ Hydrophobic -​ Bases can form hydrogen bonds with other bonds Nucleotide Polymerize to Form DNA/RNA -​ Covalent charges holding together 55 min -​ Write down what he wants us to know Polymer -​ 5’ - 3’ Orientation -​ Phosphate sugar backbone -​ Base structure (Size/Polarity) -​ Each strand held together by covalent bonds What is the nature of DNA Secondary Structure Two rules for DNA -​ Total number of purines and pyrimidenes is the same -​ Number of A and T are equal and the number of C and G are equal X Ray structure of DNA -​ Diameter of DNA (How wide it is) -​ Repeating structure  -​ Formation of Double helix -​ Hydrogen bonds (G- C three bonds, A-T two bonds) -​ Hydrophobic/Hydrophobic relationships Sugar Phosphorus on the outside -​ 5’ to 3’ on one side and 5’ to 3’ Bases in the middle being hidden bc they are hydrophobic —------------------- Hydrophobic - non polar CH bonds Hydrophilic - polar OH bonds Covalent attachment between nucleotides Nucleotides connected by phosphate DNA Association between strands -​ Hydrogen bonds What is a carbohydrate? -​ Basic definitions -​ -​ O H bonds - Polar -​ O is negative  -​ H is positive Polysaccharides - are sugar polymers -​ Don’t need to know about maltose and lactose Type of Polysaccharides -​ Storage -​ Plants store sugar as starch -​ Animals store sugar as glycogen -​ Structure -​ Cellulose in plant cells -​ Chitin in fungi -​ Peptidoglycan in bacterial cell walls for support The Role of Carbohydrates in Cell Identity -​ Display information on the outer surface of cells -​ Gycorportoes - proteins with carbohydrates Figure 5 Carbohydrates and Energy Storage -​ Store and provide chemical energy Chapter 6 The importance of Membrane -​ Plasma membranes or cell membrane separates life from nonlife Lipids -​ carbon-containing compounds the are found in organisms -​ Largely nonpolar and hydrophobic -​ C and H bonds -​ Squiggly line or straight lines Amphipathic - both hydrophilic and hydrophobic parts Three types of lipids found in cells -​ Fats -​ Steroids -​ Phospholipid Structure/ drawing of lipid -​ Head group -Polar/charged -​ Straight line - non polar Phosphate and Water  -​ Phospholipids do not dissolve in water -​ In water, phospholipids form either -​ Micelles -​ Water interacted inside and outside of the cells -​ Phospholipids bilayers - -​ Inside in hydrophobic -​ head/outsides hydrophilic Selective Permeability of lipid bilayers -​ Permeability - allowing a substance to cross a barrier -​ Phospholipid bilayers have selectively permeable Figure 6.7 Picture I took Small, nonpolar molecules more easily across bilayer Polar molecules move slower slower actress bilayer Charged molecules do NOT move actress bilayer -​ Needs help from protein to move More double bonds for fluid Fluidity= permeability Many factors affects membrane permeability -​ Number of double bonds in the tail -​ Tail length -​ Number of cholesterol molecules -​ Temperature Unsaturated fatty acids -​ Double bonds the form kinks -​ stops the ability to compact -​ Don’t allow free rotation The more double bonds, the more fluid - go back to slide Figure 6.9 time 1.02 -​ Few double bonds = less permeable Temp increase permeability Cholesterol decrease permeability Lipids are stuck on the other side -​ Diffusion -​ Every molecule moves randomly Solute Movement across the lipid bilayers -​ Materials can move across the cell's membrane in different ways  -​ Passive transport does not require energy -​ Active transport requires energy to move substances across the membrane -​ Solutes -​ Have thermal energy -​ Are inconstant, random motion -​ Diffusion -​ Random movement of solute molecules -​ A form of passive transport -​ Concentration gradient - difference in solute concentration -​ Solute molecules from high to low concentration Net movement from high to low concentration -​ Equilibrium - molecules or ion are readonly distribution throughout a solution -​ Molecules are still moving randomly but there is no net movement Diffusion works for small, nonpolar or small uncharged molecules Osmosis -​ Water moves quickly actress lipid bilayers -​ This is special case of diffusion is called osmosis -​ Water moves from regions of low solute concentration to regions of high solute concentration -​ -​ Higher solutes the less water is there -​