Biology Notes PDF

Biological Science 1/13/25 Biology: The Study of Life Page 1 of 18 What does it mean to say that something is alive? 5 characteristics - cells, replication, information, energy, evolution - information: genes & environment...

Biological Science 1/13/25 Biology: The Study of Life Page 1 of 18 What does it mean to say that something is alive? 5 characteristics - cells, replication, information, energy, evolution - information: genes & environment Theory: - Explanation for something that is happening of phenomena or observations that is supported by wide body of evidence - di ers from everyday usage of word “theory”, meaning “speculation” or “guess” - three theories form frame work - cell theory: - what are organisms made of? - theory of evolution by natural selection - chromosome theory of inheritance: - how is hereditary info transmitted form one generation to the next? ____________________________________________________________________ 1665 Robert Hooke devises microscope with 30x magni cation - termed them “cells” Anton Van Leeuwenhoek: devised more powerful microscopes observed single celled organisms Robert and Leeuwenhoek were the rst to observe cells Cells: - highly organized compartments - - separated from their environment by membrane barrier - All organisms are made up of cells - All cells come from preexisting cells ____________________________________________________________________ Terminology - theory refers to explanation for broad patterns Hypothesis: testable statement Experiment: test e ects of factor on phenomenon Prediction: measurable or observable result Cell theory vs spontaneous generation - cell theory challenged spontaneous generation all cells from cells explanation was a hypothesis Spontaneous generation was an alternative hypotheses _______________________________________________________________ Louis Pasteur’s hypothesis: cells arise from cells cells do not arise by spontaneous cells ____________________________________________________________________ Life replicates through cell division cells must replicate for life to exist as predicted by cell theory: ff ff fi fi Biological Science 1/13/25 Biology: The Study of Life Page 2 of 18 all cells present come from preexisting cells they are connected by common lineage Evidence now shows that it arose by process of chemical evolution ____________________________________________________________________ How is hereditary info encoded & passed on during cell divisions - chromosomal theory of inheritance proposed by Sutton and Boveri - hereditary/genetic info is encoded in genes and genes are united located on chromosomes 1950s—chromosomes are molecules of (DNA) - DNA is the hereditary material - genes are segments of DNA that code for cell membrane ____________________________________________________________________ DNA is a double helix - each strand is made up of four building blocks: A, T, C, and G - DNA carries info needed for growth and reproduction - the two strands of double helix are joined by interactions between pairs of bases A pares with T C parties with G ____________________________________________________________________ The central dogma describes the ow of genetic info The central dogma: - describes ow of info in cells - dogma means framework for understanding - DNA codes for RNA which codes for proteins The centra dogma DNA -> RNA -> Proteins RNA: Carry out functions in cells Proteins Form structures to promote chemical reactions MRNA is read to make proteins ____________________________________________________________________ DNA is copied to pass from one generation to the next DNA sequences changes may lead to changes in proteins DNA sequence changes lead to heritable variations that underlie diversity of life ____________________________________________________________________ Life requires energy - chemical reactions that take place inside cells require energy - Acquiring chemical energy in form of ATP (Adenosine triphosphate) - Molecules that can be used as building blocks to make DNA, RNA, proteins, etc. How organisms aquaria energy is central to diversi cation of life fl fl fi Biological Science 1/13/25 Biology: The Study of Life Page 3 of 18 ____________________________________________________________________ Life evolves What is evolution? Darwin and Wallace made 2 claims regarding natural world: species are related by common ancestry: characteristics of species can be modi ed from generation to generation Darwin called this “decent with modi cation” Natural selection explains how evolution occurs 1. Individuals must vary in characteristics that are heritable 2. In particular environment, certain versions of these heritable traits help individuals reproduce more than other versions ____________________________________________________________________ Evolution and natural selection Evolution change in characteristics of population over time species are related to one another and can change through time Population group of individuals of same species ____________________________________________________________________ Natural selection and evolutionary change certain heritable traits lead to increase success in producing o spring Natural selection acts on individuals Evolutionary change occurs in pop. Speciation occurs when pop. diverge to form new species ____________________________________________________________________ The phylogenetic tree of life used to show the relationships between species branches that share recent common ancestor branches that do not share recent common ancestors represent species that are more distantly related The tree of life estimated from genetic data: * Fewer sequence variations between 2 species may indicate closer relationship ____________________________________________________________________ Biology Science 1/15/25 The tree of life was produced by comparing genetic sequence date Tree of life indicates three major groups of organs. (Domains): 1) eukaryotes (have nucleus) Eukarya Two groups of prokaryotes (lack nucleus) 2) bacteria and 3) archaea fi fi ff  Biological Science 1/13/25 Biology: The Study of Life Page 4 of 18 ____________________________________________________________________ Doing Biology The nature of science: all scientists ask questions that can be answered by measuring things Science involves formulating hypotheses nding evidence that supports it con icts with those hypotheses. Critical to include a control group ____________________________________________________________________ Pedometer hypotheses ants always know how far they are form the nest track number of steps taken Null hypothesis speci es what should be observes when the hypotheses is incorrect if pedometer hypothesis is wrong, should have no e ect on the way back to the nest ____________________________________________________________________ Chapter 2: water and carbon: the chemical basis of life Chemical evolution: leading explanation of origin of life on earth switch from chemical to biological evolution led to molecule that could replicate itself Evolution by natural selection took over orignal molecule multiplied ve characteriects of life ful lled Four types of atoms make up 96% of matter in organism hydrogen, carbon, nitrogen, and oxygen ____________________________________________________________________ Basic atomic structure Nucleus made up of protons and neutrons: protons—positive charge neutrons—neutral charge Surrounded by orbiting electrons negative charge Atom with equal number of protons and electrons charges balance electrically neutral ____________________________________________________________________ fi fi fi fi fl ff Biological Science 1/13/25 Biology: The Study of Life Page 5 of 18 Elements: consist entirely of a single type of atom Atomic number written as subscript left of its symbol Mass number sum of protons and neutrons in atom ____________________________________________________________________ Dalton (Da): each proton and each neutrons has a mass of one dalton Mass of electron so small that it can be ignored Therefore Nass of atom is equal to its mass number Neutrons in element may vary Forms element with di erent numbers of neutrons (isotope): Isotopes of elements have di erent masses All carbon atom has 6 protons Atomic weight of element average of all masses of naturally occurring isotopes based on their abundance Radioactive isotopes unstable ____________________________________________________________________ Mole refers to 6.o22 x 10^23 mass of one mole of an atom is the same as its atomic weight expressed in grams molecular weight mass of one mole of molecule sum of atomic weights of all atoms in molecule C,H,N,O,P, and S make up 99% of all organisms ____________________________________________________________________ Electrons move around atomic nuclei in speci c regions called orbitals Orbitals grouped into levels called electron shells Electron shells number 1,2,3, and so on numbers indicate their relative distance from nucleus each electron shell contains speci c number of orbitals Outermost shells of elements atom’s valence shell is outermost shell Electrons in this shell called valence electrons ____________________________________________________________________ Atoms become more stable by main covalent binds Hydrogen does not have full valence shell two hydrogen atoms share electrons outer shell lled—more stable fi ff ff fi fi Biological Science 1/13/25 Biology: The Study of Life Page 6 of 18 Nonpolar covalent bond in hydrogen molecule electrons are halfway between the two atoms, shared equally Polar covalent bonds in water molecule electrons are not shared equally electrons in polar covalent binds spend most of their time close to nucleus of more electronegative atoms Water is an ex. Of a compound—which are molecules in which atoms of di erent elements are bonded together ____________________________________________________________________ Atoms electronegativity determined by number of protons distance of valence shells ____________________________________________________________________ Ionic bonding electrons are not Sheries; it is completely transferred from one atom to another transfer gives each atom a full valence shell Ions—atom or molecule that carries charge cation—atom loses electron and becomes positively charge anion—atom gains an electron and becomes negatively charge Number of unpaired electrons determines number of bonds an atom can make ____________________________________________________________________ 1/17/25 Quiz on Wednesday Worth 10 pts 5-6 MC Short answer ____________________________________________________________________ Nonpolar covalent bonds = no charge Polar covalent bonds = partial charge Ionic = full charge Number of unpaired electrons determines # of bonds an atom can make ____________________________________________________________________ Single bond water, ammonia methane ____________________________________________________________________ Tetrahedron forms due to repulsive forces between electrons Water is planar and bend b/c of 2 unshared electron pairs ____________________________________________________________________ ff Biological Science 1/13/25 Biology: The Study of Life Page 7 of 18 Life is based on water 75% of cell is water Water is an excellent solvent: solute dissolved into solvent makes solution substances more likely to react when they are dissolved in solvent like water ____________________________________________________________________ Water is polar oxygen atoms have partial negative charge hydrogen atoms have partial positive charge Water is polar and participates in hydrogen bonds: water molecules have bent geometry partial charge on hydrogen attracts partial negative charge on oxygen these weak electron interactions are called hydrogen bonds ____________________________________________________________________ Hydrogen bonds can also form between water molecules and polar solutes Hydrophilic (water loving) molecules ions and polar molecules stay in solution due to their interactions with water’s partial charges Hydrogen bonding makes it possible for almost any charged or polar molecule to dissolve in water ____________________________________________________________________ Hydrophobic (water fearing) molecules uncharged and non polar compounds do not dissolve in water Hydrophobic molecules interact with each other through hydrophobic interaction Van der Waals interactions increase stability of clustered hydrophobic molecules Hydrophilic = polar or charged Hydrophobic = uncharged or non polar Amphipathic = polar and non polar reactions on same region ____________________________________________________________________ Cohesion and adhesion: attraction between like molecules is called cohesion attraction between unlike molecules is called adhesion Water is cohesive: stays together b/c of hydrogen bonds adheres to surface with polar or charged components ____________________________________________________________________ Cohesion instrumental in phenomenon known as surface tension surface tension cohesive force caused by attraction between molecules at surface of liquid Water resists any force that increase its surface area resistance makes water surface act like elastic membrane ____________________________________________________________________  Biological Science 1/13/25 Biology: The Study of Life Page 8 of 18 Water expands as it freezes denser as a liquid than a solid forms relatively open crystal structure Speci c heat—around of energy needed to raise temp. Of 1 gram of substance by 1 degrees C. water has a very high speci c heat many hydrogen bonds must be broken for water molecules to move faster As molecules increase in polarity, it takes more energy to change their temp. ____________________________________________________________________ Chemical reactions occur when substances is combined with another broken down into another substance In most chemical reactions, chemical bonds are broken and new bonds form Reactions -> products Chemical equilibrium reactions is reversible, happens in both directions at the same time ____________________________________________________________________ Molecular weight mass of one mole of molecule sum of atomic weights of all atoms in molecule Molarity (M) concentration of substance in solution number of moles of solute present per liter of solution ____________________________________________________________________ Acids—substance gives up protons bases—substances that acquire protons pH (power of hydrogen) express concentration of protons in solution The pH scale acids have a p H of less than 7 bases have p H of greater than 7 natural indicates neither acidic or basic solution inside cells ins about p H 7 bu ers minimise changes in p H bu ers help maintain homeostasis ____________________________________________________________________ Expression is balanced: same number of atoms on each side System—set of interacting components If this system absorbs enough thermal energy from environment liquid water will convert to gas fi ff ff fi  Biological Science 1/13/25 Biology: The Study of Life Page 9 of 18 Endothermic reaction—absorbed heat;—reaction must absorb thermal energy to proceed Exothermic reaction—release heat ____________________________________________________________________ Energy—capacity to do work or supply heat Stored potential—potential energy object gains/loses ability to store energy due to its position Shared electrons are far from atoms nuclei—bonds are long and weak Electrons are shifted closer to one/both nuclei—bond becomes shorter and stronger Active molecular motion—kinetic energy—thermal energy molecules are constantly in motion temp—measure of thermal energy in molecules heat—measure of thermal energy being transferred between 2 objects ____________________________________________________________________ The rst law of thermodynamics energy is conserved it cannot be created or destroyed it can be transferred or transformed Energy transformation heat of chemical evolution molecules of early earth where exposed to massive inputs of energy Kinetic energy in form of heat presents in gradually cooling molten mass that formed planet The second law of thermodynamics entropy (disorder) always increases Physical and chemical processes proceed in direction that results in: Lower potential energy Increases entropy Or both ____________________________________________________________________ Chemical reaction are spontaneous if they proceed on their own—without external in uence no added energy is needed 2 factors determine if reaction will proceed spobtanrouly products have lower potential energy than the reactions product are less ordered than reactants Entropy is the amount of disorder in system ____________________________________________________________________ Stanley millers spark discharge experiment in 1953 experimental setup designed to produce microcosm of early earth Formed precursors to life molecules samples contained newly synthesized amino acids—building blocks of proteins Concluded that chemical evolution occurs readily if simple molecules with high free energy exposed to kinetic energy ____________________________________________________________________ fi fl  Biological Science 1/13/25 Biology: The Study of Life Page 10 of 18 Carbon except for water, almost all molecules found in organism have this atom forms 4 covalent bonds due to its 4 valence electrons Organic compounds—molecules that contain carbon limitless array of molecular shapes with di erent combinations of single and double bonds ____________________________________________________________________ ____________________________________________________________________ Wednesday Jan 22 Macromolecules: large molecule made of smaller molecular subunits (monomers) joined together polymer—larger number of monomers bonded together via polymerization (process of linking monomers together) ____________________________________________________________________ Condensation reactions (dehydration reactions) monomers polymerize via condensation reactions newly formed bond results production of a water molecule Reverse reaction is called hydrolysis—(water breaking): water molecules reacts with bond linking monomers, separating them from polymer chain ____________________________________________________________________ Hydrolysis dominates increase entropy is favorable energetically polymerization would occur only in high concentration of monomers to push reaction Equilibrium favors free monomers over polymers Macromolecules of life (protein, nucleic acids, carbohydrates etc.): may have polymerized early in chemical evolution ____________________________________________________________________ Chapter 3—portion structure and function Amino acids—building block of proteins: found in meteorites were most likely abundant during chemical evolution The type of molecule responsible for the origins of life must possess three attributes of life info replication evolution ____________________________________________________________________ ff  Biological Science 1/13/25 Biology: The Study of Life Page 11 of 18 Structure of amino acids Composed of central carbon atom bonded to H—hydrogen atom NH2—amino functional group COOH—carboxyl function group R group—variable “side chain” ____________________________________________________________________ Structure of amino acids in water, amino and carboxyl groups ionize to NH3^+ and COO^- respectfully Chargers on ctional groups necessary: helps amino acids stay in solution a ect amino acids chemical reactivity ____________________________________________________________________ R-group or side chain side chains contain functional groups: can participate in chemical reactions Some side chains have no functional groups: ff fi Biological Science 1/13/25 Biology: The Study of Life Page 12 of 18 solely consists of carbon and hydrogen atoms ____________________________________________________________________ Polarity and charge of R—group a ects solubility R-group types + chartered - basic - chaergers - acidic polar - oxygen non polar - no oxygen Non polar R-group[s are hydrophobic Lost a portion-must be acidic Has taken on proton-must be basic Highly electronegative oxygen will form polar covalent bind If answers to all three are no it is non polar amino acid ____________________________________________________________________ Amino acids polymerize when bond forms between carboxyl group of one amino acids and an amino group of another Peptide bond: C-N covalent bond resulting from condensation reaction ____________________________________________________________________ Peptide bond R-group orientation—side chains extend out of backbone so they can interact with each other or with water Directionality end with free amino group is the N-terminus end with free carboxyl group is the C-terminus by convention, written with N-terminus on left ff Biological Science 1/13/25 Biology: The Study of Life Page 13 of 18 Flexibility—peptide bond cannon rotate ____________________________________________________________________ Oligopeptide (few) or peptide chain of fewer than 50 amino acids Polypeptide (many) more than 50 amino acids Protein term used to describe amino acid chain residues complete, functional form of molecule ____________________________________________________________________ Proteins have unparalleled diversity of side, shape, and chemical properties of amino acid residues Proteins serve diverse function in cells b/c structure gives rise to function ____________________________________________________________________ Friday Jan 24th Notes What do proteins look like Structure rise to function proteins have unpara eled diversity of size, shape, and chemical properties of amino acid residues proteins serve diverse functions in cells b/c structure gives rise to function ____________________________________________________________________ Primary structure Fundamental to higher levels of protein structure: secondary, tertiary, and quaternary Each protein has unique sequences of amino acids Number of primary structures practically limitless 20 types of amino acids available Over 10,000 billion variations Lengths range from three amino acid residues to tens of thousands ____________________________________________________________________ Changes in primary structure a ect protein function Amino acid R-groups a ect polypeptide’s properties and function: single amino acid change can radically alter protein function example: hemoglobin: change in R-group product hemoglobin molecules that stick to one another ____________________________________________________________________ ff ll ff Biological Science 1/13/25 Biology: The Study of Life Page 14 of 18 Secondary structure Protein secondary structure formed by hydrogen bonds between: carbonyl group of one amino acid amino group of another amino acid Types of secondary structures: helix (alpha helix) beta pleated sheets Spiral - alpha helix Zigzag - beta helix ____________________________________________________________________ Tertiary structure Protein”s tertiary structure: results from interactions between residues between R-group and R-group or R-group and backbone these interactions cayuse backbone to bend and fold Bending and folding contribute to of polypeptide distinctive three-dimensional shape Five important types of R-group interactions: hydrogen bonding—form between polar side chains and opposite partial charges hydrophobic interactions—water forces hydrophobic side chains together van der Waals interactions—weak electrical interactions between hydrophobic side chains covalent bonding—covalent bonds between side chains of sul ydryl groups (disul de bonds) ionic bonding—form between groups with full and opposing charges ____________________________________________________________________ Quaternary structure bonding of 2 or more distinct polypeptide subunits produces quaternary structure multiple polypeptides interact to form single functional structure dimers—proteins with 2 polypeptide subunits homodimers—structure consists of 2 identical subunits heterodimer—subunits are not identical macromolecular machines: some cells contain molecular machines: complex of multiple proteins that carry out a particular function example: ribosome: consists of several nucleic acid molecules as well as over 50 di erent proteins ____________________________________________________________________ fh ff fi  Biological Science 1/13/25 Biology: The Study of Life Page 15 of 18 Protein structure is hierarchical primary structure (order of amino acids) responsible for secondary structure secondary structure fold up to form tertiary structure quaternary structure based on interactions between tertiary structure of polypeptide subunits ____________________________________________________________________ Protein folding directed by sequence of amino acids present in primary structure Normal protein folding is crucial and often spontaneous result of chemical bonds and interactions folded molecule more energetically stable than unfolded molecule—less potential energy Denatured (unfolded) protein unable to function normally ____________________________________________________________________ Cells contain proteins called molecular chaperones facilitate protein folding responsible for blocking inappropriate interactions between unfolded portions example: heat shock protein Hsp90: polypeptides can clump together and disturb normal folding process Hsp90 attaches to hydrophobic patches before aggregates can form ____________________________________________________________________ Each protein has characteristics folded shape necessary for its function many proteins are exible and dynamic when in an inactive state Protein folding is regulated: some proteins do not complete their folding until they bind with certain molecules ____________________________________________________________________ Mis ling can be “infectious” prions—altered folded forms of normal proteins prions protein (PrP) responsible for “mad cow disease” Prions can induce normal protein molecules to change their shape to the altered form ____________________________________________________________________ Proteins are crucial to most tasks required by cells: catalysis—speed up chemical reactions structure—shape cells and comprise body structures movement—motor proteins move cells or molecules within cells signaling—convey signals between cells transport—allow molecules to enter and exit cells or carry them throughout the body defense—antibodies attack pathogens ____________________________________________________________________ fi fl Biological Science 1/13/25 Biology: The Study of Life Page 16 of 18 Catalyzed reactions involve reactants called substrates Enzymes: proteins that function as catalysts hold subtracts in precise orientation: makes a reaction more likely to occur have active site—location on an enzyme where subtracts binds and react ____________________________________________________________________ Is it possible a protein catalyst was the rst molecule capable of replication researches have shown amino acids could have polymerized to form small proteins yet, attempt to simulate origin of like with proteins not successful Nucleic acids, however, do carry info ____________________________________________________________________ The tertiary structure of DNA Dna forms more compact three dimensional structures in cells compassion evident length of dan in each cell is approximately 6 ft long 2 forms of dan tertiary structure dna is wound too tightly or loosely; twists to form supercoils dna wraps around dna-binding proteins called histones ____________________________________________________________________ Watson and cricks model revealed DNA as the biological reservoir of info: stores info required for organisms growth and reproduction info consists of sequences of nucleotides in nucleic acid 4 nitrogenous bases function like letters in an alphabet ____________________________________________________________________ DNA replication has 3 steps 2 stands are separated by breaking hydrogen bonds free deoxribonucleotides form hydrogen bonds with complementary bases on original strand of DNA (template strand) phosphodiester linkages form to create new strand, called complementary strand complementary base pairing allows each strand to be copied exactly producing 2 identical daughter molecules ____________________________________________________________________ DNA double helix is a stable structure Double helix is highly structured held together by phosphodiester linkages, hydrogen bonds, and hydrophobic interactions functional groups participate in chemical reactions makes molecule stable and resistant to dentition stability of DNA key to e ectiveness of reliable info-storage molecule yet no support for hypothesis that rst life consisted of DNA alone ____________________________________________________________________ ff fi fi Biological Science 1/13/25 Biology: The Study of Life Page 17 of 18 Primary structure of RNA 4 types of nitrogenous bases extending from sugar-phosphate backbone Primary structure of RNA di ers from DNA RNA contains ribose instead of deoxyribose RNA contrains uracil instead of thymine 2’ —OH group on ribose is more reactive than —H RNA much less stable than DNA ____________________________________________________________________ DNA nucleotide seq. ATCG double helix supercoils histone complexes RNA sequence nucleotides AVCG hairpin loop 3D folded shape ____________________________________________________________________ Secondary structure RNA’s secondary structure results from complementary base pairing: A with U; G with C bases of RNA typically form hydrogen bonds with complementary bases on the same strand RNA strand folds over, forming hairpin structure two sugar-phosphate strands are anti-parallel ____________________________________________________________________ RNA molecules can have tertiary structure forms when secondary structure fold into more complex shapes RNA much more diverse in size, shape, and reactivity than DNA ____________________________________________________________________ RNA highly versatile folds into complex 3-dimensional shapes structure exibility allows them to perform many tasks as intermediate between DNA and protein, mRNA transmits info also helps regulate production of mRNA from DNA capable of catalyzing reactions Ribozymes (catalytic RNA molecule) RNAs can catalyze reactions three-dimensional structure vital to catalytic activity have active sites, like proteins ability to catalyze phosphodiester bonds that RNA could replicate itself ____________________________________________________________________ fl ff  Biological Science 1/13/25 Biology: The Study of Life Page 18 of 18 Theory of chemical evolution life began as naked self-replicators molecule in solution not enclosed in membrane To copy itself, rst living molecule had to ____________________________________________________________________ Evolution of protein enzymes would have marked end of RNA world 3 characteristics of life solidly on place: info processing replication of hereditary info evolution by random changes in nucleic acids ____________________________________________________________________ fi