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BIOLOGY STUDY GUIDE for Ms.Reep by Keshara Senanayake BIO QUIZ #1 CHAPTERS 24, 3, 2, and 1 24: The first cells 3: Carbon and the Molecular Diversity of Life 2: The Chemical Context of Life 1: Introduction: Evolution and the Foundations of Biology #THERETURN THE FIRST CELLS (Chapter 24 short notes 10th edition) -Our planet formed 4.6 billion years ago condensing from vast clouds of dust and rock that surrounded the young sun next hundred million years bombarded by rocks that made so much heat that vaporized all the water this bombardment ended 4 billion years ago - Chemical signatures of life date back 3.8 billion years the earliest evidence for fossils came 3.5 billions years were prokaryotes (for bacteria / archea) prokaryotes were earths first organisms and their descents had the planet for ~ 1.5 billion years until eukaryotes appeared about 1.8 billion years ago - Descendants of earth’s first cells have given rise to the diversity in prokaryotes today some prokaryotes live in extreme conditions (archea extremophiles) - Prokaryotes are also seen in “normal” habitats ability to live in a broad range of habitats is the reason why prokaryotes are the most abundant organism on earth Scientist hypothesize that the chemical and physical processes that could have produced simple cells through a sequence of four main stages 1) Abiotic synthesis of small organic molecules, such as amino acids and nitrogenous bases 2) The joining of these small molecules into macromolecules (protein + nucleic acids) 3) Packing of these molecules into protocells (droplets with membranes that maintained an internal chemistry different from their surroundings 4) The origin of self-replicating molecules that eventually made inheritance possible After bombardment of earth stopped, the first atmosphere probably had little oxygen and was probably thick with water vapor + compounds from volcanic eruptions (nitrogen + oxides +CO2 CH4 NH3 and H2) as earth cooled the water vapor condensed into oceans and hydrogen escaped into space In the 1920’s Russian scientist A. I oparin and British scientist Haldane independently hypothesized that was earth’s early atmosphere was a reducing environment in which organic compounds could have formed from simpler molecules. Energy for this organic synthesis could come from lightening and/or UV radiation. - Haldane said that early oceans were a solution of organic molecules, a “primitive soup from which life arose - In 1953 Stanley Miller (working under Harold uery at University of Chicago) tested the Oparin-Haldane hypothesis by creating laboratory conditions comparable to those that scientist at the time though existed on early Earth. yielded a variety of amino acids found in organisms today *** From “Origin of life experiment” sheet Miller used a flask which he created an “ocean” of water which he heated forcing water vapor to circulate. The flask at top contained the “atmosphere” consisting of CH4, NH3, and H2 with water vapor exposed gases to discharge (“lightening”) causing the gases to interact water soluble products of those reactants then passed through the condenser and was dissolved in the mock ocean. This yielded many amino acids ****************** some evidence points out that the early atmosphere was mostly nitrogen and CO2 (neither reducing or oxidizing) such neutral atmospheres have produced organic molecules also evidence shows small pockets of early atmosphere near volcanic openings might be reducing (maybe first organic compounds formed near volcanoes or deep sea vents Miller also did an experiment stimulating a volcanic eruption Miller-Urey type experiments show that the abiotic synthesis of organic molecules is possible under various assumptions 2nd source might be meteorites (Murchison meteorite had 80 amino acids in large amounts and other key organic molecules) a 2009 study showed that the abiotic synthesis of RNA can occur spontaneously from simple precursor molecules dripping solutions of amino acids or RNA nucleotides on hot sand/clay/rock had shown that the polymers form spontaneously without enzymes or ribosomes. amino acid polymers are a complex mix of linked/cross-linked amino acids such polymers might have acted as weak catalysts for a variety of reactions Life can not permit without reproduction and metabolism DNA molecules carry genetic information including the info to replicate required enzymatic machinery + supply of nucleotide building blocks suggests that the self-replicating molecules and a metabolism-like source of building blocks may have appeared together in early protocells. needed conditions might have been met in vesicles (fluid-filled compartments enclosed by a membrane-like structure) research shows idiotically produced vesicles can exhibit certain life properties of life including simple reproduction and metabolism as well as the maintenance of an internal chemical environment different from that of their surroundings abiotically produced vesicles can reproduce on their own and they can increase in size without dilution of their contents experiments have shown they have a selectively permeable bilayer and can perform metabolic reactions using an external source of reagents First genetic material was mostly likely RNA RNA is important for protein synthesis but It can perform many enzyme-like catalytic functions such RNA catalyst are called ribozymes and some of them can make complementary copies of short pieces of RNA if they are supplied with nucleotide building blocks Natural selection on the molecular level has produced ribozymes capable of self-replication in the lab unlike DNA’s helical form RNA is single stranded and can take on a variety of 3D shapes mandated by their nucleotide sequences RNA replicates fast w/ fewer errors than others and is best suited to the environment and has the greatest ability to replicate itself and leave the most descendant molecules. An occasional copying error will result in a molecule to have a shape that is more adept at self-replication > Life is produced by an “RNA World” in which small RNA could replicate and store genetic information about the vesicle that carried them vesicle can grow/split/pass its RNA molecules to its daughters, the daughters would be protocells that had some of the properties of their parent first protocells likely carried only limited amount of genetic information it had been acted on by natural selection the most successful of early protocells would have increased in number once RNA sequences that carried genetic info appeared it protocells many additional changes was made possible RNA could have been the template on which DNA was assembled double stranded RNA is more chemically stable storage for genetic information and DNA can be replicate more accurately this was advantageous as genomes grew larger through gene duplication and other processes and as more properties of the protocells became coded in genetic information. Once DNA appeared new forms of life did also. oldest known fossils are of stromatolites layered in rocks that formed the activities of certain prokaryotes earliest date 3.5 billion years ago for several hundred million years all such fossils were similar in overall structure by 3.1 billion years stromatolites with two distinctly different morphologies appeared and by 2.8 billion years stromatolites appeared in salty lakes and marine environments these shows early signs of ecological and evolutionary change over time Cynobacteria was the main photosynthesis organism for over billions years and they continue to be the most important groups of photosynthesis organisms alive today. early Cynobacteria had the greatest impact organisms have ever had on our planet the release of oxygen to the earth’s atmosphere during watersplitting step of photosynthesis --Chapter 3 - CARBON AND THE MOLECULAR DIVERSITY OF LIFE Carbon, can bond to 4 atoms and this is the basis for the structural/functional diversity of organic molecules a small # of monomers are joined to form a large variety of molecules FOUR CLASSES Carbohydrates monomer: monosaccharides functions: energy source, raw materials, energy storage, structural compounds Lipids monomer: glycerol and fatty acids fats; phospholipids; steroids function: Energy Storage (fats), membrane components (phospholipids), hormones (steroids) Proteins monomer: amino acids functions: enzymes, transport, movement, receptors, defense, structure, storage, hormones Nucleic acids monomer: nucleotides functions: heredity, various functions in gene expression Organic compounds contain carbon and hydrogen include lipids and huge macromolecules (carbs/proteins/nucleic acids) Carbon’s valence shell is the reason why it can form large and complex molecules carbon forms 4 single covalent bonds the resulting portion is in a tetrahedral shape when two carbons are joined by a double bond, the other atoms bonded to the carbon are in the same plane, forming a flat molecule Carbon skeletons vary in length/placement of double bonds/having rings hydrocarbons consist of only carbon + hydrogen are hydrophobic due to nonpolar C-H bond (release energy when broken) Properties of organic molecules are largely determined by characteristic chemical groups attached to a carbon skeleton six main functional groups first five are hydrophilic groups which also increase the solubility of organic compounds in water 1) The hydroxyl group consists of hydrogen and oxygen (-OH) organic molecules with hydroxyl group are called alcohol (usually end in -ol) 2) Carbonyl group has carbon double bonded to oxygen (> CO) if the carbonyl group is at the end of the carbon skeleton it is an aldehyde (otherwise this is an ketone) 3)Carboxyl group has carbon double bonded to an oxygen also attached to an -OH group (-COOH) Compounds with a carboxyl group are called carboxylic acids (organic acids) tend to release H+ to become carboxyl ate ion 4) amino group nitrogen atom bonded to two hydrogen atoms (-NH2) compounds with amino groups are amines and can act as bases (picks up H+ to become -NH3) both amino and carboxyl group are ionized at normal cellular pH 5) Phosphate group bonded to carbon skeleton by an oxygen attached to a phosphorus atom that is bonded to three other oxygen atoms (-OPO3^2-) this anion contributes to a negative charge to organic phosphates 6) Methyl group carbon bonded to three hydrogens (-CH3) Methylated compounded may have their function modified due to the addition of the methyl group nonpolar methyl might alter molecule shape and may serve as a single on organic molecules 7 )Sulfhydryl group has sulfur atom bonded to an hydrogen (-SH) Thiols are compounds w/ sulfhydryl group ATP is an important source of energy for cellular processes ATP consists of the organic molecule adenosine to which the phosphate groups are attached when ATP reacts with water the third phosphate splits off and energy is released Polymers are chainlike molecules formed from linking together monomers monomers are joined by dehydration synthesis in which one monomer provides a hydroxyl group (-OH) and the other contributes a hydrogen (-H) to release a water molecules in hydrolysis the bond between monomers is broken by the addition of water. The hydroxyl group of a water molecule is join to one monomer while the hydrogen is bonded with the other - enzymes are catalysts in both reactions Carbohydrates serve as fuel and building material carbs include sugars and their polymers has the general formula of (CH2O)n -- n of these units forming sugar varies from three to seven. Hexoses, trioses, and pentoses are most common Glucose is broken down to yield energy for cellular respiration monosaccarahides serve as raw materials for the synthesis of other organic molecules two monosaccharides are joined by glycosidic linkage to form a disaccharide Polysaccharides are storage or structural macromolecules starch is a storage molecule in plants (polymer made up of glucose molecules joined by 1-4 linkage that gives starch a helical shape) animals use glycogen a highly branched polymer of glucose as their energy source cellulose, the major component of plant cell walls is the most abundant organic compound on earth differs in that its ring form of glucose is in the beta form and has a flipped geometry of the glycosidic bonds. In plant cell wall, hydrogen bonds between hydroxyl groups hold parallel cellulose molecules together to form strong micro fibril Enzymes that digest alpha linkage in starch are unable to hydrolyze beta in cellulose (in diagram beta has OH up and alpha has OH below) only certain prokaryotes/protists/fungi can digest cellulose >chitin is a structural polysaccharide formed from glucose monomers with a nitrogen containing group LIPIDS are a diverse group. Fats, phosolipids, and steroids are part of lipids based on their hydrophobic behavior (lipids do not form polymers) Fats are composed of fatty acids attached to the three-carbon glycerol fatty acids consist of a long hydrocarbon chain with a carboxyl group at one end a triacylglycerol (or fat) consist of three fatty acid molecules, each linked to a glycerol with an ester linkage bond that forms between hydroxyl and a carboxyl group (triglyceride is another name for fats) Fatty acids with double bonds in their carbon chain are called unsaturated fatty acids the double bond creates a kink in the hydrocarbon chain and prevents fat molecules with unsaturated fatty acids from packing closely together (can’t add more hydrogens) saturated fatty acids have no double bonds and most animal fats are saturated fats are excellent storage molecules, containing twice the energy of carbohydrates such as starch Phospholipids consists of glycerol linked to two fatty acids and a negatively charged phosphate group, to which other small molecules are attached phosphate head is hydrophilic and water soluble while the two fatty phospholipids acid chains are hydrophobic makes them ideal for cell membranes hydrophilic head faces aqueous environment tails are associated with the center and is shielded from water steroids are a class of lipids distinguished by four connected carbon rings with various chemical groups attached cholesterol is a common component of animal cell membranes and a precursor to many steroids which includes hormones Proteins include a diversity of structures so it has many functions most enzymes functions as catalyst that relatively speed up chemical reactions are proteins protein is a functional molecule that consist of 1 or more polypeptides each in a specific 3D shape a polypeptide is a polymer of amino acids Amino acids are composed of a central carbon (called alpha carbon) bonded to a hydrogen atom, carboxyl group, an amino group, and a R (variable) group the pH of the cell makes it that the amino and carboxyl groups are usually ionized R group gives a unique physical/chemical property to each amino acid side chains can be polar/nonpolar (hydrophilic/hydrophobic) a peptide links the carboxyl group or one amino acid with the amino group of another. A string of amino acids make up a polypeptide had an amino end (N-terminus) and a carboxyl end (C-terminus) a protein has a unique 3D shape created by the folding of 1 or more polypeptide chains usually arise spontaneously depening on the sequence of the amino acids various types of bonds form between parts of the chain as the protein is synthesized in the cell unique structure of a protein enables it to recognize and bind to other molecules gobular proteins are roughly spherical, fibrous proteins are long fibers Primary structure genetically coded sequence of amino acids within a protein Secondary structure involves regions of coiling or folding of the polypeptide backbone stabilized by hydrogen bonds between oxygen (negative partial charge) of one peptide bond and the partially positive hydrogen attached to the nitrogen of another peptide bond >alpha helix is a coil produced by hydrogen bonding between every 4 th amino acid beta pleated sheet is held by repeated hydrogen bonds along regions of the polypeptide backbone lying parallel to each other tertiary structure 3D shape of a proteins results from the interaction between the various side chains (R groups) of the amino acid following chemical interactions produce the unique shape of the protein: hydrophobic interactions between nonpolar side groups clumped in the center of the molecule due to their repulsion of water Van Der Waals interactions among those nonpolar chains, and ionic bonds between negatively and positively charged side chains >strong covalent bonds called DISULFIDE BRIDGES may occur between the sulfhydryl side groups of Cysteine monomers that have been brought together by the folding of the polypeptide Quaternary structure occurs in proteins that have more than 1 polypeptide individual polypeptide unites are held together by a precise functional protein sick-cell disease is a change in one amino acid affecting the structure of a hemoglobin molecule causing red blood cells to become sickle shaped the bonds/interactions/shape of a protein can be interrupted by changed in pH/salt concentration/temperature Denaturation also occurs if a protein is transferred to an organic solvent its hydrophobic regions are on the outside interaction with the nonpolar solvent using X-ray crystallography biochemist have identified the structure of thousands of proteins can be related to the specific functions of different regions of a protein Nucleic acids store, transmit, and help express hereditary information Genes are the units of inheritance that determine the primary structure of proteins Nucleic acids are polymers made of nucleotide monomers DNA (deoxyribonucleic acid) is the genetic material that is inherited from one generation to the next and is replicated when cells divide (so that all cells have identical DNA in an organism) instructions coded in DNA are transcribed to RNA (ribonucleic acid) this directs the synthesis of proteins which is the “ultimate enactors of the genetic program” in a eukaryotic cell DNA is in the nucleus messenger RNA (mRNA) carried instructions for protein synthesis to ribosomes located in the cytoplasm Polynucleotides are polymers of nucleotides monomers that consist of a pentose (5-carbon sugar) covalently bonded to a phosphate group and to a nitrogenous base a nucleotide may contain more than one phosphate group without the phosphate group is is called a nucleoside Nitrogenous bases are either pyrimidines or purines which each respectively contains one or two nitrogen containing rings Adenine, Guanine, and Cytosine are in both DNA and RNA thymine is only in DNA and uracil is only in RNA in DNA the sugar is deoxyribose while in RNA it is ribose in a nucleotide the base attached to the 1’ carbon and a phosphate group attached to the 5’ carbon of the sugar Nucleotides are linked together into a polynucleotide by phosphodiester linkage which join the sugar of one nucleotide with the phosphate of the next the polymer had 2 distinct ends: a 5’ end w/ a phosphate attached to the 5’ carbon sugar and a 3’ end with a hydroxyl group on the 3’ carbon of a sugar nitrogenous bases extend from the backbone of repeating sugar phosphate units unique sequences of bases in a gene codes for the specific amino acid sequences of a protein DNA molecules consist of two polynucleotide (Strands) spiraling in a double helix two sugar-phosphate backbones run in a opposite 5’ to 3’ direction an arrangement that is ant parallel >nitrogenous bases pair and hydrogen bond together inside the molecule Adenine pairs with thymine; guanine pairs with cytosine so the sequences of nitrogenous bases on the two strands or DNA are complementary because of this specific base pairing DNA can replicate itself Genes form the heredity link between generations closely related members of the same species share many common DNA sequences and proteins. More closely related species have a large proportion of their DNA/proteins in common this “Molecular genealogy” provides evidence of evolutionary relationships Chapter 2 CHEMICAL CONTEXT OF LIFE elements cannot be broken down chemically to other substances a compound contains two or more different elements in a fixed ratio an atom is the smallest unit of an element. It’s nucleus has protons (+ charged) + neutrons (neutral) and electrons (- charge) around the nucleus protons determine element / neutrons for isotope / electron for chemical behavior an electrical neutral atom has equal numbers of electrons and protons unstable isotopes gives off particles and energy as radioactivity >in an atom electrons occupy specific electron shells; the electrons in a shell have a characteristic energy level electron distribution in shells determines the chemical behavior of an atom an atom that has an incomplete outer shell (valence shell) is reactive Chemical bonds form when atoms interact and complete their valence shells covalent bonds form when pairs of electrons are shared single bond H-H double bond is sharing two pairs of electrons ( O2) molecules consist of two or more covalently bonded atoms. The attraction of an atom for the electrons of a covalent bond is its electro negativity electrons of a polar covalent bond are pulled closer to the more electronegative atom ions form when an atom or molecule becomes charged (loss/gain of electron) weak bonds reinforce the shapes of large molecules and help molecules adhere to each other a hydrogen bond is an attraction between hydrogen and F O or N Van der Waals interactions occur between transiently positive and negative regions of molecules molecular shape is usually the basis for the reorganization of one biological molecule by another chemical reactions change reactants into products while conserving matter chemical equilibrium is reached when forward and reverse reaction rates are equal hydrogen bonding is responsible to cohesion (waters attraction to itself) also responsible for waters high surface tension water has a high specific heat heat is absorbed when hydrogen bonds break and is released when hydrogen bonds form this helps keep temperatures relatively steady within which permits life evaporative cooling is based on water’s high heat of vaporization the evaporative loss of the most energetic water molecules cools a surface ice floats because it is less dense than liquid water allows life to exist under the frozen surfaces of lakes and seas water is an “universal solvent” because its polar molecules are attracted to ions and polar substances that can form hydrogen bonds hydrophilic substance have an affinity for water (while hydrophobic substances do not) molarity is the # of moles of solute per liter solution is used as a measure of solute concentration in solutions a mole is a certain number of molecules of a substance a mass of a mole of a substance in grams is the same of the molecule mass in Daltons a water molecule can transfer an H+ to another water molecule to form H3O+ (hydronium ion) represented by H+ and OH a concentration of H+ is expressed a pH pH is -log[H+] a buffer consists of an acid-base pair that combines reversibly with hydrogen ions allowing it to resist pH change the burning of fossil fuels increases the amount of CO2 in the atmosphere. Some CO2 dissolves in the oceans causing ocean acidification which is dangerous to the coral reefs CHAPTER 1 : EVOLUTION AND (oh my hands) THE FOUNDATIONS OF BIOLOGY reductionism is the approach of reducing complex systems to simpler components that are more manageable to study emergent properties are due to the arrangement and interactions of parts as complexity increases results from the structural arrangement and interaction of parts a reductionist approach to biology lacks some of the properties that energy at higher levels of organization to fully understand emergent properties biologists today complement reductionism with systems biology the exploration of a biological system by analyzing the interactions amount the parts Biosphere ecosystems communities populations organism organ and organ systems molecules organelles tissues cells At all levels of biological hierarchy, we find a correlation of structure and function analyzing biological structures gives us clues about what it does and how it works knowing function also helps us find structure/organization Cell is the smallest unit of organization that can perform all required activities all cells share certain characteristics every cell is enclosed by a membrane that regulates the passage of materials between the cell and its surroundings -> we recognize two main forms of cells: prokaryotes and eukaryotes the cells of two groups of single celled microorganisms -- bacteria and archea are prokaryotic. all other forms of life, including plants and animals are composed of eukaryotic cells the eukaryotic cell contains membrane-enclosed organelles some organelles such as DNA containing nucleus, are found in the cells of all eukaryotes; other organelles are specific to particular cell types chloroplast are only found in eukaryotic cells a prokaryotic cell lacks a nucleus or other membraneenclosed organelles also prokaryotic cells are generally smaller within cells, structures called chromosomes contain genetic material in the form of DNA (deoxyribonucleic acid) the substances of genes genes are the units of inheritance that transmit information from parents to offspring genes are located on chromosome long DNA molecules that replicate before cell division and provide identical copies to daughter cells the biological instructions for the development and functioning of organisms are coded in the arrangement of the four kinds f nucleotides on the two strands of DNA double helix most genes program the cell’s production of proteins and almost all cellular structures and actions gene expression is the process by which a gene’s information is transcribed to RNA and then translated into protein genes also code for RNAs that serve other functions like regulating gene expression all the genetic instructions of an organism inherits make up its genome under a system called genomics scientist study whole sets of genes in one or more species bioinformatics provides the computational tools to process and analyze the resulting data from technology Life required energy producers transform light energy to chemical energy in sugars which powers cellular activities in plants consumers eat plants and other organisms, using the chemical energy in their good to power their movement, growth and other activities. In each energy is lost (as heat) to surroundings Interactions between organisms can be mutually beneficial or harmful. evolution helps explain how diverse organisms of the past and present are related through descent from common ancestors and how organisms become adapted to their environment Scientist have identified 1.8 million of 10-100 million species biologist have grouped species into group categories from genera to family, to order, class phylum and kingdom three domains. Prokaryotes are divided into Bacteria and Archea. All eukaryotes are in domain Eukarya. within this diversity of life we all share the universal genetic language of DNA Charles Darwin’s presented a case for “descent with modification” the idea that present forms have diverged from a succession of ancestral forms. Darwin proposed natural selection as the mechanism of evolution drawing an inference from three observations: Individuals vary in many heritable traits, the overproduction of offspring sets up a competition for survival, and species are generally matched to their environment Darwin used this to infer that individuals with traits best suited to the environment leave more offspring than “less-fit” individuals do this natural selection (or unequal reproductive success) within a population results in the general accumulation of favorable adaptations to the environment the diversity of life results from natural selection acting over millions of generations as populations adapted to different environments the tree-like diagram of evolutionary relationships reflect the branching genealogy extending from ancestral species. similar species share a common ancestor at a more recent branch on the tree of life. distantly related species share a more ancient common ancestor science is an approach to understanding the natural world that involved inquiry (search for information by asking questions and endeavoring to answer them) careful/veritable observation and analysis of data are the basis of scientific inquiry observations involve our sense and tools that extend our senses data quantitative (#’s) and qualitative are recorded observations using inductive reasoning generalizations can be drawn from collections of observations (observation pattern tentative hypothesis theory this is specific to broader generalizations) observations and inductions lead to search for causes/explanation hypothesis is a tentative answer to a question or an explanation of observation leads to predications that can be tested deductive reasoning uses “if…then” logic proceeds from general to the specific (theory hypothesis observation confirmation “support”) test multiple hypothesizes a hypothesis cannot be proven to be true; the more attempts to falsify it that fail, however, the more a hypothesis gains credibility controlled experiment is which subjects are divided into experimental and control groups both groups are alike except for one variable that the experiment is trying to test a theory is a broader in scope than a hypothesis generated many specific hypothesis and is supported by a large body of evidence. Still, a theory can be modified or even rejected when results and new evidence no longer supports it Science is applied technology Class notes (that apply) -When counting carbon start clockwise PEEP THESE ESTER BONDS THAT FORM #AMINO ACID LIFE Good to know Glycine ( R = Hydrogen) Cysteine (R = CH2 -SH) and Alanine (R = CH3) #TEAMCARBS Forming peptide bond