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BIO 121
Jason Wiles

Chapter 8: Introduction to Metabolism ▯ Metabolism: totality of an organisms chemical reactions o Emergent property of life o Manages material & energy resources of cells ▯ Metabolic pathway: starts with a specific molecule, then altered in a series of steps o ▯ lead to a certain product o each step catalyzed by a specific enzyme o Specific mechanisms regulate enzymes, balance metabolic supply & demand ▯ Catabolic pathways: degradative process (breakdown) o Major pathway is cellular respiration ▯ Converts chemical energy in (food energy), ▯ Glucose ▯ chemical energy in ATP ▯ By products: (heat, CO2, H20) • Organic fuels broken down ▯CO 2& H 2O with the presence of Oxygen • The stored energy can now be used for work with in cell o Exergonic o Large complex molecules ▯ smaller ▯ Anabolic pathways: consume energy to build complicated molecules from simpler ones o Endergonic ▯ Bioenergetics: the study of how energy flows through living organisms ▯ Energy: the capacity to cause change ▯ Some kinds can be used to do work ▯ Ability to rearrange collection of matter o Kinetic Energy: the relative motion of objects – energy of motion ▯ Performs work by imparting motion to other matter • Ex. Playing pool (cue ▯ ball ▯ ball) • Space station orbiting earth ▯ Heat (thermal energy): kinetic energy associated with random movement of atoms or molecules ▯ Light energy: photosynthesis o Potential Energy: energy that matter possesses because of its location or structure ▯ Ex. Water behind a dam because of its altitude ▯ Its source of energy: covalent bonds of sugar molecules o Chemical Energy: the potential energy available for release in a chemical reaction ▯ Complex molecules such as glucose increase in chemical energy ▯ Thermodynamics: study of the energy transformations that occur in a collection of matter o System: the matter understudy o Surroundings: everything else ▯ Isolated system: unable to exchange energy or matter with surroundings (ex. Liquid in thermos) ▯ Open system: energy and matter can be transferred between system and surroundings 1. First law of thermodynamics: the energy of the universe is constant, energy can be transferred or transformed by not created or destroyed • Conservation of energy – energy cannot by created or destroyed • Converts energy to the useful form o Sunlight ▯ chemical energy (plants) 2. Second law of thermodynamics • During every energy transfer/transformation some energy becomes unavailable to do work o More usable forms of energy are at least partly converted to heat, energy associated with random motion of atoms and molecules • No energy transfer is 100% efficient (dissipates as heat) o Random motion contributes to entropy o Entropy: quantity a measure of disorder, or randomness (a closed system (universe), continuously increasing) – total energy ▯ Spreading out of energy • Every energy transfer or transformation increases the entropy of the universe o Total energy available to do work in CS decreases over time • Spontaneous process: a process that can occur w/o an input of energy o Ex. Explosion or rusting of an old car ▯ Free energy: portion of a system’s energy that can perform work when temp. and pressure are uniform throughout the system, as in a living cell o ∆G = change in free energy o Change in systems enthalpy: helps predict spontaneity of a process ▯ ∆G = ∆H - T∆S ▯ change in systems entrophy • T = absolute temp (k) • ∆G represents the difference between the free energy of final state and initial state • ∆G = G fina– Ginitial ▯ a measure of a systems instability – tendency to ∆ to a more stable state o Equilibrium: describes state of max stability o A process is spontaneous and can perform work only when it is moving toward equalibrium ▯ In a spontaneous change o ∆G < O free energy decreases o System becomes more stable o Released free energy can be harnessed to do work ▯ Exergonic reaction: proceeds with a net release of free energy o G decreases therefore ∆G is negative (greater amount of work can be done) o Spontaneous reactions o Downhill o Ex. A ▯ B+C+heat = free energy ▯ Endergonic reaction: absorbs free energy from surroundings, stores free energy in molecule o G increases ▯ ∆G is positive o Nonspontaneous o Anabolism o Uphill o ATP – immediate source of energy ▯ ADP + P ▯ ATP o Products have > potential energy than reactants o Constant flow of materials in and out of cell is what keeps it alive ▯ never reaches equilibrium ▯ 3 main kinds of work 1. Chemical work: pushing of endergonic reactions that would not occur spontaneously o Ex. Synthesis of polymers from monomers 2. Transport work: pumping of substances across membranes against the direction of spontaneous movement 3. Mechanical work: beating of cilia, or contraction of muscle cells ▯ Energy coupling: use of an exergonic process to drive an endergonic one o ATP is responsible for mediating most energy in coupling in cells ▯ ATP: is the high-energy source of adenosine because it has the most phosphate groups (3) ▯ Hydrolysis of ATP o Bonds between phosphate groups can be broken by hydrolysis ▯ Phosphorylated intermediate: recipient with the phosphate group covalently bonded to it o Coupling exergonic and endergonic reactions in this form - more reactive & less stable ▯ Enzyme: a macromolecule that acts as a catalyst, a chemical agent which speeds up a chemical reaction without being consumed by the reaction o Chemical reactions include bond breaking and forming ▯ (EA) activation energy: energy required to contort the reactant molecule so that bonds can break. Energy used to start a reaction o Enzymes lower activation energy o Amount of energy needed to push reactants to top of an energy barrier ▯ Often in form of heat energy ▯ AB+CD ▯ AD+BC ▯ Reactants Products ▯ Substrate: the reactant on enzyme acts on is referred to as the enzyme’s substrate ▯ Enzyme – substrate complex: formed from the enzyme binding to its substrate Enzyme + enzyme- Enzyme + Substrate(s) substrate product(s) Complex ▯ Active site: a pocket or grove on the surface of the enzyme where catalysis occurs o Restricted region of enzyme where it bonds to substrate ▯ Induced fit: a clasping handshake, brings chemical groups of the active site into positions that enhance ability to catalyze enzyme reaction o Helps break and form bonds ▯ Cofactors: adjusts nonprotein helpers for catalytic activity binds to enzyme o May be bound tightly to enzymes as permanent residents o Ex. Vitamin ▯ Coenzyme: if a cofactor is an organic molecule o Ex. Important vitamins in nutrition ▯ Inhibitors: disrupts normal interactions between enzymes and substrate o But is reversible, must add a new enzyme after inhibitor o Competitive inhibitors: reduce the productivity of enzymes by blocking substrates from entering active sites (competes with substrate for active site) o Noncompetitive inhibitors: don’t directly compete with the substrate to bind to the enzyme at the active site (not competing for active site) ▯ Distorts shape of enzyme o Irreversible inhibition: inhibitor forms a covalent bond with an amino acid side group within active site, which prevents the substrate from entering active site or prevents catalytic activity ▯ Allosteric regulation: describes any case in which a proteins function at one site is affected by the binding of a regulatory molecule to a separate site o Inhibition or stimulation of activity ▯ Cooperativity: this mechanism amplifies the response of enzymes to substrates o A substrate molecule binding to one active site in a multisubunit enzyme triggers a shape change in all subunits ▯ increasing catalytic activity at other sights ▯ Feedback inhibition: a metabolic pathway is switched off by the inhibitory binding of its end product to an enzyme that acts early in the pathway (end product inhibits earlier reaction in metabolic pathway) ▯ Temp & pH influencing enzymes o Cold – stops working o Hot – changes and do different things ▯ Curve of activity Chapter 9: Cellular respiration and fermentation ▯ Chemical Cycling System ▯ Cellular respiration & breathing differ in that cellular respiration is at cellular level and breathing is at organism level Chapter 10: Photosynthesis ▯ Photosynthesis: 6CO 2 + 6H 0 ▯ C 6H12O 6+ 6O 2 ▯ Photosynthetic membranes found in chloroplasts in plant cells ▯ Light reactions of photosynthesis use water and produce NADPH ▯ Sunlight is the ultimate source of energy to support most life on earth o Plants – photoautotroph: use light energy to drive the synthesis of organic molecules from inorganic ▯ Role of CO 2in photosynthesis o Is fixed or incorporated into organic molecules ▯ Plants are classified as producers because they fix inorganic carbon into organic molecules ▯ > 1/billion of the suns totally energy reaches earth o all solar energy is eventually re-radiated to space as heat Chapter 26: Phylogeny and the Tree of Life ▯ All living things are related ▯ Phylogeny: evolutionary history of a species or group of species o Systematics: a discipline focused on classifying organisms and determining their evolutionary relationships ▯ Taxonomy: how organisms are named and classified ▯ Binomial: 2-part format of scientific name 1. Genus: to which the species belongs 2. Specific epithet, each species within genus ▯ Taxonomic System – figuring out how closely related organisms are o Species ▯ Genus▯Family▯ Order▯ Class▯ Phylum▯ Kingdom▯Domain o Taxon: the named taxonomic unit at any level of the hierarchy ▯ Phylogenetic tree: a branching diagram where the evolutionary history of a group of organisms can be represented o Most readjust certain classifications because of evolution ▯ *C. Darwin “I think..” ▯ Phylocode: only names groups that include a common ancestor and all of its descendants ▯ Analogy: constructing a phylogeny is similarity due to its convergent evolution o Homology: similarity due to shared ancestry o Homoplasies: analogous structures that arose independently ▯ Cladistics: common ancestry is the primary criterion used to classify organisms o Clades: includes an ancestral species and descendants groups within cladistics o Monophylectic: (taxon = to a clad), signifying that it consists of an ancestral species and all its descendants o Paraphylectic: an ancestral species and some of its descendents o PolyphyleticL includes taxa with different ancestors ▯ Shared ancestral character: a character that is originated in an ancestor of the taxon o Even if all ancestors don’t have to characteristic ▯ Shared derived character: an evolutionary novelty unique to a clade ▯ Molecular clock: regions of DNA change at a rate consistent enough to serve o The amount of genetic change is used to estimate the date of past evolutionary events ▯ Outgroup: a species or group of species from an evolutionary lineage that is know to have diverged before the lineage that includes the species we are studying – in group ▯ Maximum parsimony: first investigate the simplest explanation that in is consistent with the facts ▯ Maximum likelihood: given certain probability rules about how DNA sequences change over time, a tree can be found the reflects the most likely sequence of evolutionary events ▯ Gene duplication plays a big role in evolution, increasing number of genes in the genome o Further evolutionary change ▯ Gene families: groups of related genes within an organisms genome ▯ Orthologous genes: those found in different species and their divergences traces back to the speciation events that produce the species ▯ Paralogous genes: the homology results from gene duplication ▯ multiple copies of these genes have diverged from one another within a species ▯ Neutral theory: much evolutionary change in genes and proteins has no effect on fitness and therefore is not influenced by natural selection ▯ 3 Domains of all life: Chapter 27: Bacteria and Archaea ▯ First organisms – prokaryotes o Unicellular o Form colonies o Different shapes ▯ Spiral, spherical, rod like ▯ Cell wall of prokaryotic cells o Maintains cell shape, protects, prevents from bursting in a hypotonic environment ▯ Peptidoglycan: a polymer composed of modified sugars cross-linked by short polypeptides o Bacterial cell walls – antibiotics work here o Archaeal cell walls contain polysaccharides & proteins but not poptidoglycan ▯ Gram stain; allows scientists to classify many bacterial species into two groups based on differences in cell wall composition o Gram-positive bacteria have simpler walls (large amount of peptidoglycan), staining outer layer, cell wall o Gram-negative bacteria have less peptidoglycan and are structurally more complex with lipopolysaccharides ▯ Ex. Ancestors of mitochondria ▯ Double membranes more likely to be antibiotic resistant ▯ Capsule: surround cell wall; sticky layer of polysaccharide or protein – covers many prokaryotes ▯ Fimbriae: hair like appendages – allows prokaryotes to stick to their substrate or one another ▯ Pili: appendages that pull two cells together prior to DNA transfer from one cell to another ▯ Taxis: (half of prokaryotes are capable) a directed movement toward or away from a stimulus ▯ Genes for the resistance of antibiotics are usually located on plasmids ▯ Genetic recombination: combining of DNA from two sources – additional diversity ▯ Transformation: the genotype and possibly phenotype of a prokaryotic cell are altered by the uptake of foreign DNA from its surroundings o Take in DNA fragments released by other cells ▯ Transduction: phages carry prokaryotic genes from one host cell to another o Usually results from accidents that occur during the phage replicative cycle ▯ Conjugation: DNA is transferred between two prokaryotic cells that are temporarily joined o In bacteria DNA transfer is always one-way, one cell donates the other receives it o F factor of E coli, 25 genes, most required for production of pili o In a plasmid form: functions as DNA donors during conjugation o R plasmids: carry resistance genes ▯ Phototrophs: organisms that obtain energy from light ▯ Chemotrophs: those that obtain energy from chemicals ▯ Autotrophs: organisms that only need CO 2 in a form of carbon ▯ Heterotrophs: require at least on organic nutrient ▯ Photoheterotrophs: heterotrophs that use light energy, and cannot use CO 2as a sole carbon source ▯ Chemoheterotrophs: heterotrophs, use inorganic/organic energy sources, and cannot fix carbon to form their own ▯ Chemoautotrophs: get energy from chemical reactions and get all other organic compounds from CO 2 o Use inorganic energy ▯ Photoautotrophs: use light energy, converts CO 2▯ organic materials ▯ Obligate aerobes: must use O 2 for cellular respiration, and cant grow without it ▯ Olbigate anaerobes: poisoned by O 2, some live by fermentation o Anaerobic respiration – a way to extract chemical energy ▯ Facultative anaerobes: use O2 if it is present but can also carry out fermentation or anaerobic respiration in an anaerobic environment (w/ or w/o O2) ▯ Nitrogen is essential for the production of amino acids and nucleic acids in all organisms o Prokaryotes can metabolize nitrogen in a wide variety of forms o Eukaryotes can obtain nitrogen from a limited group of nitrogen compounds o Nitrogen fixation: a process where some cyanobacteria and some methanogens convert atmospheric nitrogen to ammonia ▯ Heterocysts – carry out only nitrogen fixation ▯ Biofilms: surface-coated colonies where metabolic cooperation between different prokaryotic species o Cells secret signaling molecules that recruit nearby cells ▯ colonies grow Archaea ▯ Share certain traits with bacteria and other traits with eukaryotic cells ▯ Extremeophiles: first prokaryotes in archaea domain live in environments so extreme that few other organisms can survive there ▯ Extreme halopiles: live in highly saline environments, great salt lake ▯ Extreme thermophiles: thrive in very hot environments Chemical Recycling ▯ Decomposers: break down dead organisms as well as waster products ▯ unlocking supplies of carbon, nitrogen and other elements Pathogenic Bacteria ▯ Exotoxins: proteins secreted by certain bacteria and other organisms o Cholera is caused by an exotoxin ▯ Endotoxins: lipopolysaccharide composed of the outer membrane of gram-negative bacteria o Are released only when the bacteria die and their cell well breaks down Chapter 28: Protists ▯ Protist: unicellular group of eukaryotes o Organisms in most eukaryotic lineages are protists o Colonies are loosely collected group of protists o Coenocytes: large masses of cytoplasm o Multicellular means composed of many cells ▯ Mixotroph: combine photosynthesis and heterotrophic nutrition o Photoautotrophs contain chloroplasts o Heterotrophs: absorbing organic molecules or ingesting larger food particles ▯ Some reproduce sexually, others asexually, or at least use the sexual process, meiosis or fertilization ▯ Endosymbiosis: the process in which certain unicellular organisms engulf other cells, endosymbionts and ultimately organelles in the host cell ▯ The protist kingdom was abandoned because o Kingdom protists is polyphyletic o Some protists are more closely related to other eukaryotes than to each other ▯ Scientists recognize just the domain eukarya ▯ Secondary endosymbiosis: ingested in the food vacuoles of heterotrophic euaryotes and became endosymbionts themselves ▯ Protists vary in body structure, mobility, nutrition and reproduction o Locomotion ▯ Flagella ▯ Pseudopodia ▯ Cilla o Interactions ▯ Free living ▯ Symbiotic ▯ Mutualism ▯ Parasitism o Nutrition ▯ Autotrophy ▯ Heterotrophic o Reproduction ▯ Sexually and asexually • Many can do both Chapter 12: The Cell Cycle ▯ Ability of organisms to produce more of their own kind is a characteristic which best distinguishes living things from nonliving matter ▯ Cell division: reproduction of cells o In unicellular eukaryotes and prokaryotic cells cell division produces an entire organism o Allows multicellular eukaryotes to form from single cells ▯ Cell cycle: the life of a cell fro when it is first formed from the dividing parent cell until its own division into two daughter cells – passing identical genetic material o Cell division involves distribution of DNA to two daughter cells – except meiosis ▯ Genome: genetic information o Prokaryotes: single DNA molecule o Eukaryotic: consists of a number of DNA molecules ▯ Chromosomes: structures where DNA molecules are packaged o Associated proteins maintain the structure of the chromosome and help control activity of the genes ▯ Chromatin: entire complex of DNA and proteins – building material of chromosomes ▯ Eukaryotic species have characteristic number of chromosomes in each cell nucleus o Somatic cells (human cell, all body cells except reproductive): each contain 46 chromosomes, 2 sets of 23, o Gametes: reproductive cells, one set of 23 chromosomes each ▯ Eukaryotic cell division o When cell isn’t dividing, it is in preparation for cell division o Each duplicated chromosome has two sister chromatids: joined copies of the same original chromosome ▯ Cohesion: proteins that attach two chromatids along their lengths – sister chromatid cohesion ▯ Centromere: a region containing specific DNA sequences where the chromatids are attached most closely to its sister chromatids o Once sister chromatids separate ▯ called individual chromosomes ▯ Mitosis: the division of the genetic material in the nucleus o Usually followed by cytokinesis: division of cytoplasm ▯ Phases of cell cycle o Mitotic (M) Phase: includes mitosis and cytokinesis ▯ Shortest part of the cell cycle o Interphase: 90% of the cell cycle ▯ A cell that is about to divide, grows and copies its chromosomes in preparation for cell division ▯ G1 phase, S phase (syntheis), G2 phase • Grows by producing proteins and cytoplasmic organelles, ex. Mitochondria and ER • Chromosomes duplicated during S phase • G1 – cell grows • S – copies chromosomes and continues to grow • G2 – grows more as it completes prep. For cell division • M – divides o Mitosis ▯ Prophase • Chromatin condenses • Duplicated chromosomes are seen as two identical sister chromatins ▯ Prometaphase • Each of 2 chromatids of each chromosomes now has a kinetochore ▯ Metaphase • Chromosomes line up at metaphase plate • Centrosomes at opp. poles of cell
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