DE BIO MIDTERM PDF

CHAPTER ONE ○ Cellular Organization: all organisms consist of one or more cells, bounded by a membrane that separates them from their surroundings ○ Ordered Complexity: all living things are both complex and highly ordered ○ Sensitivity: all organis...

CHAPTER ONE ○ Cellular Organization: all organisms consist of one or more cells, bounded by a membrane that separates them from their surroundings ○ Ordered Complexity: all living things are both complex and highly ordered ○ Sensitivity: all organisms respond to stimuli ○ Growth, development, and reproduction: all organisms are capable of growing and reproducing and they all possess hereditary molecules that are passed to their offspring ○ Energy utilization: all organisms take in energy to perform many different kinds of work ○ Homeostasis: all organisms maintain relatively constant internal conditions different from their environment ○ Evolutionary Adaptation: all organisms interact with each other and the nonliving environment in ways that influence their survival The cellular level: atoms are joined together into molecules. Molecules then assemble into organelles within cells. The organismal level: tissues (groups of similar cells that function as one unit), organs (groups of tissues), and organ systems (organs are grouped into these). The populational level: population (group of organisms of the same species living in the same place), all populations of a particular kind of organisms form a species. A biological community consists of all the populations of different species living together in one place The ecosystem level: populations and their environments constitute an ecosystem The biosphere: the entire planet can be thought of as an ecological system we call the biosphere. Deductive reasoning applies general principles to predict specific results. Used to test the validity of general ideas in all branches of knowledge Inductive reasoning uses specific observations to construct general scientific principles, leading to generalizations that can then be tested. Scientific method: ○ Observation: watching something occur and wanting to figure out the reasoning behind it ○ Hypothesis: a suggested explanation that accounts for those observations, proposition that might be true ○ Experiment: the test of a hypothesis ○ Conclusion: whether or not the hypothesis is correct ○ Result: If it is correct, more experiments similar can be tried to form a scientific theory and if not a new hypothesis can be formulated. Models: provide a way to organize how we think about a problem, closer to the big  picture, away from the minute details Theory: 1) proposed explanation for some natural phenomenon, 2) the body of interconnected concepts supported by scientific reasoning and experimental evidence that explains the facts in some area of study Basic vs applied research SELECTION: individuals with attributes that give them an advantage in their environment are more likely to survive and reproduce and pass on those traits to their offspring. - Artificial selection: animal breeders, humans choosing which traits to keep - Natural selection: selection occurring naturally by “survival of the fittest” Homologous vs Analogous: - H: same evolutionary origin but they now differ in structure and function - A: same structure/function but different evolutionary origin - Phylogenetic trees provide a graphic representation of these evolutionary relationships 5 core concepts 1) Life is subject to chemical and physical laws 2) Structure determines function 3) Living systems transform energy and matter a) Energy from the sun is trapped by photosynthetic organisms, we need a constant source of energy and carbon 4) Living systems depend on information transactions a) Most obvious in DNA which transports the genetic information, continuity of life relies on the copying of a cell’s DNA b) Living systems can collect information about the environment and then respond to this information 5) Evolution explains the unity and diversity of life CHAPTER TWO Mass refers to the amount of a substance, weight refers to the force gravity exerts on a substance Orbitals: negatively charged electrons are located in this regions in various distances around the nucleus Isotopes: atoms of a single element that possess different numbers of neutrons are called this ○ Radioactive isotopes: isotopes that decay in radioactive decay Half life: the time it takes for one-half of the atoms in a sample to decay Reduction-oxidation reactions Valence electrons: their interactions are the basis for the differing chemical properties of the elements ○ Octet rule: atoms tend to establish completely full outer energy levels  Specific heat: the amount of head 1g of a substance must absorb or lose to change its temperature by 1 degree Celsius Heat of vaporization: the amount of energy required to to change 1g of a substance from a liquid to a gas Hydration shell: every time a sucrose molecule dissociates/breaks away from a solid sugar crystal, the water molecules surround it forming a hydration shell Hydrophobic exclusion: the tendency of nonpolar molecules to aggregate in water Ionization: the process of random ion formation ○ H20 →OH- + H+ Covalent bonds build stable molecules because (2 hydrogen atoms): 1) It has no net charge: diatomic molecule formed is not charged bc it contains equal numbers of protons and electrons 2) The octet rule is satisfied: each of the two atoms can be considered to have two orbiting electrons in its outer energy level 3) It has no unpaired electrons: the bond between the 2 atoms also pairs the two free electrons Electronegativity increases left to right across a row of the periodic table and decreases down the column For bonds between identical atoms the bonds are termed nonpolar Atoms that differ in electronegativity results in regions of partial negative charge near the more electronegative atom, and regions of partial positive charge near the less electronegative atom (polar covalent bonds) Chemical reactions are influenced by 1) Temperature: heating the reactants INCREASES the rate of a reaction 2) Concentration of reactants and products: reactions proceed more quickly when more reactants are available (causes more frequent collisions) 3) Catalysts: a substance that increases the rate of a reaction Adhesion: the polarity of water causes it to be attracted to other polar molecules as well Cohesion: when water sticks to itself ★ Ice is less dense than liquid water ★ Bodies of water freeze from the top down Nonpolar: hydrophobic Polar: hydrophilic ACIDITY + BASICITY pH= -log [H+] Acids: any substance which increases the [H+] and lowers the pH Bases: A substance that combines with H+ when dissolved in water and lowers the [H+] and has at pH value above 7 Often even a small change in pH will alter the shape of the enzyme ○ Cell must maintain a constant pH Buffer: resists change in pH ○ Release hydrogen ions when a base is added and absorbing hydrogen ions when an acid is added to maintain the [H+] Review questions: 1) The property that distinguishes an atom of one element (carbon, for example) from an atom of another element (oxygen for example) is a) The number of protons 2) If an atom has one valence electron, that is a single electron in its outer energy level, it will most likely form a) An ionic bond 3) An atom with a net positive charge must have more a) Protons than electrons 4) The isotopes carbon 12 and carbon 14 differ in a) The number of neutrons 5) Which is NOT a property of the elements most commonly found in living organisms a) The elements possess eight electrons in their outer energy level 6) Ionic bonds arise from a) attractions between ions of opposite charges 7) A solution with a high concentration of hydrogen ions a) Is called an acid 8) A molecule with polar covalent bonds would a) Be soluble in water 9) Hydrogen bonds are formed a) When hydrogen is part of the bond 10) If you shake a bottle of oil and vinegar then let it sit, it will separate into two phases because a) Nonpolar oil is not soluble in water CHAPTER THREE Hydrocarbons are polar and can be thought of as a C–H core to which specific molecular groups (FUNCTIONAL GROUPS) attach to  ○ Ex. –OH (hydroxyl), COOH (acidic carboxyl), PO4– (phosphate), NH2 (basic amino groups) Isomers: same molecular/empirical formula but exist in different forms Structural isomer: if there are differences in the ACTUAL structure of the carbon skeleton Stereoisomers: have the same carbon skeleton but differ in how the groups attached are arranged ○ Enantiomers: mirror images of each other ○ Polymer: a long molecule built by linked up monomers Dehydration reaction: to form a covalent bond between two monomers, an –OH group is removed from one monomer and a H atom is removed from the other ○ Joining nucleotides, synthesizing DNA, joining glucose units, link fatty acids Hydrolysis: (disassembling polymers into their monomers) a hydrogen atom is attached to one subunit and a hydroxyl group to the other, breaking the covalent bond joining the subunits Disaccharides: serve as effective reservoirs of glucose because the enzymes that normally use glucose in the organism cannot break the bond linking the two monosaccharide subunits Polysaccharides: made up of monosaccharides that have been joined through dehydration reactions ○ Starch: entirely of a-glucose molecules ○ Cellulose: B-glucose ○ A-linkages and B-linkages Glycogen: insoluble polysaccharide containing branched amylose chains Chitin: the structural material found in arthropods + many fungi ○ Forms a tough, resistance surface material that serves as a hard exoskeleton of insects and crustaceans The Ose’s ★ Sucrose: what plants use to transport glucose, the sugar humans/animals eat ○ glucose + fructose →sucrose ★ Lactose: mammals supply their young with lactose ○ Glucose + (stereoisomer) galactose →lactose  ○ Lactose intolerance: when adults have reduced levels of lactase (the enzyme required to cleave lactose into its two monosaccharide components) ★ Amylose: starch with the simplest structure ○ Hundreds of a-glucose molecules linked together ○ Tend to coil up in water →insoluble ○ Amylopectin: variant of amylose Short amylose branches (branched from the original chain) 20 to 30 glucose subunits ★ Cellulose: polymer of B glucose ○ Make tough fibers ○ Chief component of plant cell walls ○ Can not be broken down readily by animals MACROMOLECULES Carbohydrates (all contain carbon, hydrogen, + oxygen 1:2:1) : ○ Starch, glycogen→glucose, energy storage ○ Cellulose→glucose, structural support in cell walls ○ Chitin→modified glucose, structural support Nucleic Acids: ○ DNA→ nucleotides, encodes genes ○ RNA→ nucleotides, needed for gene expression Proteins: ○ Functional→ amino acids, catalysis/transport ○ Structural→amino acids, support Lipids: ○ Triglycerides→glycerol + three fatty acids, energy storage ○ Phospholipids→glycerol + 2 fatty acids + phosphate + polar R groups, cell membranes ○ Prostaglandins→5 carbon rings + 2 nonpolar tails, chemical messengers ○ Steroids→ four fused carbon rings, membranes/hormones ○ Terpenes→long carbon chains, pigments/structural support DNA + RNA DNA stores genetic information vs RNA contains short lived copies of genetic information used to direct the SYNTHESIS OF PROTEINS - RNA can also regulate the process of gene expression - mRNA: transcribed single stranded copies of portions of the DNA, specifying the amino acid sequences of the proteins - Nucleotides: long polymers of repeating subunits - 5 carbon sugar + a phosphate group + an organic nitrogenous base  - Nitrogenous bases: - Purines: adenine + guanine - Pyrimidines: cytosine + thymine + uracil mRNA: carries information rRNA: part of the ribosome tRNA: carries amino acids ATP (Adenosine Triphosphate): energy currency of the cell NAD+ (Nicotinamide adenine dinucleotide): electron carrier FAD (Flavin adenine dinucleotide): electron carrier The function of proteins 1) Enzyme catalysis: enzymes are biological catalysts that facilitate chemical reactions 2) Defense: other globular proteins use their shapes to “recognize” foreign microbes and cancer cells 3) Transport: a variety of globular proteins transport small molecules and ions 4) Support: protein fibers play structural roles 5) Motion: muscles contract through the sliding motion of two kinds of protein filaments: actin and myosin 6) Regulation: small proteins called hormones serve as intercellular messengers in animals 7) Storage: calcium and iron are stored in the body by binding as ions to storage proteins Amino acids: contain an amino group and an acidic carboxyl group The unique character of each amino acid is determined by the nature of their R group ○ Also determines the chemistry of amino acids 5 chemical classes ○ Nonpolar amino acids: R groups that contain –CH2 or –CH3 ○ Polar uncharged amino acids: R groups that contain Oxygen or –OH ○ Charged amino acids: R groups that contain acids or bases that can ionize ○ Aromatic amino acids: R groups that contain an organic carbon ring with alternating single and double bonds (nonpolar) ○ Amino acids that have special functions have unique properties (methionine, proline, cystine) Peptide bond: links two amino acids Polypeptide: an unbranched chain of amino acids linked by peptide bonds Structures Primary structure: its amino acid sequence  Secondary structure: the amino acid and carboxyl groups could interact with one another if the peptide was coiled into a spiral he called the a-helix Tertiary structure: determines how the secondary structures are further arranged to produce the overall structure ○ Driven into this by hydrophobic exclusion from water Quaternary structure: when 2+ polypeptide chains associate to form a functional protein Motifs: similarities between otherwise dissimilar structures ○ Many proteins use it to bind to the DNA double helix ○ If amino acids are letters in the language of proteins, then motifs are repeated words/phrases Domains: functional units within a larger structure ○ Domains are paragraphs ^^^^ ○ Help the protein fold into its proper shape ○ A single polypeptide chain connects the domains of a protein Chaperone proteins: accompany proteins on its path to a properly folded state ○ High temperatures cause proteins to unfold, heat shock chaperone proteins help refold them properly ○ Used to both accomplish original folding of some proteins and restore structure of incorrectly folded ones Denaturation: if a protein’s environment is altered the protein may change its shape or even unfold completely Renaturation: when a protein’s natural environment is restored after denaturation Dissociation: for proteins with a quaternary structure, the subunits may be separated without losing their individual tertiary structure Lipids INSOLUBLE IN WATER Many spontaneously cluster together and expose what polar groups they have to the surrounding water Triglyceride: 3 fatty acids ○ Don't need to be identical  ○ If all are bonded to two hydrogen atoms it is SATURATED ○ A fatty acid with double bonds between one or more pairs of successive carbon atoms will have fewer hydrogen atoms UNSATURATED When an organism consumes excessive carbohydrate, it is converted into starch, glycogen, or fats reserved for future use. Phospholipids: a triglyceride with a phosphate replacing one of the fatty acids 1) Glycerol: 3 carbon alcohol, backbone of the phospholipid 2) Fatty acids: long chains of –CH2 groups, attached to the glycerol backbone 3) A phosphate group: attached to one end of the glycerol Polar head and nonpolar tails Review Questions 1) How is a polymer formed from multiple monomers? a) By the removal of an –OH group and a hydrogen atom 2) Why are carbohydrates important molecules for energy storage? a) The C–H bonds found in carbohydrates store energy 3) Plant cells store energy in the form of —- and animal cells store energy in the form of — a) Starch, glycogen 4) Which carbohydrate would you find as part of a molecule of RNA? a) Ribose 5) A molecule of DNA or RNA is a polymer of a) Nucleotides 6) What makes cellulose different from starch? a) Cellulose forms long filaments and starch is highly branched 7) What monomers make up a protein? a) Amino acids 8) A triglyceride is a form of — composed of — 9) Lipid, fatty acids + glycerol 10) You can use starch or glycogen as an energy source but not cellulose because a) Starch and glycogen have similar structures 11) Which is not a difference between DNA and RNA a) Phosphodiester versus hydrogen bonds 12) Which part of an amino acid has the greatest influence on the overall structure of a protein a) The R group 13) A mutation that alters a single amino acid within a protein can alter a) All levels of the protein structure 14) Two different proteins can have the same domain in the structure, from this we can infer a) Similar function 15) What aspect of triglyceride structure accounts for their insolubility in water?  a) The nonpolar C–H bonds in fatty acids 16) The spontaneous formation of a lipid bilayer in an aqueous environment occurs because a) The polar head groups of the phospholipids can interact with water + the fatty acid tails of the phospholipids are hydrophobic Unit 2 CHAPTER FOUR 1) All organisms are composed of one or more cells, and the life processes of metabolism and heredity occur within these cells. 2) Cells are the smallest living things, the basic units of organization of all organisms 3) Cells arise only by division of a previously existing cell What affects the rate of diffusion? Surface area available Temperature Concentration gradient of diffusion substance The distance over which diffusion must occur Surface area-to-volume ratio: as a cell’s size increases, its volume increases much more rapidly than its surface area Parts of the cell Nucleoid: consists primarily of a single circular molecule of DNA ○ Found near the center of the cell in the nucleoid region Nucleus: eukaryotic cells have this, DNA organized into linear chromosomes segregated into this Nuclear envelope: a double membrane structure that surrounds the nucleus Cytoplasm: a semifluid matrix which fills the interior of the cell, contains all the sugars, amino acids, and proteins the cell uses to carry out its everyday functions Cytosol: the fluid part of the cytoplasm, contains organic molecules and ions in a solution Ribosomes: large, macromolecular machines composed of RNA and protein that synthesize all cellular proteins Plasma membrane: encloses a cell and separates its contents from its surroundings ○ Phospholipid bilayer about 5 to 10 nm thick with proteins embedded in it Prokaryotes 2 main domains: archaea and bacteria Magnetosome: the best studied of particular prokaryotes with specialized functions ○ Found in bacteria that can move along a magnetic field ○ Consist of spherical membranes containing iron oxide crystals Bacterial microcompartments (BMCs): some bacteria contain cellular compartments bounded by a semipermeable protein shell ○ Act to isolate a specific metabolic process or store a particular substance Cell wall: most bacterial cell are encased by this, composed of peptidoglycan (consists of a carbohydrate matrix cross linked with short polypeptide chains)  ○ Antibiotic drugs used to combat bacterial infection often target their cell walls ○ Cell walls of archaea are more diverse than bacteria, containing polysaccharides and proteins Archaeal membrane lipids include saturated hydrocarbons that are covalently attached to glycerol at both ends (forms a monolayer membrane) Bacterial flagella: consists of protein rings embedded in the plasma membrane, and a cell wall with long protein fibers extending from this ○ Called and archaellum Convergent evolution: the independent evolution of different structures with similar function is called Eukaryotes Achieved through a combination of an extensive endomembrane system that weaves through the cell interior and by numerous organelles Central vacuole: in plants, large membrane-bound sac which stores proteins, pigments, and waste materials Vesicles: in both plant and animal, smaller sacs that store and transport a variety of materials Chromosomes: the DNA is wound tightly around proteins and packaged into compact units Cytoskeleton: all eukaryotic cells are supported by an internal protein scaffold Nucleolus: a region where intensive synthesis of ribosomal RNA is taking place  Nuclear pores: allow ions and small molecules to diffuse freely between nucleoplasm and cytoplasm, while controlling the passage of proteins and RNA–protein complexes. Chromatin: in eukaryotes, the DNA is divided into multiple linear chromosomes which are organized with proteins into a complex structures called chromatin rRNA: ribosomal RNA, each ribosome is composed of two subunits each of which is composed of a combination of RNA mRNA: carries coding information from DNA tRNA: carries amino acids The endomembrane system endoplasmic reticulum: the largest internal membrane composed of a phospholipid bilayer embedded with proteins ○ Rough ER: the proteins synthesized on the surface of the RER are destined to be exported from the cell, sent to lysosomes or vacuoles, or embedded in the plasma membrane ○ Smooth ER: steroid hormones are synthesized in the SER, the majority of membrane lipids are also assembled in the SER To store intracellular Ca2+ To modify foreign substances and make them less toxic Golgi apparatus: ○ Cisternae: the individual stacks of membrane ○ Functions in the collection, packaging and distribution of molecules synthesized at one location and used at another within the cell ○ Proteins and lipids manufactures on the RER and SER membranes are transported into the golgi apparatus and modified as they pass through it ○ Synthesis of cell-wall components Lysosomes: digestive vesicles that arise from the golgi apparatus ○ Break down old organelles and recycle their component molecules ○ Activated by fusing with a food vesicle produced by phagocytosis  ○ Tay-Sachs disease is caused by the loss of function of a single lysosomal enzyme ○ Eliminate other cells that the cell has engulfed by phagocytosis Lipid droplets: consist of neutral lipid core surrounded by a single layer of phospholipids ○ Form storage deposits for lipids that ate used for energy metabolism, and to form membranes Microbodies: one of the principal ways eukaryotic cells organize their metabolism Peroxisomes: microbodies that contain enzymes used to oxidize fatty acids Tonoplast: the membrane surrounding the vacuole Mitochondria: bounded by 2 membranes, a smooth outer membrane and an inner folded membrane with numerous contiguous layers called cristae ○ Cristae: partition the mitochondria into two compartments: Matrix: lying inside the inner membrane Intermembrane space: outer compartment, lying between the 2 mitochondrial membranes Chloroplasts: they manufacture their own food ○ Contain the photosynthetic pigment chlorophyll that gives most plants their green color ○ Grana: compartments of stacked membranes ○ Thylakoids: several dozen disk-shaped structures ○ Stroma: fluid matrix that surround the thylakoid Actin filaments ○ Long fibers composed of 2 protein chains loosely twined together ○ They have (+) and (-) ends ○ Responsible for cellular movements such as contraction, crawling, “pinching” during division, and formation of cellular extensions Microtubules ○ Hollow tubes ○ Form from nucleation centers near the center of the cell and radiate toward the periphery ○ Ends are (+) away from the nucleation center and (-) towards the nucleation center Intermediate filaments ○ Tough, fibrous protein molecules twined together in an overlapping arrangement ○ Provide structural stability for many kinds of cells Centrioles ○ Barrel shaped organelles found in the cells of animals and most protists ○ Pericentriolar material: surrounding the centrioles in the centrosome, can nucleate the assembly of microtubules in animal cells 4 components required to move material along microtubules 1) A vesicle or organelle that is to be transported  2) A motor protein that provides the energy-driven motion 3) A connector molecule that connects the vesicle to the motor molecule 4) Microtubules on which the vesicle will ride Kinesin: uses ATP to power its movement toward the cell periphery, dragging the vesicle with it Primary walls→laid down when the cell is still growing Middle lamella→between the walls of adjacent cells, a sticky substance glues the cells together Secondary walls→deposited inside the primary walls of fully expanded cells Type of Connection Structure Function Example Surface markers Variable, integral Identify the cell MHC complexes, proteins or blood groups, glycolipids in the antibodies plasma membrane Septate junctions Tightly bound, Hold cells together Junctions between Tight junctions leakproof, fibrous such that materials epithelial cells in the claudin protein seal can pass through but gut that surrounds the cell not between the cells Adhesive junction Variant cadherins, Creates strong epithelium (desmosome) desmocollins, bind to flexible connections intermediate between cells filaments of the cytoskeleton Adhesive junction Integrin proteins bind Provides attachment Involved in cell (hemidesmosome, cell to extracellular to a substrate movement and focal adhesion) matrix important during development Communication Six transmembrane Allows passage of Excitable tissue such junction connexon/pannexin small molecules from as heart muscle (gap junction) proteins creating a cell to cell in a tissue pore that connects cells Communicating Cytoplasmic Communicating Plant tissues junction connections between junction between (plasmodesmata) gaps in adjoining plant cells plant cell walls  Adhesive junction Classical cadherins, Connects cells Tissues with high (adherens junction) bind to together mechanical stress, the microfilaments of the skin cytoskeleton Adhesive junction: have been the first to evolve ○ Mechanically attach the cytoskeleton of a cell to the cytoskeletons of other cells or to the ECM Adherens junctions: formed by cadherin molecules on the surface of cells Cadherin: a single-pass transmembrane protein with an extracellular domain that can interact with the extracellular domain of a cadherin in and adjacent cell Desmosomes: join adjacent cells, support tissues against mechanical stress Hemidesmosomes + focal adhesions: connect cells to the basal lamina or other ECM Septate junctions: form a barrier that can seal off a sheet of cells Tight junctions: occlude or block substances from passing between cells CHAPTER FIVE The lipid layer that forms the foundation of a cell’s membrane is a bilayer composed of phospholipids Cellular membranes consist of 4 component groups 1) Phospholipid bilayer: every cell membrane is composed of phospholipids in a bilayer 2) Transmembrane proteins: transport and communication across the membrane, not fixed in position, crowded with proteins or sparsely distributed 3) Interior protein network: membranes are structural supported by intracellular proteins that reinforce the membrane’s shape 4) Cell-surface markers: different cell types exhibit different varieties of these glycoproteins and glycolipids on their surfaces, which act as cell identity markers Phospholipid bilayer is made up of phospholipid molecules which provide for a permeability barrier, matrix for proteins ○ Excludes water-soluble molecules from non-polar interior of bilayer and cell Transmembrane proteins ○ Carriers: actively or passively transport molecules across the membrane ○ Channels: passively transport molecules across the membrane ○ Receptors: transmit information into the cell Interior protein network ○ Spectrins: determine the shape of the cell ○ Clathrins: anchor certain proteins to specific sites, especially on the exterior plasma membrane in receptor-mediated endocytosis Cell-surface markers ○ Glycoproteins: “self” recognition  ○ Glycolipid: tissue recognition Phospholipids spontaneously form bilayers because of their amphipathic structure. ○ Polar head groups are hydrophilic and the tails are hydrophobic Classes of membrane protein 1) Transporters: membranes are selective, only allow certain solutes in or out 2) Enzymes: carry out many chemical reactions using enzymes on the interior surface of the plasma membrane 3) Cell-surface receptors: membranes are exquisitely sensitive to chemical messages, which are detected by these receptor proteins on their surfaces 4) Cell-surface identity markers: identify them to other cells, specific combinations of cell-surface proteins and protein complexes 5) Cell-to-cell adhesion proteins: use specific proteins to glue themselves together 6) Attachments to the cytoskeleton: surface proteins that interact with other cells are often anchored to the cytoskeleton by linking proteins 7) Proteins that affect the membrane structure: wedge-shape proteins can cause membranes to bend Transmembrane domain: each membrane-spanning region Osmotic pressure: the amount of water that enters the cell depends on the difference in solute concentration between the cell and the extracellular fluid, measured as osmotic pressure Maintaining osmotic balance  - Extrusion - Contractile vacuoles remove water - Collect water from parts of cytoplasm and transport it to the outside of the cell - Vacuole pumps out through a small pore the water that is continuously drawn into the cell - Isosmotic Regulation - Some organisms that live in the ocean adjust their internal concentration of solutes to match that of the surrounding seawater - Turgor - Turgor pressure presses the plasma membrane firmly against the interior of the cell wall, making the cell rigid Mechanisms for transport across cell membranes PASSIVE ○ Diffusion Direct: random molecular motion produces net migration of nonpolar molecules toward region of lower concentration ○ Facilitated diffusion Protein channel: polar molecules or ions move through a protein channel, net movement is toward region of lower concentration Protein carrier: molecule binds to carrier protein in membrane and is transported across, net movement is toward region of lower concentration ○ Osmosis Aquaporins: diffusion of water across the membrane via osmosis, requires osmotic gradient ACTIVE ○ Active transport Na/K pump: carrier uses energy to move a substance across a membrane against its concentration gradient Coupled transport: molecules are transported across a membrane against their concentration gradients by the cotransport of sodium ions or protons down the concentration gradients ○ Endocytosis Phagocytosis: particle is engulfed by membrane, which fold around it and forms a vesicle Pinocytosis: fluid droplets are engulfed by membrane which forms vesicles around them Receptor-mediated endocytosis: endocytosis triggered by a specific receptor, forming clathrin-coated vesicles ○ Exocytosis Membrane vesicle: vesicles fuse with plasma membrane and eject contents Unit 3 Kinetic energy: energy of motion Potential energy: stored energy, not actively moving but have the potential to do so Oxidation-reduction reactions (redox) Reduction: gaining electrons Oxidation: losing electrons They transfer energetic electrons when bonds are made/broken Thermodynamics The branch of chemistry concerned with energy changes Laws: 1) Energy cannot be created or destroyed, it can only change from one form to another 2) Energy cannot be transformed from one form to another with 100% efficiency, some energy is always unavailable a) Increase in random motion of molecules Disorder is more likely than order Free energy: the energy available to do work at constant temperature in a system ○ Gibbs free energy Endergonic reaction: the bond energy is higher, or the disorder is lower. If products have more free energy than reactants Exergonic reaction: the bond energy is lower, or the disorder is higher. If the products have less free energy than the reactants. Activation Energy: the extra energy needed to destabilize existing chemical bonds and initiate a chemical reaction The rate of reactions can be increased by 1) Increasing the energy of reacting molecules 2) By lowering the activation energy Catalysis: the process of influencing chemical bonds in a way that lowers the activation energy needed to initiate a reaction - Affecting the transition state - Cannot violate the basic laws of thermodynamics ATP: 5 carbon sugar, ribose, adenine, an organic molecule composed of 2 carbon-nitrogen rings, three phosphates Stores energy lies in its triphosphate group  ○ Highly negatively charged The unstable bonds holding the phosphates together in the ATP molecules have a low activation energy and are easily broken by hydrolysis ○ Exergonic Cells use ATP to drive endergonic processes Energy released by the hydrolysis of ATP can supply the energy needed by the endergonic reactions Active sites: most enzymes are globular proteins with one or more pockets/clefts called active sites Substrates bind to the enzyme at active sites which forms an enzyme substrate complex Multienzyme complexes: ○ The rate of any enzyme reaction are limited by how often the enzyme collides with its substrate ○ Unwanted side reactions are prevented ○ All of the reactions that take place within the multienzyme complex can be controlled as a unit Nonprotein enzyme: Increasing the temperature of an uncatalyzed reaction increases its rate because the additional heat increases random molecular movement Optimum temperature: the rate of an enzyme-catalyzed reaction also increases with temperature up to the point called optimum temperature Optimum pH: Inhibitor: a substance that binds to an enzyme and decreases its activity Competitive inhibitors: compete with the substrate for the same active site, preventing other substances from binding Noncompetitive inhibitors: bind to the enzyme in a location other than the active site, changing the shape of the enzyme and making it unable to bind to the substrate Allosteric site: most noncompetitive inhibitors bind to this specific portion of the enzyme Allosteric inhibitor: a substance that binds to an allosteric site and reduces enzyme activity Allosteric activator: binds to allosteric sites to keep an enzyme in its active configuration Cofactors: enzyme function is often assisted by additional chemical components Coenzyme: when the cofactor is a nonprotein organic molecule Metabolism - Metabolism: the total of all chemical reactions carried out by a living organism - Anabolism: the chemical reactions that expend energy to build up molecules - Catabolism: reactions that harvest energy by breaking down molecules are called Many reactions in a cell occur in sequences called biochemical pathways  ○ The product of one reaction becomes the substrate for the next ○ Organizational units of metabolism Feedback inhibition: the end product of the pathway binds to an allosteric site on the enzyme that catalyzes the first reaction in the pathway Cellular respiration: Autotrophs: harvest the energy of sunlight through photosynthesis, converting radiant energy into chemical energy Heterotrophs: obtain organic compounds by eating either autotrophs or other heterotrophs Cellular respiration: the process by which energy is harvested Dehydrogenations: the reactions that break down molecules share a common feature, they are oxidations, not just the simple transfer of electrons, what is really lost is a hydrogen atom, not just an electrons Nicotinamide adenine dinucleotide (NAD+) ○ W hydrogen atoms are removed from the substrate with a proton and two electrons transferred to NAD+ to form NADH ○ The substrate is oxidized and NAD+ reduced to NADH Aerobic respiration: when the acceptor is oxygen Anaerobic respiration: when the final electron acceptor is an inorganic molecule other than oxygen Fermentation: when the final acceptor is an organic molecule Aerobic respiration: Glucose is oxidized to CO2 Many electron carriers are used ○ NAD+: moves electrons from one molecule to another Composed of 2 nucleotides bound together Joined head to head by their phosphate groups When it acquires 2 electrons and a proton from the active site of an enzyme, it is reduced to NADH ○ Membrane-bound carriers: form a redox chain ○ Carriers that moves membrane within the membrane Electron transport chain: the electrons are passed to another set of electron carriers called ____, sequential redox reaction of these electron carriers release energy that is converted into potential energy Cells make ATP: - Substrate level phosphorylation: ATP is formed by transferring a phosphate group directly to ADP - During glycolysis, the initial breakdown of glucose, the chemical bonds of glucose are shifted around in reactions that provide the energy required to form ATP by slp - Oxidative phosphorylation: ATP is synthesized by the enzyme ATP synthase GLYCOLYSIS Priming reactions: the first three reactions prime glucose by changing into a compound that can readily be cleaved into two 3-carbon phosphorylated molecules. ○ Requires 2 ATP molecules Cleavage: the 6-carbon sugar is split into 2 3-carbon sugars ○ One is G3P and the other is converted into G3P Oxidation and ATP formation: each G3P is oxidized, transferring 2 electrons and 1 proton to NAD+ forming NADH CITRIC ACID CYCLE Reaction 1: condensation ○ Citrate is formed from acetyl-CoA and oxaloacetate  Reaction 2 + 3: isomerization ○ Before the oxidation reactions, the hydroxyl group of citrate must be repositioned ○ A water molecule is removed from one carbon ○ A water molecule is added to a different carbon ○ H and OH change positions Reaction 4: the first oxidation ○ Isocitrate undergoes an oxidative decarboxylation reaction ○ Isocitrate is oxidized→a pair of electrons that reduce NAD+ to NADH ○ The oxidized intermediate is decarboxylated, central carboxyl group splits off to form CO2 Reaction 5: the second oxidation ○ A-ketoglutarate is decarboxylated by a multienzyme complex similar to pyruvate dehydrogenase ○ 2 electrons are extracted and reduce another molecule of NAD+ to NADH Reaction 6: substrate level phosphorylation ○ The linkage between the 4-carbon succinyl group and CoA is a high-energy bond ○ This bond is cleaved and the energy released drives the phosphorylation of GDP, forming GTP, which can transfer a phosphate group to ADP, making it ATP Reaction 7: the third oxidation ○ Succinate is oxidized to fumarate by an enzyme in the inner mitochondrial membrane ○ FAD is the electron acceptor Reactions 8 and 9: regeneration of oxaloacetate ○ A water molecule is added to fumarate, forming malate ○ Malate is then oxidized, yielding a 4-carbon molecule of oxaloacetate and 2 electrons that reduce a molecule of NAD+ to NADH