Chapter LS2 1: Studying Life 1.1 What is biology? A. Biology is the scientific study of living things B. All living things diversified from the same ancestor 4 billion years ago C. Most living things 1. Consist of one or more cells 2. Contain genetic information 3. Use genetic information to reproduce themselves 4. Are genetically related and have evolved 5. Can convert molecules obtained in from the environment into new biological molecules 6. Can extract energy from the environment and use it to do biological work 7. Can regulate their internal environment D. Living organisms consist of cells 1. Cell theory a. Cells are the basic structural and physiological units of all life b. Cells are both distinct entities and building blocks of more complex organisms c. All cells come from preexisting cells d. All cells are similar in composition e. Complete sets of genetic information are replicated and passed on during cell division 2. Spontaneous generation: the idea that life emerges from non-life E. The diversity of life is due to evolution by natural selection 1. Species: a group of organisms that are morphologically similar and can breed successfully 2. Adaptation: Structural, physiological, or behavioral trains that enhance and organisms chance of survival 3. Natural selection: any trait that increases an organisms' ability to reproduce would be favored and increase in the population F. Biological information is contained in a genetic language common to all organisms 1. Genome: sum total of all DNA molecules in the cell 2. DNA: molecules made of long sequences of four subunits called nucleotides 3. Genes: specific segments of DNA which contain the information cells use to make proteins 4. Proteins make up much of an organisms structure and are the molecules that govern the chemical reactions within cells 5. All cells of a multicellular organisms contain the same genome, yet cells have different structures and have different functions 6. Therefore, different types of cells must express different parts of their genome 7. Alteration of genes is called mutation 8. Mutations are spontaneous and can be caused by outside factors 9. Sometimes, a mutation can improve the function of an organism G. Cells use nutrients to supply energy and to build new structures
1. Cells take in nutrient molecules and break them into smaller chemical units 2. Breaking bonds releases energy that can be used for work (mechanical/ synthesis) H. Living organisms control their internal environment 1. Organisms made of more than one cell have an internal environment that is not cellular 2. The cells are bathed in extracellular liquids from which they receive nutrients and excrete wastes 3. Assemblies of similar cells are organized into tissue. 4. Tissues types are organized to form organs 5. Organ systems are composed of organs whose functions are interrelated I. Living organisms interact with one another 1. Interactions a. Territorial b. Cooperation 2. Interaction of different populations (a species in an area) form communities 3. Interacting communities form ecosystems, in which populations modify the environment J. Discoveries in biology can be generalized 1. Model systems: discoveries on one organism can be applied to others, as they are all interrelated
1.2 How is all life on earth related? A. All organisms are genetically related, meaning they share a common ancestor B. The fossil record is useful for investigating the history of life C. The greater the difference between the genomes of two species, the more distantly they are related D. Life arose from non-life via chemical evolution 1. The conditions of early Earth allowed complex biological molecules to be formed 2. First critical step: organisms that could reproduce themselves and serves as templates for the synthesis of larger molecules E. Biological evolution began when cells formed 1. Second critical step: enclosure of complex biological molecules in membranes 2. Fat-like molecules form membrane like films 3. Earliest organisms were unicellular prokaryotes that lived in the ocean F. Photosynthesis changed the course of evolution 1. Metabolism: the sum total of all chemical reactions that go on inside a cell 2. Photosynthesis (2.5 bya) transforms energy of sunlight into a form of energy that can synthesize large biological molecules. 3. Earliest: cyanobacteria 4. Oxygen (product of photosynthesis) accumulated in atmosphere 5. Aerobic metabolism: based on oxygen 6. The formation of the ozone layer blocked UV radiation and allowed organisms to live on land
G. Eukaryotic cells evolved from prokaryotes 1. Organelles: discrete intracellular compartments which specialize in cellular functions 2. Some organelles may have evolved from ingestion of a small molecule (chloroplast): Endosymbiosis theory H. Muliticellularity arose and cells became specialized 1. Multicellularity arose from failure of eukaryotes to separate after cell division 2. Cells specialized to improve efficiency I. Biologists can trace the evolutionary Tree of Life 1. Speciation arises when populations are separated from reproduction and differences accumulate 2. Genus species 3. Autotrophy- self feeders that use photosynthesis 4. Heterotrophy _feed on biological molecules produced by other organisms 1.3 How do biologists investigate life: The scientific method! A. Observation 1. Advancement in technology has better enabled us to observe the world around us B. The scientific method combines observation and logic 1. Making observations 2. Asking questions 3. Forming a hypothesis (inductive logic) 4. Making predictions based on the hypothesis (deductive logic) accept premise, accept conclusion 5. Testing the predictions by conducting experiment C. Good experiments have the potential of falsifying hypothesis 1. Comparative: there will be a difference in samples based upon hypothesis a. Do not know or cannot control critical variables 2. Controlled: Start with similar groups and introduce a variable D. Statistical methods are essential scientific tools 1. Statistics can tell us whether the deviation among samples is significant 2. Calculate the probability that the differences were due to random variation 3. Null hypothesis no difference exists (T-test and P value) E. Not all forms of inquiry are scientific 1. Science must be testable 1.4 How does biology influence public policy?
Chapter 2 The Chemistry of life "Where there is water, there can be life" A. Water makes up 70% of bodies B. Mechanistic view- life is chemically based and obeys the universal laws of chemistry and physics 2.1 What are them chemical elements that like up all living organisms? A. All matter is composed of atoms B. An element is a pure substance that consists of only 1 type of atom C. Organisms are composed mainly of carbon, hydrogen, nitrogen, oxygen, phosphorous and sulfur D. The number of protons (atomic number) identifies an element E. Mass number: total number of protons and neutrons F. The number of neutrons differs among isotopes 1. Unstable, radioisotopes give of alpha, beta, or gamma radiation (radioactive decay) 2. Radioactive decay can change the element G. Electrons: their behavior determines chemical bonding 1. Orbital: the region in which an electron can be found 90% of the time ( 2 electrons) a. First shell 1S b. Second 1S 3P 2. The higher the shell number, the higher the energy of the electron 3. Outermost shell determines how an atom will react 4. Stable elements have complete valence shells (8 electronsoctet rule) 5. There is a "quest for stability" that drives chemical reactions 2.2 How do atoms bond to form molecules? 1. Chemical bond- and attractive force that links two atoms together 2. Covalent bonds consist of shared pairs of electrons 3. Compound: molecule made up of 2+ atoms bonded together in a fixed ratio 4. Covalent bonds are strong and require a lot of energy to break 5. The length, angle, and direction of covalent bonds is the same regardless of the large molecule of which the bond is a part 6. Unequal sharing of electrons results from electronegativity (attractive force) 7. If similar electronegativity nonpolar, else polar 8. Ionic bonds form from electrical attraction a. Sodium chloride b. Anion(-) and cation(+) formed c. Complex ion: group of covalently bonded atoms that carries a charge d. Form stable, solid salts e. Ion bond strength is weaker in biological systems than covalent bonds 9. Hydrogen bonds may form within or between molecules with polar covalent bonds
a. A bond between a strong electronegative atom and a hydrogen adom covalently bonded to another atom b. Ex: water c. Weaker than ionic or covalent, but large numbers have influence 10. Polar and Nonpolar substances: Each interacts best with its own kind a. Polar molecules interact with other molecules (hydrophilic) b. Nonpolar molecules do not react with polar molecules (hydrophobic) c. Nonpolar molecules react with non polar molecules by van der Walls forces 2.3 How do atoms change partners in chemical reactions? A. A chemical reaction occurs when atoms combine or change their bonding partners B. Matter is neither created nor destroyed, yielding balanced equations C. Energy is neigher created nor destroyed, but the form can be changed 1. Potential verse kinetic energy 2.4 What properties of water make it so important to biology? A. Solid, liquid, or gas B. Water has unique structure and special properties 1. Polar molecule that forms hydrogen bonds 2. Tetrahedral shape C. Ice floats 1. Solid water is less dense than liquid water, because 2. Allows life in water to survive freezing over the winter D. Melting, freezing, and heat capacity 1. Ice requires a great deal of energy to melt 2. Relatively constant temperature for bodies of water throughout the year a. Water helps minimize variations throughout the planet 3. This can be explained by waters high heat capacity E. Cohesion and surface tension 1. Cohesion is explained by hydrogen bonding (root system) 2. Surface tension is explained by hydrogen bonding F. Water is the solvent of life G. Aqueous solutions may be acidic or basic 1. Acids release hydrogen, bases accept hydrogen 2. Weak acids do not fully ionize in water 3. Acid-base reactions may be reversible a. direction of the reaction depends on starting concentrations b. The ionization of strong acids and bases is virtually irreversible c. The ionization of weak acids and bases is somewhat reversible H. Water is a weak acid I. pH is the measure of hydrogen ion concentration 1. ph=log10[H+] 2. pH<7 acidic 3. pH>7 basec
J. Buffers minimize pH change 1. Homeostasis: maintenance of internal consistency 2. A buffer is a solution of weak acid and its corresponding base 3. Buffering range (4-6) I. Life's chemistry began in water Chapter 3 Macromolecules and the Origin of life 3.1 What kind of molecules characterize living things? A. Proteins, carbohydrates, lipids, nucleic acids B. These biological molecules are polymers, which are constructed by covalent bonding of smaller monomers C. Functional groups give specific properties to molecules 1. Functional groups within macromolecules confer their properties D. Isomers have the different arrangements of the same molecular formula 1. Structural: differs in how atoms are joined together 2. Optical: Mirror image isomers (carbon bonding) E. The structures of macromolecules reflect their functions 1. Biochemical unity: organisms can acquire needed biochemicals by eating one another 2. Each macromolecule performs some type of function a. Energy storage, structural support, protection, catalysis, transport, defense, regulation, movement, information storage (nucleic acids) F. Most macromolecules are formed by condensation and broken down by hydrolysis 1. Polymers are constructed from monomers using condensation a. Release a water molecule for each covalent bond formed b. Polymers form i.f.f. energy is added to the system c. Hydrolysis breaks polymers back down into monomers 3.2 What are the chemical structures and functions of proteins A. Proteins are mainly for structural support and protection B. Monomers of protein consist of the 20 amino acids C. Proteins consist of a single unbranched polymer of amino acids, folded into a 3 dimesnional shape D. Composition: relative amounts of different amino acids in polypeptide chain E. Sequence variation is the source of diversity in protein structure and function F. Amino acids are the building block of proteins 1. All amino acids have a carboxyl (COO-), amino (NH3+) and hydrogen bonded, as well as a unique R chain 2. L-amino acids are commonly found in proteins in most organisms G. Peptide bonds form the backbone of a protein 1. Peptide bond is the bond inbetween the carboxyl and amino groups 2. The first amino acid is the N terminus 3. The last amino acid is the c terminus 4. C-N bonds cannot rotate freely 6. Carboxyl group and amino group have partial charges
H. The primary structure of a protein is its amino acid sequence 1. Four levels of protein structure: primary, secondary, tertiary, quaternary 2. Primary: the precise sequence of amino acids in a polypeptide chain a. Primary structure is determined by covalent bond 3. The secondary structure consists of regular, repeated spatial patterns in different regions of the polypeptide chain a. Secondary structure is determined by hydrogen bonding on partial charges b. a- helix is a right handed coil - Keratin c. B- pleated sheet forms when 2 polypeptide chains are extended and aligned 4. The tertiary structure of a protein is formed by bending and folding a. Tertiary structure determined by R groups 5. The quaternary structure consists of subunits a. Many functional proteins contain more than one polypeptide chain b. Quaternary structure results from the ways in which these subunits bind and interact I. Both Shape and chemistry contribute to protein specificity 1. The specific shape and structure allows the protein to bond noncovalently to another molecule Ex: Cause cells to stick together Ex: Antibodies recognize the shape of a virus coat and bond to it 2. A small molecule will only react if there is a general fit 3. The functional groups on the surface of a protein promote chemical interactions with other substances J. Environmental conditions affect protein structure 1. Because protein structure is determined by weak forces, it is sensitive to environmental conditions -Temp, pH, concentrations of polar substances 2. Denaturation: the loss of a proteins normal 3-D structure 3. Denaturation causes loss of normal biological function 4. Often irreversible K. Chaperonins help shape proteins 1. 2 Occasions that a protein may bind to wrong ligand a. Denaturation b. When a protein has just been made or not folded completely c. Chaperonins prevent inappropriate interactions (molecular cage) 3.3 What are the chemical structures and functions of carbohydrates? A. Carbohydrates are molecules containing the carbon atoms flanked by hydrogen atoms and hydroxyl groups. B. Major biochemical roles 1. Source of energy that can be released in a form usable by body tissue 2. Carbon skeletons that can be rearranged to form new molecules
C. Four categories or biologically important carbohydrates 1. Monosaccharide 2. Disaccharides 3. Oligosaccharides 4. Polysaccharides D. Monosaccharides and simple sugars 1. All living cells contain monosaccharide glucose, which is made in photosynthesis 2. Pentose: deoxyribose, ribose 3. Hexose: Fructose, gluctose, mannose, galactose E. Glycosidic linkages bond monosaccharides 1. Disaccharides, oligosaccharides, and polysaccharides are all constructed from monosaccharides through covelent bonds called glycosidic linkages formed by condensation 2. Different sugars can be made depending on a/b bonding 3. Carbohydrate isomers undergo different reactions and are recognized by different enzymes F. Polysaccharides store energy and provide structural material 1. Starch is a polysaccharide wish a-glycosidic linkages a. Distinguished by branching at carbons 1/6 2. Glycogen is a highly branched polysaccharide of glucose a. Stores glucose in animal livers and muscles b. Broken down to glucose monomers for fuel 3. Cellulose is polysaccharide connected by b-glycosidic linkages a. Strong bonds difficult to break down G. Chemically modified carbohydrates contain additional functional groups 3.4 What are the chemical structures and functions of lipids? A. Lipids are hydrocarbons that are insoluble in water B. Van der Walls forces cause hydrophobic hydrocarbons to stick together C. Roles 1. Store Energy 2. Phospholipids play an important structural role in cell membranes 3. Carotenoids help plants capture light energy 4. Steroids and modified fatty acids play regulatory roles as hormones and vitamins 5. The fat in animal bodies serves as thermal insulation 6. A lipid coating around nerves provides electrical insolation 7. Oil or wax on the surfaces of skin, fur, and feathers repels water D. Fats and oils (triglycerides) store enery 1. Composed of (3)fatty acid and glycerol a. Fatty acid is a long nonpolar hydrocarbon chain b. Glycerol is a small molecule with three hydrocarbon groups 2. Saturated a. All C-H bonds are single 3. Unsaturated
b. Some double bonds cause kinks that separate the hydrocarbon chains E. Phospholipids form biological membranes 1. Contain fatty acids bound to glycerol by estrogen linkages 2. A phosphate compound replaces the fatty acid 3. The head interacts with water, the tail is hydrophobic, forming a bilayer F. Not all lipids are tryglycerides 1. Cartenoids 2. Steroid: 4 rings 3. Vitamins A, D, K, E 4. Wax is made of an ester linkage between a long alchohol and long fatty acid 3.6 What are the chemical structures and functions of nucleic acids? A. Nucleic acids are polymers specialized for storage, transmission, and use of genetic information 1. DNA (pentose- deoxyribose) 1 chain, RNA (pentose- ribose)2 chains B. Nucleotides are the building blocks of nucleic acids 1. Nucleotide: pentose sugar, nitrogen containing base, phosphate group C. Pyrimidine: single ring 1. Cytosine (C) 2. Thymine (T) 3. Uracil D. Purine: fused ring 1. Adenine (A) 2. Guanine (G) E. Nucleotide joined by phosphodiester linkages F. The uniqueness if a nucleic acid resides in its nucleotide sequences 1. Complementary base paring (AT) or (CG) in double stranded DNA 2. RNA uses the base Uracil instead of thymine 3. A double helix shape results from hydrogen bonding G. DNA reveals evolutionary relationships 1. The closer the genome, the more closely related H. Nucleotide have other important roles 1. ATP (energy transducer) 2. GTP (energy source for protein synthesis) 3. cAMP (hormone action and nervous system) 3.6 How did life on earth begin? A. Biological molecules are not found in inanimate material B. Could life have come from outside Earth? 1. Rock from mars contained cyclic aromatic hydrocarbons C. Did life originate on Earth? 1. Hydrogen gas, ammonia, and methane composed the Earth's atmosphere 2. In-lab experiments caused complex molecules to form under simulated conditions
D. Chemical evolution may have lead to polymerization 1. In water, polymers hydrolyze into monomers (hydrothermal vents) E. RNA may have been the first biological catalyst 1. Protein and nucleic acids: The chicken and the egg 2. Ribozymes can explain, if living in an RNA world 3. Retroviruses catalyze synthesis of DNA from RNA F. Experiments disprove spontaneous generation of life Chapter 4: Cells: The Working Units of Life 4.1 What features of Cells make them the fundamental unit of life A. Cell theory 1. Cells are the fundamental units of life 2. All organisms are composed of cells 3. All cells come from preexisting cells B. Implications of the cell theory 1. Studying cell biology is in some sense the same as studying life 2. Life is continuous 3. The origin of life on Earth was marked by the origin of the first cells C. Cell size is limited by the surface-area to volume ratio 1. As an object increases in volume, the surface area does not increase to the same extent a. The volume determines the rate at which chemical reactions take place b. The surface area determines the rate at which cells can import and export into the environment c. Cells that are too big have demands for energy/ waste that can not be met d. That is why large organisms must still be composed of many tiny cells rather than a few large ones 2. Microscopes are needed to visualize cells a. Light microscope and electron microscope 3. Cells are surrounded by a plasma membrane a. Phospholipid bilayer b. Helps regulate internal environment c. Selectively permeable barrier d. Plasma membrane assists with intracellular communication and receiving signals from environment e. Protruding protein bind to adjacent cells 4. Cells are prokaryotic or eukaryotic 1. Life can be classified into archaea, bacteria, eukarya 2. Archaea and bacteria are prokaryotes 3. Prokaryotes do not have membrane enclosed internal compartments 4. Eukaryotes include protists, plants, fungi, and animals 5. Eukaryotes have a membrane bound nucleus, containing DNA 4.2 What are the Characteristics of Prokaryotic cells?
A. Prokaryotes have a diverse set of energy sources B. Prokaryotic cells are typically smaller than eukaryotic cells C. Prokaryotic cells share certain features 1. Plasma membrane 2. Nucleoid containing DNA 3. Cytoplasm a. Cytosol: water, dissolved ions, water-soluble macromolecules b. Ribosomes: Synthesize protein D. Some prokaryotic cells have specialized features 1. Cell walls a. Located outside plasma membrane b. Peptidoglycan c. Not a major permeable barrier d. Capsule: slime like coating outside cell-wall for protection in bacteria 2. Internal Membranes a. Photosynthetic bacteria use internal membranes for energy-releasing reactions 3. Flagella and Pili a. Flagella: Movement b. Pili: adhere to other cells to exchange genetic material, food, protection 4. Cytoskeleton a. Helical filaments composed of actin to maintain cell shape 4.2 What are the characteristics of eukaryotic cells? A. Compartmentalization is the key to eukaryotic cell function 1. Organelles a. Nucleus: genetic information, replication of DNA b. Mitochondrion: Converts energy stored in carbs/fat to ATP c. Endoplasmic reticulum and Golgi apparatus: protein package and delivery d. Lysosomes vacuoles: cellular digestive system- hydrolysis of large molecules e. Chloroplasts: Perform photosynthesis 2. Purpose of organelle membrane a. Separate from rest of cell to avoid inappropriate reaction b. Traffic regulator c. Specialization B. Organelles can be studied by microscopy or isolated for chemical analysis 1. Cell fractioning: breaking up of plasma membrane C. Some organelles process information 1. Roles of the nucleus a. Site of DNA replication b. Site of genetic control of cells activities c. Nucleolus assembles ribosomes from RNA and proteins 2. Membrane of nucleus a. 2 membranes form nuclear envelope
b. Pores i. Composed of over 100 proteins, inging hydrophobically ii. Surrounded by pore complex with 8 large protein aggregates iii. Small molecules pass through freely iv. Large molecules require nuclear localization signal (short sequence of amino acids) c. Signal sequence required to move from cytoplasm to nucleus d. Some viruses have signal sequence e. Signal sequence bonds noncovalently to receptor protein, which stretches the pore 3. The nucleus folds to be continuous with endoplasmic reticulum at some points 4. Inside nucleus, DNA combines with proteins to form chromatin, which aggregates to form chromosomes 5. During replication, nuclear envelope breaks down to distribute replicated DNA, and reforms when the process is complete D. Ribosomes 1. Found in cytoplasm and mitochondria/chloroplasts 2. Ribosomal RNA E. The endomembrane system is a group of interrelated organelles 1. Endomembrane consists of golgi apparatus and endoplasmic reticulum 2. Rough ER (ribosomes attatched) a. Segregates newly synthesized protein and transports them b. Proteins can be chemically modified i. Glycoproteins: addition of a carbohydrate ii. Protein "addressing" system 3. Smooth ER (no ribosomes) a. Breaks down toxins b. Glycogen hydrolysis c. Lipid and steroid synthesis F. Golgi apparatus 1. Further modify proteins form ER 2. Concentrates, packages, sorts proteins before they are send off 3. Synthesis of polysaccharides in the plant cell wall 4. Vesicles bud off from ER to fuse to Gogli apparatus, carrying proteins with them G. Lysosomes 1. Carbs/fats/nucleic acids/proteins are hydrolyzed into monomers 2. Autophagy- lysosomes break down its own material 3. Food gets into cell by phagocytosis E. Mitochondria 1. Break down fuel molecules and convert energy in bonds to ATP 2. If oxygen is used to make ATP, this is called cellular respiration 3. 2 membranes a. Outer membrane- little resistance b. Inner membrane- folds form cristae i. Controls what enters and leaves the cell
ii. Mitochondrial matrix is inside inner membrane F. Plastids 1. Only found in cells of plants and certain protists 2. Chloroplasts are sites for photosynthesis a. Chemical energy from light into strong bonds 3. Chromoplasts- flowers and fruit 4. Leucoplasts: storage deposits for starches and fats G. Peroxisomes 1. Collect toxic peroxides to break down 2. Plant corollary-glyoxysome 3. Vacuoles a. Storage of toxic byproducts b. Contribute to survival of plants c. Large vacuoles provide tructure d. Contain pigments that attract pollinators e. Digestion: vacuoles in seed i. If no digestive system, fuse food vacuole with lysosome ii. Sponges, protists f. Contracticle vacules help export water from cell H. The cytoskeleton 1. Roles a. Supports cell and maintains shape b. Provides for various types of movement c. Positions organelles within cell d. Move organelles within cell e. Anchors cell in place 2. Cause and effect proof a. Inhibition: remove the cause, remove the effect b. Mutation: If no cause, no effect 3. Microfilaments (smallest) a. Roles i. Help the entire cell or parts of cell move ii. Determine and stabilize cell shape b. Composed of actin, long helical chains c. Reaction of microfilament and "motor protein" myosin causes muscle contraction 4. Intermediate filaments a. Roles i. Stabalize cell structure ii. Resist tension 5. Microtubules (largest) a. Roles i. Form a rigid internal skeleton ii. Framework along which motor proteins can move structures in cell (cell division) b. Assembled from tubulin
c. Associated with cilia and flagella 6. Cilia and flagella: movement through an aqueous environment 7. Motor proteins 1. Motion results from sliding of microtubule doublets past each other 2. Motor protein dynin (slide microtubules), kinesin(walking vesicles), mysosin 4.4 What are the roles of extracellular structures? A. The plant cell wall is an extracellular structure a. Plasmodesmata are gaps in cell wall that allow molecules to pass from cell to cell B. The extracellular matrix supports tissue function in animals a. Holds cells together in tissues b. Contributes to physical properties of cartilage, skin, and other tissues c. Helps filter materials passing between different tissues d. Helps orient cell movement during embryonic development and tissue repair e. Chemical signaling from one cell to another f. Collagen 4.5 How did Eukaryotic Cells Originate? A. The endosympbiosis theory 1. Chloroplasts and mitochondria in eukaryotes was from engulfing a prokaryote 2. These organelles have their own DNA and are similar in size to prokaryotes 3. Synthesize some of their own materials 4. There has been evidence for movements DNA between organelles 5. Many biological similarities between chloroplasts and photosynthetic bacteria 6. Strong DNA similarities between chloroplasts and photosynthetic material B. Both prokaryotes and eukaryotes continue to evolve 1. Similarities between prokaryotes and eukaryotes a. Use nucleic acids in genetic material b. Use same 20 amino acids in proteins c. Use D sugars and L amino acids
Chapter 5: The Dynamic Cell Membrane 5.1 What is the Structure of a Biological membrane? A. Fluid mosaic model: proteins float unfixed around the phospholipids bilayer B. Proteins in the membrane move materials through membrane and receive chemical signals from the extern environment C. Phospholipids constitute the bulk of the membrane 1. Hydrophilic, polar head faces aqueous environment, hydrophobic tails face inward 2. Phospholipids vary in hydrocarbon chain length, degree of unsaturation, and polar groups present 3. 25% of lipid content is cholesterol 4. Phospholipid molecules can roam laterally across the membrane
a. More fluidity if low cholesterol, short fatty acid tails, and more unsaturated fatty acids, and higher temps b. Some organisms change membrane composition in lower temps Hibernation D. Membrane proteins are asymmetrically distributed 1. Proteins are embedded in phospholipids bilayer at a ratio of about 25:1 2. Proteins have hydrophobic and hydrophilic regions, determined by amino acid side chains a. Hydrophilic: faces aqueous environment b. Hydrophobic: faces inward 3. Two types of membrane proteins: a. Integral membrane protein hydrophobic domains and can penetrate phospholipids bilayer i.) a. Transmembrane proteins (integral) protrude on both sides of membrane b. Peripheral membrane proteins lack hydrophobic domains and are not embedded in bilayer 5. Movement restrictions a. The cytoskeleton may be attached b. Lipid rafts (long fatty acid chains) may trap proteins within a region E. Membranes are dynamic 1. Membranes are constantly forming, transforming, fusing, and breaking down a. Phospholipids are synthesized on smooth E.R. b. Membrane proteins inserted to rough E.R. c. Vesicles carry rough E.R. membrane to plasma membrane i.) Proteins are added according to destination d. Membranes are removed from plasma membrane through phagocytosis F. Membrane carbohydrates are recognition sites for other cells and molecules 1. Membrane-associated carbohydrates are covalently bonded to p.bilayer or membrane protein a. Glycolipid- carbohydrate covalently bonded to lipid b. Glycoprotein-carbohydrate covalently bonded to protein 2. Cells adhere based on size and shape of attached oligosaccharides 5.2 How is the Cell Membrane Involved in Cell Adhesion and Recognition? 1. Tissues, formed in multicellular organisms, form through 2 ways a. Cell recognition: one cell specifically binds to another of a certain type b. Cell Adhesion: the connection between two cells is strengthened 2. Cell recognition and cell adhesion involve proteins at the cell surface a. Glycoprotein with exposed carbohydrate is responsible b. Homotypic: if the same molecule is exposed, they will bind c. Heterohypic: different exposed molecules bind A. Three types of cell junctions connect adjacent cells 1. Tight junctions seal tissues a. Intestines b. Prevent substance from moving through spaces between cells
c. Membrane protein movement is restricted d. Ensure directional movement of materials 2. Desosomes hold cells together a. Desosomes connect adjacent plasma membranes through plaques 3. Gap junctions are means of communication a. Made of specialized channel proteins called connexons b. Ions and small molecules can pass through channel 5.3 What are the passive processes of membrane transport? A. Selective permeability 1. Passive transport does not require outside energy a. Fusion and facilitated fusion 2. Active transport requires outside energy B. Diffusion is the proves of random movement toward the state of equilibrium 1. Equilibrium: there is no net change in concentration 2. Diffusion is the net movement from regions of greater concentration to lesser 3. Diffusion rate depends on a. size b. Temp c. Electric charge d. Concentration gradient 4. Diffuion within cells and tissues a. Diffusion can not be used for long distance, but works between close cells 5. Diffusion across membranes a. Permeable molecules have equal concentrations on each side of membrane C. Simple Diffusion takes place through the phospholipids bilayer 1. Hydrophobic molecules pass easily through membrane 2. Charged or polar molecules do not pass though readily 3. Reasons a. Aquous environment prevents polar molecules from escaping into membrane b. Hydrophobic interior excludes hydrophilic substances D. Osmosis is the diffusion of water across membranes 1. Osmosis depends on number, not type of solute molecules present 2. Water diffuses from high concentration to low concentration a. Isotonic: solution has unique concentration b. Hypertonic: solution has higher solute concentration than the other side c. Hypotonic: solution has less solute concentration than other side 3. Water moves from hypotonic to hypertonic region 4. Turgor pressure in organisms with cell walls that limit volume of cell E. Diffusion may be aided by channel proteins 1. Polar and charged substances pass passively in to ways a. Integral membrane proteins form channels b. Binding to membrane protein called a carrier protein
c. Channel proteins have central pore lined with polar amino acids and water d. Pore can open if stimulated 2. Ion channels and the membrane potential a. Most ion channels are gated b. When the gate is opened, ion movement depends on 2 factors i. Concentration ii. Electrochemical gradient c. There are more ions inside the cell d. Charge imbalance is called membrane potential 3. The specifity of ion channels a. Potassium/ Sodium channels are specific b. Due to nature of pore c. These ions lose water F. Carrier proteins aid diffusion by binding substances a. Carrier proteins change shape to allow material to move into plasma membrane b. Rate of transport depends on concentration c. There is a maximum rate, when all carrier proteins are saturated 5.4 How do Substances cross membranes against a concentration gradient? A. Active transport is required when molecules move against concentration gradient B. Active transport is directional 1. Three types of membrane proteins a. Uniports: move a single substance in one direction b. Symports: Move two substances in the same direction c. Antiports: Move two substances in opposite directions i. Sodium potassium pump C. Primary and secondary transport rely on different energy sources 1. Primary active transport requires direct parcipitation of ATP a. Energy released by hydrolysis of ATP b. Sodium potassium pump 2. Secondary active transport uses ATP to create a concentration gradient 5.5 How do large molecules enter and leave a cell? A. Proteins, polysaccarides, and nucleic acids are too large to pass through biological membranes B. Macromolecules and particles enter cell through endocytosis 1. Three types of endocytosis a. Phagocytosis: Part of plasma membrane engulfs large particles b. Pinocytosis: Vesicles form to engulf small dissolved substances or fluid c. Receptor mediated endocytosis: specific reations at cell surface trigger the uptake of specific molecules C. Receptor-mediated endocytosis is highly specific 1. Depends on receptor proteins 2. Receptor protein binds to specific ligand, forming a coated vesicle around macromolecule
3. Once inside, the coat of clathrin dissolves and the vesicle fuses with the lysosome 4. Ex: cholesterol a. LDLs require endocytosis to be broken down b. High levels of cholesterol result from a difficient protein receptor D. Exocytosis moves materials outside cell 1. Exocytosis is the process by which materials packaged in vesicles are secreted when vesicle membrane fuses with plasma membrane 5.6 What are some other functions of membranes A. Keep different materials separate B. Some organelle membranes help transform energy 1. Ex: inner mitochondrial membrane C. Some membrane proteins organize chemical reactions D. Some membrane proteins process information 1. Specific binding of membrane carbohydrates sends signals to the cell Chapter 6: Energy, Enzymes, and Metabolism 6.1 What physical priciples underlie biological energy transformations? A. Metabolic reactions and catalysts are essential to biological transformation of energy by living things B. Energy is the capacity to work, or the capacity for change C. There are two basic types of energy and of metabolism 1. Potential Energy: stored energy in chemical bonds, concentration gradient for chemicals or charge 2. Kinetic Energy: moving energy D. Metabolism is the sum total of all chemical reactions in the body 1. Anabolic reactions: link simple molecules to form more complex molecules, require energy input 2. Catabolic reactions: break down complex molecules to simple molecules, releasing energy E. The first law of thermodynamics: Energy is neither created or destroyed F. The second law of thermodynamics: Disorder tends to decrease 1. When energy is converted from one form to another, some of that energy is unable to do work a. Gibbs free energy: energy available to do work b. G=H-TS (G: free, H: total energy, T: temp, S: entropy 2. Change in free energy can be measured a. Positive, free energy is required b. Negative: free energy is released 3. If you have more products than reactants, the disorder has increased 4. Disorder tends to increase as a result of energy transformations a. Why isn't the building of tissue a violation? 1. Requires 10x input energy to build energy 2. Reactions make CO2, H20, and many other small molecules 3. Therefore, Gibbs free energy is increased overall!
G. Chemical reactions release or consume energy 1. Catabolic reactions are exergonic, meaning they release energy 2. Anabolic reactions are endergonic, and require free energy 3. All reactions can go forward and backward 4. When concentration or A and B are the same, there is no net change a. Equilibrium: change in free energy is 0 H. Chemical Energy and free energy are related 1. The further toward completion the point of equilibrium lies, the more free energy is released 2. Positive Gibb's free energy means that the equilibrium lies against completion 6.2 What is the Role of ATP in biochemical energetics A. Cells rely on ATP (adenosine triphosate) to capture free energy needed to do chemical work B. Energy is trapped during exergonic reactions and used for endergonic reactions C. ATP releases a lot of energy when hydrolyzed D. ATP hydrolysis releases energy 1. ATP + H20 ADP + Free energy + Pi 2. P-O bond has more free energy than H-O 3. It takes a lot of energy to get phosphate close to one another E. ATP couples exergonic and endergonic reactions 1. ATP production is endergonic 2. ADP + Pi + Free energy ATP + H20 3. Cellular respiration provides the free energy 4. Coupling of exergonic and endergonic reactions are very common in metabolism a. Cycle: ADP picks up energy from exergonic reactions to become ATP, which donates energy to endergonic reactions to become ADP
6.3 What are Enzymes? A. Catalysts speed up the rate of reaction toward equilibrium B. Enzyme proteins are catalysts C. A biological catalyst is the framework in which chemical catalysis takes place D. For a reaction to proceed, an energy barrier must be overcome 1. Even exergonic reactions require some energy, called activation energy 2. Activation energy takes molecules into unstable forms called transition-state species 3. Enzymes reduce activation energy without excess heat input E. Enzymes bind specific reactant molecules 1. Unlike nonbiological catalysts, biological catalysts are very specific 2. In an enzyme catalyzed reactions, the reactants are called substrates 3. Substrates bind to a particular site on enzyme, called the active site 4. Specifity depends on three-dimensional shape and structure of active sites 5. Only a narrow range of substrates fit
6. The binding of a substrate to the active site is called the enzyme-substrate complex 7. The enzyme-substrate complex gives rise to a product and free enzyme 8. E + S ES E+P F. Enzymes lower the energy barrier but do not affect equilibrium 6.4 How do Enzymes work? A. Mechanisms used 1. Orient substrates 2. Induce strain in the substrate, which create transition-state species 3. Temporarily add chemical groups a. Acid base catalysis: Transfer of H+ destabilizes covalent bond b. Covalent catalysis: Functional group in side chains forms temporary covalent bond c. Metal ion catalysis: metals gain or loose ions, catalyzing oxidation/reduction reactions B. Molecular structure determines enzyme function 1. An enzyme is a protein that contains hundreds of amino acids, and is folded 2. The active site is usually 6-12 amino acids 3. The active site is specific to the substrate a. Depends on hydrogen bonds, attraction and repulsion of charged groups, and hydrophobic interactions b. Lock and key 4. An enzyme changes shape when it binds a substrate a. A change in shape is called induced fit b. Induced fit explains why amino acids are so large i. Provide a framework ii. Induced fit C. Some enzymes require other molecules in order to function 1. Prosthetic groups: distinctive, non-amino acid atoms or groups that are permanently bound to enzyme a. Flavin: mitochondrial enzyme plays role in cellular respiration b. Heme, of hemeglobin 2. Cofactors: Inorganic ions that bind to enzymes 3. Coenzymes: Carbon containing molecules that are required for the action of one or more enzymes a. Binds to active site b. ATP/ADP c. Vitamins D. Substrate concentration affects reaction rate 1. Adding the appropriate enzyme steeds up a reaction in logarithmic form a. Saturation: all enzymes are being used 2. Adding substrate increases reaction rate linearly 6.5 How are enzyme activities regulated?
A. A major characteristic of life is homeostasis, the maintenance of stable internal conditions B. Metabolic pathways: the product of one reactant is the reactant of the next C. Each reaction in a pathway is catalyzed by a specific enzyme D. Enzymes can be regulated by inhibitors 1. Inhibitors bind to enzymes to slow the rates of enzyme catalyzed reactions 2. Irreversible inhibition a. Covalent bonds to certain side chains b. Example: nerve gas 3. Reversible inhibition a. Noncovalent bonding to active site b. Competitive inhibitors compete with the substrate for the active site c. When the concentration is reduced, the enzyme is active again d. Noncompetitive inhibitors bind away from active site, and change shape (allostery) to reduce rate of reaction E. Allosteric enzymes control their activity by changing their shape 1. Active form has proper shape for substrate binding 2. Inactive form cannot bind to substrate but can bind to an inhibitor in site away from active site. This stabilizes inactive form, making it less likely to convert to active 3. The active form ca be stabilized by adding an activator to a third site 4. Binding of activators and inhibitors is specific 5. Allosterically regulated enzymes are proteins with quaternary structure a. The active site is located on the catalytic subunit b. The regulatory site(s) are located on regulatory subunits 6. Plot for allosteric regulated substrates are s shaped, and are sensitive for certain concentrations D. Allosteric effects regulate metabolism 1. Commitment step: the first step in a metabolic pathway 2. Feedback inhibition: the final product allosterically inhibits the enzyme that catalyzed the commitment step E. Enzymes are affected by their environment 1. Enzymes are highly sensitive to P.H a. Each enzyme is most active in a certain pH b. Reasons i. Ionization of functional groups on substrate of enzyme, altering folding 2. Temperature affects enzyme activity a. Warming increase rate of enzyme catalyzed-reaction b. Temperatures that are too high inactivate enzymes c. All enzymes have an optimal temperature for activity d. Isohyets catalyze the same reaction, but have different properties i. Different isozymes have different optimal temperatures ii. Ex: fish in freezing water e. Enzymes adapted to warm temperatures are held together mostly by covalent bonds i. Fever denatures bacteria enzymes but not human enzymes
Chapter 7: Pathways that harvest chemical energy 7.1 How does glucose oxidation release chemical energy? A. Principles that govern metabolic pathways 1. Complex chemical transformations in the cell occur in a series of separate reactions that form a metabolic pathway 2. Each reaction in a pathway is catalyzed by a specific enzyme 3. Metabolic pathways are similar in all organisms, from bacteria to humans 4. Most metabolic reactions are compartmentalized in eukaryotes, with certain reactions occurring inside a specific organelle 5. Each metabolic pathway is regulated by key enzymes that can be inhibited or activated, thereby determining how fast the reaction will go B. Cells trap free energy while metabolizing glucose 1. C6H12O6 + 6O2 6CO2 +6H20 + free energy 2. ADP + Pi + free energy ATP C. Three metabolic pathways for harvesting energy from glucose 1. Glycolysis: No O2. Begins glucose metabolism in all cells and produces two pyruvate molecules 2. Cellular Respiration: Uses O2 and converts each pyruvate into three CO2, and the energy stored in the pyruvate bonds is converted to ATP. Most efficient 3. Fermentation: Does not use O2. Converts pyruvate into lactic acid or ethanol D. An overview: Harvesting energy from glucose 1. When O2 is available, four pathways operate a. Glycolysis b. Pyruvate oxidation c. Citric acid cycle d. Electron transport chain 2. When O2 is not available a. Glycolysis b. Fermentation E. Redox reactions transfer electrons and energy 1. Energy can be transferred using ATP OR electrons 2. A redox reaction transfers one or more elections to another substance a. Reduction: gain of one or more electrons b. Oxidation: loss of one or more electrons c. When a molecule loses a hydrogen, it is oxidized d. Reduction and oxidation always occur together e. The reactant that becomes reduced is an oxidizing agent f. The reactant that becomes oxidized is the reacting agent g. Energy remains in the reduced product F. The coenzyme NAD is a key electron carrier in redox reactions 1. NAD+ 2H NADH + H+ 2. The proton transferred to NAD is hydride ion, which has 2 electrons 3. NADH + H+ +1/2O2 NAD+ + H2O (exergonic) 4. Oxygen acts as the oxidizing reagent
5. This reaction packages 4x more energy than ATP 7.2 What are the Aerobic Pathways of glucose metabolism? A. 10 enzyme catalyzed reactions convert glucose into two molecules of pyruvate, 4 molecules of ATP, and two molecules of NADH B. Glycolysis has reactions that use and produce ATP C. The energy-investing reactions of glycolysis that require ATP 1. The first 5 reactions are endergonic 2. Reaction 1: a phosphate group from ATP is attached to glucose 3. Reaction 2: six membered ring is rearranged into 5 membered fructose ring 4. Reaction 3: Enzyme phosphofructokinase attaches second phosphate (from ATP) to fructose ring, forming six-carbon sugar fructose 1, 6 biphosphate 5. Reaction 4: Opens fructose 1,6 biphosphate and cleaves it into two 3-carbon sugar phosphates 6. Reaction 5: Dihydroxyacetone is converted to glycalderhyde 3- phosphate (G3P) D. The energy harvesting reactions of glycolysis yield NADH + H+ and ATP 1. Each reaction occurs twice, once for each G3P 2. Producing NADH and H+ (reaction 6) a. Oxidation reaction resulting in a large drop of energy b. This energy is stored in NADH and H+ c. Enzyme triose phosphate dehydrogenase makes phosphate ester BPG (1, 3 biphosphoglycerate) 3. Producing ATP (reactions 7-10) a. BPG phosphates are transferred to ADP to form 2 ATP b. Substrate-level phosphorylation: enzyme catalyzed transfer of phosphate groups from donor molecules to ADP form to ATP i. Carried out by electron transport chain c. 2 ATP are invested to make 4 ATP d. Each glucose yields i. 2 pyruvate ii. 2 NADH + 2 H+ iii. 2 ATP E. Pyruvate oxidation links glycolysis and the citric acid cycle. 1. The oxidation of pyruvate to acetate and the subsequent conversion to acetyl CoA is the link between glycolysis and all other reactions of cellular respiration 2. Acetyl CoA formation is a multi-step reaction catalyzed by the pyruvate dehydrogenase complex, which is attached to the inner mitochondrial membrane 3. Pyruvate diffuses into the mitochondrion, where several reactions take place a. Pyruvate is oxidized into acetate, releasing CO2 b. Part of the energy from this oxidation is captured by reduction of NADH and H+ c. Some of the remaining group is stored temporarily in acetyl CoA d. pyruvate +NAD+ +CoA --_ acetyl CoA + NADH + H+ + CO2 4. Acetyl CoA donates acetyl group to receptor oxaloacetate to form citrate, the compound that initiates the citric acid cycle
F. The citric acid cycle completes the oxidation of glucose into CO2 1. 8 reaction pathway completely oxidizes acetyl into 2CO2 2. Free energy released is stored in ADP, NAD and FAD 3. Steady state reaction 4. Inputs : Acetyl CoA, H20, NAD+, FAD 5. Outputs : 10NADH + 10H+, 2 FADH2, 3CO2, 4 ATP G. The citric acid cycle is regulated by concentrations or starting materials 1. In order to restart the cycle, starting molecules must be renewed 2. Acetyl CoA is recycled 3. Electron carriers are reoxidized a. NADHNAD+ + H+ +eb. FADH2 FAD + 2H + 2e4. When NADH is oxidized, some other molecule X is reduced 5. This can happen through Fermentation of oxidative phosphorylation 6. If O2 is absent, X is pyruvate, reducing to lactic acid or ethyl alcohol 7. If O2 is present, X is O2 and the electron carriers can be reoxidized 7.3 How is energy Harvested from Glucose in the absence of oxygen A. Fermentation, like glycolysis, occurs in the cytosol B. Pyruvate is reduced to form NAD+ in lactic acid formation C. Pyruvate serves as the electron acceptor in lactic acid fermentation D. In alcohol fermentation, C)2 is removed from pyruvate, forming acetaldehyde E. Acetaldyhyde is reduced By NADH + H_, reducing NAD+ and ethanol F. The NAD + is used to begin glycolysis again G. No ATP is formed in fermentation 7.4 How does the oxidation of glucose form ATP? A. ATP synthesis from reoxidation of electron carriers in the presence of O2 is called oxidative phophorylation B. Two stages 1. Electron transport chain Why so many steps? So there are small, harvestable amounts of energy 2. Chemiosmosis C. The electron transport chain shuttles electrons and releases energy Chapter 8: What is Photosynthesis? 8.1 What is photosynthesis? A. Light +12H20 + 6CO2C6H12O6 + 6H2O +6O2 B. Plants take in carbon dioxide and release water and O2 through stomata C. Oxygen gas produced in photosynthesis is from water D. Photosynthesis involves 2 Pathways 1. Light Reactions convert light energy into chemical energy in form of ATP and NADPH 2. Light Independent reactions use ATP and NADPH to form glucose 1. Calvin cycle
2. C4 Photosynthesis 3. Crasslucacean acid metabolism 3. Both light and dark reactions stop in the dark because there is no more ATP 4. The rate of each pathway depends on the rate of the other 8.2 How does photosynthesis convert light energy to chemical energy? A. Light Acts as both a particle and a wave a. Particle like photon, but travels at certain wavelength b. The shorter the wavelength, the higher the energy of the photon c. To be active in biological processes, a photon must be absorbed by a receptor molecule B. Absorbing a photon excites a pigment molecule a. When a photon meets a molecule, it can be scattered, transmitted, or absorbed b. With absorption, the photon disappears and the molecule acquires the energy from the photon c. Energy level is raised from ground state to excited state d. An electron is boosted to farther valence shell, causing it to be held less tightly and therefore more reactive C. Absorbed wavelengths correlate with biological activity a. The electromagnetic spectrum encompasses the range of wavelengths of photons, from gamma to radio b. Molecules that absorb wavelengths in the visible spectrum are pigments c. Absorption spectrum: wavelengths absorbed by a particular pigment d. Action spectrum, or biological/photosynthetic activity, correlates with the absorption spectrum D. Photosynthesis uses energy absorbed by several pigments a. Chlorophylls, carotenoids, and phycobilins are different pigments involved in photosynthesis b. Chlorophylls a and b have complex ring structure, magnesium atom at center of ring, and hydrocarbon tail which anchors chlorophyll to thylakoid membrane c. Accessory pigments absorb energy in the middle of the spectrum, making the best use of the visible spectrum d. Carotenoids absorb blue/green e. Phycobilins absorb yellow/green/orange E. Light absorption results in photochemical change a. When a molecule moves from excited state to ground state, some energy is lost as heat or florescence. No work is done b. Pigment molecule may pass energy to another molecule, if it has the right orientation and structure c. Pigments are arranged into energy storing antennae systems, which can absorb energy d. Arranged from pigments that absorb high energy to pigments that absorb low energy e. The pigment that absorbs the longest wavelength is the reaction center
f. The reaction converts energy from light into chemical energy g. Reaction center is always chlorophyll a F. Excited chlorophyll at reaction center acts as a reducing agent a. 2 vital roles of chlorophyll i. conversion or light energy to chemical energy of an electron ii. Transferring the electron to other molecules b. Excited chlorophyll Chl* is a good reducing agent (electron donor) G. Reduction leads to electron transport a. NADP+ is oxidized to NADPH b. NADP+ is used in catabolic reactions, NADPH is used in anabolic reactions c. Two different systems of electron transport i. Noncyclic electron transport ii. Cyclic electron transport H. Noncyclic electron transport produces ATP and NADPH a. Noncyclic cycle: light energy is used to oxidize water, forming H+, O2, and electrons b. CHl* is a strong oxidizing agent because it has an electron fill that needs to be filled c. As electrons are passed from water to chlorophyll to NADP+, they pass through a chain of electron carriers in thylakoid membrane d. Exergonic reactions release energy that is used to form ATP e. Two photosystems are required i. Photosystem I uses light energy to reduce NADP+ to NADPH ii. Photosystem 2 uses light energy to oxidize water molecules, producing electrons, protons, and oxygen 1. Electron travels through ECT, becomes slightly lower energy, and enters Photosystem 1 2. ECT forms concentration gradient, which passes through ATP synthase to generate ATP 3. P 700 absorbs electron, exciting electron storing it in ferrodoxin. 4. Ferrodoxin passes electron to NADP+ reductase, which produces NADPH iii. Photosystem 2 requires photons at 680 nm, while photosystem 1 requires 700 nm iv. Photosystem 2 happens before photosystem 1 v. Z scheme shape vi. Overall, noncyclic electron transport uses water and photons to produce H+, NADPH, ATP, and O2 G. Cyclic transport chain produces ATP but no NADPH a. Calvin cycle requires more ATP than NADPH b. High ratio of NADPH to NADP+ causes cyclic electron transport to take place c. Electron is passed back to same chlorophyll after a set of reactions i. Chl* passes electrons to oxidizing agent ferodoxin, leaving positively charged Chl+
ii. Carriers of electron transport are reduced iii. Proton gradient is formed, and energy is stored in ATP iv. Electron with ground-state energy is passed back to chlorophyll, which can in turn be excited by another photon v. Occurs only in photosystem 1 A. H. Chemiosmosis is the source of ATP produced in phosphorylation a. Photophosphorylation: light driven production of ATP from ADP b. Movement of electrons through electron transport chain produces proton gradient in thylakoid membrane c. Protons move from stoma to thylakoid membrane d. ATP synthase couples diffusion of protons to production of ATP e. However, in plants protons flow out of thylakoid, whereas in animals protons flow into mitochondria 8.3 How is chemical energy used to synthesize carbohydrates? a. Formation of carbohydrates occurs in the stoma b. ATP and NADPH are coenzymes of the dark cycle A. Radioisotope labeling experiments revealed the steps of the Calvin cycle a. Used carbon dioxide isotope b. Killed cells after 3 seconds and thirty seconds, and used TLC to identify compounds containing carbon 14 c. Death after 3 seconds yielded only a 3PG (3 phosphocylgerate) molecule d. By allowing slightly longer exposures each trial, Calvin and Benson were able to map out the cycle B. The Calvin Cycle is made up of three processes a. Carbon fixation, catalyzed by rubsico b. Reduction of 3PG to form G3P c. Regeneration of CO2 receptor, RuBP d. The product of 6CO2 +6RuBP is 2 G3P, which is used to make starch, glucose, and fructose. The other 10 G3P are recycled C. Light stimulates the Calvin cycle a. Production of ATP and NADPH b. Light induced pH changes in the stoma activate some enzymes c. Light induced electron flow reduces disulfide bonds to activate four Calvin cycle enzymes 8.4 How do plants adapt to the inefficiencies of photosynthesis? A. Oxygen tends to compete with carbon dioxide for rubisco B. Rubsico catalyzes RuBG reaction with O2 as well as CO2 a. RuBP+O2 phosphoglycolate + 3PG b. Phosphoglycerateglycerate c. Enters peroxisomes, which glycerateglycine d. Glycine diffuses into mitochondrion 2 glycineglycerate + CO2 e. Same pathway as Calvin cycle, only less efficient C. This pathways is photorespiration, uses O2 to form CO2 a. Requires 4 CO2 to form 3 carbon glycerate plus CO2
75% efficient, reduces efficiency of Calvin cycle by 25% Rubisco has more affinity for CO2 If oxygen is abundant, rubsico acts as oxygenase Photorespiration is more likely to be used at high temperatures, when stomata are closed and oxygen builds up in stoma D. C4 plants can bypass photorespiration a. Mesophyll cells in roses, wheat, rice b. Close stomata on hot days to conserve water, oxygen levels rise in cell c. Operate via photorespiration, producing 3PG, a 3 carbon sugar d. Are considered C3 plants e. Corn, sugarcane, tropical grasses are C4 plants f. Maintain high CO2 to O2 ratio by forming oxaloacetate ( 4 carbon sugar) rather than 3PG g. PEP Carboxyl's, the catalyzing enzyme, fixes carbon dioxide even at low levels and does not act as an oxygenase h. Oxaloacetate loses carbon to form 3 carbon sugar in the bundle sheath cells (which contain abundant rubisco) , forming CO2 and regenerating PEP i. This process pumps up CO2 concentration around rubisco j. This stimulates the Calvin cycle k. C4 evolved from decline of CO2 in the atmosphere E. CAM plants also use PEP carboxylase a. Succulents store water b. Similar to metabolism of C4 plants, where carbon dioxide is fixed into 4 carbon compound c. CO2 fixation and Calvin cycle are separated by time d. At night, stomata open and CO2 is fixed in mesophyll cells to from oxaloacetate, which is converted to malic acid e. During the day, the stomata is closed and malic acid is shipped to chloroplasts, where decarboxylation provides CO2 necessary for Calvin cycle f. Light reactions supply necessary NADPH and ATP 8.5 How is photosynthesis connected to other metabolic pathways in plants? a. Plants use carbohydrates to fuel anabolic reactions and active transport b. Some G3P is converted to pyruvate, which enters cellular respiration in mitochondria c. Overall carbon fixation must exceed respiration for plant growth CHAPTER 9 Chromosomes, the Cell cycle, and cell division 9.1 How do prokaryotic and eukaryotic cells divide? A. Unicellular organisms divide to reproduce, cells of multicellular organisms divide to repair tissue and grow B. 4 events must occur a. Reproductive signal that initiates cell division
b. c. d. e.
b. Replication of DNA c. Distribution of DNA via segregation d. Separation into 2 cells through cytokinesis C. Cells divide by binary fission 1. Prokaryotic cells divide by binary fission 2. Cell division results in the reproduction of a single celled-organism 3. Reproductive signal a. External factors such as environmental conditions and nutrient concentrations are signals for the initiation of cell division D. Replication of DNA 1. A chromosome is a DNA molecule containing genetic information a. Most prokaryotes have 1 circular chromosome b. DNA is folded by positive/negative attractions in DNA i. Ori: site where replication of circle starts ii. Ter: site were replication of circle ends c. Replication takes place as DNA is threaded through replication complex of proteins, forming 2 daughter DNA d. Cell grows E. Segregation of DNA 1. Daughter DNAs separate led by region including ori. Cell begins to divide 2. Active process requiring the hydrolysis of ATP F. Cytokinesis 1. Pinching of plasma membrane 2. 2 new cells are formed G. Eukaryotic cells divide by mitosis or meiosis 1. Many complex eukaryotes originate from a single fertilized egg 2. Sex cells are called gametes: sperm and egg 3. Formation of a multicellular organism to a fertilized egg is called development 4. Four steps to cell reproduction in eukaryotes a. Divide: cell signal is not based upon external environment, rather the needs of the entire organism b. Eukaryotes have many chromosomes, which divide to form sister chromatids, which are separated via mitosis c. Distinct nucleus must be divided into 2 nuclei . Cytokinesis can only occur after duplication of the entire nucleus d. Cytokinesis occurs differently in animal cells and plant cells 5. Meiosis occurs only in cells that produce gametes involved in reproduction a. Only in cells that produce sperm in the egg b. Meiosis generates diversity by shuffling genetic material 9.2 How is eukaryotic cell division controlled? A. A cell lives and functions until it dies or divides B. The events that occur to produce 2 eukaryotic cells from 1 is known as the cell cycle C. If a cell is not dividing, it is in interphase D. Interphase has 3 subphases: G1, DNA synthesis, and G2 1. G1: preparation for synthesis
2. G1 to S transition: Commitment to sell division 3. S phase: DNA replication forms 2 joined sister chromatids from a chromosome 4. G2: cell makes preparation for mitosis E. Cyclins and other proteins trigger events in the cell cycle 1. Transitions from phase to phase depend on activation of protein cyclindependent kinase (Cdk) 2. Kinase is an enzyme that catalyzes transition of phosphate to a protein via phosphorylation 3. Phosphorylation changes the shape of a protein by changing its charges 4. Activation of a Cdk to a cyclin activates them, and is regulated allosterically 5. The phosphorylated protein regulates the cell cycle 6. Different cyclin-Cdk combinations act at various stages of the cell cycle F. RB (retinoblastoma protein) inhibits the cell cycle 1. When RB is phosphorylated, it becomes inactive and the cell cycle can progress 2. Damaged DNA can be stopped from replication if p21 binds to Cdks, preventing their activation by cyclins 3. Cancerous cells group exponentially because they have too much cyclin G. Growth factors can stimulate cells to divide 1. Cells that divide rarely are stimulated by external chemical signals called growth factors 2. When cut, platelets release growth factor to stimulate division of skin cells 3. Cancer cells divide inappropriately because they make their own growth factor or stop requiring growth factor to divide 9.3 What happens during mitosis A. Segregation of DNA by packaging huge DNA and proteins on chromosomes B. Eukaryotic DNA is packed onto very compact chromosomes 1. Chromosomes are made up pf dense material called chromatin 2. Sister chromatids form during S phase, and are held together by a protein called cohesin 3. During mitosis, cohesion is removed and proteins are held together only at centromere 4. Chromosomes contain large quantities of the protein histones 5. Positive charge on histone interacts with negative charge on DNA, forming nucleosomes 6. Nucleosome contains 1. 8 histone molecules united to form a core or spool 2. 146 base pairs of DNA 3. Histone H1 on the outside of the DNA, clamping it to histone core C. Overview: Mitosis segregates exact copies of genetic information " In mitosis, a single nucleus gives rise to 2 nuclei which are genetically identical to each other and the parent nucleus" D. The centrosomes determine the plane of cell division 1. The centrosome some doubles itself forming 2 centrosomes 2. The centrosomes move to opposite ends of the nuclear envelope
3. Tubulin dimmers initiate the formation of microtubules, which orchestrate chromosomal movement E. Chromatids become visible and the spindle forms during prophase 1. Cohesin is removed and individual chromatids are visible under the microscope 2. Microtubules form a spindle for which chromosomes move on toward centromere 3. Two types of microtubules a. Polar microtubules: form framework of the spindle b. Kinetochore microtubules attach to the kinetochores on the chromosomes c. Kinetochores are formed on centromere region for each chromotid d. Kinetochore microtubules ensure one chromatid will go to each side of cell F. Chromosome movements are highly organized 1. Premataphase: disappearance of nuclear envelope and nucleoli. The centromeres gradually approach metaphase plate 2. Metaphase: All centromeres arrive at equatorial plate - Best time to see chromosomes -All the chromatid pairs separate simultaneously using separase 3. Anaphase: Starts when chomatids separate - Sister chomotids move to opposite ends of the spindle -Chromotids now referred to as daughter chromosome -Kinetochores use ATP to more chromotids - Distance between poles is doubled G. Nuclei re-form during telophase H. Cytokinesis is the division of the cytoplasm 1. Animal cells divide cytoplasm by pinching off in the middle a. Thread is microfilaments of actin and mysosin 2. Plants have cell walls, and golgi apparatus forms membrane between 2 daughter cells b. Organelles need not be distributed evenly between daughter cells 9.4 What is the role of cell division in sexual life cycles? A. Reproduction by mitosis results in genetic constancy 1. Asexual reproduction stems from mitosis B. Reproduction my meiosis results in genetic diversity 1. Offspring is no identical to parent 2. Each parent contributes one gamete 3. Gametes differ genetically from one another in same organism 4. Somatic cells are non-reproductive cells 5. Each somatic cell contains two sets of chromosomes, one maternal and one paternal (diploid) forming a homologous pair 6. Gametes contain only a single set of chromosomes, and are haploid 7. Two haploid gametes fuse to form a diploid zygote during fertilization C. Haplontic organisms: The zygote is the only diploid cell and the rest is haploid 1. The zygote undergoes mitosis to form haploid spores D. Alternation of generations
1. Meiosis gives rise to haploid spores 2. Spores divide my mitosis to form gametophyte 3. Gametes are formed by mitosis 4. Gametes fuse to form diploid zygote, which divides by mitosis to form diploid sporophyte E. Diplontic organisms: The only haploid cells are gametes, and the organism is diploid F. The number, shapes, and sizes of metaphase chromosomes constitute the karyotype 1. Homologous pairs can be identified by size, shape, and staining 9.5 What happens when a cell undergoes meiosis A. Meiosis consists of two nuclear divisions, but only 1 replication of DNA B. The products of meiosis are different from one another and the parent cell C. Meiosis I 1. Early prophase: the chromatin begins to condense following interphase 2. Mid-prophase I: Synapsis aligns homologous pairs, and the chromosomes condense further 3. Late prophase 1-prometaphase: The chromosomes continue to coil and shorten. Crossing over results in exchange of genetic material. Sister chomatids are no longer identical. Nuclear envelope breaks down. Chiasmata connects homologous pairs and cohesion connects sister chromatids 4. Metaphase 1: The homologous pairs line up on the metaphase plate at random orientation via independent assortment 5. Anaphase 1; The homologous chromosomes move to opposite poles of the cell 6. Telophase I: The chromosomes begin to gather into nuclei, and the original cell divides D. Meiosis II 1. Prophase II: The chromosomes condense again, following a brief interphase where DNA does not replicate 2. Metaphase II: The centrosomes of the paired chromatids line up on the equatorial plate of each cell 3. Anaphase II: The chromatids finally separate, becoming chromosomes, and are polled to opposite poles. Because of crossover, each new cell will have different genetic makeup 4. Telophase II: Chromosomes gather into nuclei and cells divide 5. Each of the for cells has a nucleus with haploid number of chromosomes E. The activities and movements of chromosomes during meiosis result in genetic diversity 1. Crossing over and random assortment F. Meiotic errors lead to abnormal chromosome structures and numbers 1. Nondisjunction: sister chromatids or homologous pairs fail to separate 2. Aneuploidy is a condition in which there is a lack or excess of chromosomes 3. Causes a. Lack of cohesion: trisomy 21 -Homologous pair go to same pole during anaphase 1
4. Translocation: a piece of a chromosome breaks away to form another chromosome 5. Most aneuploidy zygotes are spontaneously aborted G. Polyploids can have difficulty in cell division 1. Polyploid: 3+ sets of homologous chromosomes 2. If one chromosome has not homolog (3N), anaphase 1 cannot send representatives of both chromosomes to each pole 9.6 How do cells die? A. Necrosis: damaged by toxins or starved of oxygen or essential nutrients -Scab/inflammation B. Apoptosis: cell suicide - The cell is no longer needed by the organism -The longer a cell lives, the more prone they are to genetic damage that could lead to cancer C. Signals such as lack of mitotic signal and recognition of damaged DNA stimulate cell death D. External signals can cause plasma membrane protein to change shape and activate enzymes called caspases. E. Caspases hydrolyze proteins, nucleosomes, and plasma membrane Chapter 42: Animal reproduction 42.1 How do animals reproduce without sex? Advantage: no mate needed Disadvantage: if climate changes, lack of genetic diversity leads to poor adaptability A. Budding and regeneration produce new individuals by mitosis 1. Budding: new individuals form as outgrowths 2. Regeneration: replacement of limbs can generate new organisms B. Parthonogenesis is the development of unfertilized eggs 1. Fish, amphibians, reptiles, honeybees 42.2 How do animals reproduce sexually? Disadvantage: Time and energy expenditure, dangerous Advantage: Genetic diversity A. Requires joining of two haploid cells to form a diploid B. Haploid gametes are produced through gameotogenesis C. Three fundamental steps 1. Gametogenesis (making gametes) 2. Mating (getting gametes together) 3. Fertilization (fusing gametes) D. Gametogenesis produces egg and sperm 1. Gameotogenesis occurs in gonads (testes for men, ovaries for women) 2. Gametes are produced from germ cells 3. Germ cells migrate to gonads producing spermatogonia and oogonia 4. Meisosis reduces diploid cpermatocytes and oocytes to haploid cells
E. Spermatogenesis 1. Germ cell proliferates into spermatagonium(2n) 2. Spermatagonium undergoes mitosis to form primary smerpatocyte 3. Primary spermatocytes(4n) undergo meiosis to form secondary spermatocytes(2n) 4. Spermatocytes go through second mitotic division to form spermatids (n) 5. Half spermatids receive X chromosome, half receive Y chromosome 6. Remain in cytoplasmic contact because genes on X chromosome are needed for development 7. Spermatids are genetically unique and differentiate into sperm F. Oogenesis 1. OOginia proliferate(2N) through mitosis 2. Primary oogocytes (4N) go through first mitotic division 3. Secondary oogocyte (2n) produced, receiving almost all cytoplasm 4. First polar body receives almost no cytoplasm 5. Second mitotic division: secondary oocyte divides asymmetrically into large ootid (n) and second polar body 6. Polar bodies degenerate, forming 1 mature ovum G. Fertilization is the union of sperm and egg 1. Union of haploid sperm and haploid egg forms diploid zygote 2. Fertilization involves a complex series of events a. The sperm and the egg recognize each other b. The sperm is activated, enabling it to gain access to the plasma membrane of the egg c. The plasma membranes of sperm and egg fuse d. The egg blocks entry of additional sperm e. The egg is metabolically activated and stimulated to start development f . The egg and sperm nuclei fuse to create the diploid nucleus of the zygote H. Specifity in sperm-egg interactions 1. Important that sperm/egg of different species do not interact 2. Eggs release species specific sperm attractants 3. Acrosome: enzymes and proteins located on sperm head that drill a hole in jelly coat 4. Acrosomal process is species specific and binds with vitelline coat 5. Zone pellucids prevents fertilization of gametes of different species G. Blocks to polyspermy: mechanisms that stops more than one sperm from entering egg 1. Electric charge gradient: fast black to polyspermy 2. Release of calicium ions: slow block to polyspermy H. Egg Activation 1. Increase in calcium causes corical granules to fuse with plasma membrane and release contents 2. Formation of a fertilization envelope that prevents additional sperm 3. In mammals, cortical granules destroy sperm binding molecules in zonal pellucida but does not have fert. Envelope I. External ferlization: most correlate release of gametes among males and females
J. Internal fertilization 1. Sperm can only swim through liquid 2. Terrestrial animals must reproduce through internal fertilization 3. Accessory sex organs: penis, vagina, ducts, tubules 4. Copulation: physical joining of make and female accessory sex organs 5. Lock-key fashion of vagina/penis K. A single body can function as moth male and female 1. Dioecious: species that have separate male and female members 2. Monoecious: An individual can produce both sperm and egg 3. Sequential vs. simultaneous hermaphrodites 4. Advantage: a rare encounter is twice as likely to be successful J. The evolution pf vertebrate reproductive systems parallels the move to land 1. Reptiles: the amniotic egg prevents water loss and provides nutrients K. Reproductive systems are distinguished by where the embryo develops 1. Oviparous: animals lay eggs 2. Viviparous: retain embryo within mothers body until early developmental stages Mammals: placenta Ovoviviparity: eggs are held in body until hatched 42.3 How do the human male and female reproductive systems work? A. Male sex organs produce and deliver semen 1. Sperm are produced in testes 2. Testes are located in skin pouch (scrotum) 3. Spermatogenesis takes place within seminiferous tubules, which are coiled in each teste 4. Lydig cells between seminiferous tubules produce testosterone 5. Development from germ cell to sperm takes place in sertoli cells which provide nutrients 6. Sperm are stored in epididymis where they mature and become motile 7. Epididymis connects to urthera by vans deferens duct 8. Seminal vesicles empty fluid into vans deferens before it joins urethra 9. Prostate ground contributes 30% of volume to semen a. Neutralizes acid in vagina 10. Bulbourethral glands produce alkaline, mucoid secretion that neutralizes urethra before climax a. Secretions carry residual sperm from past sexual activity b. Reason why "pulling out" is ineffective 11. Penis has highly sensitive tip: glans penis, which is covered in foreskin 12. Erection facilitates entry into female vagina 13. At climax, semen is moved into urethra by emission and released by ejaculation 14. After ejaculation, enzymes break down cGMP, causing blood vessels to constrict 15. Erectile disfunction treatment: inhibit breakdown of cGMP B. Male sexual function is controlled by hormones 1. Gonadotropin releasing hormone stimulates testosterone production
2. Testosterone stimulates production of lutenizing hormone (LH and follicle stimulating hormone (FSH) 3. Increased testosterone during puberty causes the development of secondary sexual characteristics and increased growth rate 4. Spertmatogenesis is controlled by FSH and testosterone on sertoli cells C. Female sex organs produce eggs, receive sperm, and nurture the embryo 1. Mammilian eggs are released into oviduct, or fallopian tube to be fertilized 2. Cilia in oviduct slowly propel egg toward uterus 3. Clitoris: erectile tissue with a similar developmental origin as penis 4. Sperm travel to fallopian tubes to meet egg 5. Fertilization completes second mitotic division into ovum 6. First few divisions of cells form a blastocyst 7. The blastocyst attatches to the epithelial lining of uterus (implantation) 8. Egg matures in overy, endometrium thickens 9. If no implantation, endometrium regresses or is sloughed off D. The ovarian cycle produces a mature egg 1. Cycle is 28 days long 2. Begin with millions of primary oocytes at birth 3. Average woman will go through 450 ovarian cycles 4. Many oocytes will begin to mature, but only one will mature completely 5. Follicle: oocyte and surrounding cells 6. Largest follicle grows for 2 weeks, and ovulation occurs 7. Ovulation: rupture of follicle and release of egg 8. Following ovulation, follicle cells proliferate and produce estrogen and progesterone for 2 weeks E. The uterine cucle prepares on environment for the fertilized egg 1. Uterine cycle: buildup and breakdown of endometrium 2. Uterine wall size is maximized from 5 days after ovulation and following 9 days F. Hormones control and coordinate the ovarian and uterine cycles 1. Gonadotrophins start to be produced during puberty 2. These hormones stimulate production of FSH and LH 3. FSH and LH causes ovarian tissue to grow and produce estrogen 4. Estrogen causes maturation of accessory sex organs and secondary female characteristics 5. Menstruation marks beginning of each ovarian uterine cycle -Thinning uterine wall -Increase in FSH and LH causes 10-20 follicles to mature -Follicles release estrogen 6. Estrogen exerts negative feedback on LH and FSH on first 12 days 7. Day 12, estrogen exerts positive feedback, causing a surge of LH and FSH 8. LH surge triggers follicle rupture 9. Corpeus luteum becomes an endocrine gland, and estrogen and progesterone are secreted 10. Progesterone is responsible for thickening of uterine lining 11. If the egg is not fertilized, corpus luteum degenerates on day 26
12. Lack of progesterone causes endometrium to slough off, beginning the cycle again with menstruation. Negative feedback stimulates FSH and LH production G. IN pregnancy, hormones from the extraembryonic membrane take over 1. Blastocyst secretes human chorionic gonadotrophin (hCG) 2. hCG stimulates corpus luteum to produce estrogen and progesterone to support growth of endometrium and prevent menstruation 3. hCG is tested for in pregnancy tests 4. Birth control pills maintain high estrogen/progesterone levels that inhibit ovulation H. Childbirth is triggered by hormonal and mechanical stimuli 1. Increased estrogen : progesterone ratio stimulates contractions of uterine muscle 2. Mechanical stimuli is caused by stretching of uterus and pressure on cervix 3. Cervix is dialated by contractions 42.4 How can fertility be controlled and sexual heath maintained? A. Human sexual responses have 4 phases 1. Excitement 2. Plateau 3. Orgasm 4. Resolution B. Humans use a variety of methods to control fertility 1. Nontechnological approaches: periodic abstinence, pulling out 2. Barrier methods: condoms, diaphragms, cervical caps 3. Preventing ovulation: pill 4. Preventing implantation: IUD 5. Sterilzation: vasectomy C. Reproductive technology solves problems of infertility Chapter 41: Animal Hormones 41.1 What are hormones and how do they work? A. Hormones are chemical signals, secreted by cells of the endocrine system B. Hormones are like a radio, and broadcast signals that can be picked up by target cells C. Hormones can act locally or at a distance 1. Hormones secreted by endocrine cells into extracellular fluid diffuse into bloodstream and are carried to many areas of the body (circulating hormones) 2. Hormones that affect only target cells near release site are paracrine hormones 3. When the cell secreting the hormone is the cell affected by the hormone, the hormone is autocrine (negative feedback possible) 4. Many hormones are secreted by endocrine glands (ductless) 5. A single gland may secrete several different hormones D. Hormonal communication arose early in evolution 1. Hormones from the head control molting in insects (EXP 1) a. Growth takes place with molting b. Decapitation affects molting pattern c. Hypothesis: Some substance diffusing from the head controls molting d. Experiment: Decapitate juvenile bugs at different times after blood meal
e. Results: Decapitation 1 week after blood meal: molt. Decapitated 1 hour, does not molt. f. Conclusion: molting depends on the interval between blood meal and decapitation, suggesting a substance must pass from head to body 2. Experiment 2: a. Method: Decapitate 1 bug 1 hour after blood meal, and the other bug 1 week after blood meal. Join insects by glass tube b. Results: Both insects molted c. Conclusion: a diffusible substance is necessary for molting E. Jucenile hormone controls development in insects 1. The substance that prevents molting into adults is juvenile hormone 2. Evolutionary benefit: more growth before adulthood, more survival success H. Hormones can be divided into 3 chemical groups 1. Peptides of polypeptides: derovatoves of amino acids, water soluble, easily transported in blood, cannot pass through cell membranes. Therefore, they are released by exocytosis 2. Steroid hormones: derivatives of cholesterol, easily pass through cell membranes, bound to carrier proteins to be transported to target cells. I. Hormone receptors are found on the cell surface or interior 1. Steroid hormones: receptors within the membrane a. The complex formed alters gene expression 2. Peptide hormones: receptors on the cell membrane a. Receptors are glycoprotein complexes with 3 domains i. Binding domain: projects outside plasma membrane ii. Transmembrane domain: anchors receptor in membrane iii. Cytoplasmic domain: Extends into the cytoplasm of the cell b. When hormone binds, shape of cytoplasmic domain is changed and activates a protein kinase c. Kinase activates or inactivates enzymes, leading to the cells response d. Gene expression may be altered when chemical signals enter nucleus J. Hormone action depends on the nature of the target cell and its receptors 1. The same hormone can cause different responses in different types of cells 2. Epinephrine: Increases heart rate, increases blood flow to kidneys, decreases blood flow to stomach, suppresses immune system, stimulates breakdown of glycogen, airway dilation
Chapter 44: Neurons and Nervous Systems 44.1 What Cells are unique to the nervous system? A. Nerve cells and glial cells B. Neurons are excitable and propagate electrical signals, known as action potentials C. Neurons have long extentions called axons that allow them to conduct action potentials over long distances D. Nerve is a bundle of axons that come from many different neurons E. Efferent neurons: carry commands to physiological and behavioral effectors such as muscles and glands
F. Interneurons: store information and facilitate communitation between sensors and effectors G. Neuronal networks range in complexity 1. Ganglia: organization of neurons into clusters 2. Brain: one pair of ganglia is larger than the rest, making up the brain 3. Most cells of the nervous system are found within brain and spinal cord (CNS) 4. Peripheral nervous system (PNS): Neurons located beyond brain/spinal courd 5. Information is passed from one neuron to another at structures called synapses a. Cell sending message: presynaptic neuron b. Cell receiving message: postsynaptic neuron c. Strengh of synapses is flexible: ability to learn, remember, have emotion H. Neurons are the functional units of nervous systems 1. All organisms with nervous systems have neurons that function similarly 2. Neurons are composed of 4 regions a. Cell body: contains nucleus and most cell organells b. Dendrite: receive information from other neurons c. Axon: Conducts action potentials away from cell body d. Axon terminal: Synapse with a target cell 3. Most synapses are chemical, releasing neurotransmitters 4. Electrical synapses transmit action potential from one neuron to the next I. Glial cells are also important components of nervous systems 1. Oligodendrocytes: insulate axons with insulating plasma membrane 2. Shwann cells insulate with myelin, increasing speed of action potential 3. Astrocytes: blood-brain barrier, protecting brain from toxic chemicals in blood 4. Fat soluble compounds such as alcohol and anesthetic are permeable 44.2 How do neurons generate and conduct signals? A. Action potentials are created when ions are allowed to move across the membrane B. At rest, the nerve is electrically negative compared to the outside C. Any difference in electric potential across the membrane is called membrane potential D. When a nerve is resting, it is at resting potential (-70 mv) E. Simple electrical concepts underlie neuronal function 1. Voltage (difference in electric potential ) induces a current 2. Electric current is carried by ions (Na+, K+, Ca2+, Cl-) 3. Current can be used to do work F. Membrane potentials can be measured with electrodes 1. Electrodes measure voltages within nerves 2. If permeability of membrane is changed, positive ions enter, creating an action potential G. Ion pumps and channels generate membrane potentials 1. Plasma membranes consist of proteins that can act as ion pumps 2. Ex: sodium potassium pump increases K+ inside cell and Na+ outside cell 3. Squid experiment taught much about basic electrical properties of neurons H. Ion channels and their properties can now be studied directly 1. Patch clamping I. Gated ion channels alter membrane potential 1. Voltage, chemically, or mechanically gated channel
2. Depolarized: inside of a neuron becomes less negative, Na+ channels open 3. Hyperpolarized: K+ channels open, inside becomes more negative 4. Electron currents do not spread far because membranes are not impermeable to ions J. Sudden changes in Na+ and K+ channels generate action potentials 1. Open K+ channels create resting potential 2. Activation gates of some Na+ channels open, depolarizing the cell to threshold 3. Additional Na+ channels open, causing rapid depolarization (action metential) 4. Na+ gates close, gated K+ channels open, hypolarizing the cell 5. All gated channels close and the cell returns to resting potential K. Action potentials travel along axons without loss of signal 1. Voltage gated Na+ channels open in response to stimulus 2. Depolarizing current spreads down axon 3. Upstream Na+ channels inactivate, making the membrane refractory 4. Voltage gated K+ channels open, hyperpolarizing the axon, then close 5. Action potential stimulates more Na+ channels to open in a self extended forward stream * Action potentials do not travel along all azons at same speed Mylinated vs unmylinated Larger diameter vs smaller diameter L. Action potentials can jump along axons 1. Mylenated neurons 2. Nodes of Ranvier allow ion movement 3. Leakage is reduced 4. Much faster speed of conduction 44.3 How do neurons communicate with other cells? A. Chemical synapse: chemical messages in the presynaptic cell induce changes in the postsynaptic cell B. Electrical synapse: action potential spreads directly from a presynaptic cell to a post synaptic cell C. The neuromuscular junction is a model chemical synapse 1. Neuromuscular junctions are synapses between motor neurons and muscle cells 2. Axons branch to form many neuromuscular junctions with the muscle cell (button) 3. Neurotransmitter: acetylcholine synthesized and packaged in vesicles 4. Space between presynaptic membrane and post synaptic membrane is synaptic cleft D. The arrival of an action potential causes the release of a neurotransmitter 1. Arrival of action potential opens calcium channels 2. Calcium enters cell causes vesicles to fuse to presynaptic membrane and empty their contents to the synaptic cleft 3. Postsynaptic membrane is depolarized 4. Spreading depolarization fires an action potential in postsynaptic membrane 5. Acetylcholine is broken down and the components are taken back to presynaptic cell, recycling it along with vesicles E. The postsynaptic membrane responds to neurotranspitter
F. Synapses between neurons can be excitatory or inhibitory 1. Synapses between motor neurons and muscles are always excitatory (Motor end plates respond to Ach by depolarizing) 2. A hyperpolarization response is classified as inhibitory -Reason: neuron may receive many signals at the same time 3. The postsynaptic cell sums excitatory and inhibitory input a. When the sum of the potentials surpass the threshold, and action potential b. For most neurons, summation takes place in axon hillock at base of axon c. Synapses closest to hillock have highest effect d. Spatial summation: adds influnces at several sites e. Temporal summation: adds influences rapidly taking place at same site G. Synapses can be fast or slow 1. Ionotropic receptors: ion channels that enable fast, short lived responses 2. Metabotropic" Induce signaling cascades that lead to changes in ion channels -Slower and longer lived a. Neurotransmitter binds to receptor b. Receptor changes shape and actives a G protein c. GTP replaces GDP on subunit d. Subunit activates a ion channel directly or indirectly through second messenger H. The action of a neurotransmitter depends on the receptor to which it binds 1. Inhibitory or excitatory effects depending on which cell it reaches I. Glutamate receptors may be involved in learning and memory J. To turn off the responses, synapses must be cleared of the neurotransmitter 1. Enzmes Chapter 48: Respiration 48.1 What physical factors govern respiratory gas exchange? A. Diffusiton is driven by concentration differences 1. Substances move down concentration gradient 2. Fick's law: Q(rate of diffusion) = DA(C1-C2)/L a. D: diffusion constant depends on material and temp (high temp is higher constant, use air rather than water) 3. Reasons why air is better than water 1. Higher oxygen content in air 2. Oxygen diffuses more rapidly in air 3. Less energy is required to use air over gas exchange surfaces 4. Diffusion in liquid in cytoplasm and extracellular matrix limits distance allowed 5. High temps= less oxygen solubility + higher metabolic rate + more energy to move water across exchange surface =trouble 6. Lower atmospheric pressure at high altitudes yields lower atmospheric pressure 7. CO2 must diffuse out
48.2 What adaptations maximize respiratory gas exchange? 1. Respiratory organs have large surface areas 2. Partial pressure is maximized by path length, ventilation, and perfusion 3. Insects a. Tracheal system b. Spiracle openings, trachea, trachioles, air capillaries 4. Fish gills use countercurrent flow to maximize gas exchange a. Lamellae: gas exchange surface b. Countercurrent flow maximizes oxygen gradient making gas exchange more efficient 5. Birds use uidirectional ventilation to maximize gas exchange a. Most mammals do not completely exhade, and have dead space b. Birds fresh air is not mixed with stale air, maintaining high PO2 c. Air sacs 1. Breath 1: pure O2 is inhaled into posterior air acks 2. During exhalation the breath flows into lungs 3. During the next breath, the break flows from lungs into anterior air sacks 4. During the next exhalation, breath is expelled 6. Tidal ventilation produces dead space that limits gas exchange effieciency 48.3 How do human lungs work? 1. Air Mouth tracheal ( pharynx larynx ) broncibronciolesalvioli 2. Respiratory tract secretions aid ventilation a. Mucus: remove dirt and pollutant before it reaches lung b. Suffactant: reduce surface tention to reduce work necessary to inflate lungs 3. Lungs are ventilated by the pressure changes in the thoracic cavity 4. Hemoglobin combines reversibly with oxygen a. Red blood cells contain hemoglobin b. Hemoglobin has for fubunits, each of which can bind a molecule of O2 c. Hemoglobin oxygen carrying depends on partial pressure of O2 1. four oxygen in lungs 2. usually 3 oxygen in body d. Relationship between PO2 and O2 bound in hemoglobin is S shaped e. After binding O2 to one subunit (18), 2nd (25)and 3rd (40) bind by positive cooperitivity f. 4th is more difficult to bind (100) g. PO2 after flowing through body is 40. If it goes lower, in times of stress, additional O2 will be lost 5. Myoglobin is oxygen reserve a. Can bind one oxygen b. High affinity for O2, and aids diffusion into muscle cells c. If PO2 is low, myoglobin releases O2 d. Seals have high myoglobin, and can stay under water a long time 6. The affinity of hemoglobin for oxygen is variable a. Three factors influence oxygenen binding properties of hemoglobin
1. Chemical composition 2. pH 3. Presence of BPG b. Composition 1. Adults: 2 A, 2B. Babies: 2 A. 2 Y 2. Fetal hemoglobin has higher affinity for oxygen 3. Curve is shifted to the left 4. Same with llamas, who live at high altitude and must bind O2 with lower PO2 c. Hemoglobin and pH 1. Bohr effect 2. As blood flows through muscle, it picks up fatty acid and CO2, which lowers its affinity for oxygen, as H+ takes its place 3. Curve shifts to right, providing muscles with needed oxygen d. 2,3-biphosphoglyceric acid 1. Combines with hemoglobin, reducing its affinity for oxygen 2. Curve shifts to right 3. In excersise/high altitude, BPG in muscles rise and allow more oxygen to be delivered 4. Fetus is shifted to left because Y hemoglobin has low BPG affinity e. Carbon dioxide is transported as bicarbonate ions in blood 1. Carbonic andydrase speeds up CO2H2CO3 in capillaries 2. Reduces PCO2 and allows CO2 to diffuse from tissue into endothelial cells 3. In lungs, CO2 concentration is low, and CO2H2CO3 favors carbon dioxide 48.5 How is breathing regulated a. Breathing is controlled in the brain stem b. Basic breathing is generated by the medulla Chapter 49: Circulatory Systems 49.1 Why do animals need a circulatory system? A. Circulatory system= heart + blood + vessels B. Some animals do not have circulatory systems 1. All needs can be served with direct exchange from environment 2. Larger animals need a system to take nutrients and deliver waste 3. Open: extracellular fluid is continuous with circulatory system 4. Closed: blood is contained in a continuous set of vessels C. Open circulatory systems move extracellular fluid 1. Arthropods, mollusks D. Closed circulatory systems circulate blood through a system of heart vessels 1. Vertebrates and annelids 2. Advantages over open systems 1. Fluid flows more rapidly through blood
2. By changing resistance in vessels, closed systems can direct blood to specific tissues 3. Specialized cells and molecules can be carried to vessels and transported to other tissues 49.2 How have vertebrate circulatory systems evolved?