CHAPTER ONE: A View of Life

1.1 How to Define LifeA. Living Things Are Organized

1. Organization of living systems begins with atoms, which make up basic building blocks called elements.

2. The cell is the basic structural and functional unit of all living things.

3. Different cells combine to make up tissues (e.g., myocardial tissue).

4. Tissues combine to make up an organ (e.g., the heart).

5. Specific organs work together as a system (e.g., the heart, arteries, veins, etc.).

6. Multicellular organisms (each an "individual" within a particular species) contain organ systems (e.g., cardiovascular, digestive, respiratory, etc.).

7. A species in a particular area (e.g., gray squirrels in a forest) constitutes a population.

8. Interacting populations in a particular area comprise a community.

9. A community plus its physical environment is an ecosystem.

10. The biosphere is comprised of regions of the Earth's crust, waters, and atmosphere inhabited by organisms.

11. Each level of organization is more complex than the level preceding it.

12. Each level of organization has emergent properties due to interactions between the parts making up the whole; all emergent properties follow the laws of physics and chemistry.

B. Living Things Acquire Materials and Energy

1. Maintaining organization and conducting life-sustaining processes require an outside source of energy, defined as the capacity to do "work."

2. The ultimate source of energy for nearly all life on earth is the sun; plants and certain other organisms convert solar energy into chemical energy by the process of photosynthesis.

3. Food provides nutrient molecules used as building blocks for energy.

4. Metabolism is all the chemical reactions that occur in a cell.

5. All organisms must maintain a state of biological balance, or homeostasis. Temperature, moisture level, pH, etc. must be maintained within the tolerance range of the organism. Organisms have intricate feedback and control mechanisms to maintain homeostatic balance.

C. Living Things Respond

1. Living things interact with the environment and with other living things.

2. Response often results in movement of the organism (e.g., a plant bending toward the sun to capture solar energy, a turtle withdrawing into its shell for safety, etc.).

3. Responses help ensure survival of the organism and allow the organism to carry out its biological activities.

4. The collective responses of an organism constitute the behavior of the organism.

D. Living Things Reproduce and Develop

1. Reproduction is the ability of every type of organism to give rise to another organism like itself.

2. Bacteria, protozoans, and other unicellular organisms simply split in two (binary fission).

3. Multicellular organisms often unite sperm and egg, each from a different individual, resulting in an immature individual which develops into the adult.

4. The instructions for an organism's organization and development are encoded in genes.

5. Genes are comprised of long molecules of DNA (deoxyribonucleic acid); DNA is the genetic code in all living things.

E. Living Things Have Adaptations

1. Adaptations are modifications that make organisms suited to their way of life.

2. Natural selection is the process by which species become modified over time.

a. A species is a group of interbreeding individuals.

b. In natural selection, members of a species may inherit a genetic change that makes them better suited to a particular environment.

c. These members would be more likely to produce higher numbers of surviving offspring.

3. Evolution is defined as "descent with modification over time."

a. The fact that all life forms are composed of cells, contain genes comprised of DNA, and conduct the same metabolic reactions suggests all living things have a common ancestor.

b. One species can give rise to several species, each adapted to to a particular set of environmental conditions.

c. Evolution is responsible for the great diversity of life on Earth.

1.2 How the Biosphere is OrganizedA. Levels of Complexity

1. The biosphere is the zone of air, land, and water where organisms exist.

2. A population consists of all members of one species in a particular area.

3. A community consists of all of the local interacting populations.

4. An ecosystem includes all aspects of a living community and the physical environment (soil, atmosphere, etc.).

5. Interactions between various food chains make up a food web.

6. Ecosystems are characterized by chemical cycling and energy flow.

7. Ecosystems stay in existence because of a constant input of solar energy and the ability of photosynthetic organisms to absorb it.

B. The Human Population

1. The human population modifies existing ecosystems for its own purposes.

2. Two biologically diverse ecosystems, rain forests and coral reefs, are severely threatened by the human population.

3. Human beings depend on healthy working ecosystems for food, medicines, and raw materials.

C. Biodiversity

1. Biodiversity is the total number of species, their variable genes, and their ecosystems.

2. Extinction is the death of a species or larger group; perhaps 400 species become extinct every day.

3. The continued existence of the human species is dependant on the preservation of ecosystems and the biosphere.

1.3 How Living Things Are ClassifiedA. Taxonomy is the discipline of identifying and classifying organisms according to

certain rules.1. Taxonomic classification changes as more is learned about living things,

including the evolutionary relationships between species.

B. Categories of Classification

1. From smaller (least inclusive) categories to larger (more inclusive), the sequence of classification categories is: species, genus, family, order, class, phylum, kingdom, domain.

2. The species within one genus share many specific characteristics and are the most closely related.

3. Species in the same kingdom share only general characteristics with one another.

C. Domains

1. Biochemical evidence suggests that there are three domains: Bacteria, Archaea, and Eukarya.

2. The domains Bacteria and Archaea contain unicellular prokaryotes; organisms in the domain Eukarya have a membrane-bound nucleus.

3. The prokaryotes are structurally simple but are metabolically complex.

4. Archaea can live in water devoid of oxygen, and are able to survive harsh environmental conditions (temperatures, salinity, pH).

5. Bacteria are variously adapted to living almost anywhere (water, soil, atmosphere, in/on the human body, etc.).

D. Kingdoms

1. The domains Archaea and Bacteria are not yet categorized into kingdoms.

2. Eukarya contains four kingdoms: Protista, Fungi, Plantae, and Animalia.

3. Protists (kingdom Protista) range from unicellular forms to multicellular ones.

4. Fungi (kingdom Fungi) are the molds and mushrooms.

5. Plants (kingdom Plantae) are multicellular photosynthetic organisms.

6. Animals (kingdom Animalia) are multicellular organisms that ingest and process their food.

E. Scientific Name

1. A binomial name is a two-part scientific name: the genus (first word, capitalized) and the specific epithet of a species (second word, not capitalized).

2. Binomial names are based on Latin and are used universally by biologists.

3. Either the genus name or the specific epithet name may be abbreviated.

1.4 The Process of ScienceA. Scientific Method

1. Biology is the scientific study of life, and it consists of many disciplines.

2. The scientific process differs from other ways of learning in that science follows the scientific method, which is characterized by observation, development of a hypothesis, experimentation and data collection, and forming aconclusion.

B. Observation

1. Scientists believe nature is orderly and measurable, and that natural laws (e.g., gravity) do not change with time.

2. Natural events, called, phenomena can therefore be understood from observations.

3. Scientists also use the knowledge and experiences of other scientists to expand their understanding of phenomena.

4. Chance alone can sometimes help a scientist get an idea (e.g., Alexander Fleming's discovery of penicillin).

C. Hypothesis

1. Inductive reasoning allows a person to combine isolated facts into a cohesive whole.

2. A scientist uses inductive reasoning to develop a possible explanation (a hypothesis) for a natural event; the scientist presents the hypothesis as an actual statement.

3. Scientists only consider hypotheses that can be tested (i.e., moral and religious beliefs may not be testable by the scientific method).

D. Experiments/Further Observations

1. Testing a hypothesis involves either conducting an experiment or making further observations.

2. Deductive reasoning involves "if, then" logic to make a prediction that the hypothesis can be supported by experimentation.

3. An experimental design is proposed to test the hypothesis in a meaningful way.

4. An experiment should include a control group which goes through all the steps of an experiment but lacks (or is not exposed to) the factor being tested.

5. Scientists may use a model (a representation of an actual object) in their experiments.

6. Results obtained from use of a model will remain a hypothesis in need of testing if it is impossible to test the actual phenomenon.

E. Data

1. Data are the results of an experiment, and are observable and objective rather than subjective.

2. Data are often displayed in a graph or table.

3. Many studies rely on statistical data which, among other things, determines the probability of error in the experiment.

F. Conclusion

1. Whether the data support or reject the hypothesis is the basis for the conclusion.

2. The conclusion of one experiment can lead to the hypothesis for another experiment.

3. Scientists report their findings in scientific journals so that their methodology and data are available to other scientists.

4. The experiments and observations must be repeatable or the research is suspect.

G. Scientific Theory

1. The ultimate goal is to understand the natural world in scientific theories, which are speculative ideas that join supported, related hypotheses, and are supported by a broad range of observations, experiments, and data.

2. Some basic theories of biology are:

a. Cell: all organisms are made of cells.

b. Homeostasis: the internal environment of an organism stays relatively constant.

c. Gene: organisms contain coded information that dictates their form, function, and behavior.

d. Ecosystem: organisms are members of populations which interact with each other and the physical environment.

e. Evolution: all living things have a common ancestor.

3. A principle or a law is a theory that is generally accepted by most scientists.

H. A Controlled Study

1. A controlled study ensures that the outcome is due to the experimental (independent) variable, the factor being tested.

2. The result is called the responding (dependent) variable because it is due to the dependent variable.

3. The Experiment

a. Hypothesis: pigeon pea/winter wheat rotation will increase winter wheat production as well as or better than the use of nitrogen fertilizer.

b. Prediction: wheat biomass following the growth of pigeon peas in the soil will surpass wheat biomass following nitrogen fertilizer treatment.

c. Control group: winter wheat that receives no fertilizer.

d. Test groups: winter wheat treated with different levels of fertilizer; winter wheat grown in soil into which pigeon pea plants had been tilled.

e. Environmental conditions and watering were identical in control and test groups.

f. Results: all test groups produced more biomass than control group, but high level of nitrogen fertilizer produced more biomass than pigeon pea test group. Thus, hypothesis is not supported.

4. Continuing the Experiment

a. To test the hypothesis that pigeon pea residues will build up over time and will increase winter wheat production compared to nitrogen fertilizer, the study is continued for another year.

b. The fertilizer-only treatment no longer exceeded biomass production with the use of pigeon peas; biomass in the pigeon pea-treated test group was highest.

c. Conclusion: at the end of two years, the yield of winter wheat is better in the pigeon pea-treated test group. Hypothesis supported.

d. Continuation of the study for another year showed that the soil was continuously improved by the pigeon peas compared to the nitrogen fertilizer test groups.

e. Results were reported in a scientific journal.

I. A Field Study

1. Hypothesis: aggression of the male mountain bluebird varies during the reproductive cycle.

2. Prediction: aggression will change after the nest is built, after the first egg is laid, and after hatching.

3. To test the hypothesis, a male bluebird model was placed near the nest while the male was gone and observations were made upon his return.

4. Control: a model of a male robin placed near certain nests.

5. Results: resident male bluebirds did not bother the control model but were aggressive toward the male bluebird model depending on the stage in the reproductive cycle.

6. Conclusion: hypothesis is supported.

7. Study was reported in scientific journal with evolutionary interpretation.

CHAPTER 2: Basic Chemistry

2.1 Chemical Elements1. Matter is defined as anything that takes up space and has mass.2. Matter exists in three states: solid, liquid, and gas.

3. All matter (both living and non-living) is composed of 92 naturally-occurring elements.

4. Elements, by definition, cannot be broken down to simpler substances with different chemical or physical properties.

5. Six elements (carbon, hydrogen, nitrogen, oxygen, phosphorus, and sulfur—acronym CHNOPS) make up 98% of the body weight of organisms.

B. Atomic Structure

1. Elements consist of tiny particles called atoms.

2. An atom is the smallest unit of an element that displays the properties of the element.

3. One or two letters (e.g., H, Na) create the atomic symbol of the element.

4. The atomic mass of an atom depends on the presence of certain subatomic particles.

a. Atoms contain specific numbers of protons, neutrons, and electrons.

b. Protons and neutrons are in the nucleus of an atom; electrons move around the nucleus.

c. Protons are positively charged particles; neutrons have no charge; both have 1 atomic mass unit (amu) of weight.

d. Electrons are negatively charged particles located in orbitals outside the nucleus.

5. All atoms of an element have the same number of protons, called the atomic number of the element.

C. The Periodic Table

1. The periodic table shows how various characteristics of atoms of elements recur.

2. Groups are the vertical columns in the table, periods are the horizontal rows; atomic mass increases as you move down a group or across a period.

3. The atomic number is above the atomic symbol and the atomic mass is below the atomic symbol.

D. Isotopes

1. Isotopes are atoms of the same element that differ in the number of neutrons (and therefore have different atomic masses). For example, carbon-12 has 6 protons and 6 neutrons, carbon-14 has 6 protons and 8 neutrons.

2. A carbon atom with 8 rather than 6 neutrons is unstable; it releases energy and subatomic particles and is thus aradioactive isotope.

3. Because the chemical behavior of a radioactive isotope is the same as a stable isotope of a particular element, low levels of the radioactive isotope (e.g., radioactive iodine or glucose) allow researchers to trace the location and activity of the element in living tissues; these isotopes are called tracers.

4. High levels of radiation can destroy cells and cause cancer; careful use of radiation can sterilize products and kill cancer cells.

E. Electrons and Energy

1. Electrons occupy orbitals within various energy levels (or electron shells) near or distant from the nucleus of the atom. The farther the orbital from the nucleus, the higher the energy level.

2. An orbital is a volume of space where an electron is most likely to be found; an orbital can contain no more than 2 electrons.

3. When atoms absorb energy during photosynthesis, electrons are boosted to higher energy levels. When the electrons return to their original energy level, the released energy is converted into chemical energy. This chemical energy supports all life on Earth.

4. The innermost shell of an atom is complete with 2 electrons; all other shells are complete with 8 electrons. This is called the octet rule.

5. Atoms will give up, accept, or share electrons in order to have 8 electrons in a electron shell.

2.2 Elements and Compounds1. When atoms of two or more different elements bond together, they form

a compound (e.g., H2O).2. A molecule is the smallest part of a compound that has the properties of the

compound.

3. Electrons possess energy, and bonds that exist between atoms in molecules therefore contain energy.

B. Ionic Bonding

1. An ionic bond forms when electrons are transferred from one atom to another atom.

2. By losing or gaining electrons, atoms fill outer shells, and are more stable (the octet rule).

3. Example: sodium loses an electron and therefore has a positive charge; chlorine gains an electron to give it a negative charge. Such charged particles are called ions.

4. Attraction of oppositely charged ions holds the two atoms together in an ionic bond.

5. A salt (e.g., NaCl) is an example of an ionically-bonded compound.

C. Covalent Bonding

1. Covalent bonds result when two atoms share electrons so each atom has an octet of electrons in the outer shell (or, in the case of hydrogen, 2 electrons).

2. Hydrogen can give up an electron to become a hydrogen ion (H+) or share an electron with another atom to complete its shell with 2 electrons.

3. The structural formula of a compound indicates a shared pair of electrons by a line between the two atoms; e.g., single covalent bond (H–H), double covalent bond (O=O), and triple covalent bond (N = N). Each line between the atoms represents a pair of electrons.

4. The three-dimensional shapes of molecules are not represented by structural formulas, but shape is critical in understanding the biological action of molecules. Different molecules have different three-dimensional shapes, depending on the number of atoms in the molecule and the types of bonds (single , double, or triple covalent).

D. Nonpolar and Polar Covalent Bonds

1. In nonpolar covalent bonds, sharing of electrons is equal, i.e., the electrons are not attracted to either atom to a greater degree.

2. With polar covalent bonds, the sharing of electrons is unequal.

a. In a water molecule (H2O), sharing of electrons by oxygen and hydrogen is not equal; the oxygen atom with more protons attracts the electrons closer to it, and thus dominates the H2O association.

b. Attraction of an atom for electrons in a covalent bond is called the electronegativity of the atom; an oxygen atom is more electronegative than a hydrogen atom.

c. Oxygen in a water molecule, more attracted to the electron pair, assumes a partial negative charge.

E. Hydrogen Bonding

1. A hydrogen bond is a weak attractive force between the slightly positive charge of the hydrogen atom of one molecule and slightly negative charge of another atom (e.g., oxygen, nitrogen) in another or the same molecule.

2. Many hydrogen bonds taken together are relatively strong.

3. Hydrogen bonds between and within complex biological molecules (e.g., DNA, proteins) help maintain their proper structure and function.

2.3. Chemistry of Water1. All living things are 70–90% water.2. Because water is a polar molecule, water molecules are hydrogen bonded to

one other.

3. Because of hydrogen bonding, water is liquid between 0° C and 100° C which is essential for the existence of life.

B. Properties of Water

1. Water has a high heat capacity

a. The temperature of liquid water rises and falls more slowly than that of most other liquids.

b. A calorie is the amount of heat energy required to raise the temperature of one gram of water 1° C.

c. Because the hydrogen bonds between water molecules hold more heat, water's temperature falls more slowly than other liquids; this protects organisms from rapid temperature changes and helps them maintain homeostatic temperature.

2. Water has a high heat of vaporization.

a. Hydrogen bonds between water molecules require a relatively large amount of heat to break.

b. This property moderates Earth's surface temperature; permits living systems to exist.

c. When animals sweat, evaporation of the sweat removes body heat, thus cooling the animal.

3. Water is a solvent.

a. Water dissolves a great number of substances (e.g., salts, large polar molecules).

b. Ionized or polar molecules attracted to water are hydrophilic ("water loving").

c. Nonionized and nonpolar molecules that cannot attract water are hydrophobic ("water fearing").

d. A solution contains dissolved substances called solutes.

4. Water molecules are cohesive and adhesive.

a. Cohesion allows water to flow freely without molecules separating.

b. Adhesion is ability to adhere to polar surfaces; water molecules have positive and negative poles.

c. Water rises up a tree from roots to leaves through small tubes.

i. Adhesion of water to walls of vessels prevents water column from breaking apart.

ii. Cohesion allows evaporation from leaves to pull water column from roots.

5. Water has a high surface tension.

a. Water is relatively difficult to break through at its surface.

b. This property permits a rock to be skipped across a pond surface, and supports insects walking on surface.

6. Unlike most substances, frozen water is less dense than liquid water.

a. Below 4° C, hydrogen bonding becomes more rigid but more open, causing expansion.

b. Because ice is less dense, it floats; therefore, bodies of water freeze from the top down.

c. If ice was heavier than water, ice would sink and bodies of water would freeze solid.

d. This property allows ice to act as an insulator on bodies of water, thereby protecting aquatic organisms during the winter.

C. Acids and Bases

1. When water ionizes or dissociates, it releases a small (107 moles/liter) but equal number of hydrogen (H+) ions and hydroxide (OH-) ions; H – O –H → H+ + OH-.

2. Acid molecules dissociate in water, releasing hydrogen (H+) ions: HCl → H+ + Cl-.

3. Bases are molecules that take up hydrogen ions or release hydroxide ions. NaOH → Na+ + OH-.

4. The pH scale indicates acidity and basicity (alkalinity) of a solution.

a. pH is the measurement of free hydrogen ions, expressed as a negative logarithm of the H+ concentration (-log [H+]).

b. pH values range from 0 (100 moles/liter; most acidic) to 14 (1014 moles/liter; most basic).

i. One mole of water has 107 moles/liter of hydrogen ions; therefore, has neutral pH of 7.

ii. An acid is a substance with pH less than 7; a base is a substance with pH greater than 7.

iii. Because it is a logarithmic scale, each lower unit has 10 times the amount of hydrogen ions as next higher pH unit; as move up pH scale, each unit has 10 times the basicity of previous unit.

5. Buffers keep pH steady and within normal limits in living organisms..

a. Buffers stabilize pH of a solution by taking up excess hydrogen (H+) or hydroxide (OH-) ions. B. Carbonic acid helps keep blood pH within normal limits: H2CO3 → H+ + HCO3-.

CHAPTER 3: The Chemistry of Organic Molecules

3.1 Organic Molecules Organic molecules contain carbon and hydrogen atoms bonded to other atoms.

1. Four types of organic molecules (biomolecules) exist in organisms: carbohydrates, lipids, proteins, and nucleic acids.

2. Organic molecules are a diverse group; even a simple bacterial cell contains some 5,000 organic molecules.

The Carbon Atom

1. The chemictry of the carbon atom allows it to form covalent bonds with as many as four other elements (generally with the CHNOPS elements).

2. Hydrocarbons are chains of carbon atoms bonded exclusively to hydrogen atoms; hydrocarbons can be branched and they can form ringed (cyclic) compounds.

3. Carbon atoms can form double or triple bonds with certain atoms (carbon, nitrogen).

A. The Carbon Skeleton and Functional Groups

1. The carbon chain of an organic molecule is called its skeleton or backbone.

2. Functional groups are clusters of specific atoms bonded to the carbon skeleton with characteristic structure and functions.

a. As an example, the addition of an –OH (hydroxyl group) to a carbon skeleton turns the molecule into an alcohol.

b. Ethyl alcohol (ethanol) is hydrophilic (dissolves in water) because the hydroxyl group is polar.

c. Nonpolar organic molecules are hydrophobic (cannot dissolve in water) unless they contain a polar functional group. An example is ethane.

d. Depending on its functional groups, an organic molecule may be both acidic and hydrophilic. An example is a hydrocarbon that contains a carboxyl group; carboxyl groups ionize in solution by releasing hydrogen ions, becoming both polar and acidic.

e. Because cells are 70–90% water, the degree to which an organic molecule interacts with water affects its function.

3. Isomers are molecules with identical molecular formulas but different arrangements of their atoms (e.g., glyceraldehyde and dihydroxyacetone).

B. The Macromolecules of Cells

1. Carbohydrates, lipids, proteins, and nucleic acids are called macromolecules because of their large size.

2. The largest macromolecules are called polymers, constructed by linking many of the same type of small subunits, calledmonomers. Examples: amino acids (monomers) are linked to form a protein (polymer); many nucleotides (monomers) are linked to form a nucleic acid (polymer).

3. Cellular enzymes carry out dehydration reactions to synthesize macromolecules. In a dehydration reaction, a water molecule is removed and a covalent bond is made between two atoms of the monomers.

a. In a dehydration reaction, a hydroxyl (—OH) group is removed from one monomer and a hydrogen (—H) is removed from the other.

b. This produces water, and, because the water is leaving the monomers, it is a dehydration reaction.

4. Hydrolysis ("water breaking") reactions break down polymers in reverse of dehydration; a hydroxyl (—OH) group from water attaches to one monomer and hydrogen (—H) attaches to the other.

5. Enzymes are molecules that speed up chemical reactions by bringing reactants together; an enzyme may even participate in the reaction but is not changed by the reaction.

3.2 CarbohydratesA. Monosaccharides: Ready Energy

1. Monosaccharides are simple sugars with a backbone of 3 to 7 carbon atoms.

a. Most monosaccharides of organisms have 6 carbons (hexose).

b. Glucose and fructose are hexoses, but are isomers of one another; each has the formula (C6H12O6) but they differ in arrangement of the atoms.

c. Glucoseis found in the blood of animals; it is the source of biochemical energy (ATP) in nearly all organisms.

2. Ribose and deoxyribose are five-carbon sugars (pentoses); they contribute to the backbones of RNA and DNA, respectively.

B. Disaccharides: Varied Uses

1. Disaccharides contain two monosaccharides joined by a dehydration reaction.

2. Lactose is composed of galactose and glucose and is found in milk.

3. Maltose is composed of two glucose molecules; it forms in the digestive tract of humans during starch digestion.

4. Sucrose (table sugar) is composed of glucose and fructose; it is used to sweeten food for human consumption.

C. Polysaccharides as Energy Storage Molecules

1. Polysaccharides are polymers of monosaccharides. They are not soluble in water and do not pass through the plasma membrane of the cell.

2. Starch, found in many plants, is a straight chain of glucose molecules with relatively few side branches. Amylose andamylopectin are the two forms of starch found in plants.

3. Glycogen is a highly branched polymer of glucose with many side branches. It is the storage form of glucose in animals.

D. Polysaccharides as Structural Molecules

1. Cellulose is a polymer of glucose which forms microfibrils, the primary constituent of plant cell walls.

a. Cotton is nearly pure cellulose.

b. Cellulose is indigestible by humans due to the unique bond between glucose molecules.

c. Grazing animals can digest cellulose due to special stomachs and bacteria.

d. Cellulose is the most abundant organic molecule on Earth.

2. Chitin is a polymer of glucose with an amino group attached to each glucose.

a. Chitin is the primary constituent of the exoskeleton of crabs and related animals (lobsters, insects, etc.).

b. Chitin is not digestible by humans.

3.3 Lipids Lipids are varied in structure.

1. Lipids are hydrocarbons that are insoluble in water because they lack polar groups.

2. Fat provides insulation and energy storage in animals.

3. Phospholipids form plasma membranes and steroids are important cell messengers.

4. Waxes have protective functions in many organisms.

A. Triglycerides: Long-Term Energy Storage

1. Fats and oils contain two molecular units: glycerol and fatty acids.

2. Glycerol is a water-soluble compound with three hydroxyl groups.

3. Triglycerides are glycerol joined to three fatty acids by dehydration reactions.

4. A fatty acid is a long hydrocarbon chain with a carboxyl (acid) group at one end.

a. Most fatty acids in cells contain 16 to 18 carbon atoms per molecule.

b. Saturated fatty acids have no double bonds between their carbon atoms.

c. Unsaturated fatty acids have double bonds in the carbon chain where there are less than two hydrogens per carbon atom.

5. Fats contain saturated fatty acids and are solid at room temperature (e.g., butter).

6. Oils contain unsaturated fatty acids and are liquid at room temperature.

7. Animals use fat rather than glycogen for long-term energy storage; fat stores more energy.

B. Phospholipids: Membrane Components

1. Phospholipids are constructed like neutral fats except that the third fatty acid is replaced by a polar (hydrophilic) phosphate group; the phosphate group usually bonds to another organic group (designated by R).

2. The hydrocarbon chains of the fatty acids become the nonpolar (hydrophobic) tails.

3. Phospholipids arrange themselves in a double layer in water, so the polar heads face toward water molecules and nonpolar tails face toward one other, away from water molecules.

4. This property enables phospholipids to form an interface or separation between two solutions (e.g., the interior and exterior of a cell); the plasma membrane is a phospholipid bilayer.

C. Steroids: Four Fused Rings

1. Steroids have skeletons of four fused carbon rings and vary according to attached functional groups; these functional groups determine the biological functions of the various steroid molecules.

2. Cholesterol is a component of an animal cell's plasma membrane, and is the precursor of the steroid hormone (aldosterone, testosterone, estrogen, calcitriol, etc.).

3. A diet high in saturated fats and cholesterol can lead to circulatory disorders.

D. Waxes

1. Waxes are long-chain fatty acids bonded to long-chain alcohols.

2. Waxes have a high melting point, are waterproof, and resist degradation.

3. Waxes form a protective covering in plants that retards water loss in leaves and fruits.

4. In animals, waxes maintain animal skin and fur, trap dust and dirt, and form the honeycomb.

3.4 Proteins Protein Functions

1. Support proteins include keratin, which makes up hair and nails, and collagen fibers, which support many of the body's structures (e.g., ligaments, tendons, skin).

2. Enzymes are proteins that act as organic catalysts to accelerate chemical reactions within cells.

3. Transport functions include channel and carrier proteins in the plasma membrane, and hemoglobin that transports oxygen in red blood cells.

4. Defense functions include antibodies that prevent infection.

5. Hormones are regulatory proteins that influence the metabolism of cells. For example, insulin regulates glucose content of blood and within cells.

6. Motion within cells and by muscle contraction is provided by the proteins myosin and actin.

A. Amino Acids: Building Blocks of Proteins

1. Amino acids contain an acidic group (— COOH) and an amino group (—NH2).

2. Amino acids differ according to their particular R group, ranging from single hydrogen to complicated ring compounds.

3. The R group of amino acid cystine ends with a sulfhydryl (—SH) that serves to connect one chain of amino acids to another by a disulfide bond (— S—S—).

4. There are 20 different amino acids commonly found in cells.

B. Peptides

1. A peptide bond is a covalent bond between two amino acids.

2. Atoms of a peptide bond share electrons unevenly (oxygen is more electronegative than nitrogen).

3. The polarity of the peptide bond permits hydrogen bonding between different amino acids in a polypeptide.

4. A peptide is two or more amino acids bonded together.

5. Polypeptides are chains of many amino acids joined by peptide bonds.

6. A protein may contain more than one polypeptide chain; it can thus have a very large number of amino acids.

a. The three-dimensional shape of a protein is critical; an abnormal sequence will have the wrong shape and will not function normally.

b. Frederick Sanger determined the first protein sequence (of the hormone insulin) in 1953.

C. Shape of Proteins

1. Protein shape determines the function of the protein in the organism; proteins can have up to four levels of structure (but not all proteins have four levels).

2. The primary structure is the protein's own particular sequence of amino acids.

a. Just as the English alphabet contains 26 letters, 20 amino acids can join to form a huge variety of "words."

3. The secondary structure results when a polypeptide coils or folds in a particular way.

a. The a (alpha) helix was the first pattern discovered.

i. In a peptide bond, oxygen is partially negative, hydrogen is partially positive.

ii. This allows for hydrogen bonding between the C=O of one amino acid and the N—H of another.

iii. Hydrogen bonding between every fourth amino acid holds the spiral shape of an a helix.

b. The b (beta) sheet was the second pattern discovered.

i. Pleated b sheet polypeptides turn back upon themselves.

ii. Hydrogen bonding occurs between extended lengths.

c. Fibrous proteins (e.g. keratin) are structural proteins with helices and/or pleated sheets that hydrogen bond to one another.

4. Tertiary structure results when proteins are folded, giving rise to the final three-dimensional shape of the protein. This is due to interactions among the R groups of the constituent amino acids.

a. Globular proteins tend to ball up into rounded shapes.

b. Strong disulfide linkages maintain the tertiary shape; hydrogen, ionic, and covalent bonds also contribute.

5. Quaternary structure results when two or more polypeptides combine.

a. Hemoglobin is globular protein with a quaternary structure of four polypeptides; each polypeptide has a primary, secondary, and tertiary structure.

D. Protein Folding Diseases

1. As proteins are synthesized, chaperone proteins help them fold into their correct shapes; chaperone proteins may also correct misfolding of a new protein and prevent them from making incorrect shapes.

2. Certain diseases (e.g., the transmissible spongiform encephalopathies, or TSEs) are likely due to misfolded proteins, called prions.

3.5 Nucleic Acids1. Nucleic acids are polymers of nucleotides with very specific functions in cells.2. DNA (deoxyribonucleic acid) stores the genetic code for its own replication

and for the amino acid sequences in proteins.

3. RNA (ribonucleic acid) allows for translation of the genetic code of DNA into the amino acid sequence of proteins; other functions for RNA in the cell exist.

4. Some nucleotides have independent metabolic functions in cells.

a. Coenzymes are molecules which facilitate enzymatic reactions.

b. ATP (adenosine triphosphate) is a nucleotide used to supply energy for synthetic reactions and other energy-requiring metabolic activities in the cell.

B. Structure of DNA and RNA

1. Nucleotides are a molecular complex of three types of molecules: a phosphate (phosphoric acid), a pentose sugar, and a nitrogen-containing base.

2. DNA and RNA differ in the following ways:

a. Nucleotides of DNA contain deoxyribose sugar; nucleotides of RNA contain ribose.

b. In RNA, the base uracil occurs instead of the base thymine. Both RNA and DNA contain adenine, guanine, and cytosine.

c. DNA is double-stranded with complementary base pairing; RNA is single-stranded.

i. Complementary base pairing occurs where two strands of DNA are held together by hydrogen bonds between purine and pyrimidine bases.

ii. The number of purine bases always equals the number of pyrimidine bases.

iii. In DNA, thymine is always paired with adenine; cytosine is always paired with guanine. Thus, in DNA: A + G = C + T.

d. Two strands of DNA twist to form a double helix; RNA does not form helices.

C. ATP (Adenosine Triphosphate)

1. ATP (adenosine triphosphate) is a nucleotide in which adenosine is composed of ribose and adenine.

2. Triphosphate derives its name from three phosphate groups attached together and to the ribose.

3. ATP is a high-energy molecule because the last two phosphate bonds release energy when broken.

4. In cells, the terminal phosphate bond is hydrolyzed, leaving ADP (adenosine diphosphate); energy is released when this occurs.

5. The energy released from ATP breakdown is used in the energy-requiring processes of the cell, such as synthetic reactions, muscle contraction, and the transmission of nerve impulses.

CHAPTER 4: Cell Structure and Function

4.1 Cellular Level of Organization1. Detailed study of the cell began in the 1830s; some of the scientists

contributing to the understanding of cell structure and function were Robert Brown, Matthais Schleiden, Theodor Schwann, and Rudolph Virchow.

2. The cell theory states that all organisms are composed of cells, that cells are the structural and functional unit of organisms, and that cells come only from preexisting cells.

B. Cell Size

1. Cells range in size from one millimeter down to one micrometer.

2. Cells need a surface area of plasma membrane large enough to adequately exchange materials.

3. The surface-area-to-volume ratio requires that cells be small.

a. As cells get larger in volume, surface area relative to volume decreases.

b. Size limits how large the actively metabolizing cells can become.

c. Cells needing greater surface area utilize membrane modifications such as folding, microvilli, etc.

C. Microscopy Today (Science Focus Box)

1. Compound light microscopes use light rays focused by glass lenses.

2. Transmission electron microscopes (TEM) use electrons passing through specimen and focused by magnets.

3. Scanning electron microscopes (SEM) use electrons scanned across metal-coated specimen; secondary electrons given off by metal are collected by a detector.

4. Magnification is a function of wavelength; the shorter wavelengths of electrons allow greater magnification than the longer wavelengths of light rays.

5. Resolution is the minimum distance between two objects at which they can still be seen as separate objects.

6. Immunofluorescence microscopy uses fluorescent antibodies to reveal proteins in cells.

7. Confocal microscopy uses laser beam to focus on a shallow plane within the cell; this forms a series of optical sections from which a computer creates a three dimensional image.

8. Video-enhanced contrast microscopy accentuates the light and dark regions and may use a computer to contrast regions with false colors.

9. Bright-field, phase contrast, differential interference, and darkfield are different types of light microscopes.

4.2 Prokaryotic Cells1. Prokaryotic cells lack a nucleus and are smaller and simpler than eukaryotic

cells (which have a nucleus).2. Prokaryotic cells are placed in two taxonomic domains: Bacteria and

Archaea. Organisms in these two domains are structurally similar but biochemically different.

B. The Structure of Bacteria

1. Bacteria are extremely small; average size is 1–1.5 μm wide and 2–6 μm long .

2. Bacteria occur in three basic shapes: spherical coccus, rod-shaped bacillus, and spiral spirillum (if rigid) or spirochete (if flexible).

3. Cell Envelope

a. Includes the plasma membrane, the cell wall, and the glycocalyx. The plasma membrane is a lipid bilayer with imbedded and peripheral proteins; it regulates the movement of substances into and out of the cell.

b. The plasma membrane can form internal pouches called mesosomes, which increase the internal surface area of the membrane for enzyme attachment.

c. The cell wall maintains the shape of the cell and is strengthened by peptidoglycan.

d. The glycocalyx is a layer of polysaccharides on the outside of the cell wall; it is called a capsule if organized and not easily removed, or a slime layer if it is not well-organized and is easily removed.

4. Cytoplasm

a. The cytoplasm is a semifluid solution containing water, inorganic and organic molecules, and enzymes.

b. The nucleoid is a region that contains the single, circular DNA molecule.

c. Plasmids are small accessory (extrachromosomal) rings of DNA; they are not part of the bacterial genetic material.

d. Ribosomes are particles with two RNA- and protein-containing subunits that synthesize proteins.

e. Inclusion bodies in the cytoplasm are granules of stored substances.

f. Cyanobacteria (also called blue-green bacteria) are bacteria that photosynthesize; they lack chloroplasts but havethylakoids containing chlorophyll and other pigments.

5. Appendages

a. Motile bacteria usually have flagella; the filament, hook, and basal body work to rotate the flagellum like a propeller to move through fluid medium.

b. Fimbriae are small, bristlelike fibers that attach to an appropriate surface.

c. Sex pili are tubes used by bacteria to pass DNA from cell to cell.

C. The Structure of Archaea

1. In addition to spheres, rods, and spirals, Archaea can be lobed, platelike, or irregular.

2. The cell wall contains various polysaccharides and proteins rather than peptidoglycan.

3. The membrane lipids are composed of glycerol bonded to hydrocarbons, not fatty acids.

4. The DNA and RNA base sequences are closer to eukaryotes than bacteria.

5. Many Archaea are found in extremely salty or hot environments; they may have been the first type of cell to evolve.

4.3 Eukaryotic Cells

1. Eukaryotic cells are members of the domain Eukarya, which includes the protists, fungi, plants, and animals.

2. A membrane-bounded nucleus houses DNA; the nucleus may have originated as an invagination of the plasma membrane.

3. Eukaryotic cells are much larger than prokaryotic cells, and therefore have less surface area per volume.

4. Eukaryotic cells are compartmentalized; they contain small structures called organelles that perform specific functions.

5. Some eukaryotic cells (e.g., plant cells) have a cell wall containing cellulose; plasmodesmata are channels in a cell wall that allow cytoplasmic strands to extend between adjacent cells.

B. The Structure of Eukaryotic Cells

1. The nucleus communicates with ribosomes in the cytoplasm.

2. The organelles of the endomembrane system communicate with one another; each organelle contains its own set of enzymes and produces its own products, which move from one organelle to another by transport vesicles.

3. The energy-related mitochondria (plant and animal cells) and chloroplasts (plant cells) do not communicate with other organelles; they contain their own DNA and are self-sufficient.

4. The cytoskeleton is a lattice of protein fibers that maintains the shape of the cell and assists in movement of the organelles.

C. Cell Fractionation and Differential Centrifugation (Science Focus Box)

1. Cell fractionation allows the researcher to isolate and individually study the organelles of a cell.

2. Differential centrifugation separates the cellular components by size and density.

3. Using these two techniques, researchers can obtain pure preparations of any cell component.

D. The Nucleus and Ribosomes

1. The nucleus has a diameter of about 5 μm.

2. Chromatin is a threadlike material that coils into chromosomes just before cell division occurs; contains DNA, protein, and some RNA.

3. Nucleoplasm is the semifluid medium of the nucleus.

4. Chromosomes are rodlike structures formed during cell division; composed of coiled or folded chromatin.

5. The nucleolus is a dark region of chromatin inside the nucleus; it is the site where ribosomal RNA (rRNA) joins with proteins to form ribosomes.

6. The nucleus is separated from the cytoplasm by the nuclear envelope, which contains nuclear pores to permit passage of substances (e.g., ribosomal subunits, messenger RNA, proteins, etc.) in and out of the nucleus

7. Ribosomes are the site of protein synthesis in the cell. In eukaryotic cells, ribosomes may occur freely or in groups calledpolyribosomes.

8. Ribosomes receive messenger RNA (mRNA) from the nucleus, which instructs the ribosomes of the correct sequence of amino acids in a protein to be synthesized.

E. The Endomembrane System

1. The endomembrane system is a series of intracellular membranes that compartmentalize the cell.

2. It consists of the nuclear envelope, the membranes of the endoplasmic reticulum, the Golgi apparatus, and several types of vesicles.

3. Endoplasmic Reticulum

a. The endoplasmic reticulum (ER) is a system of membrane channels and saccules (flattened vesicles) continuous with the outer membrane of the nuclear envelope.

b. Rough ER is studded with ribosomes on the cytoplasm side; it is the site where proteins are synthesized and enter the ER interior for processing and modification.

c. Smooth ER is continuous with rough ER but lacks ribosomes; it is a site of various synthetic processes, detoxification, and storage; smooth ER forms transport vesicles.

4. The Golgi Apparatus

a. It is named for Camillo Golgi, who discovered it in 1898.

b. The Golgi apparatus consists of a stack of slightly curved saccules.

c. The Golgi apparatus receives protein-filled vesicles that bud from the rough ER and lipid-filled vesicles from the smooth ER.

d. Enzymes within the Golgi apparatus modify the carbohydrates that were placed on proteins in the ER; proteins and lipids are sorted and packaged.

e. Vesicles formed from the membrane of the outer face of the Golgi apparatus move to different locations in a cell; at the plasma

membrane they discharge their contents as secretions, a process called exocytosis because substances exit the cell.

5. Lysosomes

a. Lysosomes are membrane-bounded vesicles produced by the Golgi apparatus.

b. Lysosomes contain powerful digestive enzymes and are highly acidic.

c. Macromolecules enter a cell by vesicle formation; lysosomes fuse with vesicles and digest the contents of the vesicle.

d. White blood cells that engulf bacteria use lysosomes to digest the bacteria.

e. Autodigestion occurs when lysosomes digest parts of cells.

f. Lysosomes participate in apoptosis, or programmed cell death, a normal part of development.

6. Endomembrane System Summary

a. Proteins produced in rough ER and lipids from smooth ER are carried in vesicles to the Golgi apparatus.

b. The Golgi apparatus modifies these products and then sorts and packages them into vesicles that go to various cell destinations.

c. Secretory vesicles carry products to the membrane where exocytosis produces secretions.

d. Lysosomes fuse with incoming vesicles and digest macromolecules.

F. Peroxisomes and Vacuoles

1. Peroxisomes are membrane-bounded vesicles that contain specific enzymes.

a. Peroxisome action results in production of hydrogen peroxide.

b. Hydrogen peroxide (H2O2) is broken down to water and oxygen by catalase.

c. Peroxisomes in the liver produce bile salts from cholesterol and also break down fats.

d. Peroxisomes also occur in germinating seeds where they convert oils into sugars used as nutrients by the growing plant.

2. Vacuoles

a. Vacuoles are mebranous sacs and are larger than vesicles.

b. Contractile vacuoles in some protists rid the cell of excess water.

c. Digestive vacuoles digest nutrients.

d. Vacuoles generally store substances, e.g., plant vacuoles contain water, sugars, salts, pigments, and toxic molecules

e. The central vacuole of a plant cell maintins turgor pressure within the cell, stores nutrients and wastes, and degrades organelles as the cell ages.

G. Energy-Related Organelles

1. Chloroplasts are membranous organelles (a type of plastid) that serve as the site of photosynthesis.

a. Photosynthesis is represented by the equation:

b. solar energy + carbon dioxide + water → carbohydrate + oxygen

c. Only plants, algae, and certain bacteria are capable of conducting photosynthesis.

d. The chloroplast is bound by a double membrane organized into flattened disc-like sacs called thylakoids formed from a third membrane; a stack of thylakoids is a granum.

e. Chlorophyll and other pigments capture solar energy, and the enzymes which synthesize carbohydrates are located in the chloroplasts.

f. Chloroplasts have both their own DNA and ribosomes, supporting the endosymbiotic hypothesis.

g. Other types of plastids, which differ in color, form, and function from chloroplasts, include chromoplasts andleucoplasts.

2. Mitochondria are surrounded by a double membrane: the inner membrane surrounds the matrix and is convoluted to formcristae.

a. Mitochondria are smaller than chloroplasts, and often vary their shape.

b. Mitochondria also can be fixed in one location or form long, moving chains.

c. Mitochondria contain ribosomes and their own DNA.

d. The matrix of the mitochondria is concentrated with enzymes that break down carbohydrates.

e. ATP production occurs on the cristae.

f. More than forty different diseases involving mitochondria have been described.

H. The Cytoskeleton

1. The cytoskeleton is a network of connected filaments and tubules; it extends from the nucleus to the plasma membrane in eukaryotes.

a. Electron microscopy reveals an organized cytosol.

b. Immunofluorescence microscopy identifies protein fibers.

c. Elements of the cytoskeleton include: actin filaments, intermediate filaments, and microtubules.

2. Actin Filaments

a. Actin filaments are long, thin fibers (about 7 nm in diameter) that occur in bundles or meshlike networks.

b. The actin filament consists of two chains of globular actin monomers twisted to form a helix.

c. Actin filaments play a structural role, forming a dense complex web just under the plasma membrane; this accounts for the formation of pseudopods in amoeboid movement.

d. Actin filaments in microvilli of intestinal cells likely shorten or extend cell into intestine.

e. In plant cells, they form tracks along which chloroplasts circulate.

f. Actin filaments move by interacting with myosin; myosin combines with and splits ATP, binding to actin and changing configuration to pull actin filament forward.

g. Similar action accounts for pinching off cells during cell division.

3. Intermediate Filaments

a. Intermediate filaments are 8–11 nm in diameter, between actin filaments and microtubules in size.

b. They are rope-like assemblies of fibrous polypeptides.

c. Some support the nuclear envelope; others support plasma membrane and form cell-to-cell junctions.

4. Microtubules

a. Microtubules are small hollow cylinders (25 nm in diameter and from 0.2–25 μm in length).

b. Microtubules are composed of a globular protein tubulin that occurs as α tubulin and β tubulin.

c. Assembly brings these two together as dimers and the dimers arrange themselves in rows.

d. Regulation of microtubule assembly is under control of a microtubule organizing center (MTOC): the main MTOC is called a centrosome.

e. Microtubules radiate from the MTOC, helping maintain the shape of cells and acting as tracks along which organelles move.

f. Similar to actin-myosin, the motor molecules kinesin and dynein are associated with microtubules.

g. Different kinds of kinesin proteins specialize to move one kind of vesicle or cell organelle.

h. Cytoplasmic dynein is similar to the molecule dynein found in flagella.

5. Centrioles

a. Centrioles are short cylinders with a ring pattern (9 + 0) of microtubule triplets.

b. In animal cells and most protists, centrosome contains two centrioles lying at right angles to each other.

c. Plant and fungal cells have the equivalent of a centrosome, but they do not contain centrioles.

d. Centrioles serve as basal bodies for cilia and flagella.

6. Cilia and Flagella

a. Cilia are short, usually numerous hairlike projections that can move in an undulating fashion (e.g., Paramecium; lining of human upper respiratory tract).

b. Flagella are longer, usually fewer, projections that move in whip-like fashion (e.g., sperm cells).

c. Both have similar construction, but differ from prokaryotic flagella.

i. Membrane-bounded cylinders enclose a matrix containing a cylinder of nine pairs of microtubules encircling two single microtubules (9 + 2 pattern of microtubules).

ii. Cilia and flagella move when the microtubules slide past one another.

iii. Cilia and flagella have a basal body at base with the same arrangement of microtubule triples as centrioles.

iv. Cilia and flagella grow by the addition of tubulin dimers to their tips.

CHAPTER 5: Membrane Structure and Function

5.1 Membrane Models1. In the early 1900s, researchers noted that lipid-soluble molecules entered

cells more rapidly than water-soluble molecules, suggesting lipids are component of plasma membrane.

2. Later, chemical analysis revealed that the membrane contained phospholipids.

3. Gorter and Grendel (1925) found that the amount of phospholipid extracted from a red blood cell was just enough to form one bilayer; they also suggested the nonpolar tails were directed inward and polar heads outward.

4. To account for the permeability of membrane to nonlipid substances, Danielli and Davson (1940s) proposed the "sandwich" model, with a phospholipid bilayer between layers of protein.

5. Robertson (1950s) proposed that proteins were embedded in an outer membrane and that all membranes in cells had similar compositions—the "unit membrane" model.

6. Additional research showed great diversity in membrane structure and function.

B. Fluid-Mosaic Model

1. In 1972, Singer and Nicolson introduced the currently accepted fluid-mosaic model.

a. The plasma membrane is a phospholipid bilayer, in which protein molecules are embedded.

b. Embedded proteins are scattered throughout membrane in an irregular pattern; this varies among membranes.

5.2 Plasma Membrane Structure and Function1. The plasma membrane is a phospholipid bilayer with embedded proteins.2. Phospholipids have both hydrophilic and hydrophobic regions; nonpolar tails

(hydrophobic) are directed inward, polar heads (hydrophilic) are directed outward to face both extracellular and intracellular fluid.

3. The proteins form a mosaic pattern on the membrane.

4. Cholesterol is a lipid found in animal plasma membranes; it stiffens and strengthens the membrane.

5. Glycolipids have a structure similar to phospholipids except the hydrophilic head is a variety of sugar; they are protective and assist in various functions.

6. Glycoproteins have an attached carbohydrate chain of sugar that projects externally.

7. The plasma membrane is asymmetrical; glycolipids and proteins occur only on outside and cytoskeletal filaments attach to proteins only on the inside surface.

B. Carbohydrate Chains

1. In animal cells, the glycocalyx is a "sugar coat" of carbohydrate chains; it has several functions.

2. Cells are unique in that they have highly varied carbohydrate chains (a "fingerprint").

3. The immune system recognizes foreign tissues that have inappropriate carbohydrate chains.

4. Carbohydrate chains are the basis for A, B, and O blood groups in humans.

C. Fluidity of the Plasma Membrane

1. At body temperature, the phospholipid bilayer has the consistency of olive oil.

2. The greater the concentration of unsaturated fatty acid residues, the more fluid the bilayer.

3. In each monolayer, the hydrocarbon tails wiggle, and entire phospholipid molecules can move sideways.

4. Phospholipid molecules rarely "flip-flop" from one layer to the other.

5. Fluidity of the phospholipid bilayer allows cells to be pliable.

6. Some proteins are held in place by cytoskeletal filaments; most drift in the fluid bilayer.

D. The Functions of the Proteins

1. Plasma membrane and organelle membranes have unique proteins; red blood cells (RBC) plasma membrane contains 50+ types of proteins.

2. Membrane proteins determine most of the membrane's functions.

3. Channel proteins allow a particular molecule to cross membrane freely (e.g., Cl-channels).

4. Carrier proteins selectively interact with a specific molecule so it can cross the plasma membrane (e.g., Na+-K+ pump).

5. Cell recognition proteins are glycoproteins that allow the body's immune system to distinguish between foreign invaders and body cells.

6. Receptor proteins are shaped so a specific molecule (e.g., hormone) can bind to it.

7. Enzymatic proteins carry out specific metabolic reactions.

5.3 Permeability of the Plasma Membrane1. The plasma membrane is differentially (selectively) permeable; only

certain molecules can pass through.a. Small non-charged lipid molecules (alcohol, oxygen) pass through the

membrane freely.

b. Small polar molecules (carbon dioxide, water) move "down" a concentration gradient, i.e., from high to low concentration.

c. Ions and charged molecules cannot readily pass through the hydrophobic component of the bilayer and usually combine with carrier proteins.

2. Both passive and active mechanisms move molecules across membrane.

a. Passive transport moves molecules across membrane without expenditure of energy; includes diffusion andfacilitated transport.

b. Active transport requires a carrier protein and uses energy (ATP) to move molecules across a plasma membrane; includes active transport, exocytosis, endocytosis, and pinocytosis.

B. Diffusion and Osmosis

1. Diffusion is the movement of molecules from higher to lower concentration (i.e., "down" the concentration gradient).

a. A solution contains a solute, usually a solid, and a solvent, usually a liquid.

b. In the case of a dye diffusing in water, the dye is a solute and water is the solvent.

c. Once a solute is evenly distributed, random movement continues but with no net change.

d. Membrane chemical and physical properties allow only a few types of molecules to cross by diffusion.

e. Gases readily diffuse through the lipid bilayer; e.g., the movement of oxygen from air sacs (alveoli) to the blood in lung capillaries depends on the concentration of oxygen in alveoli.

f. Temperature, pressure, electrical currents, and molecular size influence the rate of diffusion.

2. Osmosis is the diffusion of water across a differentially (selectively) permeable membrane.

a. Osmosis is illustrated by the thistle tube example:

i. A differentially permeable membrane separates two solutions.

ii. The beaker has more water (lower percentage of solute) and the thistle tube has less water (higher percentage of solute).

iii. The membrane does not permit passage of the solute; water enters but the solute does not exit.

iv. The membrane permits passage of water with a net movement of water from the beaker to the inside of the thistle tube.

b. Osmotic pressure is the pressure that develops in such a system due to osmosis.

c. Osmotic pressure results in water being absorbed by the kidneys and water being taken up from tissue fluid.

3. Tonicity is strength of a solution with respect to osmotic pressure.

a. Isotonic solutions occur where the relative solute concentrations of two solutions are equal; a 0.9% salt solution is used in injections because it is isotonic to red blood cells (RBCs).

b. A hypotonic solution has a solute concentration that is less than another solution; when a cell is placed in a hypotonic solution, water enters the cell and it may undergo cytolysis ("cell bursting").

c. Swelling of a plant cell in a hypotonic solution creates turgor pressure; this is how plants maintain an erect position.

d. A hypertonic solution has a solute concentration that is higher than another solution; when a cell is placed in a hypertonic solution, it shrivels (a condition called crenation).

e. Plasmolysis is shrinking of the cytoplasm due to osmosis in a hypertonic solution; as the central vacuole loses water, the plasma membrane pulls away from the cell wall.

C. Transport by Carrier Proteins

1. The plasma membrane impedes passage of most substances but many molecules enter or leave at rapid rates.

2. Carrier proteins are membrane proteins that combine with and transport only one type of molecule or ion; they are believed to undergo a change in shape to move the molecule across the membrane.

3. Facilitated transport is the transport of a specific solute "down" or "with" its concentration gradient (from high to low), facilitated by a carrier protein; glucose and amino acids move across the membrane in this way.

4. Active transport is transport of a specific solute across plasma membranes "up" or "against" (from low to high) its concentration gradient through use of cellular energy (ATP).

a. Iodine is concentrated in cells of thyroid gland, glucose is completely absorbed into lining of digestive tract, and sodium is mostly reabsorbed by kidney tubule lining.

b. Active transport requires both carrier proteins and ATP; therefore cells must have high number of mitochondria near membranes where active transport occurs.

c. Proteins involved in active transport are often called "pumps"; the sodium-potassium pump is an important carrier system in nerve and muscle cells.

d. Salt (NaCl) crosses a plasma membrane because sodium ions are pumped across, and the chloride ion is attracted to the sodium ion and simply diffuses across specific channels in the membrane.

5. Membrane-Assisted Transport

a. In exocytosis, a vesicle formed by the Golgi apparatus fuses with the plasma membrane as secretion occurs; insulin leaves insulin-secreting cells by this method.

b. During endocytosis, cells take in substances by vesicle formation as plasma membrane pinches off by either phagocytosis, pinocytosis, or receptor-mediated endocytosis.

c. In phagocytosis, cells engulf large particles (e.g., bacteria), forming an endocytic vesicle.

i. Phagocytosis is commonly performed by ameboid-type cells (e.g., amoebas and macrophages).

ii. When the endocytic vesicle fuses with a lysosome, digestion of the internalized substance occurs.

d. Pinocytosis occurs when vesicles form around a liquid or very small particles; this is only visible with electron microscopy.

e. Receptor-mediated endocytosis, a form of pinocytosis, occurs when specific macromolecules bind to plasma membrane receptors.

i. The receptor proteins are shaped to fit with specific substances (vitamin, hormone, lipoprotein molecule, etc.), and are found at one location in the plasma membrane.

ii. This location is a coated pit with a layer of fibrous protein on the cytoplasmic side; when the vesicle is uncoated, it may fuse with a lysosome.

iii. Pits are associated with exchange of substances between cells (e.g., maternal and fetal blood).

iv. This system is selective and more efficient than pinocytosis; it is important in moving substances from maternal to fetal blood.

v. Cholesterol (transported in a molecule called a low-density lipoprotein, LDL) enters a cell from the bloodstream via receptors in coated pits; in familial hypocholesterolemia, the LDL receptor cannot bind to the coated pit and the excess cholesterol accumulates in the circulatory system.

5.4 Modification of Cell SurfacesA. Cell Surfaces in Animals

1. Junctions Between Cells are points of contact between cells that allow them to behave in a coordinated manner.

a. Anchoring junctions mechanically attach adjacent cells.

b. In adhesion junctions, internal cytoplasmic plaques, firmly attached to cytoskeleton within each cell are joined by intercellular filaments; they hold cells together where tissues stretch (e.g., in heart, stomach, bladder).

c. c. In desmosomes, a single point of attachment between adjacent cells connects the cytoskeletons of adjacent cells.

d. d. In tight junctions, plasma membrane proteins attach in zipper-like fastenings; they hold cells together so tightly that the tissues are barriers (e.g., epithelial lining of stomach, kidney tubules, blood-brain barrier).

e. A gap junction allows cells to communicate; formed when two identical plasma membrane channels join.

i. They provide strength to the cells involved and allow the movement of small molecules and ions from the cytoplasm of one cell to the cytoplasm of the other cell.

ii. Gap junctions permit flow of ions for heart muscle and smooth muscle cells to contract.

2. The extracellular matrix is a meshwork of polysaccharides and proteins produced by animal cells.

a. Collagen gives the matrix strength and elastin gives it resilience.

b. Fibronectins and laminins bind to membrane receptors and permit communication between matrix and cytoplasm; these proteins also form "highways" that direct the migration of cells during development.

c. Proteoglycans are glycoproteins that provide a packing gel that joins the various proteins in matrix and most likely regulate signaling proteins that bind to receptors in the plasma protein.

B. Plant Cell Walls

1. Plant cells are surrounded by a porous cell wall; it varies in thickness, depending on the function of the cell.

2. Plant cells have a primary cell wall composed of cellulose polymers united into threadlike microfibrils that form fibrils.

3. Cellulose fibrils form a framework whose spaces are filled by non-cellulose molecules.

4. Pectins allow the cell wall to stretch and are abundant in the middle lamella that holds cells together.

5. Non-cellulose polysaccharides harden the wall of mature cells.

6. Lignin adds strength and is a common ingredient of secondary cell walls in woody plants.

7. Plasmodesmata are narrow membrane-lined channels that pass through cell walls of neighboring cells and connect their cytoplasms, allowing direct exchange of molecules and ions between neighboring plant cells.

CHAPTER 6: Metabolism: Energy and Enzymes

6.1 Cells and the Flow of EnergyA. Forms of Energy

1. Energy is capacity to do work; cells continually use energy to develop, grow, repair, reproduce, etc.

2. Kinetic energy is energy of motion; all moving objects have kinetic energy.

3. Potential energy is stored energy.

4. Food is chemical energy; it contains potential energy.

5. Chemical energy can be converted into mechanical energy, e.g., muscle movement.

B. Two Laws of Thermodynamics

1. First law of thermodynamics (also called the law of conservation of energy)

a. Energy cannot be created or destroyed, but it can be changed from one form to another.

b. In an ecosystem, solar energy is converted to chemical energy by the process of photosynthesis; some of the chemical energy in the plant is converted to chemical energy in an animal, which in turn can become mechanical energy or heat loss.

c. Neither the plant nor the animal create energy, they convert it from one form to another.

d. Likewise, energy is not destroyed; some becomes heat that dissipates into the environment.

2. Second law of thermodynamics

a. Energy cannot be changed from one form into another without a loss of usable energy.

b. Heat is a form of energy that dissipates into the environment; heat can never be converted back to another form of energy.

C. Cells and Entropy

1. Every energy transformation makes the universe less organized and more disordered; entropy is the term used to indicate the relative amount of disorganization.

2. When ions distribute randomly across a membrane, entropy has increased.

3. Organized/usable forms of energy (as in the glucose molecule) have relatively low entropy; unorganized/less stable forms have relatively high entropy.

4. Energy conversions result in heat; therefore, the entropy of the universe is always increasing.

5. Living things depend on a constant supply of energy from the sun, because the ultimate fate of all solar energy in the biosphere is to become randomized in the universe as heat; the living cell is a temporary repository of order purchased at the cost of a constant flow of energy.

6.2 Metabolic Reactions and Energy Transformations1. Metabolism is the sum of all the biochemical reactions in a cell.2. In the reaction A + B = C + D, A and B are reactants and C and D

are products.

3. Free energy (DG) is the amount of energy that is free to do work after a chemical reaction.

4. Change in free energy is noted as DG; a negative DG means that products have less free energy than reactants; the reaction occurs spontaneously.

5. Exergonic reactions have a negative DG and energy is released.

6. Endergonic reactions have a positive DG; products have more energy than reactants; such reactions can only occur with an input of energy.

B. ATP: Energy for Cells

1. Adenosine triphosphate (ATP) is the energy currency of cells; when cells need energy, they "spend" ATP.

2. ATP is an energy carrier for many different types of reactions.

3. When ATP is converted into ADP + P, the energy released is sufficient for biological reactions with little wasted.

4. ATP breakdown is coupled to endergonic reactions in a way that minimizes energy loss.

5. ATP is a nucleotide composed of the base adenine and the 5-carbon sugar ribose and three phosphate groups.

6. When one phosphate group is removed, about 7.3 kcal of energy is released per mole.

C. Coupled Reactions

1. A coupled reaction occurs when energy released by an exergonic reaction is used to drive an endergonic reaction.

2. ATP breakdown is often coupled to cellular reactions that require energy.

3. ATP supply is maintained by breakdown of glucose during cellular respiration.

4. Only 39% of the chemical energy of glucose is transformed into ATP; 61% is lost as heat.

D. ATP can have any of three functions.

1. Chemical Work: ATP supplies energy to synthesize molecules that make up the cell.

2. Transport Work: ATP supplies energy to pump substances across the plasma membrane.

3. Mechanical Work: ATP supplies energy needed to perform mechanical processes (e.g., muscle contraction, propel cilia, etc.).

6.3 Metabolic Pathways and Enzymes1. A metabolic pathway is an orderly sequence of linked reactions; each step

is catalyzed by a specific enzyme.2. Metabolic pathways begin with a particular reactant, end with a particular end

product(s), and may have many intermediate steps.

3. In many instances, one pathway leads to the next; since pathways often have one or more molecules in common, one pathway can lead to several others.

4. Metabolic energy is captured more easily if it is released in small increments.

5. A reactant is the substance that is converted into a product by the reaction; often many intermediate steps occur.

6. Each step in a series of chemical reactions requires a specific enzyme.

7. Enzymes are catalysts that speed chemical reactions without the enzyme being affected by the reaction.

8. Every enzyme is specific in its action and catalyzes only one reaction or one type of reaction.

9. A substrate is a reactant for an enzymatic reaction.

B. Energy of Activation

1. Molecules often do not react with each other unless activated in some way.

2. For metabolic reactions to occur in a cell, an enzyme must usually be present.

3. The energy of activation (Ea) is the energy that must be added to cause molecules to react; without an enzyme (i.e., in a reaction vessel in the laboratory) this energy may be provided by heat, which causes an increase in the number of molecular collisions.

C. Enzyme-Substrate Complex

1. Enzymes speed chemical reactions by lowering the energy of activation (Ea) by forming a complex with their substrate(s) at the active site.

a. An active site is a small region on the surface of the enzyme where the substrate(s) bind.

b. When a substrate binds to an enzyme, the active site undergoes a slight change in shape that facilitates the reaction. This is called the induced fit model of enzyme catalysis.

2. Only a small amount of enzyme is needed in a cell because enzymes are not consumed during catalysis.

3. Some enzymes (e.g., trypsin) actually participate in the reaction.

4. A particular reactant(s) may produce more than one type of product(s).

a. Presence or absence of enzyme determines which reaction takes place.

b. If reactants can form more than one product, the enzymes present determine which product is formed.

5. Every cell reaction requires its specific enzyme; enzymes are sometimes named for substrates by adding "-ase."

D. Factors Affecting Enzymatic Speed

1. Substrate concentration.

a. Because molecules must collide to react, enzyme activity increases as substrate concentration increases; as more substrate molecules fill active sites, more product is produced per unit time.

2. Temperature and pH

a. As temperature rises, enzyme activity increases because there are more enzyme-substrate collisions.

b. Enzyme activity declines rapidly when enzyme is denatured at a certain temperature, due to a change in shape of the enzyme.

c. Every enzyme has optimal pH at which its rate of reaction is optimal.

d. A change in pH can alter the ionization of the R groups of the amino acids in the enzyme, thereby disrupting the enzyme's activity.

3. Enzyme concentration

a. The amount of active enzyme can regulate the rate of an enzymatic reaction.

b. Cells can activate specific genes when certain enzymes are needed.

c. Enzyme Cofactors

i. Many enzymes require an inorganic ion or non-protein cofactor to function.

ii. Inorganic cofactors are ions of metals.

iii. A coenzyme is an organic cofactor, which assists the enzyme (i.e., it may actually contribute atoms to the reaction).

iv. Vitamins are small organic molecules required in trace amounts for synthesis of coenzymes; they become part of a coenzyme's molecular structure; vitamin deficiency causes a lack of a specific coenzyme and therefore a lack of its enzymatic action.

v. Phosphorylation of enzymes occurs when signal proteins turn on kinases, which then activate specific enzymes; some hormones use this mechanism.

d. Enzyme inhibition occurs when a substance (called an inhibitor) binds to an enzyme and decreases its activity; normally, enzyme inhibition is reversible.

i. In competitive inhibition, the substrate and the inhibitor are both able to bind to the enzyme's active site.

ii. In noncompetitive inhibition, the inhibitor binds to the enzyme at a location other than the active site (theallosteric site), changing the shape of the enzyme and rendering it unable to bind to its substrate.

iii. Competitive and noncompetitive inhibition are both examples of feedback inhibition.

iv. In irreversible inhibition, the inhibitor permanently inactivates or destroys the enzyme; cyanide, mercury, and lead are irreversible inhibitors for several specific enzymes.

6.4 Oxidation-Reduction and the Flow of Energy1. In oxidation-reduction (redox) reactions, electrons pass from one molecule to

another.2. Oxidation is the loss of electrons.

3. Reduction is the gain of electrons.

4. Both reactions occur at the same time because one molecule accepts electrons given up by another molecule.

B. Photosynthesis

1. Photosynthesis uses energy to combine carbon dioxide and water to produce glucose in the formula:

6 CO2 + 6 H2O + energy = C6H12O6 + 6 O2

2. When hydrogen atoms are transferred to carbon dioxide from water, water has been oxidized and carbon dioxide has been reduced.

3. Input of energy is needed to produce the high-energy glucose molecule.

4. Chloroplasts capture solar energy and convert it by way of an electron transport system into the chemical energy of ATP.

5. ATP is used along with hydrogen atoms to reduce glucose; when NADP+

(nicotinamide adenine dinucleotide phosphate)donates hydrogen atoms (H+ + e-) to a substrate during photosynthesis, the substrate has accepted electrons and is therefore reduced.

6. The reaction that reduces NADP+ is:

NADP+ + 2e- + H+ = NADPH

C. Cellular Respiration1. The overall equation for cellular respiration is opposite that of photosynthesis:

C6H12O6 + 6 O2 = 6 CO2 + 6 H2O + energy

2. When NAD removes hydrogen atoms (H+ + e-) during cellular respiration, the substrate has lost electrons and is therefore oxidized.

3. At the end of cellular respiration, glucose has been oxidized to carbon dioxide and water and ATP molecules have been produced.

4. In metabolic pathways, most oxidations involve the coenzyme NAD+ (nicotinamide adenine dinucleotide); the molecule accepts two electrons but only one hydrogen ion: NAD+ + 2e- + H+ = NADH

D. Electron Transport Chain

1. Both photosynthesis and respiration use an electron transport chain consisting of membrane-bound carriers that pass electrons from one carrier to another.

2. High-energy electrons are delivered to the system and low-energy electrons leave it.

3. The overall effect is a series of redox reactions; every time electrons transfer to a new carrier, energy is released for the production of ATP.

E. ATP Production

1. ATP synthesis is coupled to the electron transport system.

2. Peter Mitchell received the 1978 Nobel Prize for his chemiosmotic theory of ATP production.

3. In both mitochondria and chloroplasts, carriers of electron transport systems are located within a membrane.

4. H+ ions (protons) collect on one side of the membrane because they are pumped there by specific proteins.

5. The electrochemical gradient thus established across the membrane is used to provide energy for ATP production.

6. Enzymes and their carrier proteins, called ATP synthase complexes, span the membrane; each complex contains a channel that allows H+ ions to flow down their electrochemical gradient.

7. In photosynthesis, energized electrons lead to the pumping of hydrogen ions across the thylakoid membrane; as hydrogen ions flow through the ATP synthase complex, ATP is formed.

8. During cellular respiration, glucose breakdown provides energy for a hydrogen ion gradient on the inner membrane of the mitochondria that also couples hydrogen ion flow with ATP formation.

CHAPTER 7: Photosynthesis

7.1 Photosynthetic Organisms

1. Photosynthetic organisms (algae, plants, and cyanobacteria) transform solar energy into carbohydrates.

2. Photosynthetic organisms (plants, algae, cyanobacteria) are called autotrophs because they produce their own food.

3. Organisms that must take in preformed organic molecules are called heterotrophs.

4. Both autotrophs and heterotrophs use organic molecules produced by photosynthesis as chemical building blocks and as a source of energy.

B. Flowering Plants as Photosynthesizers

1. Raw materials for photosynthesis are carbon dioxide and water.

2. Roots absorb water that moves up vascular tissue in the stem until it reaches the leaf veins.

3. Carbon dioxide enters a leaf through small openings called stomata.

4. Carbon dioxide and water diffuse into the chloroplasts, the organelles that carry on photosynthesis.

5. In chloroplasts, a double membrane encloses a fluid-filled space called the stroma.

6. An internal membrane system within the stroma forms flattened sacs called thylakoids, which in some cases are organized into stacks to form grana.

7. Spaces within all thylakoids are connected to form an inner compartment, the thylakoid space.

8. Chlorophyll and other pigments involved in absorption of solar energy reside within thylakoid membranes; these pigments absorb solar energy, and energize electrons prior to reduction of CO2 to a carbohydrate.

7.2 Plants as Solar Energy Converters1. Only 42% of the solar radiation that hits the Earth's atmosphere reaches

surface; most is visible light.2. Higher energy wavelengths are screened out by the ozone layer in the upper

atmosphere.

3. Lower energy wavelengths are screened out by water vapor and CO2.

4. Both the organic molecules within organisms and certain processes (e.g., vision, photosynthesis) are adapted to visible light, the radiation that is most prevalent in the environment.

B. Photosynthetic Pigments

1. Photosynthetic pigments use primarily the visible light portion of the electromagnetic spectrum.

2. Pigments found in chlorophyll absorb various portions of visible light; this is called their absorption spectrum.

3. Two major photosynthetic pigments are chlorophyll a and chlorophyll b.

4. Both chlorophylls absorb violet, blue, and red wavelengths best.

5. Very little green light is absorbed; most is reflected (this is why leaves appear green).

6. Carotenoids are yellow-orange pigments that absorb light in violet, blue, and green regions.

7. When chlorophyll breaks down in the fall, the yellow-orange pigments in leaves show through.

8. Absorption and action spectrum

a. A spectrophotometer measures the amount of light that passes through a sample.

i. As light is shone on a sample, some wavelengths are absorbed and others pass through the sample.

ii. A graph of percent of light absorbed at each wavelength is a compound's absorption spectrum.

b. Action spectrum

i. Photosynthesis produces oxygen; the production rate of oxygen is used to measure the rate of photosynthesis.

ii. Oxygen production and therefore photosynthetic activity is measured for plants under each specific wavelength; when plotted on a graph, this gives an action spectrum for a compound.

iii. The action spectrum for chlorophyll resembles its absorption spectrum, thus indicating that chlorophyll contributes to photosynthesis.

C. Photosynthetic Reaction

1. In 1930, van Niel showed that O2 given off by photosynthesis comes from water and not from CO2.

2. The net equation of photosynthesis reads: 6CO2 + 6H2O = C6 H12O6 + 6O2.

D. Two Sets of Reactions

1. In 1905, Blackman proposed two sets of reactions for photosynthesis.

2. Light reactions take place only in the presence of light.

a. Light reactions are the energy-capturing reactions.

b. Chlorophyl within thylakoid membranes absorbs solar energy and energizes electrons.

c. When energized electrons move down an electron transport chain, energy is captured and used for ATP production.

d. Energized electrons are also taken up by NADP+, converting it to NADPH.

3. Calvin cycle reactions

a. These reactions take place in the stroma; the reactions can occur in either the presence or the absence of light.

b. These are synthetic reactions that use NADPH and ATP to reduce CO2.

7.3 Light Reactions1. Two electron pathways operate in the thylakoid membrane:

the noncyclic pathway and the cyclic pathway.2. Both pathways produce ATP; only the noncyclic pathway also produces

NADPH.

3. ATP production during photosynthesis is called photophosphorylation; therefore these pathways are also known as cyclicand noncyclic photophosphorylation.

B. Noncyclic Electron Pathway

1. This pathway occurs in the thylakoid membranes and requires participation of two light-gathering units: photosystem I (PS I) and photosystem II (PS II).

2. A photosystem is a photosynthetic unit comprised of a pigment complex and an electron acceptor; solar energy is absorbed and high-energy electrons are generated.

3. Each photosystem has a pigment complex of chlorophyll a, chlorophyll b, carotenoid, and electron acceptor molecules.

4. Absorbed energy is passed from one pigment molecule to another until concentrated in reaction-centerchlorophyll amolecules.

5. Electrons in reaction-center chlorophyll a become excited, and escape to the electron-acceptor molecule.

6. The noncyclic pathway begins with PSII; electrons move from H2O through PS II to PS I and then on to NADP+.

7. The PS II pigment complex absorbs solar energy; high-energy electrons (e-) leave the reaction-center chlorophyll amolecule.

8. PS II takes replacement electrons from H2O, which splits, releasing O2 and H+ ions: H2O = 2 H+ + 2 e- + ½ O2.

9. Oxygen is released as oxygen gas (O2).

10. The H+ ions temporarily stay within the thylakoid space and contribute to a H+ ion gradient.

11. As H+ flow down electrochemical gradient through ATP synthase complexes, chemiosmosis occurs.

12. Low-energy electrons leaving the electron transport system enter PS I.

13. When the PS I pigment complex absorbs solar energy, high-energy electrons leave reaction-center chlorophyll a and are captured by an electron acceptor.

14. The electron acceptor passes them on to NADP+.

15. NADP+ takes on an H+ to become NADPH: NADP+ + 2 e- + H+ = NADPH.

16. NADPH and ATP (produced by noncyclic-flow electrons in the thylakoid membrane) are used by enzymes in the stroma during the light-independent (dark) reactions.

C. Cyclic Electron Pathway

1. The cyclic electron pathway begins when the PS I antenna complex absorbs solar energy.

2. High-energy electrons leave PS I reaction-center chlorophyll a molecule.

3. Before they return, the electrons enter and travel down an electron transport chain.

a. Electrons pass from a higher to a lower energy level.

b. Energy released is stored in the form of a hydrogen (H+) gradient.

c. When hydrogen ions flow down their electrochemical gradient through ATP synthase complexes, ATP production occurs.

d. The electrons return to PSI rather than move on to NADP+--this is why it is called cyclic and also why no NADPH is produced.

4. It is possible that in plants, the cyclic flow of electrons is utilized only when CO2 is in such limited supply that carbohydrate is not being produced.

D. The Organization of the Thylakoid Membrane

1. PS II consists of a pigment complex and electron-acceptor molecules; it oxidizes H2O and produces O2.

2. The electron transport system consists of cytochrome complexes and transports electrons and pumps H+ ions into the thylakoid space.

3. PS I has a pigment complex and electron-acceptor molecules; it is associated with an enzyme that reduces NADP+ to NADPH.

4. ATP synthase complex has an H+ channel and ATP synthase; it produces ATP.

E. ATP Production

1. The thylakoid space acts as a reservoir for H+ ions; each time H2O is split, two H+ remain.

2. Electrons move carrier-to-carrier, giving up energy used to pump H+ from the stroma into the thylakoid space.

3. Flow of H+ from high to low concentration across thylakoid membrane provides energy to produce ATP from ADP + P by using an ATP synthase enzyme.

4. This is called chemiosmosis because ATP production is tied to an electrochemical (H+) gradient.

7.4 Calvin Cycle Reactions1. The Calvin cycle is a series of reactions producing carbohydrates; these

reactions follow the light reactions.2. The cycle is named for Melvin Calvin who used a radioactive isotope of

carbon to trace the reactions.

3. The Calvin cycle includes carbon dioxide fixation, carbon dioxide reduction, and regeneration of ribulose 1,5-bisphosphate (RuBP).

B. Fixation of Carbon Dioxide

1. CO2 fixation is the attachment of CO2 to an organic compound called RuBP.

2. RuBP (ribulose bisphosphate) is a five-carbon molecule that combines with carbon dioxide; the resulting 6-carbon molecule then splits into two 3-carbon molecules.

3. The enzyme RuBP carboxylase (rubisco) speeds this reaction; this enzyme comprises 20–50% of the protein content of chloroplasts--it is an unusually slow enzyme.

C. Reduction of Carbon Dioxide

1. With the reduction of carbon dioxide, a 3PG (3-phosphoglycerate) molecule forms.

2. Each of two 3PG molecules undergoes reduction to G3P (glyceraldehyde-3-phosphate) in two steps.

3. Light-dependent reactions provide NADPH (electrons) and ATP (energy) to reduce 3PG to G3P.

D. Regeneration of RuBP

1. For every three turns of the Calvin cycle, five molecules of G3P are used to re-form three molecules of RuBP.

2. This reaction also uses ATP produced by the light reactions.

E. The Importance of the Calvin Cycle

1. G3P, the product of the Calvin Cycle can be converted into many other molecules.

2. Glucose phosphate is one result of G3P metabolism; it is a common energy molecule.

3. Glucose phosphate can bond with fructose to form sucrose.

4. Glucose phosphate is the starting point for synthesis of starch and cellulose.

5. The hydrocarbon skeleton of G3P is used to form fatty acids and glycerol; the addition of nitrogen forms various amino acids.

7.5 Other Types of Photosynthesis1. In C3 plants, the Calvin cycle fixes CO2 directly; the first molecule following

CO2 fixation is 3PG.2. In hot weather, stomata close to save water; CO2 concentration decreases in

leaves; O2 increases.

3. This is called photorespiration since oxygen is taken up and CO2 is produced; this produces only one 3PG.

B. C4 Photosynthesis

1. In a C3 plant, mesophyll cells contain well-formed chloroplasts, arranged in parallel layers.

2. In C4 plants, bundle sheath cells as well as the mesophyll cells contain chloroplasts.

3. In C4 leaf, mesophyll cells are arranged concentrically around the bundle sheath cells.

4. C3 plants use RuBP carboxylase to fix CO2 to RuBP in mesophyll; the first detected molecule is G3P.

5. C4 plants use the enzyme PEP carboxylase (PEPCase) to fix CO2 to PEP (phosphoenolpyruvate, a C3 molecule); the end product is oxaloacetate (a C4 molecule).

6. In C4 plants, CO2 is taken up in mesophyll cells and malate, a reduced form of oxaloacetate, is pumped into the bundle-sheath cells; here CO2 enters Calvin cycle.

7. In hot, dry climates, net photosynthetic rate of C4 plants (e.g., corn) is 2–3 times that of C4 plants.

8. Photorespiration does not occur in C4 leaves because PEPCase does not combine with O2; even when stomates are closed, CO2 is delivered to the Calvin cycle in bundle sheath cells.

9. C4 plants have advantage over C3 plants in hot and dry weather because photorespiration does not occur; e.g., bluegrass (C3) dominates lawns in early summer, whereas crabgrass (C4) takes over in the hot midsummer.

C. CAM Photosynthesis

1. CAM (crassulacean-acid metabolism) plants form a C4 molecule at night when stomates can open without loss of water; found in many succulent desert plants including the family Crassulaceae.

2. At night, CAM plants use PEPCase to fix CO2 by forming C4 molecule stored in large vacuoles in mesophyll.

3. C4 formed at night is broken down to CO2 during the day and enters the Calvin cycle within the same cell, which now has NADPH and ATP available to it from the light-dependent reactions.

4. CAM plants open stomates only at night, allowing CO2 to enter photosynthesizing tissues; during the day, stomates are closed to conserve water but CO2 cannot enter photosynthesizing tissues.

5. Photosynthesis in a CAM plant is minimal, due to limited amount of CO2 fixed at night; but this does allow CAM plants to live under stressful conditions.

D. Photosynthesis and Adaptation to the Environment

1. Each method of photosynthesis has its advantages, depending on the environment.

2. C4 plants are adapted to areas of high light intensities, high temperatures, and limited rainfall.

3. C3 plants do better in cooler climates.

4. CAM plants do well in an arid environment.

CHAPTER 8: Cellular Respiration

8.1 Cellular Respiration1. Cellular respiration involves various metabolic pathways that break down

carbohydrates and other metabolites with the concomitant buildup of ATP.2. Cellular respiration consumes oxygen and produces CO2; because oxygen

is required, cellular respiration is aerobic.

3. Cellular respiration usually involves the complete breakdown of glucose into CO2 and H2O.

4. The net equation for glucose breakdown is: C6H12O6 + 6 O2 = 6 CO2 + 6 H2O + energy

5. Glucose is a high-energy molecule; CO2 and H2O are low-energy molecules; cellular respiration is thus exergonic because it releases energy.

6. Electrons are removed from substrates and received by oxygen, which combines with H+ to become water.

7. Glucose is oxidized and O2 is reduced.

8. The buildup of ATP is an endergonic reaction (i.e., requires energy).

9. The reactions of cellular respiration allow energy in glucose to be released slowly; therefore ATP is produced gradually.

10. In contrast, if glucose were broken down rapidly, most of its energy would be lost as non-usable heat.

11. The breakdown of glucose yields synthesis of 36 or 38 ATP (depending on certain conditions); this preserves about 39% of the energy available in glucose.

12. This is relatively efficient compared to, for example, the 25% efficiency of a car burning gasoline.

B. NAD+ and FAD

1. Each metabolic reaction in cellular respiration is catalyzed by a specific enzyme.

2. As a metabolite is oxidized, NAD+ (nicotinamide adenine dinucleotide) accepts two electrons and a hydrogen ion (H+); this results in NADH + H+.

3. Electrons received by NAD+ and FAD are high-energy electrons and are usually carried to the electron transport chain.

4. NAD+ is a coenzyme of oxidation-reduction since it both accepts and gives up electrons; thus, NAD+ is sometimes called aredox coenzyme

5. Only a small amount of NAD+ is needed in cells because each NAD+ molecule is used repeatedly.

6. FAD coenzyme of oxidation-reduction can replace NAD+; FAD accepts two electrons and two hydrogen ions to become FADH2.

C. Phases of Cellular Respiration

1. Cellular respiration includes four phases:

a. Glycolysis is the breakdown of glucose in the cytoplasm into two molecules of pyruvate.

i. Enough energy is released for an immediate yield of two ATP.

ii. Glycolysis takes place outside the mitochondria and does not utilize oxygen; it is therefore an anaerobicprocess.

b. In the preparatory (prep) reaction, pyruvate enters a mitochondrion and is oxidized to a two-carbon acetyl group and CO2 is removed; this reaction occurs twice per glucose molecule.

c. The citric acid cycle:

i. occurs in the matrix of the mitochondrion and produces NADH and FADH2;

ii. is a series of reactions that gives off CO2 and produces one ATP;

iii. turns twice because two acetyl-CoA molecules enter the cycle per glucose molecule;

iv. produces two immediate ATP molecules per glucose molecule.

d. The electron transport chain:

i. is a series of carriers in the inner mitochondrial membrane that accept electrons from glucose--electrons are passed from carrier to carrier until received by oxygen;

ii. passes electrons from higher to lower energy states, allowing energy to be released and stored for ATP production;

iii. accounts for 32 or 34 ATP, depending on certain cell conditions.

2. Pyruvate is a pivotal metabolite in cellular respiration.

a. If O2 is not available to the cell, fermentation, an anaerobic process, occurs in the cytoplasm.

b. During fermentation, glucose is incompletely metabolized to lactate, or to CO2 and alcohol (depending on the organism).

c. Fermentation results in a net gain of only two ATP per glucose molecule.

8.2 Outside the Mitochondria: Glycolysis1. Glycolysis occurs in the cytoplasm outside the mitochondria.2. Glycolysis is the breakdown of glucose into two pyruvate molecules.

3. Glycolysis is universally found in organisms; therefore, it likely evolved before the citric acid cycle and electron transport chain.

B. Energy-Investment Steps

1. Glycolysis begins with the activation of glucose with two ATP; the glucose splits into two C3 molecules known as G3P, each of which carries a phosphate group.

C. Energy-Harvesting Steps

1. Oxidation of G3P occurs by removal of electrons and hydrogen ions.

2. Two electrons and one hydrogen ion are accepted by NAD+, resulting in two NADH; later, when the NADH molecules pass two electrons to another electron carrier, they become NAD+ again.

3. The oxidation of G3P and subsequent substrates results in four high-energy phosphate groups, which are used to synthesize four ATP molecules; this process is called substrate-level phosphorylation.

4. Two of four ATP molecules produced are required to replace two ATP molecules used in the initial phosphorylation of glucose; therefore there is a net gain of two ATP from glycolysis.

5. Pyruvate enters a mitochondrion (if oxygen is available) and cellular respiration ensues.

6. If oxygen is not available, fermentation occurs and pyruvate undergoes reduction.

8.3 Inside the Mitochondria1. The next reactions of cellular respiration involve the preparatoryreaction,

the citric acid cycle, and the electron transport chain.2. In these reactions, the pyruvate from glycolysis is broken down completely to

CO2 and H2O.

3. CO2 and ATP are transported out of the mitochondria into the cytoplasm.

4. The H2O can remain in the mitochondria or within the cell, or it can enter the blood and be excreted by the kidneys.

5. A mitochondrion has a double membrane with an intermembrane space (between the outer and inner membrane).

6. Cristae are the inner folds of membrane that jut into the matrix, the innermost compartment of a mitochondrion that is filled with a gel-like fluid.

7. The prep reaction and citric acid cycle enzymes are in the matrix; the electron transport chain is in the cristae.

8. Most of the ATP produced in cellular respiration is produced in the mitochondria; therefore, mitochondria are often called the "powerhouses" of the cell.

B. Preparatory Reaction

1. The preparatory reaction connects glycolysis to the citric acid cycle.

2. In this reaction, pyruvate is converted to a two-carbon acetyl group, and is attached to coenzyme A, resulting in the compound acetyl-CoA.

3. This redox reaction removes electrons from pyruvate by a dehydrogenase enzyme, using NAD+ as a coenzyme.

4. This reaction occurs twice for each glucose molecule.

C. Citric Acid Cycle

1. The citric acid cycle occurs in the matrix of mitochondria.

2. The cycle is sometimes called the Krebs cycle, named for Sir Hans Krebs, who described the fundamentals of the reactions in the 1930s.

3. The cycle begins by the addition of a two-carbon acetyl group to a four-carbon molecule, forming a six-carbon citrate (citric acid) molecule.

4. In the subsequent reactions, at three different times two electrons and one hydrogen ion are accepted by NAD+, forming NADH.

5. At one time, two electrons and one hydrogen ion are accepted by FAD, forming FADH2.

6. NADH and FADH2 carry these electrons to the electron transport chain.

7. Some energy is released and is used to synthesize ATP by substrate-level phosphorylation.

8. One high-energy metabolite accepts a phosphate group and transfers it to convert ADP to ATP.

9. The citric acid cycle turns twice for each original glucose molecule.

10. The products of the citric acid cycle (per glucose molecule) are 4 CO2, 2 ATP, 6 NADH and 2 FADH2.

11. The six carbon atoms in the glucose molecule have now become the carbon atoms of six CO2 molecules, two from the prep reaction and four from the citric acid cycle.

D. The Electron Transport Chain

1. The electron transport chain is located in the cristae of mitochondria and consists of carriers that pass electrons successively from one to another.

2. Some of the protein carriers are cytochrome molecules, complex carbon rings with a heme (iron) group in the center.

3. NADH and FADH2 carry the electrons to the electron transport system..

4. NADH gives up its electrons and becomes NAD+; the next carrier then gains electrons and is thereby reduced.

5. At each sequential redox reaction, energy is released to form ATP molecules.

6. Because O2 must be present for the proteins to work, this process is also called oxidative phosphorylation.

7. Oxygen serves as the terminal electron acceptor and combines with hydrogen ions to form water.

8. By the time electrons are received by O2, three ATP have been made.

9. When FADH2 delivers electrons to the electron transport system, two ATP are formed by the time the electrons are received by O2.

10. Coenzymes and ATP undergo recycling.

a. Cell needs a limited supply of coenzymes NAD+ and FAD because they constantly recycle.

b. Once NADH delivers electrons to the electron transport chain, it can accept more hydrogen atoms.

c. ADP and phosphate also recycle.

d. Efficiency of recycling NAD+, FAD, and ADP eliminates the need to continuously synthesize them anew.

E. The Cristae of a Mitochondrion

1. The electron transport chain consists of three protein complexes and two protein mobile carriers that transport electrons.

2. The three protein complexes include NADH-Q reductase complex, the cytochrome reductasecomplex, and the cytochrome oxidase complex; the two protein mobile carriers are coenzyme Q and cytochrome c.

3. Energy released from the flow of electrons down the electron transport chain is used to pump H+ ions, which are carried by NADH and FADH2, into intermembrane space.

4. Accumulation of H+ ions in this intermembrane space creates a strong electrochemical gradient.

5. ATP synthase complexes are channel proteins that serve as enzymes for ATP synthesis.

6. As H+ ions flow from high to low concentration, ATP synthase synthesizes ATP by the reaction: ADP + P = ATP.

7. Chemiosmosis is the term used for ATP production tied to an electrochemical (H+) gradient across a membrane.

8. Respiratory poisons confirm the chemiosmotic nature of ATP synthesis (i.e., a poison that inhibits ATP synthesis increases the H+ gradient).

9. Once formed, ATP molecules diffuse out of the mitochondrial matrix through channel proteins.

10. ATP is the energy currency for all living things; all organisms must continuously produce high levels of ATP to survive.

F. Energy Yield From Glucose Metabolism

1. Substrate-Level Phosphorylation

a. Per glucose molecule, there is a net gain of two ATP from glycolysis in cytoplasm.

b. The citric acid cycle in the matrix of the mitochondria produces two ATP per glucose.

c. Thus, a total of four ATP are formed by substrate-level phosphorylation outside of the electron transport chain.

2. Electron Transport Chain and Chemiosmosis

a. Most of the ATP is produced by the electron transport chain and chemiosmosis.

b. Per glucose, ten NADH and two FADH2 molecules provide electrons and H+ ions to the electron transport chain.

c. For each NADH formed within the mitochondrion, three ATP are produced.

d. For each FADH2 formed by the citric acid cycle, two ATP are produced.

e. For each NADH formed outside mitochondria by glycolysis, two ATP are produced as electrons are shuttled across the mitochondrial membrane by an organic molecule and delivered to FAD.

3. Efficiency of Cellular Respiration

a. The energy difference between total reactants (glucose and O2) and products (CO2 and H2O) is 686 kcal.

b. An ATP phosphate bond has an energy of 7.3 kcal; 36 to 38 ATP are produced during glucose breakdown for a total of at least 263 kcal.

c. This efficiency is 263/686, or 39% of the available energy in glucose is transferred to ATP; the rest of the energy is lost as heat.

8.4 Fermentation1. Fermentation is an anaerobic (i.e., occurs in the absence of oxygen) process

which consists of glycolysis plus reduction of pyruvate to either lactate or to alcohol and CO2 (depending on the organism).

2. NADH passes its electrons to pyruvate instead of to an electron transport chain; NAD+ is then free to return and pick up more electrons during earlier reactions of glycolysis.

3. Alcoholic fermentation, carried out by yeasts, produces carbon dioxide and ethyl alcohol; this process is used in the production of alcoholic spirits and breads.

4. Lactic acid fermentation, carried out by certain bacteria and fungi, produces lactic acid (lactate); this process is used commercially in the production of cheese, yogurt, and sauerkraut.

5. Other bacteria produce chemicals anaerobically, including isopropanol, butyric acid, proprionic acid, and acetic acid.

B. Advantages and Disadvantages of Fermentation

1. Despite a low yield of two ATP molecules, fermentation provides a quick burst of ATP energy for muscular activity.

2. Lactate is toxic to cells.

a. When blood cannot remove all lactate from muscles, lactate changes pH and causes muscles to fatigue.

b. The individual is in oxygen debt because oxygen is needed to restore ATP levels and rid the body of lactate.

c. Recovery occurs after lactate is sent to the liver where it is converted into pyruvate; some pyruvate is then respired or converted back into glucose.

C. Efficiency of Fermentation

1. Two ATP produced per glucose molecule during fermentation is equivalent to 14.6 kcal.

2. Complete glucose breakdown to CO2 and H2O during cellular respiration represents a potential yield of 686 kcal of energy.

3. Efficiency of fermentation is 14.6/686 or about 2.1%, far less efficient than complete breakdown of glucose.

8.5 Metabolic Pool1. Degradative reactions (catabolism) break down molecules; they tend to be

exergonic.2. Synthetic reactions (anabolism) build molecules; they tend to be endergonic.

B. Catabolism

1. Just as glucose is broken down in cellular respiration, other molecules in the cell undergo catabolism.

2. Fat breaks down into glycerol and three fatty acids.

a. Glycerol is converted to G3P, a metabolite in glycolysis.

b. An 18-carbon fatty acid is converted to nine acetyl-CoA molecules that enter the citric acid cycle.

c. Respiration of fat products can produce 108 kcal in ATP molecules; fats are an efficient form of stored energy.

3. Amino acids break down into carbon chains and amino groups.

a. Hydrolysis of proteins results in amino acids.

b. R-group size determines whether carbon chain is oxidized in glycolysis or the citric acid cycle.

c. A carbon skeleton is produced in the liver by removal of the amino group, by the process of deamination.

d. The amino group becomes ammonia (NH3), which enters the urea cycle and ultimately becomes part of excreted urea.

e. The size of the R-group determines the number of carbons left after deamination.

C. Anabolism

1. ATP produced during catabolism drives anabolism.

2. Substrates making up pathways can be used as starting materials for synthetic reactions.

3. The molecules used for biosynthesis constitute the cell's metabolic pool.

4. Carbohydrates can result in fat synthesis: G3P converts to glycerol, acetyl groups join to form fatty acids.

5. Some metabolites can be converted to amino acids by transamination, the transfer of an amino acid group to an organic acid.

6. Plants synthesize all the amino acids they need; animals lack some enzymes needed to make some amino acids.

7. Humans synthesize 11 of 20 amino acids; the remaining 9 essential amino acids must be provided by the diet.

CHAPTER 9: The Cell Cycle and Cellular Reproduction

9.1 The Cell Cycle1. The cell cycle is an orderly set of stages from the first division to the time

the daughter cells divide.2. When a cell is preparing for division, it grows larger, the number of organelles

doubles, and the DNA replicates.

B. Interphase

1. Most of a cell's life is spent in interphase, in which the cell performs its usual functions.

2. Time spent in interphase varies by cell type: nerve and muscle cells do not complete the cell cycle and remain in the G0stage while embryonic cells complete the cycle every few hours.

3. The G1 stage is just prior to DNA replication; a cell grows in size, organelles increase in number, and material accumulates for DNA synthesis.

4. The S stage is the DNA synthesis (replication) period; proteins associated with DNA are also synthesized; at the end of the S stage, each chromosome has two identical DNA double helix molecules, called sister chromatids.

5. The G2 stage occurs just prior to cell division; the cell synthesizes proteins needed for cell division, such as proteins in microtubules.

6. Interphase therefore consists of G1, S, and G2.

C. M (Mitotic) Stage

1. M stage (M = mitosis) is the entire cell division stage, including both mitosis and cytokinesis.

2. Mitosis is nuclear division, cytokinesis is division of the cytoplasm.

3. When division of the cytoplasm is complete, two daughter cells are produced.

D. Control of the Cell Cycle

1. The cell cycle is controlled by both internal and external signals.

2. A signal is a molecule that either stimulates or inhibits a metabolic event.

3. Growth factors are external signals received at the plasma membrane.

4. Cell Cycle Checkpoints

a. There appear to be three checkpoints where the cell cycle either stops or continues onward, depending on the internal signals it receives.

b. Researchers have identified a family of proteins called cyclins, internal signals that increase or decrease during the cell cycle.

c. Cyclin must be present for the cell to move from the G1 stage to the S stage, and from the G2 stage to the M stage.

d. The cell cycle stops at the G2 stage if DNA has not finished replicating; stopping the cell cycle at this stage allows time for repair of possible damaged DNA.

e. Also, the cycle stops if chromosomes are not distributed accurately to daughter cells.

f. DNA damage also stops the cycle at the G1 checkpoint by the protein p53; if the DNA is not repaired, p53 triggers apoptosis.

E. Apoptosis

1. Apoptosis is programmed cell death and involves a sequence of cellular events involving:

a. fragmenting of the nucleus,

b. blistering of the plasma membrane, and

c. engulfing of cell fragments by macrophages and/or neighboring cells.

2. Apoptosis is caused by enzymes called caspases.

3. Cells normally hold caspases in check with inhibitors.

4. Caspases are released by internal or external signals.

5. Apoptosis and cell division are balancing processes that maintain the normal level of somatic (body) cells.

6. Cell death is a normal and necessary part of development: frogs, for example, must destroy tail tissue they used as tadpoles, and the human embryo must eliminate webbing found between fingers and toes.

7. Death by apoptosis prevents a tumor from developing.

9.2 Mitosis and CytokinesisA. Eukaryotic Chromosomes

1. DNA in chromosomes of eukaryotic cells is associated with proteins; histone proteins organize chromosomes.

2. When a cell is not undergoing division, DNA in the nucleus is a tangled mass of threads called chromatin.

3. At cell division, chromatin becomes highly coiled and condensed and is now visible as individual chromosomes.

4. Each species has a characteristic number of chromosomes.

a. The diploid (2n) number includes two sets of chromosomes of each type.

i. The diploid number is found in all the non-sex cells of an organism's body (with a few exceptions).

ii. Examples include humans (46), crayfish (200), etc.

b. The haploid (n) number contains one of each kind of chromosome.

i. In the life cycle of many animals, only sperm and egg cells have the haploid number.

ii. Examples include humans (23), crayfish (100), etc.

5. Cell division in eukaryotes involves nuclear division and cytokinesis.

a. Somatic cells undergo mitosis for development, growth, and repair.

i. This nuclear division leaves the chromosome number constant.

ii. A 2n nucleus replicates and divides to provide daughter nuclei that are also 2n.

b. A chromosome begins cell division with two sister chromatids.

i. Sister chromatids are two strands of genetically identical chromosomes.

ii. At the beginning of cell division, they are attached at a centromere, a region of constriction on a chromosome.

B. Stages of Mitosis

1. The centrosome, the main microtubule organizing center of the cell, divides before mitosis begins.

2. Each centrosome contains a pair of barrel-shaped organelles called centrioles.

3. The mitotic spindle contains many fibers, each composed of a bundle of microtubules.

4. Microtubules are made of the protein tubulin.

a. Microtubules assemble when tubulin subunits join, disassemble when tubulin subunits become free, and form interconnected filaments of cytoskeleton.

b. Microtubules disassemble as spindle fibers form.

5. Mitosis is divided into five phases: prophase, prometaphase, metaphase, anaphase, and telophase.

6. Prophase

a. Nuclear division is about to occur: chromatin condenses and chromosomes become visible.

b. The nucleolus disappears and the nuclear envelope fragments.

c. Duplicated chromosomes are composed of two sister chromatids held together by a centromere; chromosomes have no particular orientation in the cell at this time.

d. The spindle begins to assemble as pairs of centrosomes migrate away from each other.

e. An array of microtubules called asters radiates toward the plasma membrane from the centrosomes.

7. Prometaphase (Late Prophase)

a. Specialized protein complexes (kinetochores) develop on each side of the centromere for future chromosome orientation.

b. An important event during prometaphase is attachment of the chromosomes to the spindle and their movement as they align at the metaphase plate (equator) of the spindle.

c. The kinetochores of sister chromatids capture kinetochore spindle fibers.

d. Chromosomes move back and forth toward alignment at the metaphase plate.

8. Metaphase

a. Chromosomes, attached to kinetochore fibers, are now aligned at the metaphase plate.

b. Non-attached spindle fibers, called polar spindle fibers, can reach beyond the metaphase plate and overlap.

9. Anaphase

a. The two sister chromatids of each duplicated chromosome separate at the centromere.

b. Daughter chromosomes, each with a centromere and single chromatid, move to opposite poles.

i. Polar spindle fibers lengthen as they slide past each other.

ii. Kinetochore spindle fibers disassemble at the kinetochores; this pulls daughter chromosomes to poles.

iii. The motor molecules kinesin and dynein are involved in this sliding process.

iv. Anaphase is the shortest stage of mitosis.

10. Telophase

a. Spindle disappears in this stage.

b. The nuclear envelope reforms around the daughter chromosomes.

c. The daughter chromosomes diffuse, again forming chromatin.

d. The nucleolus reappears in each daughter nucleus.

C. Cytokinesis in Animal and Plant Cells

1. Cytokinesis in Animal Cells

a. A cleavage furrow indents the plasma membrane between the two daughter nuclei at a midpoint; this deepens to divide the cytoplasm during cell division.

b. Cytoplasmic cleavage begins as anaphase draws to a close and organelles are distributed.

c. The cleavage furrow deepens as a band of actin filaments, called the contractile ring, constricts between the two daughter cells.

d. A narrow bridge exists between daughter cells during telophase until constriction completely separates the cytoplasm.

2. Cytokinesis in Plant Cells

a. The rigid cell wall that surrounds plant cells does not permit cytokinesis by furrowing.

b. The Golgi apparatus produces vesicles, which move along the microtubules to a small flattened disc that has formed.

c. Vesicles fuse forming a cell plate; their membranes complete the plasma membranes of the daughter cells.

d. The new membrane also releases molecules from the new plant cell walls; the cell walls are strengthened by the addition of cellulose fibrils.

D. The Functions of Mitosis

1. Mitosis permits growth and repair.

2. In flowering plants, the meristematic tissue retains the ability to divide throughout the life of the plant; this accounts for the continued growth, both in height and laterally, of a plant.

3. In mammals, mitosis is necessary as a fertilized egg becomes an embryo and as the embryo becomes a fetus; throughout life, mitosis allows a cut to heal or a broken bone to mend.

E. Stem Cells

1. Many mammalian organs contain stem cells (or adult stem cells), which retain the ability to divide.

2. Red bone marrow stem cells repeatedly divide to produce the various types of blood cells.

3. Therapeutic cloning to produce human tissues can begin with either adult stem cells or embryonic stem cells.

4. Embryonic stem cells can be used for reproductive cloning, the production of a new individual.

9.3 The Cell Cycle and Cancer1. A neoplasm is an abnormal growth of cells.2. A benign neoplasm is not cancerous; a malignant neoplasm is cancerous.

3. Cancer is a cellular growth disorder that results from the mutation of genes that regulate the cell cycle; i.e., cancer results from the loss of control and a disruption of the cell cycle.

4. Carcinogenesis, the development of cancer is gradual—it may take decades before a cell has the characteristics of a cancer cell.

B. Characteristics of Cancer Cells

1. Cancer cells lack differentiation.

a. Unlike normal cells that differentiate into muscle or nerves cells, cancer cells have an abnormal form and are nonspecialized.

b. Normal cells enter the cell cycle only about 50 times; cancer cells are immortal in that they can enter the cell cycle repeatedly.

2. Cancer cells have abnormal nuclei.

a. The nuclei may be enlarged and may have an abnormal number of chromosomes.

b. The chromosomes have mutated; some chromosomes may be duplicated or deleted.

c. Gene amplification, extra copies of genes, is more frequent in cancerous cells.

d. Whereas ordinary cells with DNA damage undergo apoptosis, cancer cells do not.

3. Cancer cells form tumors.

a. Normal cells are anchored and stop dividing when in contact with other cells; i.e., they exhibit contact inhibition.

b. Cancer cells invade and destroy normal tissue and their growth is not inhibited.

c. Cancer cells pile on top of each other to form a tumor.

4. Cancer cells undergo metastasis and angiogenesis.

a. A benign tumor is encapsulated and does not invade adjacent tissue.

b. Cancer in situ is a tumor in its place of origin but is not encapsulated—it will invade surrounding tissues.

c. Many types of cancer can undergo metastasis, in which new tumors form which are distant from the primary tumor.

d. Angiogenesis, the formation of new blood vessels, is required to bring nutrients and oxygen to the tumor.

e. A cancer patient's prognosis depends on whether the tumor has invaded surrounding tissue, whether there is lymph node involvement, and whether there are metastatic tumors elsewhere in the body.

C. Origin of Cancer

1. A DNA repair system corrects mutations during replication; mutations in genes encoding the various repair enzymes can cause cancer.

2. Proto-oncogenes specify proteins that stimulate the cell cycle while tumor-suppressor genes specify proteins that inhibit the cell cycle; mutations of either of these genes can cause cancer.

3. DNA segments called telomeres form the ends of chromosomes and shorten with each replication, eventually signaling the cell to end division; cancer cells

produce telomerase that keeps telomeres at a constant length and thus the cells to continue dividing.

D. Regulation of the Cell Cycle

1. Proto-oncogenes are at the end of a stimulatory pathway from the plasma membrane to the nucleus; a growth factor binding at the plasma membrane can result in turning on an oncogene.

2. Tumor-suppressor genes are at the end of an inhibitory pathway; a growth-inhibitory factor can result in turning on a tumor suppressor gene that inhibits the cell cycle.

3. The balance between stimulatory and inhibitory signals determines whether proto-oncogenes or tumor-suppressor genes are active, and therefore whether or not cell division occurs.

E. Oncogenes

1. Proto-oncogenes can undergo mutation to become oncogenes (cancer-causing genes).

2. An oncogene may code for a faulty receptor in the stimulatory pathway, or,

3. An oncogene can specify an abnormal protein product or abnormally high levels of a normal product that stimulates the cell cycle.

4. About 100 oncogenes have been described; the ras gene family includes variants associated with lung, colon, pancreatic cancers as well as leukemias, lymphomas, and thyroid cancers; the BRCA1gene is associated with certain forms of breast and ovarian cancer.

F. Tumor-suppressor Genes

1. Mutation of a tumor-suppressor gene results in unregulated cell growth.

2. Researchers have identified about a half dozen tumor-suppressor genes.

3. The RB tumor-suppressor gene prevents retinoblastoma, a cancer of the retina, and has been found to malfunction in cancers of the breast, prostate, bladder, and small-cell lung carcinoma.

4. The p53 tumor-suppressor gene is more frequently mutated in human cancers than any other known gene; it normally functions to trigger cell cycle inhibitors and stimulate apoptosis.

9.4 Prokaryotic Cell Division1. Unicellular organisms reproduce via asexual reproduction, in which the

offspring are genetically identical to the parent.B. The Prokaryotic Chromosome

1. Prokaryotic cells (bacteria and archaea) lack a nucleus and other membranous organelles.

2. The prokaryotic chromosome is composed of DNA and associated proteins, but much less protein than eukaryotic chromosomes.

3. The chromosome appears as a nucleoid, an irregular-shaped region that is not enclosed by a membrane.

4. The chromosome is a circular loop attached to the inside of the plasma membrane; it is about 1,000 times the length of the cell.

C. Binary Fission

1. Binary fission of prokaryotic cells produces two genetically identical daughter cells.

2. Before cell division, DNA is replicated--both chromosomes are attached to a special site inside the plasma membrane.

3. The two chromosomes separate as a cell lengthens and pulls them apart.

4. When the cell is approximately twice its original length, the plasma membrane grows inward, a septum (consisting of new cell wall and plasma membrane) forms, dividing the cell into two daughter cells.

5. The generation time of bacteria depends on the species and environmental conditions; Escherichia coli's generation time is about 20 minutes.

D. Comparing Prokaryotes and Eukaryotes

1. Both binary fission and mitosis ensure that each daughter cell is genetically identical to the parent.

2. Bacteria and protists use asexual reproduction to produce identical offspring.

3. In multicellular fungi, plants, and animals, cell division is part of the growth process that produces and repairs the organism.

4. Prokaryotes have a single chromosome with mostly DNA and some associated protein; there is no spindle apparatus.

5. Eukaryotic cells have chromosomes with DNA and many associated proteins; histone proteins organize the chromosome.

6. The spindle is involved in distributing the daughter chromosomes to the daughter nuclei.

CHAPTER 10: Meiosis and Sexual Reproduction

10.1 Halving the Chromosome Number1. Meiosis is nuclear division, reducing the chromosome number from

the diploid (2n) to the haploid (n) number.2. The haploid (n) number is half of the diploid number of chromosomes.

3. Sexual reproduction requires gamete (reproductive cell, often sperm and egg) formation and then fusion of gametes to form a zygote.

4. A zygote always has the full or diploid (2n) number of chromosomes.

5. If gametes contained same number of chromosomes as body cells, doubling would soon fill cells.

B. Homologous Pairs of Chromosomes

1. In diploid body cells, chromosomes occur as pairs.

a. Each set of chromosomes is a homologous pair; each member is a homologous chromosome or homologue.

b. Homologues look alike, have the same length and centromere position, and have a similar banding pattern when stained.

c. A location on one homologue contains gene for the same trait that occurs at this locus on the other homologue, although the genes may code for different variations of that trait; alternate forms of a gene are called alleles.

2. Chromosomes duplicate immediately prior to nuclear division.

a. Duplication produces two identical parts called sister chromatids; they are held together at the centromere.

3. One member of each homologous pair is inherited from the male parent, the other member from the female parent.

4. One member of each homologous pair will be placed in each sperm or egg.

C. Overview of Meiosis

1. Meiosis involves two nuclear divisions and produces four haploid daughter cells.

2. Each daughter cell has half the number of chromosomes found in the diploid parent nucleus.

3. Meiosis I is the nuclear division at the first meiotic division.

a. Prior to meiosis I, DNA replication occurs, each chromosome thus has two sister chromatids.

b. During meiosis I, homologous chromosomes pair; this is called synapsis.

c. During synapsis, the two sets of paired chromosomes lay alongside each other as a bivalent (sometimes called atetrad).

4. In meiosis II, the centromeres divide and daughter chromosomes (derived as sister chromatids) separate.

a. No replication of DNA is needed between meiosis I and II because chromosomes are already doubled (DNA replication occurred prior to meiosis I).

b. Chromosomes in the four daughter cells have only one chromatid.

c. Counting the number of centromeres verifies that parent cells were diploid; each daughter cell is haploid.

d. In the animal life cycle, daughter cells become gametes that fuse during fertilization.

e. Fertilization restores the diploid number in cells.

10.2 Genetic VariationA. Genetic Recombination

1. Due to genetic recombination, offspring have a different combination of genes than their parents.

2. Without recombination, asexual organisms must rely on mutations to generate variation among offspring; this is sufficient because they have great numbers of offspring.

3. Meiosis brings about genetic recombination in two ways: crossing-over and independent assortment.

4. Crossing-over of non-sister chromatids results in exchange of genetic material between non-sister chromatids of a bivalent; this introduces variation.

5. At synapsis, homologous chromosomes are held in position by a nucleoprotein lattice (the synaptonemal complex).

6. As the lattice of the synaptonemal complex breaks down at the beginning of anaphase I, homologues are temporarily held together by chiasmata, regions where the non-sister chromatids are attached due to crossing-over.

7. The homologues separate and are distributed to daughter cells.

8. Due to this genetic recombination, daughter chromosomes derived from sister chromatids are no longer identical.

B. Independent Assortment of Homologous Chromosomes

1. During independent assortment, the homologous chromosomes separate independently or in a random manner.

2. Independent assortment in a cell with only three pairs of chromosomes is 23 or eight combinations of maternal and paternal chromosomes.

3. In humans with 23 pairs of chromosomes, the combinations possible are 223 or 8,388,608, and this does not consider the variation from crossing-over.

C. Fertilization

1. When gametes fuse at fertilization, chromosomes donated by parents combine.

2. The chromosomally different zygotes from same parents have (223)2 or 70,368,744,000,000 combinations possible without crossing-over.

3. If crossing-over occurs once, then (423)2 or 4,951,760,200,000,000,000,000,000,000 genetically different zygotes are possible for one couple.

D. Significance of Genetic Recombination

1. A successful parent in a particular environment can reproduce asexually and produce offspring adapted to that environment.

2. If the environment changes, differences among offspring provide the sexual parents with much improved chances of survival.

10.3 The Phases of Meiosis1. Both meiosis I and meiosis II have four phases: prophase, metaphase

anaphase, and telophase.B. Prophase I

1. Nuclear division is about to occur: nucleolus disappears; nuclear envelope fragments; centrosomes migrate away from each other; and spindle fibers assemble.

2. Homologous chromosomes undergo synapsis to form bivalents; crossing-over may occur at this time in which case sister chromatids are no longer identical.

3. Chromatin condenses and chromosomes become microscopically visible.

C. Metaphase I

1. Bivalents held together by chiasmata have moved toward the metaphase plate at the equator of the spindle.

2. In metaphase I, there is a fully formed spindle and alignment of the bivalents at the metaphase plate.

3. Kinetochores, protein complexes just outside the centromeres attach to spindle fibers called kinetochore spindle fibers.

4. Bivalents independently align themselves at the metaphase plate of the spindle.

5. Maternal and paternal homologues of each bivalent may be oriented toward either pole.

D. Anaphase I

1. The homologues of each bivalent separate and move toward opposite poles.

2. Each chromosome still has two chromatids.

E. Telophase I

1. In animals, this stage occurs at the end of meiosis I.

2. When it occurs, the nuclear envelope reforms and nucleoli reappear.

3. This phase may or may not be accompanied by cytokinesis.

F. Interkinesis

1. This period between meiosis I and II is similar to the interphase between mitotic divisions; however, no DNA replication occurs (the chromosomes are already duplicated).

G. Meiosis II

1. During metaphase II, the haploid number of chromosomes align at the metaphase plate.

2. During anaphase II, the sister chromatids separate at the centromeres; the two daughter chromosomes move toward the poles.

3. Due to crossing-over, each gamete can contain chromosomes with different types of genes.

4. At the end of telophase II and cytokinesis, there are four haploid cells.

5. In animals, the haploid cells mature and develop into gametes.

6. In plants, the daughter cells become spores and divide to produce a haploid generation; these haploid cells fuse to become a zygote that develops into a diploid generation.

7. The type of life cycle of alternating haploid and diploid generations is called alternation of generations.

10.4 Meiosis Compared to Mitosis1. Meiosis requires two nuclear divisions; mitosis requires only one nuclear

division.2. Meiosis produces four daughter nuclei and four daughter cells; mitosis

produces only two.

3. The daughter cells produced by meiosis are haploid; the daughter cells produced by mitosis are diploid.

4. The daughter cells produced by meiosis are not genetically identical; the daughter cells produced by mitosis are genetically identical to each other and to the parental cell.

B. A Occurrence

1. In humans, meiosis occurs only in reproductive organs to produce gametes.

2. Mitosis occurs in all tissues for growth and repair.

C. Meiosis I Compared to Mitosis

1. DNA is replicated only once before both mitosis and meiosis; in mitosis there is only one nuclear division; in meiosis there are two nuclear divisions.

2. During prophase I of meiosis, homologous chromosomes pair and undergo crossing-over; this does not occur during mitosis.

3. During metaphase I of meiosis, bivalents align at the metaphase plate; in mitosis individual chromosomes align.

4. During anaphase I in meiosis, homologous chromosomes (with centromeres intact) separate and move to opposite poles; in mitosis at this stage, sister chromatids separate and move to opposite poles.

D. Meiosis II Compared to Mitosis

1. Events of meiosis II are the same stages as in mitosis.

2. However, in meiosis II, the nuclei contain the haploid number of chromosomes.

10.5 The Human Life Cycle1. Life cycle refers to all reproductive events between one generation and next.2. In animals, the adult is always diploid [Instructors note: some bees, etc. have

haploid male adults].

3. In plants, there are two adult stages: one is diploid (called the sporophyte) and one is haploid (called the gametophyte).

4. Mosses are haploid most of their cycle; the majority of higher plants are diploid most of their cycle.

5. In fungi and some algae, only the zygote is diploid, and it undergoes meiosis.

6. In human males, meiosis is part of spermatogenesis (the production of sperm), and occurs in the testes.

7. In human females, meiosis is part of oogenesis (the production of eggs), and occurs in the ovaries.

8. After birth, mitotic cell division is involved in growth and tissue regeneration of somatic tissue.

B. Spermatogenesis and Oogenesis in Humans

1. Spermatogenesis

a. In the testes of males, primary spermatocytes with 46 chromosomes undergo meiosis I to form two secondary spermatocytes, each with 23 duplicated chromosomes.

b. Secondary spermatocytes divide (meiosis II) to produce four spermatids, also with 23 daughter chromosomes.

c. Spermatids then differentiate into sperm (spermatozoa).

d. Meiotic cell division in males always results in four cells that become sperm.

2. Oogenesis

a. In the ovaries of human females, primary oocytes with 46 chromosomes undergo meiosis I to form two cells, each with 23 duplicated chromosomes.

b. One of the cells, a secondary oocyte, receives almost all the cytoplasm; the other cell, a polar body, disintegrates or divides again.

c. The secondary oocyte begins meiosis II and then stops at metaphase II.

d. At ovulation, the secondary oocyte leaves the ovary and enters an oviduct where it may meet a sperm.

e. If a sperm enters secondary oocyte, the oocyte is activated to continue meiosis II to completion; the result is a mature egg and another polar body, each with 23 daughter chromosomes.

f. Meiosis produces one egg and three polar bodies; polar bodies serve to discard unnecessary chromosomes and retain most of the cytoplasm in the egg.

g. The cytoplasm serves as a source of nutrients for the developing embryo.

BIOLOGY 9th

Sylvia Mader

Sanchez, Ingrid Dominique P.

MEB11